2009 Vol. 22, No. 6

Special Issue
2009, 22(6): 1-1. doi: 10.1088/1674-0068/22/6/1-1
Crossed beams scattering study was carried out on the F+HD→DF+H reaction using highresolution H-atom Rydberg tagging time-of-flight technique. Vibrational state-resolved differential cross sections were measured, with partial rotational state resolution, at eight collision energies in the range of 2.51?5.60 kJ/mol. Experimental results indicated that the product angular distributions are predominantly backward scattered. As the collision energy increases, the backward scattered peak becomes broader gradually. Dependence of product vibration branching ratios on the collision energy was also determined. The experimental results show that the DF products are highly inverted in the vibrational state distribution and the DF (v′=3) product is the most populated state. Furthermore, the DF (v′=1) product has also been observed at collision energy above 3.97 kJ/mol.
The native protein structures in buffer solution are maintained by the electrostatic force as well as the hydrophobic force, salt ions play an important role in maintaining the protein native structures, and their effect on the protein stability has attracted tremendous interests. Infrared spectroscopy has been generally used in molecular structure analysis due to its fingerprint resolution for different species including macromolecules as proteins. However spectral intensities have received much less attention than the vibrational frequencies. Here we report that the spectral intensities of protein amide I band, the finger prints for the protein secondary structures, are very sensitive to the local electric field known as Onsager reaction field caused by salt ions. IR absorbance thermal titrations have been conducted for a series of samples including simple water soluble amino acids, water soluble monomeric protein cytochrome c and dimeric protein DsbC and its single-site mutant G49R. We found that at lower temperature range (10-20 oC), there exists a thermal activated salting-in process, where the IR intensity increases with a rise in the temperature, corresponding to the ions binding of the hydrophobic surface of protein. This process is absent for the amino acids. When further raising the temperature, the IR intensity decreases, this is interpreted as the thermal activated breaking of the ion-protein surface binding. Applying Van't Hoff plot to the thermal titration curves, the thermodynamic parameters such as ?H and ?S for salting-in and ion unbinding processes can be derived for various protein secondary structural components, revealing quantitatively the extent of hydrophobic interaction as well as the strength of the ion-protein binding.
Changes of molecular structure and associated charge distributions, and changes of anhar-monic vibrational parameters from DNA base monomers to the Watson-Crick base pairs, have been investigated at the density functional theory level. Through examination of the NH2, N-H, and C=O stretching vibrational modes that are involved in the multiple H-bonds in the base pairs, sensitivity of their diagonal and off-diagonal anharmonicities, as well as anharmonic vibrational couplings, to the structure change are predicted. Our results re-veal the intrinsic connection between the anharmonic vibrational potentials, H-bonding, and electrostatic interactions in DNA bases.
Dynamic processes of CO2 are experimentally studied in intense femtosecond laser fields with laser intensity varying from 1×1013W/cm2 to 6×1014W/cm2. When the laser intensity is below the ionization threshold, a coherent rotational wave-packet is formed for CO2 at room temperature through nonadiabatic rotational excitation. The evolution of the wave-packet leads to transient alignment. The field-free alignment revives periodically after the laser pulse is over. The revival structure can be modified by a second laser pulse for the rotational wave-packet through precisely adjusting the time delays between the two laser pulses. When the laser intensity excesses the ionization threshold, ionization and Coulomb explosion occur. The atomic ions Cm+ (m=1-3) and On+ (n=1-3) observed in the experiment exhibit highly anisotropic angular distributions relative to the laser polarization. Using two linearly polarized laser pulses with crossed polarization, we conclude that the anisotropic angular distribution results from dynamic alignment, in which the rising edge of the laser pulse aligns the neutral CO2 along the laser polarization direction prior to ionization.
Density functional theory (DFT) calculations are reported for the structures of neutral andzwitterionic glycine-(CH3OH)n where n=1-6. Initial geometries of the clusters of neutral and zwitterionic glycine with 1-6 methanol molecules are fully optimized at B3LYP/6-31+G* level of theory. The lowest energy configurations are located and their hydrogen bond structures are analyzed. Theoretical prediction reveals that the methanols prefer to locate near the carboxylic acid group for the small clusters (n≤3) with the neutral form while the configurations with the methanols bridging the acid and the amino group are favorite in the zwitterionic form clusters. When the number of the methanol molecules in the clusters reaches five and six,the two forms tend to be isoenergetic.
The ultrafast dynamics of benzaldehyde upon 260, 271, 284, and 287 nm excitations have been studied by femtosecond pump-probe time-of-flight mass spectrometry. A biexponential decay component model was applied to fit the transient profiles of benzaldehyde ions and fragment ions. At the S2 origin, the first decay of the component was attributed to the internal conversion to the high vibrational levels of S1 state. Lifetimes of the first component decreased with increasing vibrational energy, due to the influence of high density of the vibrational levels. The second decay was assigned to the vibrational relaxation of the S1 whose lifetime was about 600 fs. Upon 287 nm excitation, the first decay became ultra-short (~56 fs) which was taken for the intersystem cross from S1 to T2, while the second decay component was attributed to the vibrational relaxation. The pump-probe transient of fragment was also studied with the different probe intensity at 284 nm pump.
