2013 Vol. 26, No. 6

Content
Special Issue
This work presents a theoretical insight into the variation of the site-specific intermolecular hydrogen-bonding (HB), formed between C=O group of fluorenone (FN) and O?H groups of methanol (MeOL) molecules, induced by both the electronic excitation and the bulk solvent effect. Through the calculation of molecular ground- and excited-state properties, we not only demonstrate the characters of HB strengthening induced by electronic excitation and the bulk solvent effect but also reveal the underlying physical mechanism which leads to the HB variation. The strengthening of the intermolecular HB in electronically excited states and in liquid solution is characterized by the reduced HB bond-lengths and the red-shift IR spectra accompanied by the increasing intensities of IR absorption corresponding to the characteristic vibrational modes of the O-H and C=O stretching. The HB strengthening in the excited electronic states and in solution mainly arises from the charge redistribution of the FN molecule induced by the electronic excitation and bulk solvent instead of the intermolecular charge transfer. The charge redistribution of the solute molecule increases the partial dipole moment of FN molecule and the FN-MeOL intermolecular interaction, which subsequently leads to the HB strengthening. With the bulk solvent effect getting involved, the theoretical IR spectra of HBed FN-MeOL complexes agree much better with the experiments than those of gas-phase FN-MeOL dimer. All the calculations are carried out based on our developed analytical approaches for the first and second energy derivatives of excited electronic state within the time-dependent density functional theory.
The reaction dynamics of the F+H2O/D2O→HF/DF+OH/OD are investigated on an ac-curate potential energy surface (PES) using a quasi-classical trajectory method. For bothisotopomers, the hydrogen/deuterium abstraction reaction is dominated by a direct rebound mechanism over a very low “reactant-like” barrier, which leads to a vibrationally hot HF/DF product with an internally cold OH/OD companion. It is shown that the lowered reaction barrier on this PES, as suggested by high-level ab initio calculations, leads to a much better agreement with the experimental reaction cross section, but has little impact on the product state distributions and mode selectivity. Our results further indicate that rotational exci-tation of the H2O reactant leads to significant enhancement of the reactivity, suggesting a strong coupling with the reaction coordinate.
The time-dependent density functional-based tight-bind (TD-DFTB) method is implemented on the multi-core and the graphical processing unit (GPU) system for excited state calcu-lations of large system with hundreds or thousands of atoms. Sparse matrix and OpenMPmultithreaded are used for building the Hamiltonian matrix. The diagonal of the eigenvalue problem in the ground state is implemented on the GPUs with double precision. The GPU-based acceleration fully preserves all the properties, and a considerable total speedup of8.73 can be achieved. A Krylov-space-based algorithm with the OpenMP parallel and GPU acceleration is used for finding the lowest eigenvalue and eigenvector of the large TDDFT matrix, which greatly reduces the iterations taken and the time spent on the excited states eigenvalue problem. The Krylov solver with the GPU acceleration of matrix-vector product can converge quickly to obtain the final result and a notable speed-up of 206 times can be observed for system size of 812 atoms. The calculations on serials of small and large sys-tems show that the fast TD-DFTB code can obtain reasonable result with a much cheaper computational requirement compared with the first-principle results of CIS and full TDDFT calculation.
We have investigated creation of variable concentrations of defects on TiO2(110)-(1×1) sur-face by 266 nm laser using temperature programmed desorption technique. Oxygen-vacancy defects can be easily induced by ultraviolet light, the defects concentration has a linear dependence on power density higher than 50 mW/cm2 for 90 s irradiation. No observa-tion of O2 molecule and Ti atom desorption suggests that UV induced defects creation on TiO2(110)-(1×1) is an effective and gentle method. With pre-dosage of thin films of water,the rate of defects creation on TiO2(110)-(1×1) is slower at least by two orders of magnitude than bare TiO2(110)-(1×1) surface. Further investigations show that water can be moreeasily desorbed by UV light, and thus desorption of bridging oxygen is depressed.
