2020, 33(1): 1-7.
doi: 10.1063/1674-0068/cjcp1910173
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2020, 33(1): 13-22.
doi: 10.1063/1674-0068/cjcp1910191
Experimental vibrational spectra of heavy light XH stretching vibrations of simple molecules have been analyzed using the local mode model. In addition, the bond dipole approach, which assumes that the transition dipole moment (TDM) of the XH stretching mode is aligned along the XH bond, has helped analyze experimental spectra. We performed theoretical calculations of the XH stretching vibrations of HOD, HND\begin{document}$^-$\end{document} \begin{document}$^-$\end{document} \begin{document}$^-$\end{document} \begin{document}$^-$\end{document}
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In this work, we simulated 2D IR spectroscopy in both transmission geometry and Brewster-angle reflection geometry. Light dispersion and the leakage of s-polarized light are considered in simulating the enhancement factor of the reflection mode. Our simulation shows that the dispersion in reflection will only alter the 2D IR lineshape slightly and can be corrected. Leaking s-polarized light due to imperfectness of IR polarizers in the reflection geometry may limit the enhancement factor, but such limit is above what a typical experiment can reach. In current experiments, the enhancement factor is mainly limited by the precision of incident angle, for which ordinary rotation stages are probably not adequate enough. Moreover, traditional energy ratio of pump and probe pulses, which is 9:1, may not be ideal and could be changed to 2:1 in the reflection geometry. Considering all the above factors, the enhancement on the order of 1,000 is possible in a current experiment. Nevertheless, near-Brewster angle reflection will enhance both the signal and the noise caused by the signal itself, therefore this method only works if the noise is unrelated to the signal, particularly if the noise is caused by the fluctuation in the probe. It cannot improve the signal to noise ratio when the dominate noise is from the signal itself. The theoretical results here agree reasonably well with published experiment results and pave way for realizing even higher enhancement at nearer-Brewster angle.
Molecular packing patterns are crucial factors determining electron/energy transfer processes that are critical for the optoelectronic properties of organic thin film devices. Herein, the polarization-selective ultraviolet/infrared (UV/IR) mixed frequency ultrafast spectroscopy is applied to investigate the relative molecular orientations in two organic thin films of 7-(diethylamino)coumarin-3-carboxylic acid (DEAC) and perylene. The signal anisotropy changes caused by intermolecular energy/electron transfers are utilized to calculate the cross angles between the electronic transition dipole moment of the donor and the vibrational transition dipole moments of the acceptor, yielding the relative orientation between two adjacent molecules. Using this method, the relative orientation angle in DEAC film is determined to be 53.40, close to 600 of its single crystalline structure, and that of the perylene film is determined to be 6.20, also close to -0.20 of its single crystalline structure. Beside experimental uncertainties, the small difference between the angles determined by this method and those of single crystals also results from the fact that the thin film samples are polycrystalline where some of the molecules are amorphous.
We measured the photoelectron spectra of AuCn− (n = 3-8) and conducted theoretical study on the structures and properties of AuCn−/0 (n = 3-8). It is found that the photoelectron spectra of AuCn− exhibit odd-even alternation. The spectral features of AuC3−, AuC5−, and AuC7− are much broader than those of AuC4−, AuC6−, and AuC8−. The vertical detachment energies of AuC3−, AuC5−, and AuC7− are lower than those of AuC4−, AuC6−, and AuC8−. The most stable structures of AuCn− (n = 3-8) are chain structures. The most stable structures of neutral AuCn (n = 3-8) are linear structures except that those of AuC3 and AuC5 are slightly bent. The calculated ∠AuCC angles, Au-C bond lengths, and the charges on Au atom also show odd-even alternations, consistent with the experimental observations.
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We perform accurate quantum dynamics calculations on the isomerization of vinylidene-acetylene. Large-scale parallel computations are accomplished by an efficient theoretical scheme developed by us, in which the basis functions are customized for the double-H transfer process. The A<sub>1</sub>′ and B<sub>2</sub>″ vinylidene and delocalization states are obtained. The peaks recently observed in the cryo-SEVI spectra are analyzed, and very good agreement for the energy levels is achieved between theory and experiment. The discrepancies of energy levels between our calculations and recent experimental cryo-SEVI spectra are of similar magnitudes to the experimental error bars, or ≦ 30 cm<sup>−1</sup> excluding those involving the excitation of the CCH<sub>2</sub> scissor mode. A kind of special state, called the isomerization state, is revealed and reported, which is characterized by large probability densities in both vinylidene and acetylene regions. In addition, several states dominated by vinylidene character are reported for the first time. The present work would contribute to the understanding of the double-H transfer.
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Metal-organic frameworks (MOFs) draw more and more attentions due to their abundant properties and potential applications in materials science. Developing new MOFs structures often gets unexpected material properties. Herein, we report the properties of a copper [2,2]paracyclophane dicarboxylate MOF (CuCP-MOF). The magnetic properties of both CuCP-MOF and activated CuCP-MOF are investigated. CuCP-MOF shows the triplet state EPR spectrum at room temperature due to the antiferromagnetic coupling of the copper(II) paddlewheel (Cu-PW) dimer centers. The MOF has strong intramolecular antiferromagnetic interactions inside the paddlewheel dimer centers and very weak intermolecular interactions, while activated CuCP-MOF exhibits strong intramolecular and intermolecular interactions due to the existence of unpaired Cu(II) centers. We also investigate the electronic structure and semiconductor behavior of CuCP-MOF. The MOF is assigned to direct bandgap semiconductors. Moreover, CuCP-MOF could selectively adsorb cationic organic dyes. By utilizing the synergistic effects of adsorption and photodegradation, we successfully apply CuCP-MOF to organic dye removal.
Full-dimensional adiabatic potential energy surfaces of the electronic ground state X ̃ and nine excited states A ̃, I ̃, B ̃, C ̃, D ̃, D ̃', D ̃", E ̃' and F ̃ of H2O molecule are developed at the level of internally contracted multireference configuration interaction with the Davidson correction. The potential energy surfaces are fitted by using Gaussian process regression combining permutation invariant polynomials. With a large selected active space and extra diffuse basis set to describe these Rydberg states, the calculated vertical excited energies and equilibrium geometries are in good agreement with the previous theoretical and experimental values. Compared with the well-investigated photodissociation of the first three low-lying states, both theoretical and experimental studies on higher states are still limited. In this work, we focus on all the three channels of the highly excited state, which are directly involved in the vacuum ultraviolet photodissociation of water. In particular, some conical intersections of D ̃-E ̃', E ̃^'-F ̃, A ̃-I ̃ and I ̃-C ̃ states are clearly illustrated for the first time based on the newly developed PESs. The nonadiabatic dissociation pathways for these excited states are discussed in detail, which may shed light on the photodissociation mechanisms for these highly excited states.
Six-dimensional quantum dynamics calculations for the state-to-state scattering of H2/D2 on the rigid Cu(100) surface have been carried out using a time-dependent wave packet approach, based on an accurate neural network potential energy surface fit to thousands of density functional theory data computed with the optPBE-vdW density functional. The present results are compared with previous theoretical and experimental ones regarding to the rovibrationally (in)elastic scattering of H2 and D2 from Cu(100). In particular, we test the validity of the site-averaging approximation in this system by which the six-dimensional (in)elastic scattering probabilities are compared with the weighted average of four-dimensional results over fifteen fixed sites. Specifically, the site-averaging model reproduces vibrationally elastic scattering probabilities quite well, though less well for vibrationally inelastic results at high energies. These results support the use of the site-averaging model to reduce computational costs in future investigations on the state-to-state scattering dynamics of heavy diatomic or polyatomic molecules from metal surfaces, where full-dimensional calculations are too expensive.
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As the major and abundant type of glucosinolates (GL) in plants, sinigrin has potential functions in promoting health and insect defense. The final step in the biosynthesis of sinigrin core structure is highly representative in GL compounds, which corresponding to the process from 3-methylthiopropyl ds-GL to 3-methylthiopropyl GL catalyzed by sulfotransferase (SOT). However, due to the lack of the crystallographic structure of SOT complexed with the 3-methylthiopropyl GL, little is known about this sulfonation process. Fortunately, the crystal structure of SOT 18 from Arabidopsis thaliana (AtSOT18) containing the substance (sinigrin) similar to 3-methylthiopropyl GL has been determined. To understand the enzymatic mechanism, we employed molecular dynamics (MD) simulation and combined quantum mechanics and molecular mechanics (QM/MM) methods to study the conversion from ds-sinigrin to sinigrin catalyzed by AtSOT18. The calculated results demonstrate that the reaction occurs through a concerted dissociative mechanism. Moreover, Lys93, Thr96, Thr97, Tyr130, His155 and two enzyme peptide chains (Pro92-Lys93 and Gln95-Thr96-Thr97) play a role in positioning the substrates and promoting the catalytic reaction by stabilizing the transition state geometry. Particularly, His155 acts as a catalytic base while Lys93 acts as a catalytic acid in the reaction process. The presently proposed concerted dissociative mechanism explains the role of AtSOT18 in sinigrin biosynthesis, and could be instructive for the study of GL biosynthesis catalyzed by other SOTs.
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Excited-state double proton transfer (ESDPT) is a controversial issue which has long been plagued with theoretical and experimental communities. Herein, we took 1,8-dihydroxy-2-naphthaldehyde (DHNA) as a prototype and used combined complete active space self-consistent field (CASSCF) and multi-state complete active-space second-order perturbation (MS-CASPT2) methods to investigate ESDPT and excited-state deactivation pathways of DHNA. Three different tautomer minima of S1-ENOL, S1-KETO-1, and S1-KETO-2 and two crucial conical intersections of S1S0-KETO-1 and S1S0-KETO-2 in and between the S<sub>0</sub> and S<sub>1</sub> states were obtained. S1-KETO-1 and S1-KETO-2 should take responsibility for experimentally observed dual-emission bands. In addition, two-dimensional potential energy surfaces (2D-PESs) and linear interpolated internal coordinate (LIIC) paths connecting relevant structures were calculated at the MS-CASPT2//CASSCF level and confirmed a stepwise ESDPT mechanism. Specifically, the first proton transfer from S1-ENOL to S1-KETO-1 is barrierless, whereas the second one from S1-KETO-1 to S1-KETO-2 demands a barrier of ca. 6.0 kcal/mol. The LIIC path connecting S1-KETO-1 [S1-KETO-2] and S1S0-KETO-1 [S1S0-KETO-2] is uphill with a barrier of ca. 12.0 kcal/mol, which will trap DHNA in the S<sub>1</sub> state awhile therefore enabling dual-emission bands. On the other hand, the S<sub>1</sub>/S<sub>0</sub> conical intersections would also prompt the S<sub>1</sub> system to decay to the S<sub>0</sub> state, which could be to certain extent suppressed by locking the rotation of the C<sub>5</sub>-C<sub>8</sub>-C<sub>9</sub>-O<sub>10</sub> dihedral angle. These mechanistic insights are not only helpful for understanding ESDPT but also useful for designing novel molecular materials with excellent photoluminescent performances.
Recently, more attention have been paid on the construction of dipole moment functions (DMF) using theoretical methods. However, the computational methods to construct DMFs are not validated as much as those for potential energy surfaces do. In this Letter, using Ar⋯He as an example, we tested how spectroscopy-accuracy DMFs can be constructed using ab initio methods. We especially focused on the basis set dependency in this scenario, i.e., the convergence of DMF with the sizes of basis sets, basis set superposition error, and mid-bond functions. We also tested the explicitly correlated method, which converges with smaller basis sets than the conventional methods do. This work can serve as a pictorial sample of all these computational technologies behaving in the context of constructing DMFs.
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Cell membrane fusion is a fundamental biological process involving in a number of cellular living functions. Regarding this, divalent cations can induce fusion of the lipid bilayers through binding and bridging of divalent cations to the charged lipids, thus leading to the cell membrane fusion. However, the elaborate mechanism of cell membrane fusion induced by divalent cations is still needed to be elucidated. Here, surface/interface sensitive sum frequency generation vibrational spectroscopy (SFG-VS) and dynamic light scattering (DLS) were applied in this research to study the responses of phospholipid monolayer to the exposure of divalent metal ionsi.e. Ca2+ and Mg2+. According to the particle size distribution results measured by DLS experiments, it was found that Ca2+ could induce inter-vesicular fusion while Mg2+ could not. An Octadecyltrichlorosilane self-assembled monolayer (OTS-SAMs)/lipid monolayer system was designed to model the cell membrane for the SFG-VS experiment. We found, Ca2+ can interact with the lipid PO2- head groups more strongly, resulting in cell membrane fusion more easily, in comparison to Mg2+. No specific interaction between the two metal cations and the C=O groups was observed. However, the C=O orientations changed more after Ca2+ -PO2- binding than Mg2+ mediation on lipid monolayer. Meanwhile, Ca2+ can induce dehydration of the lipids (which should be related to the strong Ca2+ - PO2- interaction), leading to the reduced hindrance for cell membrane fusion. .
The oxygen reduction reaction (ORR) by the nitrogen-doped fullerene (C59N) catalyst demonstrates an excellent activity in hydrogen fuel cells. However, the intermediates and catalytic active sites in pathways have not been directly characterized, hindering the understanding of the enhanced activity mechanism for ORR on C59N. By taking the inhomogeneity of spatially confined plasmon (SCP) into account, we theoretically propose that the high-resolution tip-enhanced Raman scattering (TERS) can effectively identify different intermediate configurations of ORR on C59N. With the modulation of the focused SCP center position, vibrational modes that are directly related to site-specific O2−C59N interactions in ORR can be lighted up and then selected out by TERS spectra. Furthermore, the vibration-resolved TERS images for the selected modes of different intermediate configurations give spatial hot spot around the adsorption site, providing the in-situ details of catalytic active sites of ORR on C59N. These findings serve as good references for future high-resolution TERS experiments on probing catalytic systems at the molecular scale.
氮掺杂富勒烯(C59N)催化剂在氢燃料电池的氧还原反应(ORR)中表现出良好的活性。然而，C59N上发生的ORR反应路径的中间体和催化活性位点尚未被直接表征，阻碍了我们对C59N催化剂在ORR中活性增强机制的理解。通过在模拟计算中考虑空间限制等离子体(SCP)的不均匀分布，我们从理论上提出高空间分辨针尖增强拉曼散射(TERS)可以有效地识别C59N上ORR的不同中间体构型。通过调整聚焦的SCP位置，ORR中与O2−C59N相互作用有关联的振动模式可以被TERS光谱直接选择出来，并且得到增强。此外，选择出来的振动模式对应的TERS图像在吸附位点周围给出了拉曼热点，提供了ORR在C59N上催化活性位点的原位观测细节。这些发现为今后通过高分辨率TERS技术在分子尺度上探索催化系统提供了良好的参考。
The symmetric and quadrupolar donor-acceptor-donor (D-A-D) molecules usually exhibit excited-state charge redistribution process from delocalized intramolecular charge transfer (ICT) state to localized ICT state. Direct observation of such charge redistribution process in real-time has been intensively studied via various ultrafast time-resolved spectroscopies. Femtosecond stimulated Raman spectroscopy (FSRS) is one of the powerful methods which can be used to determine the excited state dynamics by tracking vibrational mode evolution of the specific chemical bonds within molecules. Herein, a molecule, 4,4’-(buta-1,3-diyne-1,4-diyl)bis(N,N-bis(4-methoxyphenyl)aniline), that consists of two central adjacent alkyne (-C≡C-) groups as electron-acceptors and two separated, symmetric N,N-bis(4-methoxyphenyl)aniline at both branches as electron-donors is chosen to investigate the excited-state photophysical properties. It is shown that the solvation induced excited-state charge redistribution in polar solvents can be probed by using femtosecond stimulated Raman spectroscopy. The results provide a fundamental understanding of photoexcitation induced charge delocalization/localization properties of the symmetric quadrupolar molecules with adjacent vibrational markers located at central position.
The divergent behavior of C-H bond oxidations of aliphatic substrates compared to those of aromatic substrates shown in Gupta’s experiment was mechanistically studied herein by means of density functional theory (DFT) calculations. Our calculations revealed that such difference is caused by different reaction mechanisms between two kinds of substrates (the aliphatic cyclohexane, 2,3-dimethylbutane (DMB) and the aromatic toluene, ethylbenzene and cumene). For the aliphatic substrates, C-H oxidation by the oxidant Fe<sup>V</sup>(O)(TAML) is a hydrogen atom transfer (HAT) process; whereas for the aromatic substrates, C-H oxidation is a proton-coupled electron transfer (PCET) process with a proton transfer character on the transition state, that is, a PCET(PT) process. This difference is caused by the strong π-π interactions between the tetra-anionic TAML ring and the phenyl ring of the aromatic substrates, which has a “pull” effect to make the electron transfer from substrates to the Fe=O moiety inefficient.
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The industrial pollutant NO is a potential threat to the environment and to human health. Thus, selective catalytic reduction (SCR) of NO into harmless N2, NH3, and/or N2O gas is of great interest. Among many catalysts, metal Pd has been demonstrated to be most efficient for selectivity, reducing NO to N2. However, the reduction mechanism of NO on Pd, especially the route of N-N bond formation, remains unclear, impeding the development of new, improved catalysts. We report here the elementary reaction steps in the reaction pathway of reducing NO to NH3, N2O, and N2, based on density functional theory (DFT)-based quantum mechanics calculations. We show that the formation of N2O proceeds through an Eley-Rideal (E-R) reaction pathway that couples one adsorbed *NO with one non-adsorbed NO from the solvent or gas phase. This reaction requires high NO* surface coverage, leading first to the formation of the trans-(NO)2* intermediate with a low N-N coupling barrier (0.58 eV). Notably, we found that trans-(NO)2* will continue to react with NO in the solvent to form N2O that has not been reported. With the consumption of NO and the formation of N2O* in the solvent, the L-H mechanism will dominate at this time, and N2O* will be reduced by hydrogenation at a low chemical barrier (0.42 eV) to form N2. In contrast, NH3 is completely formed by the L-H reaction, which has a higher chemical barrier (0.87 eV). Our predicted E-R reaction has not previously been reported, but it explains existing experimental observations. In addition, we examine how catalyst activity might be improved by doping a single metal atom (M) at the NO* adsorption site to form M/Pd and show its influence on the barrier for forming the N-N bond to provide control over the product distribution.
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Understanding organic photovoltaic (OPV) work principles and the materials’ optoelectronic properties is fundamental for developing novel heterojunction materials with the aim of improving power conversion efficiency (PCE) of organic solar cells. Here, in order to understand more than 13% of PCE achieved by OPV device composed of the non-fullerene acceptor fusing naphtho[1,2-b:5,6-b']dithiophene with two thieno[3,2-b]thiophene (IDCIC) and the polymer donor fluorobenzotriazole (FTAZ), by the aid of extensive quantum chemistry calculations, we investigated the geometries, molecular orbitals, excitations, electrostatic potentials (ESP), transferred charges and charge transfer (CT) distances of FTAZ, IDCIC and their complexes with face-on configurations, which was constructed as heterojunction interface model. The results indicate that, the prominent OPV performance of FTAZ:IDCIC heterojunction is caused by co-planarity between the donor and acceptor fragments in IDCIC, the CT and hybrid excitations of FTAZ and IDCIC, the complementary optical absorptions in visible region, and the large ESP difference from FTAZ to IDCIC. The electronic structures and excitations of FTAZ/IDCIC complexes suggest that exciton dissociation (ED) can fulfill through the decay of local excitation exciton in acceptor by means of hole transfer, which is quite different from the OPVs based on fullerenes acceptor. The rates of ED, charge recombination and CT processes, which were evaluated by Marcus theory, support the efficient ED that is also responsible for good photovoltaic performance.