Here we report a novel twin polarization angle (TPA) approach in the quantitative chirality detection with the surface sum-frequency generation vibrational spectroscopy (SFG-VS). Generally, the achiral contribution dominates the surface SFG-VS signal, and the pure chiral signal is usually two or three orders of magnitude smaller. Therefore, it has been difficult to make quantitative detection and analysis of the chiral contributions to the surface SFG-VS signal. In the TPA method, by varying together the polarization angles of the incoming visible light and the sum frequency signal at fixed s or p polarization of the incoming infrared beam, the polarization dependent SFG signal can give not only direct signature of the chiral contribution in the total SFG-VS signal, but also the accurate measurement of the chiral and achiral components in the surface SFG signal. The general description of the TPA method is presented and the experiment test of the TPA approach is also presented for the SFG-VS from the S- and R-limonene chiral liquid surfaces. The most accurate degree of chiral excessvalues thus obtained for the 2878 cm-1 spectral peak of the S- and R-limonene liquid surfaces are (23.7±0.4)% and (-25.4±1.3)%, respectively.
New global three dimensional potential energy surfaces for the Cl+H2 reactive system have been constructed using accurate multireference configuration interaction calculations with a large basis set. The three lowest adiabatic potential energy surfaces correlating asymptotically with Cl(2P)+H2 have been transformed to a diabatic representation, which leads to a fourth coupling potential for non-linear geometries. In addition, the spin-orbit coupling surfaces have also been computed using the Breit-Pauli Hamiltonian. Properties of the new potential are described. Reaction dynamics based on the new potential agrees with the recent experimental results quite well.
Ion mobility spectra for ten alcohols have been studied in an ion mobility spectrometry apparatus equipped with a corona discharge ionization source. Using protonated water cluster ions as the reactant ions and clean air as the drift gas, the alcohols exhibit different product ion characteristic peaks in their ion mobility spectra. The detection limit for these alcohols is at low concentration pmol/L level according to the concentration calibration by exponential dilution method. Based on the measured ion mobilities, several chemical physics parameters of the ion-molecular interaction at atmosphere were obtained, including the ionic collision cross sections, diffusion coefficients, collision rate constants,and the ionic radii under the hard-sphere model approximation.
The absorption spectrum of NiI between 445 and 510 nm has been investigated using the technique of laser vaporization/reaction with free jet expansion and cavity ring down laser absorption spectroscopy. Two new transitions namely, [21.3]2?5/2~X2?5/2 and [21.9]2Π3/2~X2?5/2 systems were identified and studied. Spectra of both 58NiI and 60NiI isotopic molecules were observed. Equilibrium molecular constants for both electronic states are reported and the equilibrium bond length for the [21.3]2?5/2 state and the [21.9]2Π3/2 state was respectively determined to be 2.431 and 2.481 ?.
Resonance-enhanced multiphoton ionization of the titanium atoms has been investigated in the 293-321 nm wavelength. We couple a laser-ablated metal target into a molecular beam to produce free atoms. Ions produced from photoionization of the neutral atoms are monitored by a home-built time-of-flight mass spectrometer. Photoionization cross sections of the excited states of Ti I were deduced from the dependence of the ion signal intensity on the laser intensity for photon energies close to the ionization threshold. The values obtained range from 0.2 Mb to 6.0 Mb. No significant isotope-dependence was found from measurements of the photoionization cross sections of 46Ti, 47Ti, and 48Ti.
Based on the reaction microscope at the institute of modern physics, the reaction mechanism in molecular ion-atom collisions is investigated experimentally. The features of this system is illustrated by a kinematically complete experiment performed for the collision process.Using the so-called list-mode data recording technique and the coincidence measurement,the momentum vector of each fragment from the molecular ion were recorded event by event.The orientation of the molecular axis for H2+ dissociation reactions could be determined for each event in the off-line analysis. The measured orientation of the molecular ion is believed the same as the one at the instance of collision under axial recoil approximation. The polar angle resolution of the molecular orientation of ±8o was obtained.
The adsorption dynamics of a model protein (the human insulin) onto graphene surfaces with different sizes was investigated by molecular dynamics simulations. During the adsorption, it has different effect on the stability of the model protein in the fixed and non-fixed graphene systems. The tertiary structure of the protein was destroyed or partially destroyed,and graphene surfaces shows the selective protection for some α-helices in non-fixed systems but not in fixed systems by reason of the flexibility of graphene. As indicated by the interaction energy curve and trajectory animation, the conformation and orientation selection of the protein were induced by the properties and the texture of graphene surfaces. The knowledge of protein adsorption on graphene surfaces would be helpful to better understand stability of protein on graphene surfaces and facilitate potential applications of graphene in biotechnology.