The ultrafast excited state dynamics of trans-4-aminoazobenzene (trans-4-AAB) in ethanol was investigated by femtosecond transient absorption spectroscopy. After being excited to the S2 state by 400 nm, trans-4-AAB decays from the S2 state to the hot S1state by internal conversion with time constant of ~70 fs. The photoisomerization through inversion mechanism on the S1 potential energy surface and the internal conversion from the S1 state to the hot S0 state are observed, respectively. The average timescale of these two decay pathways is ~0.7 ps. And the vibrational cooling of the hot S0 state of cis- and trans-4-AAB occur with time constants of ~4 and ~13 ps, respectively. Furthermore, the ultrafast intersystem crossing process are also observed. The timescale of intersystem crossing from the S2 state to the T4 state is about 480 ps while from the S1 state to the T2 state is ~180 ps.
We report a theoretical study on the rotational spectra of Ar-D232S. The intermolecular po-tential energy surface was transformed from our latest ab initio three-dimensional potentialof Ar-D232S. The rotational energy levels and wavefunctions of the complex were calcu-lated by using the radial discrete variable representation/angular finite basis representation method and the Lanczos algorithm. The calculated rotational transition frequencies and structural parameters were found to be in good agreement with the available experimental
As a well known DNA photolesion product, the special UV induced pyrimidine dimmer called spore photoproduct (SP), has aroused strong research interests. The SP formation was reported solely between two adjacent thymidine residues. It remains unclear in perviousexperimental observations why there is an absence of the cytosine-derived SP-like photoprod-uct formation at the cytosine containing DNA strand, although the cytosine residue holds great similarity to thymine in terms of molecular structure. From a theoretical perspec-tive, we have explored this issue in this work by means of density functional theory at the B3LYP/6-311++G(d,p) //B3LYP/6-31G(d,p) level for the DNA dinucleotide fragment, cy-tosine phosphate thymine (CpT). Key factors blocking the formation of the SP-like product between two adjacent cytosine and thymidine residues are revealed. Instead of undergoing photochemical SP reaction, a photophysical deactivation pathway back to the ground state turns out to be favorable for the CpT dinucleotide fragment.
We have conducted a two-color visible-ultraviolet (VIS-UV) resonance-enhanced laser pho-toionization and pulsed field ionization-photoelectron (PFI-PE) study of gaseous vana-dium mononitride (VN) in the total energy range of 56900-59020 cm-1. The VN molecules were selectively excited to single rotational levels of the intermediate VN(D3∏0, v'=0) state by using a VIS dye laser prior to photoionization by employing a UV laser. This two-color scheme allows the measurements of rovibronically selected and re-solved PFI-PE spectra for the VN+(X2△; v+=0, 1, and 2) ion vibrational bands. By simulating the rotationally resolved PFI-PE spectra, J+=3/2 is determined to be the lowest rotational level of the ground electronic state, indicating that the symmetry of the ground VN+ electronic state is 23/2. The analysis of the PFI-PE spectra for VN+ also yields accurate values for the adiabatic ionization energy for the formation of VVN+(X23/2), IE(VN)=56909.5±0.8 cm-1 (7.05588±0.00010 eV), the vibrational fre-quency ωe+=1068.0±0.8 cm-1, the anharmonicity constant ωe+χe+=5.8±0.8 cm-1, the ro-tational constants Be+=0.6563±0.0005 cm-1 and αe+=0.0069±0.0004 cm-1, and the equi-librium bond length, re+=1.529 ?, for VN+(X23/2); along with the rotational constants Be+=0.6578±0.0028 cm-1 and αe+=0.0085±0.0028 cm-1, and the equilibrium bond length re+=1.527 ? for VN+(X25/2), and the spin-orbit coupling constant A=153.3±0.8 cm-1 for VN+(X25/2,3/2). The highly precise energetic and spectroscopic data obtained in the present study are valuable for benchmarking the predictions based on state-of-the-art ab initio quantum calculations.