Excited-state intramolecular proton transfer (ESIPT) is favored by researchers because of its unique optical properties. However, there are relatively few systematic studies on the effects of changing the electronegativity of atoms on the ESIPT process and photophysical properties. Therefore, we selected a series of benzoxazole isothiocyanate fluorescent dyes (2-HOB, 2-HSB, and 2-HSeB) by theoretical methods, and systematically studied the ESIPT process and photophysical properties by changing the electronegativity of chalcogen atoms. The calculated bond angle, bond length, energy gap, and infrared spectrum analysis show that the order of the strength of intramolecular hydrogen bonding of the three molecules is 2-HOB<2-HSB<2-HSeB. Correspondingly, the magnitude of the energy barrier of the potential energy curve is 2-HOB>2-HSB>2-HSeB. In addition, the calculated electronic spectrum shows that as the atomic electronegativity decreases, the emission spectrum has a redshift. Therefore, this work will offer certain theoretical guidance for the synthesis and application of new dyes based on ESIPT properties.
Understanding the excited state dynamics of donor-acceptor (DA) complexes is of fundamental importance both experimentally and theoretically. Herein, we have first explored the photoinduced dynamics of a recently synthesized paddle-wheel BODIPYhexaoxatriphenylene (BH) conjugates DA complex with the combination of both electronic structure calculations and non-adiabatic dynamics simulations. On the basis of computational results, we concluded that the BH conjugates will be promoted to the local excited (LE) states of the BODIPY fragments upon excitation, which is followed by the ultrafast LE to charge transfer (CT) exciton transfer. Instead of the photoinduced electron transfer process proposed in previous experimental work, such exciton transfer process is accompanied with the photoinduced hole transfer from BODIPY to hexaoxatriphenylene. Additionally, solvent effects are found to play an important role in the photoinduced dynamics. Specifically, the hole transfer dynamics is accelerated by the acetonitrile solvent, which can be ascribed to significant influences of the solvents on the charge transfer states, i.e. the energy gaps between LE and CT excitons are reduced greatly and the non-adiabatic couplings are increased in the meantime. Our present work not only provides valuable insights into the underlying photoinduced mechanism of BH, but also can be helpful for the future design of novel donoracceptor conjugates with better optoelectronic performance.
The interactions in complexes of XeOF2 and XeO3 with a series of different hybridization N-containing donors are studied by means of DFT and MP2 calculations. The aerogen bonding interaction energies range from 6.5-19.9 kcal/mol between XeO3 and XeOF2 with typical N-containing donors. The sequence of interaction is sp3> sp2> sp and XeO3 is higher than XeOF2. For some donors of sp2 and sp3 hybridization, the steric effect plays a fractional role in the interaction with the evidence of RDG plots. The dominant stable part is the electrostatic interaction. In complex of XeO3, the weight of polarization is larger than dispersion, while the situation is opposite for XeOF2 complexes. Except for Vs, the other five interaction parameters show great linear correlation coefficients with each other.
Magnesium monofluoride (MgF) is proposed as an ideal candidate radical for direct laser cooling. Here, the high resolution laser excitation spectra of MgF for the A<sup>2</sup>Π-X<sup>2</sup>Σ<sup>+</sup> electronic transition system were recorded by using laser induced fluorescence (LIF) technique. The MgF radicals are produced by discharging SF6/Ar gas mixtures between the tips of two magnesium needles in a supersonic jet expansion. We recorded 19 vibrational bands in total belonging to three sequences of Δv=0, ±1 in the region of 348-370 nm. Accurate spectroscopic constants for both A<sup>2</sup>Π and X<sup>2</sup>Σ<sup>+</sup> states are determined from rotational analysis of the experimental spectra. Spectroscopic parameters, including the Franck-Condon factors (FCFs), are determined from the experimental results and the Rydberg-Klein-Rees (RKR) calculations. Significant discrepancies between the experimentally measured and RKR-calculated FCFs are found, indicating that the FCFs are nearly independent on the spin-orbit coupling in the A<sup>2</sup>Π state. Potential energy curves (PECs) and Franck-Condon factors (FCFs) determined here provide necessary data for the theoretical simulation of the laser-cooling scheme of MgF.
The ethoxycarbonyl isothiocyanate has been investigated by using supersonic jet Fourier transform microwave spectroscopy. Two sets of rotational spectra belonging to conformers TCC (with the backbone of C-C-O-C, C-O-C=O, and O-C(=O)-NCS being trans, cis, and cis arranged, respectively) and GCC (gauche, cis, and cis arrangement of the C-C-O-C, C-O-C=O, and O-C(=O)-NCS) have been measured and assigned. The measurements of 13C, 15N and 34S mono-substituted species of the two conformers were also performed. The comprehensive rotational spectroscopic investigations generate accurate values of rotational constants and 14N quadrupole coupling constants, which lead to structural determinations of the two conformers of ethoxycarbonyl isothiocyanate. For conformer TCC, the values of Pcc keep constant upon isotopic substitution, indicating that the heavy atoms of TCC effectively be located in the ab plane.
In this work, mixed polymer brushes coating based on poly(2-methyl-2-oxazoline) (PMOXA)/poly(4-vinyl pyridine) (P4VP) was prepared by simultaneously grafting amine-terminated PMOXA and thiol-terminated P4VP onto poly(dopamine) (PDA)-modified substrates. The coatings were characterized by X-ray photoelectron spectroscopy (XPS), ellipsometry, zeta potential measurements, and the static water contact angle (WCA) tests. The results demonstrated that the coating based mixed PMOXA/P4VP brushes with desired surface composition could be obtained by simply maintaining their percentage in the mixture of PMOXA and P4VP solutions. Moreover, the zeta potential and the WCA of mixed brushes modified surfaces could be tuned by changing the environmental pH value and surface compositions. Finally, the switchable behavior of PMOXA/P4VP based coatings toward pepsin adsorption was investigated by fluorescein isothiocyanate-labelled pepsin assay and surface plasmon resonance. The results showed that by adjusting the fraction of PMOXA or P4VP, the PMOXA/P4VP mixed brushes coated surfaces could adsorb large amounts of pepsin at pH 3, but more than 92% of the adsorbed protein could be desorbed at pH 7.
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Crystallographic group is an important character to describe the crystal structure, but it is difficult to identify the crystallographic group of crystal only given chemical composition. Here, we present a machine-learning method to predict the crystallographic group of crystal structure from its chemical formula. 34528 stable compounds in 230 crystallographic groups are investigated, of which 72% of data set are used as training set, 8% as validation set, and 20% as test set. Based on the results of machine learning, we present a model which predicts crystallographic group among the top-1, top-5, and top-10 groups of compounds with the estimated accuracy of 60.8%, 76.5%, and 82.6%, respectively. In particular, the performance of deep-learning model presents high generalization through comparison between validation set and test set. Additionally, 230 crystallographic groups are classified into 19 new labels, denoting 18 heavily represented crystallographic groups with each containing more 400 compounds and one combination group of remaining compounds in other 212 crystallographic groups. A deep-learning model trained on 19 new labels yields a promising result to identify crystallographic group with the estimated accuracy of 72.2%. Our results provide a promising approach to identify crystallographic group of crystal structures only from their chemical composition.
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Deriving reaction coordinates (RC) for the characterization of chemical reactions has long been a demanding task. In our previous article (ACS Central Science 2017, 3(5), 407-414), the reaction coordinate of a (retro-) Claisen rearrangement in aqueous solution optimized through a Bayesian measure, 0.82d(C1-C6) - 0.18d(O3- C4), was judged to be optimal among all trails. Here, considering the nonlinearity of the transition state, we used Isometric Mapping ( Isomap) and Locally Linear Embedding (LLE) to obtain one reaction coordinate which is composed of a few collective variables. With this method, we have found a more reasonable and powerful one-dimensional reaction coordinate, which can well describe the reaction progression. To explore the reaction mechanism, we analyzed the contribution of intrinsic molecular properties and the solvent-solute interactions to the nonlinear reaction coordinate. Furthermore, a second coordinate is identified to characterize the heterogeneity of reaction mechanisms.
Revealing the relationship between electronic structures and the decomposition mechanism is the key to explore novel primary explosives. A systematic investigation on electronic structures and microscopic decomposition pathways of 4-amino-5-mercapto-1,2,4-triazole (AMTA) and 4-amino-5-mercapto-3-nitro-1,2,4- triazole (AMNTA) in the ground, charged, and excited states (S0→T1) has been analyzed with density functional theory (DFT). The effect of electrifying molecules and exciting electrons on the decomposition mechanism has been clarified by thermodynamics and kinetics. This study shows that the neutral amino dissociation from the triazole ring has an advantage among different substituents dissociation. For AMTA, electrifying the molecule can make the ring cleavage occur easily at the "N4-C5" site, and exciting electrons makes the triazole ring decompose directly and release 3.3 kcal/mol of heat. For AMNTA, positively electrifying the molecule makes CONO isomerization become the dominant reaction and hinders the H-transfer reaction. When the molecule is electrified negatively or its electrons are excited, H-transfer will take place preferentially. This work sheds light on how to control the decomposition pathways of novel primary explosives at the electronic structure level by the means of electrifying molecules and exciting electrons.
The kinetics of U(IV) produced by hydrazine reducting U(VI) with platinum as catalyst in nitric acid media was studied for revealing the reaction mechanism and optimizing the reaction process. Electron spin resonance (ESR) was used to determine the influence of nitric acid oxidation. The influence of nitric acid, hydrazine, U(VI) concentration, catalyst dosage and temperature on the reaction were studied. Concurrently, the simulation of the reaction process was performed using density functional theory (DFT). The results show that the influence of oxidation on the main reaction is limited when the concentration of nitric acid was below 0.5 mol/L. The reaction kinetics equation below the concentration of 0.5 mol/L is found as follows: –dc(UO22+)/dt) = kc0.5323(UO22+)c0.2074(N2H5+)c−0.2009(H+). When the temperature is 50°C, and the solid/liquid ratio r is 0.0667g/mL, the reaction kinetics constant is k = 0.00199 (mol/L) 0.4612/min. Between 20℃ and 80℃, with the increase of temperature, the reaction rate is gradually accelerated, and the reaction changes from chemically controlled to diffusion-controlled. The reaction process is simulated by DFT, and the influence of various factors on the reaction process is deduced. The reaction process and mechanism are determined according to the reaction kinetics and simulation results finally.
The general application of antibiotics has brought a series of negative impacts on human health and the environment, which has aroused widespread public attention to their removal from aqueous systems. In this study, a chitosan (CS)-linked graphene oxide (GO) composite (GO-CS) was synthesized by a modified Hummers/solvothermal method. It was separated from the mixed aqueous phase by low-speed centrifugation, thereby endowing the GO with high separation efficiency in water. The adsorption of tetracycline (TC), norfloxacin (NOR), and sulfadiazine (SDZ) by GO-CS were then studied by experimental techniques and theoretical calculations. In batch experiments at 298 K and optimal pH, the adsorption capacities of TC, NOR, and SDZ were 597.77, 388.99, and 136.37 mg/g, respectively, which were far better than those for pristine graphene oxide. The spectra results illustrated that the adsorption process was mainly contributed by the interactions between antibiotics and functional groups (carboxyl, hydroxyl, and amino groups) of GO-CS. Furthermore, density functional theory calculations showed that electrostatic interaction and hydrogen bonds are of vital importance for the uptake of the antibiotics; the former is extremely important for TC adsorption. This research will provide theoretical references for the removal of antibiotics by graphene-based composite materials, thus offering their promising application in environmental remediation.
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The anionic carbonyl complexes of groups IV and V metals are prepared in the gas phase using a laser vaporation-supersonic expansion ion source. The infrared spectra of the TM(CO)<sub>6,7</sub><sup>-</sup> (TM=Ti, Zr, Hf, V, Nb, Ta) anion complexes in the carbonyl stretching frequency region are measured by mass-selected infrared photodissociation spectroscopy. The six-coordinated TM(CO)<sub>6</sub><sup>-</sup> anions are determined to be the coordination saturate complexes for both the group IV and group V metals. The TM(CO)<sub>6</sub><sup>-</sup> complexes of group IV metals (TM=Ti, Zr, Hf) are 17-electron complexes having a <sup>2</sup>A<sub>1g</sub> ground state with D<sub>3d</sub> symmetry, while the TM(CO)<sub>6</sub><sup>-</sup> complexes of group V metals (TM=V, Nb, Ta) are 18-electron species with a closed-shell singlet ground state possessing O<sub>h</sub> symmetry. The energy decomposition analyses indicate that the metal-CO covalent bonding are dominated by TM-(d) → (CO)<sub>6</sub> π-backdonation and TM-(d)←(CO)<sub>6</sub> σ-donation interactions.
A better understanding of the photophysical processes occurring within organic semiconductors is important for designing and fabricating organic solar cells (OSCs). In this paper, we investigated the triplet‒triplet annihilation process in CuPc thin films with different molecular stacking configurations. The ultrafast transient absorption measurements indicate that the primary annihilation mechanism is one-dimensional exciton diffusion collision destruction. The decay kinetics shows a clearly time-dependent annihilation rate constant with γ ∝ t−1/2. Annihilation rate constants were determined to be γ0 = (2.87 ± 0.02) × 10−20 and (1.42 ± 0.02) × 10−20 cm3·s−1/2 for upright and lying-down configurations, respectively. Compared to the CuPc thin film with an upright configuration, the thin film with a lying-down configuration shows a longer exciton lifetime and a higher absorbance, which are beneficial for OSCs. The results in this paper have important implications on the design and mechanistic understanding of organic optoelectronic devices.
Vacuum ultraviolet photodissociation dynamics of N2O + hv → N2(X1Σg+) + O(1S0) in the short wavelength tail of D1Σ+ band have been performed using the time-sliced velocity-mapped ion imaging technique by probing the images of the O(1S0) photoproducts at a set of photolysis wavelengths from 121.47 to 123.95 nm. The product total kinetic energy release distributions, vibrational state distributions of the N2(X1Σg+) photofragments and angular anisotropy parameters have been obtained through analyzing the raw O(1S0) images. It is noted that an additional vibrationally excited photoproducts (3≤v≤8) with a Boltzmann-like feature start to appear except for the non-statistical component as the photolysis wavelength decreases to 123.25 nm, and the corresponding populations become more pronounced with decreasing of the photolysis wavelength. Furthermore, the vibrational state specific β-value at each photolysis wavelength exhibits a drastic fluctuation near β=1.75 at v<8, and decreases to a minimum as the vibrational quantum number further increases. While the overall β-value for the N2(X1Σg+) + O(1S0) channel presents a roughly monotonically increasing from the value of 1.63 at 121.47 nm to 1.95 at 123.95 nm. The experimental observations suggest that there is at least one fast nonadiabatic pathway from initially prepared D1Σ+ state to the dissociative state with bent geometry dominating to generate the additional vibrational structures at high photoexcitation energies.
Catalytic hydrolysis of ammonia borane for dehydrogenation is a promising way for generation and storage of hydrogen energy. Catalysts with reduced utilization of costly noble metals while high activity and stability are highly desired. Herein we show that the catalytic activity of the prototypical Pt/SiO2 catalysts towards ammonia borane hydrolysis could be significantly improved by the presence of a layer of Co(OH)2 beneath the supported Pt nanoparticles. By changing the Pt:Co molar ratio in the Pt-Co(OH)2/SiO2 catalysts, the hydrogen generation rates from ammonia borane hydrolysis show a volcano-type curve, with the maximum catalytic activity at the Pt:Co molar ratio of 1:11. The highest turnover frequency value of 829 molH2·molPt−1·min−1 at room temperature outperforms most of the reported Pt-based catalysts, and the apparent activation energy is drastically decreased to 36.2 kJ/mol from 61.6 kJ/mol for Pt/SiO2. The enhanced catalytic performance of Pt-Co(OH)2/SiO2 is attributed to the electrons donation from Co atoms on Co(OH)2 to Pt occurring at the metal-hydroxide interface, which is beneficial for optimizing the oxidation cleavage of the O−H bond of attacked H2O.
Herein, we present the decoration of NiFeCoAlOOH nanoparticles onto titanium doped nanoporous hematite (Ti-PH) utilizing a simple electroless ligand-controlled oxidation method for photoelectrochemical water splitting. Owing to the improved oxygen evolution reaction kinetics and reduced charge transfer resistance, the resulting Ti-PH/NiFeCoAlOOH photoanode presents an excellent photocurrent density of 2.46 mA/cm<sup>2</sup> at 1.23V vs. RHE and good stability compared to Ti-PH or bare hematite (H). Furthermore, the onset potential of the photocurrent density is shifted cathodically by ~ 60 mV with reference to the titanium doped nanoporous hematite. This work offers a promising method for designing high-performance, stable, and inexpensive catalysts for photoelectrochemical (PEC) applications.
Although lead-based halide perovskites have promising applications in optoelectronic devices, these applications are limited by the toxicity of the materials. Therefore, it is necessary to develop lead-free all-inorganic substitute such as tin-based halide perovskites in spite of the enormous challenges in their controllable synthesis and stability. Here, we report the controlled growth of high quality CsSnBr<sub>3</sub> microcrystals on SiO<sub>2</sub>/Si substrates by chemical vapor deposition method. The as-prepared products predominantly show the morphology of triangle star and nail-like rod and the structure of cubic phase. The control of nucleation density and size of CsSnBr<sub>3</sub> microcrystals has been realized by varying the growth temperature. The results of air-exposed samples provide direct evidences for explaining the structural instability of the tin-based perovskites, which is attributed to the production of SnO. The power and temperature dependent photoluminescence spectra reveal that CsSnBr<sub>3</sub> microcrystals with different morphologies possess different exciton binding energies and produce different photoexcitation species due to the quantum confinement effect that changes the electron-hole effect.
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Ultra-wide-bandgap semiconductors have tremendous potential to advance electronic devices, as device performance improves nonlinearly with increasing gap. In this work we employ density-functional theory with the accurate screened-hybrid functional to evaluate the electronic and optical properties of NaYO2 in two different phases. The electronic structure calculation results show that both monoclinic and trigonal phases of NaYO2 exhibit direct bandgaps of 5.6 and 5.4 eV, respectively, offering a physically realistic material platform to derive the semiconductor industry beyond the well-established diamond, and GaN semiconducting materials. Next, we investigate the optical properties and reveal that both phases of NaYO2 are transparent in the infrared and visible regions, thereby, these materials can be used as infrared window materials.