The reactions of cationic zirconium oxide clusters ZrxOy+ with ethylene (C2H4) were inves-tigated by using a time-of-flight mass spectrometer coupled with a laser ablation/supersonic expansion cluster source. Some hydrogen containing products (ZrO2)xH+ (x=1~4) were observed after the reaction. The density functional theory calculations indicate that apart from the common oxygen transfer reaction channel, the hydrogen abstraction channel can also occur in (ZrO2)x++C2H4, which supports that the observed (ZrO2)xH+ may be due to (ZrO2)x++C2H4→(ZrO2)xH++C2H3. The rate constants of different reaction channels were also calculated by Rice-Ramsberger-Kassel-Marcus theory.
Electron momentum distributions for 4a1 orbitals of serial freon molecules CF3Cl, CF2Cl2,and CFCl3 (CFxCl4-x, x=1~3) have been reanalyzed due to the severe discrepancies between theory and experiment in low momentum region. The tentative calculations using equilibrium geometries of molecular ions have exhibited a great improvement in agreement with the experimental data, which suggests that the molecular geometry distortion may be responsible for the observed high intensities at p<0.5 a.u.. Further analyses show that the severe discrepancies at low momentum region mainly arise from the influence of molecular geometry distortion on C-Cl bonding electron density distributions.
Two-color resonant two-photon mass-analyzed threshold ionization (MATI) spectroscopy was used to record the vibrationally resolved cation spectra of the selected rotamers of pethoxyphenol. The adiabatic ionization energies of the trans and cis rotamers are determined to be 61565±5 and 61670±5 cm-1, which are less than that of p-methoxyphenol by 645 and 643 cm-1, respectively. Analysis on the MATI spectra of the selected rotamers of pethoxyphenol cation shows that the relative orientation of the ethoxy group has little effect on the in-plane ring vibrations. The low-frequency OC2H5 bending vibrations appear to be active for both forms of the cation.
We introduce a modification of reflectron time-of-flight mass spectrometer for laser photodis-sociation of mass-selected ions. In our apparatus, the ions of interests were selected by amass gate near the first space focus point and decelerated right after the mass gate, were thencrossed by a laser beam for dissociation. The daughter ions and surviving parent ions werere-accelerated and analyzed by the reflectron time-of-flight mass spectrometer. Compared to the designs reported by other research groups, our selection-deceleration-dissociation-reacceleration approach has better daughter-parent-ions-separation, easier laser timing, and better overlapping between the ion beam and laser beam. We also conducted detailed calculations on the parent ion and daughter ion flight times, and provided a simplified formula for the calibration of daughter ion mass.
A cavity ring-down spectrometer (CRDS) is constructed with a single-mode continuous-waveTi:Sapphire laser. It allows attaining a minimum detectable absorption of 1.8×10-10 cm-1.The spectrometer is applied to record the overtone spectrum of 12C2H2 in the 12240-12350 cm-1. Compared with the previous CRDS and intra-cavity laser absorption spec-troscopy studies in the same region, the present measurement achieved better sensitivity and better precision as well. As a result, the ro-vibrational parameters of the high overtone bands of acetylene at 12290.12, 12311.82, and 12350.61 cm-1 have been refined. The advantages of the present CRD spectrometer is also demonstrated by the newly observed and well characterized perturbation on the f component of the very weak band near 12289 cm-1. The quantitative measurement capability of the spectrometer is verified with the measurement of the water lines and employed to give the absolute band intensities of those three acetylene bands.
The laser-induced fluorescence excitation spectrum of jet-cooled NiS molecule has been recorded in the energy range of 15500-17200 cm-1. Fifteen bands have been assigned as three transition progressions: [15.65]3Π1(v′=0-4)-X30- (v"=0), [15.69]3Π1(v′=0-4)-X30-(v"=0). Spectroscopic constants for the three newly identified electronically excited states have been determined for the first time. In addition, the lifetimes for most observed vibronic bands have also been measured.
The product channels and mechanisms of the C2HCl2+O2 reaction are investigated by step-scan time-resolved Fourier transform infrared emission spectroscopy and the G3MP2//B3LYP/6-311G(d,p) level of electronic structure calculations. Vibrationally excited products of HCl, CO, and CO2 are observed in the IR emission spectra and the product vibrational state distribution are determined which shows that HCl and CO are vibrationally excited with the nascent average vibrational energy estimated to be 59.8 and 51.8 kJ/mol respectively. In combination with the G3MP2//B3LYP/6-311G(d,p) calculations, the reaction mechanisms have been characterized and the energetically favorable reaction pathways have been suggested.
Photodissociation of p-aminobenzoic acid at 266 nm was investigated by probing the nascent OH photoproduct employing the laser-induced fluorescence technique. It was found that the nascent OH radical was vibrationally cold and its rotational state distribution conformed to be a Boltzmann behavior, characterized by a rotational temperature of 1040±110 K. The rotational energy of OH was determined to be 8.78±0.84 kJ/mol. Between the two spinorbit states of OH, 2Π3/2 and 2Π1/2, the former was found to be preferentially populated.The distribution of the Π(A′) state for the Λ-doublet was dominant. Finally, a probable mechanism for the formation of OH produced from the photodissociation of p-aminobenzoic acid is discussed.