Manganese oxide cluster cations Mnm18On+ were prepared by laser ablation and reacted with hydrogen sulfide (H2S) in a fast flow reactor under thermal collision conditions. A time-of-flight mass spectrometer was used to detect the cluster distributions before and after the interactions with H2S. The experiments suggest that oxygen-for-sulfur (O/S) ex-change reaction to release water took place in the reactor for most of the manganese oxide cluster cations: Mnm18On++H2S→Mnm18On-1S++H218O. Density functional theory cal-culations were performed for reaction mechanisms of Mn2O2+, Mn2O3+, and Mn2O4+. The computational results indicate these O/S exchange reactions are both thermodynamically and kinetically favorable, thus in good agreement with the experimental observations. The O/S exchange reactions identified in this gas-phase cluster study parallel similar behavior of related condensed phase reaction systems.
Ti+(CO2)2Ar and Ti+(CO2)n(n=3-7) complexes are produced by laser vaporization in a pulsed supersonic expansion. The ion complexes of interest are each mass-selected in a time-of-flight spectrometer, and studied with infrared photodissociation spectroscopy. For each complex, a sharp band in the CO stretching frequency region is observed, which confirms the formation of the OTi+CO(CO2)n-1 oxide-carbonyl species. Small OTi+CO(CO2)n-1 complexes (n≦5) exhibit CO stretching and antisymmetric CO2 stretching vibrational bands that are blue-shifted from those of free CO and CO2. The experimental observations indicate that the coordination number of CO and CO2 molecules around TiO+ is five. Evidence is also observed for the presence of another electrostatic bonding Ti+(CO2)2 structural isomer for the Ti+(CO2)2Ar complex, which is characterized to have a bent OCO-Ti+-OCO structure stabilized by argon coordination
The most recognized and employed model of the solvation equilibration in the ionic solutions was proposed by Eigen and Tamm, in which there are four major states for an ion pair in the solution: the completely solvated state, 2SIP (double solvent separate ion pair), SIP (single solvent separate ion pair), and CIP (contact ion pair). Eigen and Tamm suggested that the transition from SIP to CIP is always the slowest step during the whole pairing process, due to a high free energy barrier between these two states. We carried out a series of potential of mean force calculations to study the pairing free energy profiles of two sets of model mono-atomic 1:1 ion pairs 2.0:x and x:2.0. For 2.0:x pairs the free energy barrier between the SIP and CIP states is largely reduced due to the salvation shell water structure. For these pairs the SIP to CIP transition is thus not the slowest step in the ion pair formation course. Thisis a deviation from the Eigen-Tamm model
Laser-induced fluorescence excitation spectra and dispersed fluorescence spectra of cobalt sulfide (CoS) have been recorded in the energy range of 22400-24400 cm-1 (corresponding to 446-409 nm). A new electronic transition progression with six vibronic bands, stemming from the X47/2 state of CoS, was identified and assigned to be [24.00]47/2-X47/2. The new observed 4△ state most probably originates from the core[10σ2][4π3][11σ2][1δ3][5π3] electronic configuration. Strong perturbations are found to extensively exist in the transition bands of this new state. The rotational constants and lifetimes of these bands have been determined
A recent study has revealed a full 3-dimentional reactive scattering picture of the reaction Cl+CHD3(v1=1) as the Cl atoms attack CHD3 from various directions respective to the C-H stretching bond. The reported polarization-dependent differential cross sections provide the most detailed characterization of the influences of reagent alignments on reactivity. To convey the stereo-specific information more accessible to general chemists, we show here, by proper symmetry considerations, how to retrieve from the measurements the relative integral and differential cross sections of two most common collision geometries: the end-on versus side-on attacks. The results, albeit coarse-grained, provide an appealing picture that not only reinforces our intuition about chemical reactivity, but also sheds more light on the conventional (unpolarized) attributes