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Polymers are routinely used as embedding matrices for organic molecular phosphors to substantially reduce the non-radiative decay rate and promote room-temperature phosphorescence (RTP). However, most previous studies focus on how glass transition temperature and free volume of various polymers influence RTP efficiency; very little is known on how electronic coupling between the matrix and the phosphor can modulate organic RTP. The current investigation attempts to address the problem by synthesizing a monomeric version of an aromatic ketone phosphor and copolymerizing the ketone with four different types of matrix monomers. The resulting copolymers exhibit clear matrix-dependent RTP efficiency: a gradual decrease of RTP quantum yield from 22% to nearly 0 can be observed when the electronic conjugation of the matrix increases, suggesting that energy dissipation can occur in the triplet excited state via electron exchange when the triplet state of the matrix is close to that of the phosphor. The study provides a guiding principle on regulating the lifetime of triplet-excited states for organic dyes.
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A novel electrochemical non-enzymatic glucose sensor based on three-dimensional Au/MXene nanocomposites was developed. MXenes were prepared using the mild etched method, and the porous foam of Au nanoparticles was combined with the MXene by means of in situ synthesis. By controlling the mass of MXene in the synthesis process, porous foam with Au nanoparticles was obtained. The three-dimensional foam structure of nanoparticles was confirmed by scanning electron microscopy (SEM). Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) were used to study the electrochemical performance of the Au/MXene nanocomposites. The Au/MXene nanocomposites acted as a fast redox probe for non-enzymatic glucose oxidation and showed good performance, including a high sensitivity of 22.45 μA mM−1 cm−1 and a wide linear range of 1–12 mM. Studies have shown that MXene as a catalyst-supported material is beneficial to enhance the conductivity of electrons and increase the loading rate of the catalyst materials. The foam structure with Au nanoparticles can provide a larger surface area, increase the contact area with the molecule in the catalytic reaction, and enhance the electrochemical reaction signal. In summary, this study showed that Au/MXene nanoparticles have the potential to be used in non-enzymatic glucose sensors.
The yolk-shell MIL-125/TiO<sub>2</sub>/Pt/CdS and hollow TiO<sub>2</sub>/Pt/CdS visible-light catalysts were successfully synthesized from MIL-125 by γ-ray irradiation. What is interesting is that during the reduction process by γ-ray irradiation, MOFs are partially or completely hydrolyzed to TiO<sub>2</sub> nanosheets, forming the unique yolk-shell or hollow structure. The hydrogen production rate is 2983.5 μmol·g<sup>-1</sup>·h<sup>-1</sup> for yolk-shell structures and 1934.2 μmol·g<sup>-1</sup>·h<sup>-1</sup> for hollow structures under visible-light illumination, which is 7.9 and 5.1 times higher than that of CdS, respectively. The excellent properties of these photocatalysts may be attributed to the effective absorption and utilization of the light, the porous yolk-shell or hollow structure derived from MIL-125 to facilitate mass transfer, and close contact among CdS nanoparticles, TiO<sub>2</sub> nanosheets and Pt nanoparticles to improve the separation of electron-hole pairs. This research can provide a simple and new method for the construction of high efficiency photocatalysts derived from MOFs using the γ-ray irradiation.
The electrocatalytic carbon dioxide reduction reaction (CO2RR) producing HCOOH and CO is
one of the most promising approaches for storing renewable electricity as chemical energy in fuels.
The SnO2 is a good catalyst for CO2-to-HCOOH or CO2-to-CO conversion, with different crystal
planes participating the catalytic process. Among them, (110) surface SnO2 is very stable and easy
to synthesis. By changing the ratio of Sn:O for SnO2 (110), we have two typical SnO2 thin films:
fully oxidized (stoichiometric) and partially reduced. In this work, we are concerned with different
metals (Fe, Co, Ni, Cu, Ru, Rh, Pd, Ag, Os, Ir, Pt, and Au)-doped SnO2 (110) of different activity
and selectivity for CO2RR. All these changes are manipulated by adjusting the ratio of Sn:O in
(110) surface. The results show that stochiometric and reduced Cu/Ag doped SnO2(110) have
different selectivity for CO2RR. More specifically, stochiometric Cu/Ag-doped SnO2 (110) tends to
generate CO(g). Meanwhile, the reduced surface tends to generate HCOOH(g). Moreover, we also
considered the competitive reaction hydrogen evolution reaction(HER). The catalysts SnO2 (110)
doped by Ru, Rh, Pd, Os, Ir, and Pt have high activity for HER, and others are good catalysts for
CO2RR.
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In this work, we firstly elucidated the ultraviolet light protection dynamics mechanism of the typical hemicyanines of Hemicy and DHemicy by combining the theoretical calculation method and the transient absorption spectra. It was theoretically and experimentally demonstrated that both of Hemicy and DHemicy have strong absorption in UVC, UVB, and UVA regions. Moreover, after absorbing energy, Hemicy and DHemicy can jump into the excited states. Subsequently, the Hemicy and DHemicy will relax to S0 states from S1 states rapidly by the non-adiabatic transition at the conical intersection (CI) point between the potential energy curves of S1 and S0 states and accompany by the trans-cis photoisomerism. The transient absorption spectra showed that the trans-cis photoisomerization will occur within a few picoseconds. Thus, the ultraviolet energy absorbed by Hemicy and DHemicy could be relaxed ultrafast by the non-adiabatic trans-cis photoisomerization processes.
Specific energy and self-discharge are two important performances of electrochemical capacitors. In this work, we have fabricated the composite electrodes by complexing the negatively charged carboxylated multi-walled carbon nanotubes (cMWCNT) with the redox active units-containing positively charged random copolymers. 2,2,6,6-Tetramethylpiperidinyl-N-oxyl and viologen are employed as model redox active units to exemplify the strategy of the concurrent increase of specific energy and suppression of self-discharge of a two-electrode device. The enhanced specific energy is mainly attributed to the increased electrolyte decomposition window induced by the faster redox reactions than those of the hydrogen and oxygen evolution reactions. The improved performance of self-discharge is due to the suppression of the cross-diffusion and redox shuttling of the redox couples induced by the complexation between the cMWCNT and the copolymers. By employing the redox active units-containing charged copolymers, this work provides a convenient and universal strategy to concurrently increase specific energy and suppress self-discharge of electrochemical capacitors with the carbon-based electrodes.
It is important to identify non-planar deformations of porphyrin macrocycle in metallo-porphyrin proteins due to their functional relevance. The relationship between non-planar deformations of porphyrin macrocycle and low frequency Raman spectral bands of Ni(II) Meso-tetraphenyl porphyrin (NiTPP), with different coordination numbers , was studied by density functional theory (DFT) , normal coordinate structural decomposition (NSD) method and Raman experiments. The results show that the crystal of four-coordinate NiTPP has two major kinds of nonplanar deformations: ruffling and saddling. The non-planar deformations of ruffling and saddling for NiTPP are 1.473 Å and 0.493 Å determined by DFT calculation. The ruffling and saddling deformations can be identified by using the low frequency Raman characteristic peaks (r12 ,r13 ) and (r16 ,r17 ), respectively. When four-coordinate NiTPP is transformed to the six-coordinate bis(pyrrolidine) NiTPP (NiTPP(Pyr)2), the large non-planar distortion of the porphyrin macrocycle almost disappears, with the non-planar deformation of saddling only about 0.213 Å estimated by DFT calculation. Experimentally, we can make use of the characteristic peaks of low frequency Raman spectra to identify the saddling deformation beyond 0.25 Å.
Though poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) has been widely adopted as hole transport material (HTM) in flexible perovskite solar cells (PSCs), arising from high optical transparency, good mechanical flexibility, and high thermal stability, its acidity and hygroscopicity would inevitably hamper the long-term stability of the PSCs and its energy level does not match well with that of perovskite materials which would lead to a relatively low open-circuit voltage (VOC). In this investigation, p-type delafossite CuCrO2 nanoparticles synthesized through hydrothermal method have been employed as an alternative HTM for triple cation perovskite [(FAPbI3)0.87(MAPbBr3)0.13]0.92[CsPbI3]0.08 (possessing better photovoltaic performance and stability than conventional CH3NH3PbI3) based inverted architecture PSCs. The average VOC of PSCs has increased from 908 mV of the devices with PEDOT:PSS HTM to 1020 mV of the devices with CuCrO2 HTM. Ultraviolet photoemission spectroscopy measurement demonstrates the energy band alignment between CuCrO2 and perovskite is better than that between PEDOT:PSS and perovskite, the electrochemical impedance spectroscopy indicates CuCrO2 based PSCs exhibit larger recombination resistance and longer charge carrier lifetime, which contribute to the high VOC of CuCrO2 HTM based PSCs.
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The burgeoning two-dimensional (2D) layered materials provide a powerful strategy to realize efficient light-emitting devices. Among them, Gallium telluride (GaTe) nanoflakes, emerging strong photoluminescence (PL) emission from multilayer to bulk crystal, relax the stringent fabrication requirements of nanodevices. However, detailed knowledge on the optical properties of GaTe varied as layer thickness is still missing. Here we perform thickness-dependent PL and Raman spectra, as well as temperature-dependent PL spectra of GaTe nanoflakes. Spectral analysis reveals a spectroscopic signature for the coexistence of both the monoclinic and hexagonal phases in GaTe nanoflakes. To understand the experimental results, we propose a crystal structure where the hexagonal phase is on the top and bottom of nanoflakes while the monoclinic phase is in the middle of the nanoflakes. On the basis of temperature-dependent PL spectra, the optical gap of the hexagonal phase is determined to 1.849 eV, which can only survive under a temperature higher than 200 K with the increasing phonon population. Furthermore, the exciton-phonon interaction of the hexagonal phase is estimated to be 1.24 meV/K. Our results prove the coexistence of dual crystalline phases in multilayer GaTe nanoflakes, which may provoke further exploration of phase transformation in GaTe materials, as well as new applications in 2D light-emitting diodes and heterostructure-based optoelectronics.
We report a measurement of electron momentum distributions of valence orbitals of cyclopentene employing symmetric noncoplanar (e, 2e) kinematics at impact energies of 1200 and 1600 eV plus the binding energy. Experimental momentum profiles for individual ionization bands are obtained and compared with theoretical calculations considering nuclear dynamics by harmonic analytical quantum mechanical and thermal sampling molecular dynamics approaches. The results demonstrate that molecular vibrational motions including ring-puckering of this flexible cyclic molecule have obvious influences on the electron momentum profiles for the outer valence orbitals, especially in the low momentum region. For π*-like molecular orbitals 3a'' and 2a''+3a' , the impact-energy dependence of the experimental momentum profiles indicates a distorted wave effect.
Red phosphorus (RP) has attracted more attention as a promising sodium storage material due to its ultra-high theoretical capacity, suitable sodiation potential. However, the low intrinsic electrical conductivity and large volume change of pristine RP lead to high polarization and fast capacity fading during cycling. Herein, surface synergistic protections on red phosphorus composite is successfully proposed by conductive poly (3, 4-ethylenedioxythiophene) (PEDOT) coating and electrolyte strategy. Nanoscale RP is confined in porous carbon skeleton and the outside is packaged by PEDOT coating via in-situ polymerization. Porous carbon provides rich access pathways for rapid Na+ diffusion and empty spaces accommodate the volume expansion of RP; PEDOT coating isolates the direct contact between electrolyte and active materials to form a stable solid electrolyte interphase. In addition, the reformulated electrolyte with 3 wt% SbF3 additive can stabilize the electrode surface and thus enhance the electrochemical performance, especially cycling stability and rate capability (433 mAh g-1 at high current density of 10 A g-1).
Metal-halide perovskite solar cells (PSCs) have attracted considerable attention during the past decade. However, due to the existence of non-radiative recombination losses, the best power conversion efficiency (PCE) is still lower than the theoretical limit defined by shockley-Queser theory. In this work, we investigate1,2,3-oxathiazin-4(3h)-one,6-methyl-2,2-dioxide (Acesulfame Potassium, abbreviated as AK) as a additional dopant for the 2,2′,7,7′-Tetrakis(N,N-di-p-methoxyphenyl-amine)-9,9′-spirobifluorene (Spiro-OMeTAD) and fabricate PSCs in the air. It is found that 12 mol % fraction of AK relative to lithium bis((trifluoromethyl)sulfonyl)-amide (Li-TFSI) reduced the non-radiative recombination from 86.05 % to 69.23 %, resulting in an average 0.08 V enhancement of Voc. The champion solar cell gives a PCE up to 21.9% and over 84% retention of the initial value during 720 h aging in dry air with 20%~30% humidity.
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We have investigated the adsorption of 9 different adatoms on the (111) and (100) surfaces of
Iridium (Ir) using first principles density functional theory. The study explores surface functionalization
of Ir which would provide important information for further study towards investigating its
functionality in catalysis and other surface applications. The adsorption energy, stable geometry,
density of states and magnetic moment are the physical quantities of our interest. Strong hybridization
between the adsorbates and the substrate electronic states revealed to impact the adsorption,
while the magnetic moment of the adsorbates found to be suppressed. In general, stronger binding
is observed on the (100) surface.
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Based on density functional theory (DFT), a new silicon allotrope (C2-Si) is proposed in this work. The mechanical stability and dynamic stability of C2-Si are examined based on the elastic constants and phonon spectrum. According to the BH/GH values, C2-Si has ductility under ambient pressure; compared with Si64, Si96, I4/mmm and h-Si6, C2-Si is less brittle. Within the Heyd-Scuseria-Ernzerhof (HSE06) hybrid functional, C2-Si is an indirect narrow band gap semiconductor, and the band gap of C2-Si is only 0.716 eV, which is approximately two-thirds that of c-Si. The ratios of the maximum and minimum values of the Young's modulus, shear modulus and Poisson's ratio in their 3D spatial distributions for C2-Si are determined to characterize the anisotropy. In addition, the anisotropy in different crystal planes is also investigated via 2D representations of the Young’s modulus, shear modulus and Poisson’s ratio. In addition, among more than ten silicon allotropes, C2-Si has the strongest absorption ability for visible light.
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In order to reduce the impact of CdS photogenerated electron-hole recombination on its photocatalytic performance, a narrow band gap semiconductor MoS2 and organic macromolecular cucurbit[n]urils(Q[n]) were used to modify CdS. Q[n]/CdS-MoS2 (n=6, 7, 8) composite photocatalysts were synthesized by hydrothermal method. Infrared spectroscopy (FT-IR), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), field emission scanning electron microscopy (SEM), ultraviolet-visible (UV-Vis) and photoluminescence spectrum (PL) were used to characterize the structure, morphology and optical properties of the products, and the catalytic degradation of the solutions of methylene blue, rhodamine B and crystal violet by Q[n]/CdS-MoS2 composite catalyst was investigated. The results showed that the Q[n] played a regulatory role on the growth and crystallization of CdS-MoS2 particles, Q[n]/CdS-MoS2 (n=6, 7, 8) formed flower clusters with petal-like leaves, the flower clusters of petal-like leaves increased the surface area and active sites of the catalyst, the Q[n]/CdS-MoS2 barrier width decreased, the electron-hole pair separation efficiency was improved in the Q[6]/Cds-MoS2. Q[n] makes the electron-hole pair to obtain better separation and migration. The Q[6]/CdS-MoS2 and Q[7]/CdS-MoS2 have good photocatalytic activity for methylene blue, and the catalytic process is based on hydroxyl radical principle.
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The laser-induced fluorescence excitation spectra of UF have been recorded in the range of 17000−19000 cm-1 using two-dimensional spectroscopy. High resolution dispersed fluorescence spectra and fluorescence decay curves time-resolved fluorescence spectroscopy were also recorded. Three rotationally resolved bands have been intensively analyzed, and all bands were found to be derived from the ground state X(1)4.5 with a rotational constant of 0.23421 cm-1. The low-lying electronic states have been observed near 435 and 651 cm-1 in the dispersed fluorescence spectra, which were assigned as Ωʹ = 3.5, and 2.5, respectively. The vibrational constants for the X(1)4.5 and X(1)3.5 states have been calculated. The branching ratios of the dispersed fluorescence spectra for the [18.62]3.5, [17.72]4.5, and [17.65]4.5 states were reported. Radiative lifetimes of 332(9), 825(49), and 433(15) ns for the [18.62]3.5, [17.72]4.5, and [17.65]4.5 states were obtained by fitting the fluorescence decay curves time-resolved fluorescence spectroscopy, respectively. Transition dipole moments were performed using the branching ratios and the radiative lifetimes.
Dimension-controllable supramolecular organic frameworks (SOFs) with aggregation-enhanced fluorescence are hierarchically fabricated through the host-guest interactions of CB[8] and coumarin-modified tetraphenylethylene derivatives (TPEC). The three-dimensional (3D) layered SOFs could be constructed from the gradual stacking of two-dimensional (2D) mono-layered structures via simply regulating the self-assembly conditions including the culturing time and concentration. Upon light irradiation under the wavelength of 350 nm, the photodimerization of coumarin moieties occurred, which resulted in the transformation of the resultant TPECn/CB[8]4n 2D SOFs into robust covalently-connected 2D polymers with molecular thickness. Interestingly, the supramolecular system of TPECn/CB[8]4n exhibited intriguing multicolor fluorescence emission from yellow to blue from 0 to 24 hours at 365 nm irradiation, possessing potential applicability for cell imaging and photochromic fluorescence ink.
Rational designs of electrocatalytic active sites and architectures are of great importance to develop cost-efficient non-noble metal electrocatalysts towards efficient oxygen reduction reaction (ORR) for high-performance energy conversion and storage devices. In this paper, active amorphous Fe-based nanoclusters (Fe NC) are elaborately embedded at the inner surface of balloon-like N-doped hollow carbon (Fe NC/C<sub>h</sub> sphere) as an efficient ORR electrocatalyst with an ultrathin wall of about 10 nm. When evaluated for electrochemical performance, Fe NC/C<sub>h</sub> sphere exhibits decent ORR activity with a diffusion-limited current density of ~5.0 mA cm<sup>-2</sup> and a half-wave potential of ~0.81 V in alkaline solution, which is comparable with commercial Pt/C and superior to Fe nanoparticles (NP) supported on carbon sheet (Fe NP/C sheet) counterpart. The electrochemical analyses combined with electronic structure characterizations reveal that robust Fe-N interactions in amorphous Fe nanoclusters are helpful for the adsorption of surface oxygen-relative species, and the strong support effect of N-doped hollow carbon is benefit for accelerating the interfacial electron transfer, which jointly contributes to improved ORR kinetics for Fe NC/C<sub>h</sub> sphere.
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In order to search for high energy density materials, various 4, 8-dihydrodifurazano[3,4-b,e]pyrazine based energetic materials were designed. Density functional theory was employed to investigate the relationships between the structures and properties. The calculated results indicated that the properties of these designed compounds were influenced by the energetic groups and heterocyclic substituents. The –N3 energetic group was found to be the most effective substituent to improve the heats of formation of the designed compounds while the tetrazole ring/–C(NO2)3 group contribute much to the values of detonation properties. The analysis of bond orders and bond dissociation energies showed that the addition of –NHNH2, –NHNO2, –CH(NO2)3 and –C(NO2)3 groups will decrease the bond dissociation energies remarkably. Compounds A8, B8, C8, D8, E8, and F8 were finally screened as the potential candidates for high energy density materials since these compounds possess excellent detonation properties and acceptable thermal stabilities. Additionally, the electronic structures of the screened compounds were calculated.
The photochemical reaction of potassium ferrocyanide (K4Fe(CN)6}) exhibits excitation wavelength dependence and non-Kasha rule behavior. In this study, the excited-state dynamics of K4Fe(CN)6 were studied by transient absorption spectroscopy. Excited state electron detachment (ESED) and phtoaquation reactions were clarified by comparing the results of 260 , 320 , 340 , and 350 nm excitations. ESED is the path to generate a hydrated electron (eaq-). ESED energy barrier varies with the excited state, and it occurrs even at the first singlet excited state (1T1g). The 1T1g state shows ~0.2 ps lifetime and converts into triplet [Fe(CN)6]4- by intersystem crossing. Subsequently, 3[Fe(CN)5]3- appears after one CN- ligand is ejected. In sequence, H2O attacks [Fe(CN)5]3- to generate [Fe(CN)5H2O]3- with a time constant of approximately 20 ps. The 1T1g state and eaq- exhibit strong reducing power. The addition of UMP to the K4Fe(CN)6 solution decreased the yield of eaq- and reduced the lifetimes of the eaq- and 1T1g state. The obtained reaction rate constant of 1T1g state and UMP was 1.7×1014 M-1 s-1, and the eaq- attachment to UMP was ~8×109 M-1 s-1. Our results indicate that the reductive damage of K4Fe(CN)6 solution to nucleic acids under ultraviolet irradiation cannot be neglected.
Rhodium-catalyzed cycloaddition reaction was calculated by density functional theory (DFT) M06-2X method to directly synthesize benzoxepine and coumarin derivatives. In this paper, we conducted a computational study of two competitive mechanisms in which the carbon atom of acetylene or carbon monoxide attacked and inserted from two different directions of the six-membered ring reactant to clarify the principle characteristics of this transformation. The calculation result reveal (1) the insertion process of alkyne or carbon monoxide is the key step of the reaction; (2) For the (5 + 2) cycloaddition reaction of acetylene, higher energy is required to break the Rh-O bond of the reactant, and the reaction tends to complete the insertion from the side of the Rh-C bond; (3) For the (5 + 1) cycloaddition of carbon monoxide, both reaction paths have lower activation free energy, and the two will generate a competition mechanism.
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Methyl 2-furoate (FAME2) is a renewable biofuel with the development of the new synthesis method of dimethyl furan-2,5-dicarboxylate. The potential energy surfaces (PES) of H-abstractions and OH-additions between FAME2 and hydroxyl radical (OH) were studied at the CCSD(T)/CBS//M062X/cc-pVTZ level. The following isomerization and decomposition reactions were also determined for the main radicals produced. The results show that the H-abstraction on the branch methyl group is the dominant channel and that the OH-addition reactions on the furan ring has a significant pressure dependency. The current rate coefficients provide important kinetic data for the further improving of the combustion mechanism of FAME2, which bring a trusty reference for further research on practical fuels.
The vacuum ultraviolet (VUV) photodissociation of OCS via the F 31Π Rydberg states was investigated in the range of 134–140 nm, by means of the time-sliced velocity map ion imaging technique. The images of S (1D2) products from the CO (X1Σ+) + S (1D2) dissociation channel were acquired at five photolysis wavelengths, corresponding to a series of symmetric stretching vibrational excitations in OCS (F 31Π, v1=0-4). The total translational energy distributions, vibrational populations and angular distributions of CO (X1Σ+, v) coproducts were derived. The analysis of experimental results suggests that the excited OCS molecules dissociate to CO (X1Σ+) and S (1D2) products via non-adiabatic couplings between the upper F 31Π states and the lower-lying states both in the C∞v and Cs symmetry. Furthermore, strong wavelength dependent behavior has been observed: the greatly distinct vibrational populations and angular distributions of CO (X1Σ+, v) products from the lower (v1=0-2) and higher (v1=3,4) vibrational states of the excited OCS (F 31Π, v1) demonstrate that very different mechanisms are involved in the dissociation processes. This study provides evidence for the possible contribution of vibronic coupling and the crucial role of vibronic coupling on the VUV photodissociation dynamics.
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The hierarchical stochastic Schrödinger equations (HSSE) are a kind of numerically exact wavefunction-based approaches suitable for the quantum dynamics simulations in a relatively large system coupled to a bosonic bath. Starting from the influence-functional description of open quantum systems, this review outlines the general theoretical framework of HSSEs and their concrete forms in different situations. The applicability and efficiency of HSSEs are exemplified by the simulations of ultrafast excitation energy transfer processes in large-scale systems.
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Stars with masses between 1 and 8 solar masses (M⊙) lose large amounts of material in the form of gas and dust in the late stages of stellar evolution, during their Asymptotic Giant Branch phase. Such stars supply up to 35% of the dust in the interstellar medium and thus contribute to the material out of which our solar system formed. In addition, the circumstellar envelopes of these stars are sites of complex, organic chemistry with over 80 molecules detected in them. We show that internal ultraviolet photons, either emitted by the star itself or from a close-in, orbiting companion, can significantly alter the chemistry that occurs in the envelopes particularly if the envelope is clumpy in nature. At least for the cases explored here, we find that the presence of a stellar companion, such as a white dwarf star, the high flux of UV photons destroys H2O in the inner regions of carbon-rich AGB stars to levels below those observed and produces species such as C+ deep in the envelope in contrast to the expectations of traditional descriptions of circumstellar chemistry.
Two-photon fluorescence dyes have shown promising applications in biomedical imaging. However, the substitution site effect on geometric structures and photophysical properties of fluorescence dyes is rarely illustrated in detail. In this work, a series of new lipid droplets detection dyes are designed and studied, molecular optical properties and non-radiative transitions are analyzed. The intramolecular weak interaction and electron-hole analysis reveal its inner mechanisms. All dyes are proved to possess excellent photophysical properties with high fluorescence quantum efficiency and large stokes shift as well as remarkable TPA cross section. Our work reasonably elucidates the experimental measurements and the effects of substitution site on two-photon absorption and excited states properties of Lipid droplets detection NAPBr dyes are highlighted, which could provide a theoretical perspective for designing efficient organic dyes for lipid droplets detection in biology and medicine fields.
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We predict two novel group 14 element alloys Si2Ge and SiGe2 in P6222 phase in this work through first-principles calculations. The structures, stability, elastic anisotropy, electronic and thermodynamic properties of these two proposed alloys are investigated systematically. The proposed P6222-Si2Ge and -SiGe2 have a hexagonal symmetry structure, and the phonon dispersion spectra and elastic constants indicate that these two alloys are dynamically and mechanically stable at ambient pressure. The elastic anisotropy properties of P6222-Si2Ge and -SiGe2 are examined elaborately by illustrating the surface constructions of Young’s modulus, the contour surfaces of shear modulus, and the directional dependences of Poisson’s ratio, as well as discussing and comparing the differences with their corresponding group 14 element allotropes P6222-Si3 and -Ge3. Moreover, the Debye temperature and sound velocities are analyzed to study the thermodynamic properties of the proposed P6222-Si2Ge and -SiGe2.
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Herein we present a facile approach for the preparation of a novel hierarchically porous carbon, in which seaweeds serve as carbon source and KOH as activator. The fabricated KOH-activated seaweed carbon (K-SC) displays strong affinity towards tetracycline (TC) with maximum uptake quantity of 853.3 mg g–1, significantly higher than other TC adsorbents. The superior adsorption capacity ascribes to large specific surface area (2614 m2 g−1) and hierarchically porous structure of K-SC, along with strong π–π interactions between TC and K-SC. In addition, the as-prepared K-SC exhibits fast adsorption kinetics, capable of removing 99% of TC in 30 min. Meanwhile, the exhausted K-SC can be regenerated for four cycling adsorption without an obvious degradation in capacities. More importantly, pH and ionic strengths barely affect the adsorption performance of K-SC, implying electrostatic interactions hardly play any role in TC adsorption process. Furthermore, the K-SC packed fixed-bed column (0.1 g of adsorbents) can continually treat 2780 mL solution spiked with 5.0 mg g–1 TC before reaching the breakthrough point. All in all, the fabricated K-SC equips with high adsorption capacity, fast adsorption rate, glorious anti-interference capability and good reusability, which make it holding great feasibilities for treating TC contamination in real applications.
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Theoretical study was carried out with OX2 (X = Halogen) molecules and calculation results showed that delocalized π36 bonds exists in their electronic structures and O atoms adopt the sp2 type of hybridization, which violated the VSEPR theory’s prediction of sp3 type. Delocalization stabilization energy (DSE) was proposed to measure delocalized π36 bond’s contribution to energy decrease and proved that it brings extra-stability to the molecule. According to our analyses, these phenomena can be summarized as a kind of coordinating effect.
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The boom in ultra-thin electronic devices and the growing need for humanization greatly facilitated the development of wearable flexible micro-devices. But the technology to deposit electrode material on flexible substrate is still in its infancy. Herein, the flexible symmetric micro-supercapacitors made of carbon nanotubes (CNTs) on commercial printing paper as electrode materials were fabricated by combining tetrahedral preparator auxiliary coating method and laser-cutting interdigital configuration technique on a large scale. The electrochemical performance of obtained micro-supercapacitors can be controlled and tuned by simple choosing the different model of tetrahedral preparatory to obtain CNTs film of different thickness. As expected, the micro-supercapacitor based on CNTs film can deliver an areal capacitance of up to 4.56 mF cm-2 at current of 0.02 mA. Even if, micro-supercapacitor undergo continuous 10000 cycles, the performance of device can still remain nearly 100%. The as-demonstrated tetrahedral preparator auxiliary coating method and laser-cutting interdigital configuration technique provide new perspective for preparing microelectronics in an economical way. The paper electrode appended by CNTs achieves steerable areal capacitance, showing broad application prospect in fabricating asymmetric micro-supercapacitor with flexible planar configurations in the future.
Smart functional microgels hold great potential in a variety of applications, especially in drug transportation. However, current drug carriers based on physiological internal stimuli cannot efficiently orientate to designated locations. Therefore, it is necessary to introduce the self-propelled particles to the drug release of the microgels. In order to study self-propulsion of microgels induced by light, it is also a challenge to prepare micron-sized microgels so that they can be observed directly under optical microscopes. This paper presents a method to prepare phototactic microgels with photoresponsive properties. The microgel particles is observed by confocal laser scanning microscopy (CLSM). The photoresponsive properties of microgels are fully investigated by various instruments. Light can also regulate the state of the microgel solution, making it switch between turbidity and clarity. The phototaxis of particles irradiated by UV light was studied, which may be used for microgels enrichment and drug transportation and release.
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In this study, the application of bovine serum albumin (BSA) to glucose- sensitive materials was proposed for the first time. Au-CuO bimetallic nanoclusters (Au-CuO/BSA) were prepared using BSA as a template, the new sensing material (Au-CuO/BSA/MWCNTs) was synthesized by mixing with multi-walled carbon nanotubes (MWCNT) and applied to non-enzymatic electrochemical sensors to detect glucose stably and effectively under neutral conditions. The scanning electron microscopy was used to investigate the morphology of the synthesized nanocomposite. The electrochemical properties of the sensor were studied by cyclic voltammetry. Glucose detection experiments showed that Au-CuO/BSA/MWCNTs/Au electrode had good glucose detection ability, stability, accuracy, repeatability, and high selectivity in neutral environment. Unlike existing glucose-sensitive materials, due to the use of BSA, the composite material is firmly fixed to the electrode surface without a Nafion solution, which reduces the current blocking effect on the modified electrode. The composite materials can be effectively preserved for extremely long periods, higher than 80% activity was maintained at room temperature in a closed environment for 3 to 4 months, due to the special effects of BSA. In addition, the feasibility of using BSA in glucose-sensitive materials was confirmed.
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Our experimental progresses on the reaction dynamics of dissociative electron attachment (DEA) to carbon dioxide (CO2) are summarized in this review. First, we introduce some fundamentals about the DEA dynamics and provide an epitome about the DEAs to CO2. Second, our development on the experimental techniques is described, in particular, on the high-resolution velocity map imaging apparatus in which we put a lot of efforts during the past two years. Third, our findings about the DEA dynamics of CO2 are surveyed and briefly compared with the others’ work. At last, we give a perspective about the applications of the DEA studies and highlight the inspirations in the production of molecular oxygen on Mars and the catalytic transformations of CO2.
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Si (111) electrode has been widely used in electrochemical and photoelectrochemical studies. The potential dependent measurements of the second harmonic generation (SHG) were performed to study Si (111) electrolyte interface. At different azimuthal angles of the Si (111) and under different polarization combinations, the curve of the intensity of SHG with extern potential have different form of line or parabola. A quantitative analysis showed that this differences of the potential-dependence can be explained by the isotropic and anisotropic contribution of the Si (111) electrode. The change in isotropic and anisotropic contribution of the Si (111) electrode may be attributed to the increase in doping concentration of Si (111) electrodes.
Reactions of gas-phase species with small molecules are being actively studied to understand the elementary steps and mechanistic details of related condensed-phase processes. Activation of the very inert N≡N triple bond of dinitrogen molecule by isolated gas-phase species has attracted considerable interest in the past few decades. Apart from molecular adsorption and dissociative adsorption, interesting processes such as C–N coupling and degenerate ligand exchange were discovered. The present review article focuses on the recent progress on adsorption, activation, and functionalization of N2 by gas-phase species (particularly metal cluster ions) using mass spectrometry, infrared photo-dissociation spectroscopy, anion photoelectron spectroscopy, and quantum chemical calculations including density functional theory and high-level ab-initio calculations. Recent advances including characterization of adsorption products, dependence of clusters' reactivity on their sizes and structures, and mechanisms of N≡N weakening and splitting have been emphasized and prospects have been discussed.
Defect-mediated processes in two-dimensional transition metal dichalcogenides have a significant influence on their carrier dynamics and transport properties, however, the detailed mechanisms remain poorly understood. Here, we present a comprehensive ultrafast study on defect-mediated carrier dynamics in ion exchange prepared few-layer MoS<sub>2</sub> by femtosecond time-resolved Vis-NIR-MIR spectroscopy. The broadband photobleaching feature observed in the near-infrared transient spectrum discloses that the mid-gap defect states are widely distributed in few-layer MoS<sub>2</sub> nanosheets. The processes of fast trapping of carriers by defect states and the following nonradiative recombination of trapped carriers are clearly revealed, demonstrating the mid-gap defect states play a significant role in the photoinduced carrier dynamics. The positive to negative crossover of the signal observed in the mid-infrared transient spectrum further uncovers some occupied shallow defect states distributed at less than 0.24 eV below the conduction band minimum. These defect states can act as effective carrier trap centers to assist the nonradiative recombination of photo-induced carriers in few-layer MoS<sub>2</sub> on the picosecond time scale.
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Silicon bulk etching is an important part of micro-electro-mechanical system (MEMS) technology. In this work, a novel etching method is proposed based on the vapor from TMAH solution heated up to boiling point. The monocrystalline silicon wafer is positioned over the solution surface and can be anisotropically etched by the produced vapor. This etching method does not rely on the expensive vacuum equipment used in dry etching. Meanwhile, it presents several advantages like low roughness, high etching rate and high uniformity compared with the conventional wet etching methods. The etching rate and roughness can reach 2.13 μm/min and 1.02 nm, respectively. To our knowledge, this rate is the highest record for the wet etching based on TMAH. Furthermore, the diaphragm structure and Al-based pattern on the non-etched side of wafer can maintain intact without any damage during the back-cavity fabrication. Finally, an etching mechanism has been proposed to illustrate the observed experimental phenomenon. It is suggested that there is a water thin film on the etched surface during the solution evaporation. It is in this water layer that the ionization and etching reaction of TMAH proceed, facilitating the desorption of hydrogen bubble and the enhancement of molecular exchange rate.
Methyl vinyl ketone oxide (MVCI), an unsaturated four-carbon Criegee intermediate produced from the ozonolysis of isoprene has been recognized to play a key role in determining the tropospheric OH concentration. It exists in four configurations (anti_anti, anti_syn, syn_anti and syn_syn) due to two different substituents of saturated methyl and unsaturated vinyl groups. In this study, we have carried out the electronic structure calculation at the multi-configurational CASSCF and multi-state MS-CASPT2 levels, as well as the trajectory surface-hopping (TSH) nonadiabatic dynamics simulation at the CASSCF level to reveal the different fates of syn/anti configurations in photochemical process. Our results show that the dominant channel for the S1-state decay is a ring closure, isomerization to dioxirane, during which, the syn(C-O) configurations with an intramolecular hydrogen bond show slower nonadiabatic photoisomerization. More importantly, it has been found for the first time in photochemistry of Criegee intermediate that the cooperation of two heavy groups (methyl and vinyl) leads to an evident pyramidalization of C3 atom in MVCI, which then results in two structurally-independent minimal-energy crossing points (CIs) towards the syn(C-O) and anti(C-O) sides, respectively. The preference of surface hopping for a certain CI is responsible for the different dynamics of each configuration.
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The photodissociation dynamics of AlO at 193 nm is studied using time-sliced ion velocity mapping. Two dissociation channels are found through the speed and angular distributions of aluminum ions: one is one photon dissociation of the neutral AlO to generate Al(2Pu) + O(3Pg), and the other is two-photon ionization and then dissociation of AlO+ to generate Al+(1Sg) + O(3Pg). Each dissociation channel includes the contribution of AlO in the vibrational states v = 0-2. The anisotropy parameter of the neutral dissociation channel is more dependent on the vibration state of AlO than the ion dissociation channel.
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We report a study on photo-ionization of benzene and aniline with incidental subsequent dissociation by the customized reflection time-of-flight mass spectrometer utilizing a deep ultraviolet (DUV) 177.3 nm laser. Highly efficient ionization of benzene is observed with a weak C4H3+ fragment formed by undergoing disproportional C−C bond dissociation. In comparison, a major C5H6+• fragment and a minor C6H6+• radical are produced in the DUV ionization of aniline pertaining to the removal of CNH* and NH* radicals, respectively. First-principles calculation is employed to reveal the photo-dissociation pathways of these two molecules having a structural difference of just an amino group. It is demonstrated that hydrogen atom transfer (HAT) plays an important role in the cleavage of C−C or C−N bonds in benzene and aniline ions. This study helps understand the underlying mechanisms of chemical bond fracture of benzene ring and related aromatic molecules.
Recent experiments report the rotation of FA (FA= HC[NH2]2+) cations significantly influence the excited-state lifetime of FAPbI3. However, the underlying mechanism remains unclear. Using ab initio nonadiabatic (NA) molecular dynamics combined with time-domain density functional simulations, we have demonstrated that eeorientation of partial FA cations significantly inhibits nonradiative electron-hole recombination with respect to the pristine FAPbI3 due to the decreased NA coupling by localizing electron and hole in different positions and the suppressed atomic motions. Slow nuclear motions simultaneously increase the decoherence time but which is overcomed by the reduced NA coupling, extending electron-hole recombination time scales to several nanoseconds and being about 3.9 times longer than that in pristine FAPbI3, which occurs within sub-nanosecond and agrees with experiment. Our study established the mechanism for the experimentally reported prolonged excited-state lifetime, providing rational strategy for design of high performance of perovskite solar cells and optoelectronic devices.