We present a comparative study on the C-H stretching vibrations at air/DMSO (dimethyl sulfoxide) interface with both the free-induction decay (FID) coherent vibrational dynamics and the sub-wavenumber high resolution sum-frequency generation vibrational spectroscopy measurements. In principle the frequency-domain and time-domain spectroscopic measure-ments should generate identical information for a given molecular system. However, when the molecular systems are with several coupled or overlapping vibrational modes, obtain-ing detailed spectroscopic and coherent dynamics information is not as straightforward and rather difficult from either the time-domain or the frequency domain measurements. For the case of air/DMSO interface that is with moderately complex vibrational spectra, we show that the frequency-domain measurement with sub-wavenumber high-resolution sum-frequency generation vibrational spectroscopy is probably more advantageous than the time-domain measurement in obtaining quantitative understanding of the structure and coherent dynamics of the molecular interface
Equilibrium photoproduct of π-cyclopentadienyliron dicarbonyl dimer [CpFe(CO)2]2 in nonpolar solvent carbon tetrachloride (CCl4) is investigated using time-resolved 2D IR spectroscopy. One of the several possible visible-light-driven photoreaction pathways is confirmedand the product is found to contain a di-carbonyl group that exhibits quantum beating between two equivalent transitions in time-resolved 2D IR spectra, which turns out to be the anti-symmetric and symmetric stretching of the terminal carbonyl stretching modes of CpFe(CO)2Cl. This is the main product and its reaction pathway involves radical formation, followed by chloride addition. Quantum-chemistry computations support these experimental results. Our results indicate that 2D IR method can be used to identify in situ structures and dynamics of chemical species involved in condensed-phase chemical reactions
Alkali halide clusters are interesting model systems that can provide information about how crystal properties evolve. To study these properties, a high-resolution atmospheric pressure inlet time-of-flight mass spectrometry (APi-TOF-MS) study of the sequential sodium halides series, Cl-(NaCl)n and Br-(NaBr)m, has been reported, and the viability of the APi-TOF-MS equipped with an electrospray ionization source in determining cluster compositions has been demonstrated. The isotopic patterns were well resolved, as n=4 and 7 were determined to be the magic numbers for Cl-(NaCl)n clusters, which were particularly abundant in the mass spectra. A global minimum search based on density functional theory enabled basin hopping yield the most stable structures for the mentioned series. The structures exhibit several distinct motifs which can be roughly categorized as linear chain, rock salt, and hexagonal ring. This work provides an effective way to discover and elucidate the nonstoichiometry sodium halide clusters. These clusters possess very high vertical detachment energies and are generally called as superhalogens, which play important roles in chemistry because they are widely used in the synthesis of new classes of charge-transfer salts
β-Crystallins are the major structural proteins existing in the vertebrate lens, and their conformational stability is critical in maintaining the life-long transparency and refraction index of the lens. Seven subunits of β-crystallins naturally assemble into various heteroge-neous oligomers with different sizes. Here, we systematically investigated the thermal sta-bility of the different secondary structures present in β-crystallins and then the dynamic process for the thermal-induced unfolding of β-crystallins by Fourier transform infrared spectroscopy-monitored thermal titration and temperature-jump nanosecond time-resolved IR difference absorbance spectra. Our results show that the N-terminal anti-parallel β-sheets in β-crystallin are the most unstable with a transition midpoint temperature at 36.0±2.1 oC, leading to the formation of an intermediate consisting vastly of random coil structures. This intermediate structure is temporally assigned to that of the monomer generated by the thermal-induced disassembly of β-crystallin oligomers with a transition midpoint tempera-ture of 40.4±0.7 oC. The global unfolding of β-crystallins that leads to denaturation and aggregation indicated by the formation of intermolecular anti-parallel β-sheets has a transi-tion midpoint temperature determined as 72.4±0.2 oC. Temperature-jump time-resolved IR absorbance difference spectroscopy analysis further reveals that thermal-induced unfolding of β-crystallins occurs firstly in the anti-parallel β-sheets in the N-terminal domains with a time constant of 50 ns