Sum frequency generation vibrational spectroscopy (SFG-VS) is a powerful technique for determining molecular structures at both buried interface and air surface. Distinguishing the contribution of SFG signals from buried interface and air surface is crucial to the applications in devices such as microelectronics and bio-tips. Here we demonstrate that the SFG spectra from buried interface and air surface can be differentiated by controlling the film thickness and employment of surface-plasmon enhancement. Using substrate-supported PMMA films as a model, we have visualized the variations in the contribution of SFG signals from buried interface and air surface. By monitoring carbonyl and C-H stretching groups, we found that SFG signals are dominated by the moieties (-CH2, -CH3, -OCH3 and C=O) segregated at the PMMA/air surface for the thin films while they are mainly contributed by the groups (-OCH3 and C=O) at the substrate/PMMA buried interface for the thick films. At the buried interface, the tilt angle of C=O decreases from 65° to 43° as the film preparation concentration increases; in contrast, the angles at the air surface fall in the range between 38° and 21°. Surface plasmon generated by gold nanorod can largely enhance SFG signals, particularly the signals from the buried interface.
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Inspired by the branching corrected surface hopping (BCSH) method [J. Xu and L. Wang, J. Chem. Phys. 150, 164101 (2019)], we present two new decoherence time formulas for trajectory surface hopping. Both the proposed linear and exponential formulas characterize the decoherence time as functions of the energy difference between adiabatic states and correctly capture the decoherence effect due to wave packet reflection as predicted by BCSH. The relevant parameters are trained in a series of 200 diverse models with different initial nuclear momenta and the exact quantum solutions are utilized as references. As demonstrated in the three standard Tully models, the two new approaches exhibit significantly higher reliability than the widely used counterpart algorithm while holding the appealing efficiency, thus promising for nonadiabatic dynamics simulations of general systems.
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A fundamental study on C?C coupling that is the crucial step in the Fischer-Tropsch synthesis (FTS) process to obtain multi-carbon products is of great importance to tailor catalysts and then guide a more promising pathway. It has been demonstrated that the coupling of CO with the metal carbide can represent the early stage in the FTS process, while the related mechanism is elusive. Herein, the reactions of the CuC3H– and CuC3– cluster anions with CO have been studied by using mass spectrometry and theoretical calculations. The experimental results showed that the coupling of CO with the C3H– moiety of CuC3H– can generate the exclusive ion product COC3H–. The reactivity and selectivity of this reaction are greatly higher than that on the reaction of CuC3– with CO, and this H-assisted C?C coupling process was rationalized by theoretical calculations.
Photo-induced proton coupled electron transfer (PCET) is essential in the biological, photosynthesis, catalysis and solar energy conversion processes. Recently, p-nitrophenylphenol (HO-Bp-NO<sub>2</sub>) has been used as a model compound to study the photo-induced PCET mechanism using ultrafast spectroscopy. In transient absorption spectra both singlet and triplet exhibited PCET behavior. When we focused on the PCET in the triplet state, a new sharp band attracted us. This band had not been observed for p-nitrobiphenyl which is without hydroxyl substitution. To assign the new band, acidic solutions were used as an additional proton donor. Based on results in strong (~10<sup>-1</sup> M) and weak (~10<sup>-4</sup> M) acidic solutions, the new band is identified as the open shell singlet O-Bp-NO<sub>2</sub>H, which is generated through protonation of nitro O in <sup>3</sup>HO-Bp-NO<sub>2</sub> followed by deprotonation of hydroxyl. Kinetics analysis indicates the formation of radical •O-Bp-NO<sub>2</sub> competes with O-Bp-NO<sub>2</sub>H in the way of concerted electron-proton transfer and/or proton followed electron transfers and is responsible for the low yield of O-Bp-NO<sub>2</sub>H. The results in the present work will make it clear that how the <sup>3</sup>HO-Bp-NO<sub>2</sub> deactivates in aprotic polar solvents and provide a solid benchmark for the deeply studying the PCET mechanism in triplets of analogous aromatic nitro compound.
In recent decades, materials science has experienced rapid development and posed increasingly high requirements for the characterizations of structures, properties, and performances. Herein, we report on our recent establishment of a multi-domain (energy, space, time) high-resolution platform for integrated spectroscopy and microscopy characterizations, offering an unprecedented way to analyze materials in terms of spectral (energy) and spatial mapping as well as temporal evolution. We present several proof-of-principle results collected on this platform, including in-situ Raman imaging (high-resolution Raman, polarization Raman, low-wavenumber Raman), time-resolved photoluminescence imaging, and photoelectrical performance imaging. It can be envisioned that our newly established platform would be very powerful and effective in the multi-domain high-resolution characterizations of various materials of photoelectrochemical importance in the near future.
Hydrogels show versatile properties and are of great interest in the fields of bioelectronics and tissue engineering. Understanding the dynamics of the water molecules trapped in the three-dimensional polymeric networks of the hydrogels is crucial for us to elucidate their mechanical and swelling properties at the molecular level. In this report, the poly(DMAEMA-co-AA) hydrogels were synthesized and characterized by the macroscopic swelling measurements under different pH conditions. Furthermore, the microscopic structural dynamics of pH stimulus responsive hydrogels were studied using FTIR and ultrafast IR spectroscopies from the viewpoint of the SCN-anionic solute as the local vibrational reporter. Ultrafast IR spectroscopic measurements showed the time constants of the vibrational population decay of SCN- were increased from 14±1 ps to 20±1 ps when the pH of the hydrogels is varied from 2.0 to 12.0. Rotational anisotropy measurements further revealed that the rotation of SCN- anionic probe was restricted by the three-dimensional network formed in the hydrogels and the rotation of SCN- anionic probe can’t decay to zero especially at the pH of 7.0. These results presented in this study are expected to provide molecular level understanding of the microscopic structure of the cross-linked polymeric network in the pH stimulus-responsive hydrogels.
Among various photocatalytic materials, Z-scheme photocatalysts have drawn tremendous research interest due to the high photocatalytic performance in solar water splitting. Here, we perform extensive hybrid density functional theory calculations to explore electronic structures, interfacial charge transfer, electrostatic potential profile, optical absorption properties, and photocatalytic properties of a proposed two-dimensional small-lattice-mismatched GaTe/Bi2Se3 heterostructure. Theoretical results clearly reveal that the examined heterostructure with a small direct band gap can effectively harvest the broad spectrum of the incoming sunlight. Due to the relative strong interfacial built-in electric field in the heterostructure and the small band gap between the valence band maximum of GaTe monolayer and the conduction band minimum of Bi2Se3 nanosheet with slight band edge bending, the photogenerated carriers transfer via Z-scheme pathway, which results in the photogenerated electrons and holes effectively separating into the GaTe monolayer and the Bi2Se3 nanosheet for the hydrogen and oxygen evolution reactions, respectively. Our results imply that the artificial 2D GaTe/Bi2Se3 is a promising Z-scheme photocatalyst for overall solar water splitting.
The IRMPD spectrum of the protonated heterodimer of ProPheH+, in the range of 2700-3700 cm-1, has been obtained with a Fourier-transform ion cyclotron mass spectrometer combined with an IR OPO laser. The experimental spectrum shows one peak at 3560 cm?1 corresponding to the free carboxyl O-H stretching vibration, and two broad peaks centered at 2935 and 3195 cm?1. Theoretical calculations were performed on the level of M062X/6-311++G(d,p). Results show that the most stable isomer is characterized by a charge-solvated structure in which the proton is bound to the unit of Pro. Its predicted spectrum is in good agreement with the experimental one, although the coexistence of salt-bridged structures cannot be entirely excluded.
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A Mn3O4 coating is approved to modify the surface of LiNi0.5Mn1.5O4 particles by a simple wet grinding method for the first time, which realize an great improvement in electronic conductivity from 1.53?10-7 S cm-1 to 3.15?10-5 S cm-1 after 2.6% Mn3O4 coating. The electrochemical test resualts demonstrate that the Mn3O4 coating dramatically enhances both the rate performance and cycling capability (at 55 °C) of LiNi0.5Mn1.5O4. Among the samples, 2.6% Mn3O4-coated LiNi0.5Mn1.5O4 not only exhibits excellent rate capability (a large capacity of 108 mAh g-1 at 10 C rate) but also keep 78% capacity retention at 55 °C and 1 C rate after 100 cycles.
Formaldehyde and hydrogen peroxide are two important realistic molecules in atmospheric chemistry. We implement path integral Liouville dynamics (PILD) to calculate the dipole-derivative autocorrelation function for obtaining the infrared (IR) spectrum. In comparison to exact vibrational frequencies, PILD faithfully capture most nuclear quantum effects in vibrational dynamics as temperature changes and as the isotopic substitution occurs.
Two non-ionic hydro-fluorocarbon hybrid surfactants with and without hydroxyl groups were synthesized and compared. They exhibited good thermal stability and superior surface activity. It was observed that the hydroxyl group had a profound effect on modifying the surface tension of their solutions and the morphology of the formed micelles. This effect may be attributed to the rearranging of the alkane group from above the air/aqueous surface to below it and the disrupting of the interfacial water structure induced by the hydroxyl groups. This work provides a strategy to weaken the immiscibility between hydrocarbon and fluorocarbon chains by modifying their orientational structure at the interface, thus is helpful for the design of surfactants with varied interfacial properties.
Empirical potential structure refinement (EPSR) is a neutron scattering data analysis algorithm and a software package. It was developed by the British spallation neutron source (ISIS) Disordered Materials Group in 1980s, and aims to construct the most-probable atomic structures of disordered materials in the field of chemical physics. It has been extensively used during the past decades, and has generated reliable results. However, it implements a shared-memory architecture with Open Multi-Processing (OpenMP). With the extensive construction of supercomputer clusters and the widespread use of graphics processing unit (GPU) acceleration technology, it is now possible to rebuild the EPSR with these techniques in the effort to improve its calculation speed. In this study, an open source framework NeuDATool is proposed. It is programmed in the object-oriented language C++, can be paralleled across nodes within a computer cluster, and supports GPU acceleration. The performance of NeuDATool has been tested with water and amorphous silica neutron scattering data. The test shows that the software can reconstruct the correct microstructure of the samples, and the calculation speed with GPU acceleration can increase by more than 400 times, compared with CPU serial algorithm at a simulation box that consists about 100 thousand atoms. NeuDATool provides another choice to implement simulation in the (neutron) diffraction community, especially for experts who are familiar with C++ programming and want to define specific algorithms for their analysis.
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In this paper, the effect of channel length and width on the large and small-signal parameters of the Graphene Field Effect Transistor (GFET) have been explored using an analytical approach. In the case of faster saturation as well as extremely high transit frequency GFET shows outstanding performance. From the transfer curve, it is observed that there is a positive shift of Dirac point from the voltage of 0.15 V to 0.35 V because of reducing channel length from 440 nm to 20 nm and this curve depicts that graphene shows ambipolar behavior. Besides, it is found that because of widening channel the drain current increases and the maximum current is found approximately 2.4 mA and 6 mA for channel width 2μm and 5μm respectively. Furthermore, an approximate symmetrical capacitance-voltage (C–V) characteristic of GFET is obtained and found that capacitance reduces when the channel length decreases but the capacitance can be increased by raising the channel width. In addition, a high transconductance of 6.4 mS at channel length 20 nm and 4.45 mS at channel width 5 μm along with a high transit frequency of 3.95 THz has been found that demands high-speed radio frequency (RF) applications.
Two thin-film 2D organic–inorganic hybrid perovskites, i.e., 2-phenylethylammonium lead iodide (PEPI) and 4-phenyl-1-butylammonium lead iodide (PBPI) were synthesized and investigated by steady-state absorption, temperature-dependent photoluminescence, and temperature-dependent ultrafast transient absorption spectroscopy. PBPI has a longer organic chain (via introducing extra ethyl groups) than PEPI, thus its inorganic skeleton can be distorted bringing on structural disorder. The comparative analyses of spectral profiles and temporal dynamics revealed that the greater structural disorder in PBPI results in more defect states serving as trap states to promote exciton dynamics. In addition, the fine-structuring of excitonic resonances was unveiled by temperature-dependent ultrafast spectroscopy, suggesting its correlation with inorganic skeleton rather than organic chain. Moreover, the photoexcited coherent phonons were observed in both PEPI and PBPI, pointing to a subtle impact of structural disorder on the low-frequency Raman-active vibrations of inorganic skeleton. This work provides valuable insights into the optical properties, excitonic behaviors and dynamics, as well as coherent phonon effects in 2D hybrid perovskites.
In this study, we have developed a high-sensitivity, near-infrared photodetector (NIRPD)
based on PdSe2/GaAs heterojunction, which was made by transferring a multilayered PdSe2
film onto a planar GaAs. The as-fabricated PdSe2/GaAs heterojunction device exhibited
obvious photovoltaic behavior to 808 nm illumination, indicating that the NIRPD can be
used as a self-driven device without external power supply. Further device analysis showed
that the hybrid heterojunction exhibited a high on/off ratio ratio of 1.16×105 measured at
808 nm under zero bias voltage. The responsivity and specific detectivity of photodetector
were estimated to be 171.34 mA/W and 2.36×1011 Jones, respectively. Moreover, the device showed excellent stability and reliable repeatability. After 2 months, the photoelectric
characteristics of the NIRPD hardly degrade in air, attributable to the good stability of the
PdSe2. Finally, the PdSe2/GaAs-based heterojunction device can also function as a NIR
light sensor.
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Over the last few years, machine learning is gradually becoming an essential approach for the investigation of heterogeneous catalysis. As one of the important catalysts, binary alloys have attracted extensive attention for the screening of bifunctional catalysts. Here we present a holistic framework for machine learning approach to rapidly predict adsorption energies on the surfaces of metals and binary alloys. We evaluate different machine-learning methods to understand their applicability to the problem and combine a tree-ensemble method with a compressed-sensing method to construct decision trees for about 60,000 adsorption data. Compared to linear scaling relations, our approach enables to make more accurate predictions lowering predictive root-mean-square error by a factor of two and more general to predict adsorption energies of various adsorbates on thousands of binary alloys surfaces, thus paving the way for the discovery of novel bimetallic catalysts.
The simple homodinuclear M-M single bonds for Group II and XII elements are difficult to obtain as a result of the fulfilled s2 electronic configurations, consequently, a dicationic prototype is often utilized to design the M+-M+ single bond. Existing studies generally use sterically bulky organic ligands L- to synthesize the compounds in an L--M+-M+-L- manner. However, here we report the design of Mg-Mg and Zn-Zn single bonds in two ligandless clusters, Mg2B7- and Zn2B7-, using density functional theory methods. The global minima of both of the clusters are in the form of M22+(B73-), where the M-M single bonds are positioned above a quasi-planar hexagonal B7 moiety. Chemical bonding analyses further confirm the existence of Mg-Mg and Zn-Zn single bonds in these clusters, which are driven by the unusually stable B73- moiety that is both σ and π aromatic. Vertical detachment energies of Mg2B7- and Zn2B7- are calculated to be 2.79 eV and 2.94 eV, respectively, for the future comparisons with experimental data.
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We carried out first-principles calculations to investigate the electronic properties of the monolayer blue phosphorene (BlueP) decorated by the group-IVB transition-metal adatoms (Cr, Mo and W), and found that the Cr-decorated BlueP is a magnetic half metal, while the Mo- andW-decorated BlueP are semiconductors with band gaps smaller than 0.2 eV. Compressive biaxial strains make the band gaps close and reopen and band inversions occur during this process, which induces topological transitions in the Mo-decorated BlueP (with strain of ??5:75%) and W-decorated BlueP (with strain of ??4:25%) from normal insulators to topological insulators (TIs). The TI gap is 94 meV for the Mo-decorated BlueP and 218 meV for the W-decorated BlueP. Such large TI gaps demonstrate the possibility to engineer topological phases in the monolayer BlueP with transition-metal adatoms at high temperature.
We constructed two types of copper-doped metal–organic framework (MOF), i.e., Cu@UiO-66-NH2 and Cu-UiO-66-NH2. In the former, Cu2+ ions are impregnated in the pore space of the amine-functionalized, Zr-based UiO-66-NH2; while in the latter, Cu2+ ions are incorporated to form a bimetal-center MOF with Zr4+ being partially replaced by Cu2+ in the Zr–O oxo-clusters. Ultrafast spectroscopy revealed that the photoinduced relaxation kinetics associated with the ligand-to-cluster charge-transfer state are promoted for both Cu-doped MOFs relative to undoped one, but in a sequence of Cu-UiO-66-NH2 > Cu@UiO-66-NH2 > UiO-66-NH2. Such a sequence turned to be in line with the trend observed in the visible-light photocatalytic hydrogen evolution activity tests on the three MOFs. These findings highlighted the subtle effect of copper-doping location in this Zr-based MOF system, further suggesting that rational engineering of the specific metal-doping location in alike MOF systems to promote the photoinduced charge separation and hence suppress the detrimental charge recombination therein is beneficial for achieving improved performances in MOF-based photocatalysis.
In this work, p-type Co3O4 decorated n-type ZnO (Co3O4/ZnO) nanocomposite was designed with the assistance of bacterial cellulose template. Phase composition, morphology and element distribution were investigated by XRD, SEM, HRTEM, EDS mapping and XPS. Volatile organic compounds (VOCs) sensing measurements indicated a noticeable improvement of response and decrease of working temperature for Co3O4/ZnO sensor, in comparison with pure ZnO, i.e., the response towards 100 ppm acetone was 63.7 (at a low working temperature of 180 °C), which was 26 times higher than pure ZnO (response of 2.3, at 240 °C). Excellent VOCs response characteristics could be ascribed to increased surface oxygen vacancy concentration (revealed by defect characterizations), catalytic activity of Co3O4 and the special p-n heterojunction structure, and bacterial cellulose provides a facile template for designing diverse functional heterojunctions for VOCs detection and other applications.
The special mass shift coefficient, ΔKSMS, and field parameter factor, Ful of four multiples, 3〖s 〗^4 P→3〖p 〗^4 P^°, 3〖s 〗^4 P→3〖p 〗^4 D^°, 3〖s 〗^2 D→5〖p 〗^2 D^°, and 3〖s 〗^2 P→3〖p 〗^2 P^°, of 14N and 15N were studied using the multi-configuration Dirac–Hartree–Fock method and the relativistic configuration interaction approach. The normal mass shift, special mass shift, field shift, and isotope shift of N I were derived from the theoretical calculated ΔKSMS, ΔKSMS and Ful, and compared with the reported experimental measurements and theoretical results.
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The structures and electronic properties of the gaseous M2Pt20/? clusters (M represents the alkaline earth metal) are investigated using the density functional theory (B3LYP and PBE0) and wave function theory (SCS-MP2, CCSD and CCSD (T)). The results show that the D2h isomers with the planar structures are more stable than the C2V isomers with smaller dihedral angles and shorter Pt-Pt bond lengths. In this work we show that the mutual competition of M(s, p)-Pt(5d) interaction and Pt-Pt covalent bonding contributes to the different stabilizations of the two kinds of isomers. The M(s, p)-Pt(5d) interaction favors the planar isomers with D2h symmetry, while the Pt-Pt covalent bonding leads to the C2V isomers with bending structures. Two different crossing points are determined in the potential energy curves of Be2Pt2 with the singlet and triplet states. But there is just one crossing point in potential energy curves of Ra2Pt2 and Ca2Pt2? because of flatter potential energy curves of Ra2Pt2 with the triplet state or Ca2Pt2? with quartet state. The results reveal a unique example of dihedral angle-bending isomers with the smallest number of atoms and may help the understanding of the bonding properties of other potential angle-bending isomers.
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From the organization of animal ocks to the emergence of swarming behav- iors in bacterial suspension, populations of motile organisms at all scales display coherent collective motion. Recent studies showed the anisotropic interaction between the active particles plays a key role on the phase behaviors. Here we investigate the collective behaviors of active Janus particles that experience an anisotropic interaction that is opposite to the active force by using Langevin dynamics simulations in two dimensional space. Interestingly, the system shows emergence of collective swarming states upon increasing the total area fraction of particles, which is not observed for systems without anisotropic interaction or activity. The threshold value of area fraction c decreases with particle ac- tivity or interaction strength. We have also performed basic kinetic analysis to reproduce the essential features of the simulation results. Our results demon- strate that anisotropic interactions at the individual level are sucient to set homogeneous active populations into stable directed motion.
Photocatalytic degradation of organic pollutants has become a hot research topic because of its low energy consumption and environmental-friendly characteristics. Bismuth oxide (Bi2O3) nanocrystals with a bandgap ranging between 2.0-2.8 eV has attracted increasing attention due to high activity of photodegradation of organic pollutants by utilizing visible light. Though several methods have been developed to prepare Bi2O3-based semiconductor materials over recent years, it is still difficult to prepare highly active Bi2O3 catalysts in large-scale with a simple method. Therefore, developing simple and feasible methods for the preparation of Bi2O3 nanocrystals in large-scale is important for the potential applications in industrial wastewater treatment. In this work, we successfully prepared porous Bi2O3 in large scale via etching commercial BiSn powders, followed by thermal treatment with air. The acquired porous Bi2O3 exhibited excellent activity and stability in photocatalytic degradation of methylene blue (MB). Further investigation of the mechanism witnessed that the suitable band structure of porous Bi2O3 allowed the generation of reactive oxygen species, such as O2-? and ?OH, which effectively degraded MB.
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The structure-property relationship of DAE-derivative (C5F-4Py) molecular isomers which involve ring-closed status and ring-open status is investigated by employing non-equilibrium Green’s function formalism combined with density functional theory. Molecular junctions are formed by the isomers connecting to Au (111) electrodes through the flanked pyridine groups. The difference of electronic structures caused by different geometry structures for the two isomers, especially the alternative single bond and double bond in ring-closed molecule, contributes the remarkable different low-bias conductance values. The LUMO orbitals of isomers are mainly channels to transport electron. In addition, the more electrons transferred to ring-closed molecular junction in equilibrium condition drop down the LUMO orbitals closer to the Fermi energy which may be to contribute larger conductance value at Fermi level. Our findings are help to understand the mechanism of the low-bias conducting mechanism of and are conductive to design of high performance molecular switching based on DAE or DAE-derivatives molecules.
Multinanoparticles interacting with the phospholipid membranes in solution were studied by dissipative particle dynamics simulation. The nanoparticles selected have spherical or cylindrical shapes, and they have various initial velocities in the dynamical processes. Several translocation modes are defined according to their characteristics in the dynamical processes, in which the phase diagrams are constructed based on the interaction strengths between the particles and membranes and the initial velocities of particles. Furthermore, several parameters, such as the system energy and radius of gyration, are investigated in the dynamical processes for the various translocation modes. Results elucidate the effects of multiparticles interacting with the membranes in the biological processes.
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Surface passivation is one valuable approach to tune the properties of nanomaterials. The piezo- electric properties of hexagonal [001] ZnO nanowires with four kinds of surface passivations were investigated using the rst-principles calculations. It is found that in the 50% H(O), 50% Cl(Zn); 50% H(O), 50% F(Zn) passivations, the volume and surface e ects both enhance the piezoelectric coecient. This di ers from the unpassivated cases where the surface e ect was the sole source of piezoelectric enhancement. In the 100% H; 100% Cl passivations, the piezoelectric enhancement is not possible since the surface e ect is screened by surface charge with weak polarization. The study reveals that the competition between the volume e ect and surface e ect in uences the iden- ti cation of the diameter-dependence phenomenon of piezoelectric coecients for ZnO nanowires in experiments. Moreover, the results suggest that one e ective means of improving piezoelectricity of ZnO nanowires is shrinking axial lattice or increasing surface polarization through passivation.
A distributed feedback (DFB) laser with a wavelength of 2.8 m was used to measure the species produced by water vapor glow discharge. Only the absorption spectra of OH radicals and transient H2O molecules were observed using concentration modulation (CM) spectroscopy. The intensities and orientations of the absorption peaks change with the demodulation phase, but the direction of one absorption peak of H2O is always opposite to the other peaks. The different spectral orientations of OH and H2O reflect the increase or decrease of the number of particles in the energy levels. If more transient species can be detected in the discharge process, the dynamics of excitation, ionization and decomposition of H2O can be better studied. This study shows that the demodulation phase relationship of CM spectrum can be used to study the population change of molecular energy levels.
A new kind of phenyl-functionalized magnetic fibrous mesoporous silica (Fe3O4@SiO2@KCC-1-phenyl) was prepared by copolymerization as an efficient adsorbent for the magnetic extraction of phthalate esters from environmental water samples. The obtained Fe3O4@SiO2@KCC-1-phenyl showed monodisperse fibrous spherical morphology, fairly strong magnetic response (29 emu g–1), and an abundant π-electron system, which allowed rapid isolation of the Fe3O4@SiO2@KCC-1-phenyl from solutions upon applying an appropriate magnetic field. Several variables that affect the extraction efficiency of the analytes, including the type of the elution solvent, amount of adsorbent, extraction time and reusability, were investigated and optimized. Under optimum conditions, the Fe3O4@SiO2@KCC-1-phenyl was used for the extraction of four phthalate esters from environmental water samples followed by high-performance liquid chromatographic analysis. Validation experiments indicated that the developed method presented good linearity (0.1–20 ng mL-1), low limit of detection (7.5-29 μg L–1, S/N=3). The proposed method was applied to the determination of phthalate esters in different real water samples, with relative recoveries of 93-103.4% and RSDs of 0.8–8.3 %.
Developing low-cost and high-efficient noble-metal-free cocatalysts has been a challenge to achieve economic hydrogen production. In this work, molybdenum oxides (MoO3-x) were in-situ loaded on polymer carbon nitride (PCN) via a simple one-pot impregnation-calcination approach. Different from post-impregnation method, intimate coupling interface between high-dispersed ultra-small MoO3-x nanocrystal and PCN was successfully formed during the in-situ growth process. The MoO3-x-PCN-x photocatalyst without noble platinum (Pt) finally exhibited enhanced photocatalytic hydrogen performance under visible light irradiation (λ>420 nm), with the highest hydrogen evolution rate of 15.6 μmol/h, which was more than 3 times that of bulk PCN. Detailed structure-performance revealed that such improvement in visible-light hydrogen production activity originated from the intimate interfacial interaction between high-dispersed ultra-small MoO3-x nanocrystal and polymer carbon nitride as well as efficient charge carriers transfer brought by Schottky junction formed.
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Highly luminescent bulk two-dimensional covalent organic frameworks (COFs) attract much attention recently. Origin of their luminescence and their large Stokes shift is an open question. After first-principles calculations on two kinds of COFs using the GW method and Bethe-Salpeter equation, we find that monolayer COF has a direct band gap, while bulk COF is an indirect band-gap material. The calculated optical gap and optical absorption spectrum for the direct excitons of bulk COF agree with the experiment. However, calculated energy of the indirect exciton, in which the photoelectron and the hole locate at the conduction band minimum and the valence band maximum of bulk COF respectively, is too low compared to the fluorescence spectrum in experiment. This may exclude the possible assistance of phonons in the luminescence of bulk COF. Luminescence of bulk COF might result from exciton recombination at the defects sites. The indirect band-gap character of bulk COF originates from its AA-stacked conformation. If the conformation is changed to the AB-stacked one, the band gap of COF becomes direct which may enhance the luminescence.
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The geometric structures and vibration frequencies of para-chlorofluorobenzene (p-ClFPh) in the first excited state of neutral and ground state of cationic were investigated by resonance-enhanced multiphoton ionization (REMPI) and slow electron velocity-map imaging (SEVI). The infrared spectrum of S0 state and absorption spectrum for S1 ← S0 transition in p-ClFPh were also recorded. Based on the one-color resonant two-photon ionization (1C-R2PI) spectrum and two-color resonant two-photon ionization (2C-R2PI) spectrum, we measured the adiabatic excitation energy of p-ClFPh as 36302 ± 4 cm-1. In the 2C-R2PI SEVI spectra, the accurate adiabatic ionization potential (AIP) of p-ClFPh was extrapolated to be 72937 ± 8 cm?1 via a series of progressive measurements near threshold ionization region. In addition, Franck-Condon simulations were performed to help us confidently ascertain the main vibration modes in the S1 and D0 states. The wavenumber changes of vibration modes during the transition of S1 ← S0 and D0 ← S1 were discussed. Furthermore, the mixing of vibration modes both between S0 & S1 and S1 & D0 has been analyzed.
The geometric and electronic structures of several possible adsorption configurations of the pyrazine (C4H4N2) molecule covalently attached to Si(100) surface, which is of vital importance in fabricating functional nanodevices, have been investigated using X-ray spectroscopies. The Carbon K-shell (1s) X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy of predicted adsorbed structures have been simulated by density functional theory (DFT) with cluster model calculations. Both XPS and NEXAFS spectra demonstrate the structural dependence on different adsorption configurations. In contrast to the XPS spectra, it is found that the NEXAFS spectra exhibiting conspicuous dependence on the structures of all the studied pyrazine/Si(100) systems can be well utilized for structural identification, which has been discussed in detail in this article. In addition, according to the classification of carbon atoms, the spectral components of carbon atoms in different chemical environments have been investigated in the NEXAFS spectra as well.
Cancer is one of the most serious issues in human life. Blocking Programmed cell death protein 1 (PD-1) and programmed death ligand-1 (PD-L1) pathway is one of the great innovation on last few years, but a few numbers of inhibitors can be able to block it. (2-methyl-3-biphenylyl) methanol (MBPM) derivative is one of them. Here, the quantitative structure-activity relationship (QSAR) established twenty (2-methyl-3-biphenylyl) methanol (MBPM) derivatives as the programmed death ligand-1 (PD-L1) inhibitors. Density functional theory (DFT) at the B3LPY/6-31+G (d, p) level was employed to study the chemical structure and properties of the chosen compounds. Highest occupied molecular orbital energy EHOMO, lowest unoccupied molecular orbital energy ELUMO, total energy ET, dipole moment DM, absolute hardness η, absolute electronegativity χ, softness S, electrophilicity ω, energy gap ΔE, etc, properties were observed and determine. Principal component analysis (PCA), multiple linear regression (MLR) and multiple non-linear regression (MNLR) analysis were carried out to establish the QSAR. The proposed quantitative models and interpreted outcomes of the compounds were based on statistical analysis. Statistical results of MLR and MNLR exhibited the coefficient was 0.661 and 0.758, respectively. Leave-one-out cross-validation (LOO-CV), r2m metric, r2m test and “Golbraikh & Tropsha’s criteria” analyses were applied for the validation of MLR and MNLR, which indicate two models are statistically significant and well stable with data variation in the external validation towards PD-L1. The obtained values specified that the two different modelings can predict the bioactivity and may be helpful and supporting for evaluation of the biological activity of PD-L1 inhibitor.
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Zinc oxide is recently being used as magnetic semiconductor with introduction of magnetic elements in it. In this work, we report phase pure synthesis of Mg and Ni co-substituted ZnO to explore its structure, optical, magnetic and photo-catalytic properties. X-ray diffraction analysis reveal the formation of hexagonal wurtzite type structure having P63mc space group without any impurity phase. UV-Vis spectrophotometry demonstrate the variation in band gap with addition of Mg and Ni content in ZnO matrix. Magnetic measurements exhibit a clear boosted magnetization in Ni and Mg co-doped compositions with its stable value of band gap corroborating the structural stability and magnetic tuning for its advanced applications in modern day spintronic devices. Photo-catalytic measurements were performed using methyl green degradation demonstrate an enhanced trend of activity in Mg and Ni co-doped compositions.
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ATP-binding cassette (ABC) exporters transport many substrates out of cellular membranes via alternating between inward-facing (IF) and outward-facing (OF) conformations. Despite extensive research efforts over the past decades, understanding of the molecular mechanism remains elusive. As these large-scale conformational movements are global and collective, we have previously performed extensive coarse-grained molecular dynamics (CG-MD) simulations of the potential of mean force (PMF) along the conformational transition pathway [Z. Wang et. al JPCB, 119, 1295?1301 (2015)]. However, the occluded (OC) conformational state, in which both the internal and external gate are closed, was not determined in the calculated free energy profile. In this paper, we extend the above methods to the calculation of the free energy profile along the reaction coordinate, d1- d2, which are the COM distances between the two sides of the internal (d1) and the external gate (d2). The PMF is thus obtained to identify the transition pathway, along which several OF-, IF- and OC- state structures are predicted in good agreement with structural experiments. Our CG-MD free-energy simulations demonstrate that the internal gate is closed before the external gate is open during the IF to OF transition and vice versa during the IF to OF transition. Our results capture the unidirectional feature of substrate translocation via the exporter, which is functionally important in biology. This finding is different from the results, in which both the internal and external gates are open reported in an X-ray experiment [Ward A. et al, PNAS, 104, 19005?19010 (2007)]. Our study sheds light on the molecular mechanism of the state transitions in the ABC exporter.
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The initial state-selected reaction probabilities of the H + CH3D → H2 + CH2D reaction were calculated using the ten-dimensional time-dependent wave packet method developed by our group. The reaction dynamics are studied with the reactant CH3D initially from the ground state, the CH3 symmetry and asymmetry stretching excitation, the CD stretching excitation and the fundamental and overtone of the CH3 bending mode. The calculated reaction probabilities show that exciting either of the CH3 stretching modes enhances the reactivity in the collision energy range below 1.0 eV, while the CD stretching excitation does not obviously prompt the reaction. Fundamental excitation of the CH3 bending mode has nearly no effect on the reactivity. However, a significant enhancement is observed for the first overtone excitation of the CH3 bending mode, resulting from the Fermi resonance between the fundamental state of the CH3 symmetry stretching mode and the first overtone state of the CH3 bending mode.
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The excited-state double proton transfer (ESDPT) properties of 1,5-dihydroxyanthraquinone (1,5-DHAQ) in various solvents were investigated using femtosecond transient absorption spectroscopy and the DFT/TDDFT method. The steady-state fluorescence spectra in toluene, tetrahydrofuran (THF) and acetonitrile (ACN) solvents presented that the solvent polarity has an effect on ESDPT processes for the 1,5-DHAQ system. Transient absorption spectra showed that the increasing polarity of the solvent accelerates the rate of excited state dynamics. Calculated potential energy curves analysis further verified the experimental results. The ESDPT barrier decreases gradually with the increase of solvent polarity from toluene, THF to ACN solvent. It is convinced that the increase of solvent polarity can promote the occurrence of the ESDPT dynamic processes for the 1,5-DHAQ system. This work clarified the mechanism of the influence of solvent polarity on the ESDPT process of 1,5-DHAQ, which provides novel ideas for design and synthesis of new hydroxyanthraquinone derivatives.
A chemical process may involve multiple adiabatic electronic states, and non-adiabatic couplings play an important role in the reaction mechanism. In this work, the effect of non-adiabatic couplings in the H + MgH+ → Mg+ + H2 reaction are studied using the time-dependent wave packet method and trajectory surface hopping (TSH) method. The calculated results show that the reaction follows a direct abstraction process when the non-adiabatic couplings are neglected. However, when non-adiabatic couplings are included in the calculations, a long-lived excited state complex (MgH2+)* can be formed during the reaction. These direct and complex-forming reaction pathways are revealed by TSH calculations. The non-adiabatic couplings induced complex-forming mechanism not only increases the reactivity but also has significant effect on the product vibrational state distribution.
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The photodissociation dynamics of Br-C bond cleavage for BrCN in the wavelength region from 225 to 260 nm have been studied by our homebuilt time-slice velocity-map imaging setup. The images for both of the ground state Br(<sup>2</sup>P<sub>3/2</sub>) and spin-orbit excited Br*(<sup>2</sup>P<sub>1/2</sub>) channels are obtained at several photodissociation wavelengths. From the analysis of the translational energy release spectra, the detailed vibrational and rotational distributions of CN products have been measured for both of the Br and Br* channels. It is found that the internal excitation of the CN products for the Br* channel is colder than that for the Br channel. The most populated vibrational levels of the CN products are v = 0 and 1 for the Br and Br* channels, respectively. For the Br channel, the photodissociation dynamics at longer wavelengths are found to be different from those at shorter wavelengths, as revealed by their dramatically different vibrational and rotational excitations of the CN products.
Nanosystems play an important role in many applications. Due to their complexity, it is challenging to accurately characterize their structure and properties. An important means to reach such a goal is computational simulation, which is grounded on ab initio electronic structure calculations. Low scaling and accurate electronic-structure algorithms are developed in recent years. Especially, the efficiency of hybrid density functional calculations for periodic systems has been significantly improved. With electronic structure information, simulation methods can be developed to directly obtain experimentally comparable data. For example, scanning tunneling microscopy (STM) images can be effectively simulated with advanced algorithms. When the system we are interested is strongly coupled to environment, such as in the Kondo effect, solving the hierarchical equations of motion (HEOM) turns out to be an effective way of computational characterization. Furthermore, the first principles simulation on the excited state dynamics rapidly emerges in recent years, and nonadiabatic molecular dynamics method plays an important role. For nanosystem involved chemical processes, such as graphene growth, multiscale simulation methods should be developed to characterize their atomic details. In this article, we review some recent progresses in methodology development for computational characterization of nanosystems. Advanced algorithms and software are essential for us to better understand of the nanoworld.
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Our recent theoretical studies have screened out CuCs-doped Ag-based as promising catalysts for ethylene epoxidation (ACS Catalysis, 2021, 3371-3383). The theoretical results were based on surface modeling, while in the actual reaction process Ag catalysts are particle shaped. In this work, we combine Density functional theory (DFT), Wulff construction theory, and microkinetic analysis to study the catalytic performance of Ag catalysts at the particle model. It demonstrates that the CuCs-doped Ag catalysts are superior to pure Ag catalysts in terms of selectivity and activity in ethylene oxide production, which is further proved by our experimental results. The characterization analysis finds that both Cu and Cs dopants promote particle growth as well as particle dispersion, resulting in a grain boundary-rich Ag particle. Besides, CuCs also facilitates electrophilic atomic oxygen formation on catalyst surface, which is benefit for ethylene oxide formation and desorption. Our work provides a case study of Ag-based catalyst design for ethylene epoxidation by combining theory and experiment.