Reaction of laser ablated zinc and cadmium atoms with SO2 molecules was studied by low temperature matrix isolation infrared spectroscopy. Cyclic M(SO2) and anion M(SO2)- (M=Zn, Cd) were produced in excess argon and neon, which were identified by 34SO2 and S18O2 isotopic substitutions. The observed infrared spectra and molecular structures were confirmed by density functional theoretical calculations. Natural charge distributions indicated significant electron transfer from s orbitals of zinc or cadmium metal atom to SO2 ligand and cyclic M(SO2) complexes favored “ion pair” M+(SO2)- formation, which were trapped in low temperature matrices. In addition Zn-O or Cd-O bond in M(SO2) exhibited strong polarized covalent character. Reaction of Hg atom with SO2 was also investigated, but no reaction product was observed, due to the relativistic effect that resulted in the contraction of 6s valence shell and high ionization potential of Hg atom
Efficient numerical solver for the Schr?dinger equation is very important in physics and chem-istry. The finite element discrete variable representation (FE-DVR) was first proposed by Rescigno and Mc-Curdy [Phys. Rev. A 62, 032706 (2000)] for solving quantum-mechanical scattering problems. In this work, an FE-DVR method in a mapped coordinate was proposed to improve the efficiency of the original FE-DVR method. For numerical demonstration, the proposed approach is applied for solving the electronic eigenfunctions and eigenvalues of the hydrogen atom and vibrational states of the electronic state 33gof the Cs2 molecule which has long-range interaction potential. The numerical results indicate that the numeri-cal efficiency of the original FE-DVR has been improved much using our proposed mapped coordinate scheme
We present a theoretical study of the reaction of the hydroxyl radical with ethene using electronic structure calculations and direct-dynamics simulations. High-accuracy electronic structure calculations at the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVDZ level have been carried out to characterize the representative regions of the potential energy surface of various reaction pathways, including OH-addition and H-abstraction. These ab initio calculations have been employed to derive an improved set of parameters for the MSINDO semiempirical Hamiltonian specific to the OH+C2H4 reaction. The specific-reaction-parameter Hamilto-nian captures the ab initio data accurately, and has been used to perform direct quasiclas-sical trajectory simulations of the OH+C2H4 reaction at collision energies in the range of 2?10 kcal/mol. The calculated cross sections reveal that the OH-addition reaction domi-nates at all energies over H-abstraction. In addition, the excitation function of addition is reminiscent of a barrierless capture process, while that for abstraction corresponds to an activated one, and these trends can be connected to the transition-state energies of both reactions. We note that the development of an accurate semiempirical Hamiltonian for the OH+C2H4 reaction in this work required the inclusion of empirical dispersion corrections, which will be important in future applications for which long-range intermolecular attraction becomes significant
We have developed a compact photoelectron imaging facility, including an anion source with dissociative photoelectron attachment to molecules, a linear time-of-flight mass spec-trometry (TOFMS), and an orthogonal high-resolution threshold photoelectron velocity mapimaging spectrometer (VMI). Intense and cold cluster anions were prepared in photoelectron-attachment processes upon pulsed UV laser ablation of metal target. Combining this anion source with TOFMS-VMI, the achieved mass resolution is about 200, and the electron ki-netic energy resolution is better than 3%, i.e., 30 meV for 1 eV electrons. More importantly, low-energy photoelectron imaging spectra for CH3S- and S2- at 611.46 nm are obtained. In both cases, the refined electron a±nities are determined to be 1.8626±0.0020 eV for CH3S and 1.6744§±0.0035 eV for S2, respectively. Preliminary results suggest that the apparatus is a powerful tool for estimating precise electron affinities values from threshold photoelectron imaging spectroscopy
The molecular orientation of ellipsoidal C70 in carbon nanotubes is carefully studied by first principles calculations. Using (14, 7) single-wall carbon nanotube (SWCNT) as a prototype material, we explored that the weak chemical interaction between SWCNT and C70 was the crucial factor to determine the molecular orientation. However, the small energy difference makes the distinguishment of two possible molecular orientations difficult. By simulating scanning tunneling microscope images and optical properties, we found that local electronic states sensitively depended on the molecular orientation of ellipsoidal C70, which provided a practical way of using scanning tunneling microscope to recognize the molecular orientation of ellipsoidal C70
Chinese abstract