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The hydrogen abstraction reaction from H<sub>2</sub>S by OH is of key importance in understanding of the causes of acid rain, air pollution and climate change. In this work, the reaction OH + H<sub>2</sub>S → H<sub>2</sub>O + SH is investigated on a recently developed <i>ab initio</i>-based globally accurate potential energy surface by the time-dependent wave packet approach under a reduced-dimensional model. This reaction behaves like a barrier-less reaction at low collision energies and like an activated reaction with a well-defined barrier at high collision energy energies. Exciting either the symmetric or antisymmetric stretching mode of the molecule H<sub>2</sub>S enhances the reactivity more than exciting the bending mode, which is rationalized by the coupling strength of each normal mode with the reaction coordinate. In addition, the mode-specific rate constant shows a remarkable non-Arrhenius temperature dependence.
α-pinene is the most abundant monoterpene that represents an important family of volatile organic compounds (VOCs). Molecular identification of key transient compounds during the α-pinene ozonolysis has been proven to be a challenging experimental target because of a large number of intermediates and products involved. Here we exploit recently developed, hybrid instruments that integrate aerosol mass spectrometry (AMS) with a vacuum ultraviolet free-electron laser (VUV-FEL) to study the α-pinene ozonolysis. The experiments of a-pinene ozonolysis are performed in an indoor smog chamber, which reactor has a volume of 2 m3 made of fluorinated ethylene propylene film. Distinct mass spectral peaks provide direct experimental signatures of previously unseen compounds produced from the reaction of α-pinene with O3. With the aid of quantum chemical calculations, plausible mechanisms for the formation of these new compounds are proposed. These findings provide crucial information for fundamental understanding of the initial steps of α-pinene oxidation and the subsequent processes of new particle formation
The photo-induced ultrafast electron dynamics in both anatase and rutile TiO<sub>2</sub> are investigated by using the Boltzmann transport equation with the explicit incorporation of electron-phonon scattering rates. All structural parameters required for dynamic simulations are obtained from ab initio calculations. The results show that although the longitudinal optical modes significantly affect the electron energy relaxation dynamics in both phases due to strong Fröhlich-type couplings, the detailed relaxation mechanisms have obvious differences. In the case of a single band, the energy relaxation time in anatase is 24.0 fs, twice longer than 11.8 fs in rutile. This discrepancy is explained by the different diffusion distributions over the electronic Bloch states and different scattering contributions from acoustic modes in the two phases. As for the multiple-band situation involving the lowest six conduction bands, the predicted overall relaxation times are about 47 fs and 57 fs in anatase and rutile, respectively, very different from the case of the single band. The slower relaxation in rutile is attributed to the existence of multiple rate-controlled steps during the dynamic process. The present findings may be helpful to control the electron dynamics for designing efficient TiO<sub>2</sub>-based devices.
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Trend analysis and change point detection in a time series are frequent analysis tools. Change point detection is the identification of abrupt variation in the process behaviour due to natural or artificial changes, whereas trend can be defined as estimation of gradual departure from past norms. We analyze the time series data in the presence of trend, using Cox–Stuart methods together with the change point algorithms. We applied the methods to the near-surface wind speed time series for Australia as an example.
The trends in near-surface wind speeds for Australia have been investigated based upon our newly developed wind speed datasets, which were constructed by blending observational data collected at various heights using local surface roughness information. The trend in wind speed at 10m is generally increasing while at 2m it tends to be decreasing. Significance testing, change point analysis and manual inspection of records indicate several factors may be contributing to the discrepancy, such as systematic biases accompanying instrument changes, random data errors (e.g. accumulation day error) and data sampling issues. Homogenization technique and multiple-period trend analysis based upon change point detections have thus been employed to clarify the source of the inconsistencies in wind speed trends.
The hydrogen abstraction reaction of methanol with fluorine atoms can produce HF and CH3O or CH2OH radicals, and are important in the environment, combustion, radiation and interstellar chemistry. In this work, the dynamics of this typical reaction is investigated by the quasi-classical trajectory method based on a recently developed globally accurate full-dimensional potential energy surface. Particularly, the vibrational state distributions of the polyatomic products CH3O and CH2OH are determined by using the normal mode analysis (NMA) method. It is found that CH3O and CH2OH are dominantly populated in the ground state when the reactants are at the ground ro-vibrational state. The OH stretching mode, torsional mode, H2CO out-of-plane bending mode and their combination bands in the CH2OH product can be effectively excited once the OH stretching mode of the reactant CH3OH is excited to the first vibrationally excited state. Most of the available energy flows into the HF vibrational energy and the translational energy in both channels, while the radical products, CH3O or CH2OH, receives a small amount of energy, consistent with experiment, an indication of its spectator nature.
The product branching ratio between different products in multichannel reactions is as important as the overall rate of reaction, both in in terms of practical applications (e.g. models of combustion or atmosphere chemistry) in understanding the fundamental mechanisms of such chemical reactions. A global ground state potential energy surface for the dissociation reaction of deuterated alkyl halide CD3CH2F was computed at the CCSD(T)/CBS//B3LYP/aug-cc-pVDZ level of theory for all species. The decomposition of CD3CH2F is controversial concerning C–F bond dissociation reaction and molecular (HF, DF, H2, D2, HD) elimination reaction. Rice–Ramsperger–Kassel–Marcus (RRKM) calculations were applied to compute the rate constants for individual reaction steps and the relative product branching ratios for the dissociation products were calculated using the steady-state approach. At the different energies studied, the RRKM method predicts that the main channel for DF, HF elimination from 1,2-elimination of CD3CH2F is through a four-center transition state, whereas D2, H2 elimination from 1,1-elimination of CD3CH2F occurs through a direct three-center elimination. At 266, 248 and 193 nm photodissociation, the main product CD2CH2 + DF branching ratios are computed to be 96.57%, 91.47%, and 48.52%, respectively; however, at 157 nm photodissociation, the product branching ratios is computed to be 16.11%. Base on these transition state structures and energies, suggested the following photodissociation mechanism at 266, 248, 193 nm: CD3CH2F 1 → absorption of a photon → TS5 → the formation of the major product CD2CH2 + DF; at 157 nm: CD3CH2F 1 → absorption of a photon → D/F interchange of TS1 → CDH2CDF 2 → H/F interchange of TS2 → CHD2CHDF 3 → the formation of the major product CHD2 + CHDF.
Integration of non-noble transition metal oxides with graphene is known to construct high-activity electrocatalysts for oxygen evolution reduction (OER). In order to avoid the complexity of traditional synthesis process, for the first time, a facile electrochemical method is elaborately designed to engineer efficient WO3-x/graphene (photo-)electrocatalyst for OER by a two-electrode electrolysis system, where graphite cathode is exfoliated into graphene and tungsten wire anode evolves into VO-rich WO3-x profiting from formed reductive electrolyte solution. Among as-prepared samples, WO3-x/G-2 shows the best electrocatalytic performance for OER with an overpotential of 320 mV (without iR compensation) at 10 mA•cm−2, superior to commercial RuO2 (341 mV). With introduction of light illumination, the activity of WO3-x/G-2 is greatly enhanced and its overpotential decreases to 290 mV, benefited from additional reaction path produced by photocurrent effect and extra active sites generated by photogenerated carriers (h+). Characterization results indicate that both VO-rich WO3-x and graphene contribute to the efficient OER performance. The activity of WO3-x for OER is decided by the synergistic effect between VO concentration and particle size. The graphene could not only disperse WO3-x nanoparticles, but also improve the holistic conductivity and promote electron transmission. This work supports a novel method for engineering WO3-x/graphene composite for highly efficient (photo-)electrocatalytic performance for OER.
A quasi-classical trajectory study of the H(2S) + NO(X2Π) → N(4S) + OH(X2Π) reaction kinetics and dynamics is reported on an accurate potential energy surface. The total integral cross sections of the reaction were calculated at the collision energy ranging from 2.00 to 2.80 eV. It was found that the total reaction integral cross section increases monotonically with the collision energy. Specifically at the collision energy of 2.57 eV, our calculated result slightly overestimated the experimental data. The calculated thermal rate constants are in fairly good agreement with available experimental results. Through the trajectory analysis at the collision energy of 2.57 eV, it was found that the title reaction is dominated by the indirect trajectories (1.4 times more compared to the direct trajectories), which sheds lights on the reaction dynamics of the title reaction in the high collision energy range.
Performing cluster analysis on molecular conformation is an important way to find the representative conformation in the Molecular dynamics (MD) trajectories. Usually, it is a critical step for interpreting complex conformational changes or interaction mechanisms. As one of the density-based clustering algorithms, Find Density Peaks (FDP) is an accurate and reasonable candidate for the molecular conformation clustering. However, facing the rapidly increasing simulation length due to the increase in computing power, the low computing efficiency of FDP limits its application potential. Here we propose a marginal extension to FDP named the K-means Find density Peaks (KFDP) to solve the mass source consuming problem. In KFDP, the points are initially clustered by a high efficiency clustering algorithm, such as K-means. Cluster centers are defined as typical points with a weight which represents the cluster size. Then, the weighted typical points are clustered again by FDP, and then are refined as core, boundary and redefined halo points. In this way, KFDP has comparable accuracy with FDP but its computational complexity is reduced from O(n<sup>2</sup>) to O(n). We apply and test our KFDP method to the trajectory data of multiple small proteins in terms of torsion angle, secondary structure or contact map. The comparing results with K-means and DBSCAN show the validation of the proposed KFDP.
Crayfish shell is an abundant natural waste meanwhile a potential biosorbent for pollutants if the release of heavy metals can be ignored. In this study, the safety of crayfish shell as a biosorbent was first accessed by the release experiments involving primary heavy metal ions, such as Cu2+, Zn2+, and Cr3+, in aqueous solution under environmental conditions. Although the release concentrations of heavy metals were dependent on pH, ionic strength, and humic acid, the concentrations were still lower than the national standard. The removal of Cu2+ and Pb2+ by crayfish shell in synthetic wastewater was investigated. The results indicated that crayfish shell is an excellent biosorbent for the removal of Cu2+ and Pb2+, and the removal process involved biosorption, precipitation, and complexation. Particularly, the precipitation step is calcium species-, pH- and temperature-dependent. The maximum removal capacity of Pb2+ and Cu2+ reached 676.20 and 119.98 mg g-1, respectively. The related precipitation and complex products include Cu2CO3(OH)2, Ca2CuO3, CuCO3, Pb2CO3(OH)2, CaPb3O4, and PbCO3. This study evaluated a recyclable pathway of crayfish shell waste and provides a new explanation for the biosorption of heavy metals by crayfish shell.
, Available online
We calculate the interaction strength of the van der Waals force between two Rydberg atoms by applying the applications of quantum information processing using for Rydberg blockade. The alkali metals (Cs and K) in states of principal quantum number n were used to calculate the interaction strength. We use some possible angular momentum channels involving s, p, and d states for measuring interaction strength. The obtained results were then generalized for all angular momentum channels which mostly have small interactions and therefore a poor candidate for blockade experiments. The interaction strength in the atoms of Cs and K dipole matrix elements was calculated first and then relevant energy levels were determined by using the quantum defects theory. The radial wave function was calculated numerically with the integration of the radial Schrödinger equation. Also, the interaction coefficients of van der Waals for various channels were calculated here.
Rotating disk electrode systems are widely used to study the kinetics of electrocatalytic reactions that may suffer from insufficient mass transfer of the reactants. Kinetic current density (jk) at certain overpotential calculated by K-L equation is commonly used as the metrics to evaluate the activity of electrocatalysts. However, it is frequently found that the jl is not correctly identified in the literatures. Instead of jK, the measured current density normalized by diffusion limiting current density (j/jL) has also been frequently under circumstance where its validity is not justified. By taking ORR/HER/HOR as examples, we demonstrate that identify the actualjL for the same reaction under otherwise identical conditions from the experimental data is essential to accurately deduce jk. Our analysis reveals that j/jL is a rough activity metric which can only be used to qualitatively compare the activity trend under conditions that the mass transfer conditions and the roughness factor of the electrode are exactly the same. In addition, if one wants to use j/jL to compare the intrinsic activity, the concentration overpotential should be eliminated.
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The reaction H+SO$ _2 $$ \rightarrow $OH+SO is important in the combustion and atmospheric chemistry, as well as the interstellar medium. It also represents a typical complex-forming reaction with deep complexes, serving as an ideal candidate for testing various kinetics theories and providing interesting reaction dynamical phenomena. In this work, we reported a quasi-classical trajectory study of this reaction on our previously developed accurate full-dimensional potential energy surface. The experimental thermal rate coefficients over the temperature range 1400 K$ \leq $$ T $$ \leq $ 2200 K were well reproduced. For the reactant SO$ _2 $ being sampled at the ground ro-vibrational state, the calculated integral cross sections increased slightly along the collision energy ranging from 31.0 kcal/mol to 40.0 kcal/mol, and then became essentially flat at the collision energy within 40.0$ - $55.0 kcal/mol. The product angular distributions are almost symmetric with nearly identical backward-forward double peak structure. The products OH and SO vibrational state distributions were also analyzed.
2021, 34(6): 659-669.
doi: 10.1063/1674-0068/cjcp2107120
Antifreeze glycoproteins (AFGPs) facilitate the survival of various organisms in the polar region by preventing internal ice accumulation via an adsorption-inhibition mechanism. Inhibition of AFGP antifreeze activity by the borate buffers has been widely acknowledged as the direct experimental evidence supporting the hydroxyl, rather than methyl, binding mechanism. On the other hand, perturbation of borate binding on the AFGP configuration, which might have considerable influence on the binding efficiency of not only the hydroxyl but also the methyl groups, has rarely been quantitatively examined. Herein we studied, using molecular dynamics simulations, the perturbation on the configuration of a solvated AFGP8 protein induced by the binding of one single borate anion. Near the freezing point, this binding not only makes the disaccharide groups adjacent to the borate-binding disaccharide close to each other but also affects the entire AFGP8 conformation. The structural changes induced by the binding of borate on different disaccharide sidechains exhibit clear site-specificities and the effect of borate binding on the structural changes is significantly reduced at higher temperatures. Our study is valuable for further understanding the relationship between the structure and antifreeze activity of these antifreeze glycoproteins.
In the past few years, the renormalized excitonic model (REM) approach was developed as an efficient low-scaling ab initio excited state method, which assumes the low-lying excited states of the whole system are a linear combination of various single monomer excitations and utilizes the effective Hamiltonian theory to derive their couplings. In this work, we further extend the REM calculations for the evaluations of first-order molecular properties (e.g. charge population and transition dipole moment) of delocalized ionic or excited states in molecular aggregates, through generalizing the effective Hamiltonian theory to effective operator representation. Results from the test calculations for four different kinds of one dimensional (1D) molecular aggregates (ammonia, formaldehyde, ethylene and pyrrole) indicate that our new scheme can efficiently describe not only the energies but also wavefunction properties of the low-lying delocalized electronic states in large systems.
2021, 34(6): 683-694.
doi: 10.1063/1674-0068/cjcp2109150
Monte Carlo (MC) methods are important computational tools for molecular structure optimizations and predictions. When solvent effects are explicitly considered, MC methods become very expensive due to the large degree of freedom associated with the water molecules and mobile ions. Alternatively implicit-solvent MC can largely reduce the computational cost by applying a mean field approximation to solvent effects and meanwhile maintains the atomic detail of the target molecule. The two most popular implicit-solvent models are the Poisson-Boltzmann (PB) model and the Generalized Born (GB) model in a way such that the GB model is an approximation to the PB model but is much faster in simulation time. In this work, we develop a machine learning-based implicit-solvent Monte Carlo (MLIMC) method by combining the advantages of both implicit solvent models in accuracy and efficiency. Specifically, the MLIMC method uses a fast and accurate PB-based machine learning (PBML) scheme to compute the electrostatic solvation free energy at each step. We validate our MLIMC method by using a benzene-water system and a protein-water system. We show that the proposed MLIMC method has great advantages in speed and accuracy for molecular structure optimization and prediction.
Machine learning potentials are promising in atomistic simulations due to their comparable accuracy to first-principles theory but much lower computational cost. However, the reliability, speed, and transferability of atomistic machine learning potentials depend strongly on the way atomic configurations are represented. A wise choice of descriptors used as input for the machine learning program is the key for a successful machine learning representation. Here we develop a simple and efficient strategy to automatically select an optimal set of linearly-independent atomic features out of a large pool of candidates, based on the correlations that are intrinsic to the training data. Through applications to the construction of embedded atom neural network potentials for several benchmark molecules with less redundant linearly-independent embedded density descriptors, we demonstrate the efficiency and accuracy of this new strategy. The proposed algorithm can greatly simplify the initial selection of atomic features and vastly improve the performance of the atomistic machine learning potentials.
In this work, we employ electronic structure calculations and nonadiabatic dynamics simulations based on many-body Green function and Bethe-Salpeter equation (GW/BSE) methods to study excited-state properties of a zinc phthalocyanine-fullerene (ZnPc-C$ _{60} $) dyad with 6-6 and 5-6 configurations. In the former, the initially populated locally excited (LE) state of ZnPc is the lowest S$ _1 $ state and thus, its subsequent charge separation is relatively slow. In contrast, in the latter, the S$ _1 $ state is the LE state of C$ _{60} $ while the LE state of ZnPc is much higher in energy. There also exist several charge-transfer (CT) states between the LE states of ZnPc and C$ _{60} $. Thus, one can see apparent charge separation dynamics during excited-state relaxation dynamics from the LE state of ZnPc to that of C$ _{60} $. These points are verified in dynamics simulations. In the first 200 fs, there is a rapid excitation energy transfer from ZnPc to C$ _{60} $, followed by an ultrafast charge separation to form a CT intermediate state. This process is mainly driven by hole transfer from C$ _{60} $ to ZnPc. The present work demonstrates that different bonding patterns (i.e. 5-6 and 6-6) of the C$ - $N linker can be used to tune excited-state properties and thereto optoelectronic properties of covalently bonded ZnPc-C$ _{60} $ dyads. Methodologically, it is proven that combined GW/BSE nonadiabatic dynamics method is a practical and reliable tool for exploring photoinduced dynamics of nonperiodic dyads, organometallic molecules, quantum dots, nanoclusters, etc.
2021, 34(6): 717-727.
doi: 10.1063/1674-0068/cjcp2109173
Although the many-body expansion (MBE) approach is widely applied to estimate the energy of large systems containing weak interactions, it is inapplicable to calculating the energies of covalent or metal clusters. In this work, we propose an interaction many-body expansion (IMBE) to calculate the energy of atomic clusters containing covalent bonds. In this approach, the energy of a system is expressed as the sum of the energy of atoms and the interaction energy between the atom and its surrounding atoms. The IMBE method is first applied to calculate the energies of nitrogen clusters, in which the interatomic interactions are truncated to four-body terms. The results show that the IMBE approach could significantly reduce the energy error for nitrogen clusters compared with the traditional MBE method. The weak size and structure dependence of the IMBE error with respect to DFT calculations indicates the IMBE method has good potential application in estimating energy of large covalent systems.
We measured the photoelectron spectra of Al$ _n $C$ _4 $$ ^- $ ($ n $ = 2$ - $4) clusters by using size-selected anion photoelectron spectroscopy. The structures of Al$ _n $C$ _4 $$ ^{-/0} $ ($ n $ = 2$ - $4) clusters were explored with quantum chemistry calculations and were determined by comparing the theoretical results with the experimental spectra. It is found that the most stable structure of Al$ _2 $C$ _4 $$ ^- $ anion is a $ C_{2 \rm{v}} $ symmetry planar structure with two Al atoms interacting with two C$ _2 $ units. In addition, Al$ _2 $C$ _4 $$ ^- $ anion also has a $ D_{\infty \rm{h}} $ symmetry linear structure with two Al atoms located at the two ends of a C$ _4 $ chain, which is slightly higher in energy than the planar structure. The most stable structure of neutral Al$ _2 $C$ _4 $ has a $ D_{\infty \rm{h}} $ symmetry linear structure. The most stable structure of Al$ _3 $C$ _4 $$ ^- $ anion is a planar structure with three Al atoms interacting with two C$ _2 $ units. Whereas neutral Al$ _3 $C$ _4 $ cluster has a $ C_{2 \rm{v}} $ symmetric V-shaped bent structure. The global minima structures of both Al$ _4 $C$ _4 $$ ^- $ and neutral Al$ _4 $C$ _4 $ are $ C_{2 \rm{h}} $ symmetry planar structures with four Al atoms interacting with the ends of two C$ _2 $ units. Adaptive natural density partitioning analyses of Al$ _n $C$ _4 $$ ^- $ ($ n $ = 2$ - $4) clusters show that the interactions between the Al atoms and C$ _2 $ units have both $ \sigma $ and $ \pi $ characters.
2021, 34(6): 797-804.
doi: 10.1063/1674-0068/cjcp2110194
In order to investigate the origin of catalytic power for serine proteases, the role of the hydrogen bond in the catalytic triad was studied in the proteolysis process of the peptides chymotrypsin inhibitor 2 (CI2), MCTI-A, and a hexapeptide (SUB), respectively. We first calculated the free energy profile of the proton transfer between His and Asp residues of the catalytic triad in the enzyme-substrate state and transition state by employing QM/MM molecular dynamics simulations. The results show that a low-barrier hydrogen bond (LBHB) only forms in the transition state of the acylation of CI2, while it is a normal hydrogen bond in the acylation of MCTI-A or SUB. In addition, the change of the hydrogen bond strength is much larger in CI2 and SUB systems than in MCTI-A system, which decreases the acylation energy barrier significantly for CI2 and SUB. Clearly, a LBHB formed in the transition state region helps accelerate the acylation reaction. But to our surprise, a normal hydrogen bond can also help to decrease the energy barrier. The key to reducing the reaction barrier is the increment of hydrogen bond strength in the transition state state, whether it is a LBHB or not. Our studies cast new light on the role of the hydrogen bond in the catalytic triad, and help to understand the catalytic triad of serine proteases.
2021, 34(6): 805-813.
doi: 10.1063/1674-0068/cjcp2110195
In this work, we studied the electronic band structure of the halogen (F, Cl, and Br) functionalized graphdiynes (GDYs) by using hybrid density functional theory. The results revealed that the bandgap energies of modified GDYs increase as the number of halogen atoms increases. It is also found that the position of the valence band maximum (VBM) is influenced by the electronegativity of halogen atoms. The higher the electronegativity, the deeper the VBM of the GDYs modified by the same number of halogen atoms. Importantly, our results revealed that the bandgap of GDY could be effectively tuned by mixing types of halogen atoms. The new generated conduction band and valence band edges are properly aligned with the oxidation and reduction potentials of water. Further thermodynamic analysis confirms that some models with mixing types of halogen atoms exhibit higher performance of overall photocatalytic water splitting than non-mixing models. This work provides useful insights for designing efficient photocatalysts that can be used for overall water splitting.
Protein-protein interactions are vital for a wide range of biological processes. The interactions between the hypoxia-inducible factor and von Hippel Lindau (VHL) are attractive drug targets for ischemic heart disease. In order to disrupt this interaction, the strategy to target VHL binding site using a hydroxyproline-like (pro-like) small molecule has been reported. In this study, we focused on the inhibition mechanism between the pro-like inhibitors and the VHL protein, which were investigated via molecular dynamics simulations and binding free energy calculations. It was found that pro-like inhibitors showed a strong binding affinity toward VHL. Binding free energy calculations and free energy decompositions suggested that the modification of various regions of pro-like inhibitors may provide useful information for future drug design.
2021, 34(6): 825-832.
doi: 10.1063/1674-0068/cjcp2110196
Three-dimensional (3D) diabatic potential energy surfaces (PESs) of thiophenol involving the S$_0$, and coupled $^1$$\pi\pi^*$ and $^1$$\pi\sigma^*$ states were constructed by a neural network approach. Specifically, the diabatization of the PESs for the $^1$$\pi\pi^*$ and $^1\pi\sigma^*$ states was achieved by the fitting approach with neural networks, which was merely based on adiabatic energies but with the correct symmetry constraint on the off-diagonal term in the diabatic potential energy matrix. The root mean square errors (RMSEs) of the neural network fitting for all three states were found to be quite small ($<$4 meV), which suggests the high accuracy of the neural network method. The computed low-lying energy levels of the S$_0$ state and lifetime of the 0$^0$ state of S$_1$ on the neural network PESs are found to be in good agreement with those from the earlier diabatic PESs, which validates the accuracy and reliability of the PESs fitted by the neural network approach.
Ring polymer molecular dynamics (RPMD) calculations for the C($^1$D)+H$_2$ reaction are performed on the Zhang-Ma-Bian $ab$ $initio$ potential energy surfaces (PESs) recently constructed by our group, which are unique in very good descriptions of the regions around conical intersections and of van der Waals (vdW) interactions. The calculated reaction thermal rate coefficients are in very good agreement with the latest experimental results. The rate coefficients obtained from the ground $\tilde{a}^1\hspace{-0.08cm}A'$ ZMB-a PES are much larger than those from the previous RKHS PES, which can be attributed to that the vdW saddles on our PESs have very different dynamical effects from the vdW wells on the previous PESs, indicating that the RPMD approach is able to include dynamical effects of the topological structures caused by vdW interactions. The importance of the excited $\tilde{b}^1\hspace{-0.08cm}A''$ ZMB-b PES and quantum effects in the title reaction is also underscored.
2021, 34(6): 843-849.
doi: 10.1063/1674-0068/cjcp2110199
In this work, the solidification of liquid iron with or without external magnetic field was investigated by using two molecular dynamics methods, namely direct cooling and two-phase simulation. The influence of external magnetic field on the solidification is characterized by the critical temperature and radial distribution functions. Our computational results show that under external magnetic field, the solidification point tends to decrease significantly. By further analyzing the diffusion coefficients and viscosity, we attribute the effect to the stronger fluctuation of liquid iron atoms driven by the external magnetic field.
2021, 34(6): 850-860.
doi: 10.1063/1674-0068/cjcp2110200
Excess electrons are not only an important source of radiation damage, but also participate in the repair process of radiation damage such as cyclobutane pyrimidine dimer (CPD). Using ab initio molecular dynamics (AIMD) simulations, we reproduce the single excess electron stepwise catalytic CPD dissociation process in detail with an emphasis on the energy levels and molecular structure details associated with excess electrons. On the basis of the AIMD simulations on the CPD aqueous solution with two vertically added excess electrons, we exclude the early-proposed [2+2]-like concerted synchronous dissociation mechanism, and analyze the difference between the symmetry of the actual reaction and the symmetry of the frontier molecular orbitals which deeply impact the mechanism. Importantly, we propose a new model of the stepwise electron-catalyzed dissociation mechanism that conforms to the reality. This work not only provides dynamics insights into the excess electron catalyzed dissociation mechanism, but also reveals different roles of two excess electrons in two bond-cleavage steps (promoting versus inhibiting).
Optical excitations of the hybrids, which are assembled by coupling single-walled carbon nanotubes (SWCNTs) with organic molecules through van der Waals interactions, are studied using ab initio many-body Green's function theory. We take the semiconducting (7, 0) SWCNT, the squarylium and oligothiophene molecules as the example. The $ E_{11} $ and $ E_{22} $ absorption peaks of the (7, 0) tube can be redshifted by tens of meV. Most importantly, the lowest dark exciton of the (7, 0) tube at the lower-energy side of $ E_{11} $ can be brightened by the interaction between the nanotube and molecules. Position of this new satellite absorption peak is influenced by the type of adsorbed molecule. These findings may be useful for tuning the emission energy and emission efficiency of CNTs.
2021, 34(6): 867-873.
doi: 10.1063/1674-0068/cjcp2110202
The luminescence property of 2, 7-diphenyl-fluorenone (DPFO) was previously reported to be very unusual with a large aggregation-induced effect associated with a fluorescence redshift of 150 nm. The phenomenon is reexamined in this work. It is found that the abnormal observations are caused by the presence of a trace amount of impurity 2, 7-diphenyl-fluorene (DPF) in the as-synthesized DPFO. The pure DPFO molecule does have an intense fluorescence (FL) in solid (528 nm), about 4-5 times larger than in its dilute dichloromethane solutions (542 nm), but with a blueshifted rather than redshifted FL wavelength in solid. The enormous FL enhancement and redshifted FL wavelength of the as-synthesized DPFO solid are due to the presence of impurity DPF. The FL of DPF is much stronger than that of DPFO in dilute solutions and it also has shorter FL wavelengths. In a dilute solution of DPFO with a trace amount of DPF (~1%), the dominant FL peaks are from DPF. Because the electronic absorption peaks of DPF overlaps with DPFO, the electronic energy of DPF can transfer to DPFO. The energy transfer is faster with the increase of concentration because DPF and surrounding DPFO molecules become closer, which quenches the FL of DPF (356 and 372 nm) and enhances the FL of DPFO (542 nm in solution and 528 nm in solid). Therefore, at high concentrations or in solids, only peak at about 542 or 528 nm shows up, and peaks at 356 and 372 nm disappear.
2021, 34(6): 874-882.
doi: 10.1063/1674-0068/cjcp2110205
We present a new three-dimensional potential energy surface (PES) for CH$ _4 $-Ne complex. The electronic structure computations were carried out using the coupled-cluster method with singles, doubles, and perturbative triples [CCSD(T)], the augmented correlation-consistent aug-cc-pVXZ (X = T, Q) basis sets were employed with bond functions placed at the mid-point on the intermolecular axis, and the energies obtained were then extrapolated to the complete basis set limit. Analytic intermolecular PES is obtained by least-squares fitting to the Morse/Long-Range (MLR) potential function form. These fits to 664 points have root-mean-square deviations of 0.042 cm$ ^{-1} $. The bound rovibrational levels are calculated for the first time, and the predicted infrared spectra are in good agreement with the experimental values. The microwave spectra for CH$ _4 $-Ne dimer have also been predicted for the first time. The analytic PES can be used for modeling the dynamical behavior in CH$ _4 $-(Ne)$ _N $ clusters, and it will be useful for future studies of the collision-induced-absorption for the CH$ _4 $-Ne dimer.
2021, 34(6): 883-895.
doi: 10.1063/1674-0068/cjcp2110207
In this work, we explore the suitability of several density functionals with the generalized gradient approximation (GGA) and beyond for describing the dissociative chemisorption of methane on the reconstructed Pt(110)-(2$ \times $1) surface. The bulk and surface structures of the metal, methane adsorption energy, and dissociation barrier are used to assess the functionals. A van der Waals corrected GGA functional (optPBE-vdW) and a meta-GGA functional with van der Waals correction (MS PBEl-rVV10) are selected for ab initio molecular dynamics calculations of the sticking probability. Our results suggest that the use of these two functionals may lead to a better agreement with existing experimental results, thus serving as a good starting point for future development of reliable machine-learned potential energy surfaces for the dissociation of methane on the Pt(110)-(2$ \times $1) surface.
2021, 34(6): 896-904.
doi: 10.1063/1674-0068/cjcp2110210
Global optimization of Morse clusters with short-range potential is a great challenge. Here, we apply our recently developed unbiased fuzzy global optimization method to systematically study Morse clusters with the potential range $ \rho $ = 14 and the number of atoms $ N $ up to 400. All the putative global minima reported in the literature have been successfully reproduced with relatively high success ratios. Compared to the available results for $ N $$ \leq $240 and several larger Morse clusters, new global minima (and local minima) with lower energies have been found out for $ N $ = 164, 175, 188, 193, 194, 197, 239, 246, 260, 318, and 389. Clusters with magic numbers are figured out through fitting the size-dependent global minimum energies. The cluster structures tend to be close-packed for short-range potential with large $ N $.
2021, 34(6): 905-914.
doi: 10.1063/1674-0068/cjcp2110212
The hierarchical equation of motion method has become one of the most popular numerical methods for describing the dissipative dynamics of open quantum systems linearly coupled to environment. However, its applications to systems with strong electron correlation are largely restrained by the computational cost, which is mainly caused by the high truncation tier $ L $ required to accurately characterize the strong correlation effect. In this work, we develop an adiabatic terminator by decoupling the principal dissipation mode with the fastest dissipation rate from the slower ones. The adiabatic terminator leads to substantially enhanced convergence with respect to $ L $ as demonstrated by the numerical tests carried out on a single impurity Anderson model. Moreover, the adiabatic terminator alleviates the numerical instability problems in the long-time dissipative dynamics.
Calcium-release-activated calcium (CARC) channels are one of the major pathways of calcium entry in non-excitable cells. Despite a decade or two of research, its regulatory mechanism is not yet thoroughly understood. The slow progress is due to the complexity of its pores (i.e., Orai) on one hand and the difficulty in capturing its regulatory complex on the other hand. As a result, possible gating mechanisms have often been speculated by exploring the structure and properties of constitutive open mutants. However, there is much debate about how they can truly reflect the gating of CRAC channels under physiological conditions. In the present study, we combined molecular dynamics simulations with free energy calculations to study three dOrai mutants (G170P, H206A, and P288A), and further calculated their current-voltage curves. Results show that these constructs adopt different approaches to maintain their conductive state. Meanwhile they have unique pore structures and distinctive rectification properties and ion selectivity for cations compared to wild-type pores. We conclude that although the mutants may partially capture the gating motion characteristics of wild-type pores, the information obtained from these mutants is likely not a true reflection of CRAC channel gating under physiological conditions.
2021, 34(6): 925-931.
doi: 10.1063/1674-0068/cjcp2111232
The prototypical reaction of F+HD→DF+H was investigated at collision energies from 3.03 meV to 17.97 meV using a crossed molecular beam apparatus with multichannel Rydberg tagging time-of-flight detection. Significant contributions from both the Born-Oppenheimer (BO) forbidden reaction F*(2P1/2)+HD→DF+H and the BO-allowed reaction F(2P3/2)+HD→DF+H were observed. In the backward scattering direction, the contribution from the BO-forbidden reaction F*(2P1/2)+HD was found to be considerably greater than the BO-allowed reaction F(2P3/2)+HD, indicating the non-adiabatic effects play an important role in the dynamics of the title reaction at low collision energies. Collision-energy dependence of differential cross sections (DCSs) in the backward scattering direction was found to be monotonously decreased as the collision energy decreases, which does not support the existence of resonance states in this energy range. DCSs of both BO-allowed and BO-forbidden reactions were measured at seven collision energies from 3.03 meV to 17.97 meV. It is quite unexpected that the angular distribution gradually shifts from backward to sideway as the collision energy decreases from 17.97 meV to 3.03 meV, suggesting some unknown mechanisms may exist at low collision energies.
2021, 34(6): 932-948.
doi: 10.1063/1674-0068/cjcp2111242
Accurate and efficient integration of the equations of motion is indispensable for molecular dynamics (MD) simulations. Despite the massive use of the conventional leapfrog (LF) integrator in modern computational tools within the framework of MD propagation, further development for better performance is still possible. The alternative version of LF in the middle thermostat scheme (LF-middle) achieves a higher order of accuracy and efficiency and maintains stable dynamics even with the integration time stepsize extended by several folds. In this work, we perform a benchmark test of the two integrators (LF and LF-middle) in extensive conventional and enhanced sampling simulations, aiming at quantifying the time-stepsize-induced variations of global properties (e.g., detailed potential energy terms) as well as of local observables (e.g., free energy changes or bond-lengths) in practical simulations of complex systems. The test set is composed of six chemically and biologically relevant systems, including the conformational change of dihedral flipping in the N-methylacetamide and an AT (Adenine-Thymine) tract, the intra-molecular proton transfer inside malonaldehyde, the binding free energy calculations of benzene and phenol targeting T4 lysozyme L99A, the hydroxyl bond variations in ethaline deep eutectic solvent, and the potential energy of the blue-light using flavin photoreceptor. It is observed that the time-step-induced error is smaller for the LF-middle scheme. The outperformance of LF-middle over the conventional LF integrator is much more significant for global properties than local observables. Overall, the current work demonstrates that the LF-middle scheme should be preferably applied to obtain accurate thermodynamics in the simulation of practical chemical and biological systems.
2021, 34(6): 949-956.
doi: 10.1063/1674-0068/cjcp2111228
The time-dependent wave packet method has been employed to calculate the state-to-state integral cross sections and differential cross sections (DCSs) for three initial states of the title reaction on the recently constructed neural network potential energy surface. It is found that the product HBr($ v' $ = 2, 3, 4) states have the dominated population in the entire energy region considered here, indicating an inverted HBr vibrational state distribution. More than half of the available energy ends up as product internal motion, and most of which goes into the vibrational motion. Our calculations show that initial rotational excitation of Br$ _2 $ has little effect on the product ro-vibrational state distributions and DCSs of the reaction. While the initial vibrational excitation has some influences. The initial vibrational excitation to $ v_0 $ = 5 obviously enhance the product vibrational excitation in the low energy region. The DCSs for collision energy up to 0.5 eV at the ground and rotationally excited state are peaked in the backward direction, but the width of the angular distribution increases considerably with the increase of collision energy. For the vibrationally excited state, the DCSs are rather complicated with some strong forward scattering peaks for highly vibrationally excited products.
2021, 34(6): 957-969.
doi: 10.1063/1674-0068/cjcp2110218
The coarse grained (CG) model implements the molecular dynamics simulation by simplifying atom properties and interaction between them. Despite losing certain detailed information, the CG model is still the first-thought option to study the large molecule in long time scale with less computing resource. The deep learning model mainly mimics the human studying process to handle the network input as the image to achieve a good classification and regression result. In this work, the TorchMD, a MD framework combining the CG model and deep learning model, is applied to study the protein folding process. In 3D collective variable (CV) space, the modified find density peaks algorithm is applied to cluster the conformations from the TorchMD CG simulation. The center conformation in different states is searched. And the boundary conformations between clusters are assigned. The string algorithm is applied to study the path between two states, which are compared with the end conformations from all atoms simulations. The result shows that the main phenomenon of protein folding with TorchMD CG model is the same as the all-atom simulations, but with a less simulating time scale. The workflow in this work provides another option to study the protein folding and other relative processes with the deep learning CG model.
