Shan Xi Tian

A Comparative Study for Molecular Dynamics Simulations of Liquid Benzene

The classical equilibrium and nonequilibrium molecular dynamics simulations for liquid benzene, the prototypical aromatic π-π interaction system, are performed using a variety of molecular force fields, OPT-FF, AMBER 03, general AMBER force field (GAFF), OPLS-AA, OPLS-CS, CHARMM27, GROMOS 53A5, and GROMOS 53A6. The simulated results of the molecular structure and thermodynamic properties of liquid benzene are compared with the experimental data available in the literature, accounting for the superiority of each force field in the descriptions of the π-π interaction system. The OPLS-AA force field is recommended to be the best one, which reproduces quite well the properties examined in this work, while the others fail in predicting either the local structure or the thermodynamic properties. Such distinct discrepancies for the above force fields are discussed within the scheme of the pairwise interaction construction of the standard force field, which will stimulate searching for a force field with generally good quality not only in terms of microstructure descriptions but also in the predictions of the thermodynamic properties of the liquids.

Conformational Stability of 1-Butene: An Electron Momentum Spectroscopy Investigation

The valence-shell electron momentum distributions for 1-butene are measured by electron momentum spectroscopy (EMS) employing non-coplanar symmetric geometry. The experimental electron momentum distributions are compared with the density functional theory (DFT) calculations using different-sized basis sets. Although the two conformers of 1-butene in the gas phase, namely the skew and syn, have very close ionization potentials, the electron momentum distributions, especially in the low momentum region, can show prominent differences for some of the valence orbitals. By comparing the experimental electron momentum profiles with the theoretical ones, the skew conformer is found to be more stable than the syn and their relative abundances at room temperature are estimated to be (69 +/- 6)% and (31 +/- 6)%, respectively. It demonstrates that EMS has the latent potential to study the relative stability of conformers.

Positive/negative ion velocity mapping apparatus for electron-molecule reactions

In molecular dissociative ionization by electron collisions and dissociative electron attachment to molecule, the respective positively and negatively charged fragments are the important products. A compact ion velocity mapping apparatus is developed for the angular distribution measurements of the positive or negative fragments produced in the electron-molecule reactions. This apparatus consists of a pulsed electron gun, a set of ion velocity mapping optic lenses, a two-dimensional position detector including two pieces of micro-channel plates, and a phosphor screen, and a charge-coupled-device camera for data acquisition. The positive and negative ion detections can be simply realized by changing the voltage polarity of ion optics and detector. Velocity sliced images can be directly recorded using a narrow voltage pulse applied on the rear micro-channel plate. The efficient performance of this system is evaluated by measuring the angular distribution of O(-) from the electron attachments to NO at 7.3 and 8.3 eV and O(+) from the electron collision with CO at 40.0 eV.

Unique Interactions Between Diborane and π Orbitals: Blue- or Red-Shifted Hydrogen Bonding?

A new type of hydrogen-bonding interaction in the diborane (B 2H 6)...pi (benzene C 6H 6, 1,3-cyclopentadiene C 5H 6, and cyclobutadiene C 4H 4) system is identified with the natural bond orbital and atoms-in-molecules analyses based on ab initio calculations. In comparison with the symmetric and asymmetric stretching vibrational modes of the bridging hydrogen atoms in free B 2H 6, the frequencies of the symmetric mode are red-shifted for B 2H 6...C 6H 6 and B 2H 6...C 5H 6 but blue-shifted for B 2H 6...C 4H 4. The frequency blue shifts of the asymmetric mode are found for all three complexes; the most significant blue shift is 14.73 cm (-1) for the asymmetric mode in B 2H 6...C 4H 4. In these complexes, the electron-deficient three-center two-electron bond B-H 1-B facing the pi orbital is shortened, while the opposite B-H 2-B bond is elongated.

Thermal stabilities of the microhydrated zwitterionic glycine: a kinetics and dynamics study.

Thermal stabilities of the zwitterionic glycine (zg) combined with water molecules are investigated by both ab initio/RRKM calculations and the thermostatic molecular dynamics (MD) simulations. The microhydrated zg clusters, zg-nw (n = 2, 3; w = water), can transfer to the canonical clusters cg-nw through the rapid intramolecular proton transfers (PT), while the proton is shifted via the intermolecular hydrogen bonds for zg-4w --> cg-4w. Both the MD/solution model simulations and the RRKM calculations indicate that the zg and cg conformers hydrated with more water molecules have their respective higher stabilties and the transformation needs to overcome a certain energy barrier. The thermostatic MD simulations show that the dynamic PT processes are significantly influenced by both the temperatures used in the trajectory simulations and the hydrogen bonding arrangements between glycine and water molecules.

Shape resonance states of the low-energy electron attachments to DNA base tautomers

Two different types of shape resonance states, π* and σ*, formed in the low-energy electron attachments to the low-lying tautomers of DNA bases (adenine, guanine, thymine, and cytosine) in the gas phase are investigated using the quantum scattering method with the non-empirical model potentials in a symmetry-adapted, single-center expansion. Four and three π* states are predicted for purines and pyrimidines, respectively. Comparing the different tautomers of a certain DNA base, we find distinct differences both in the resonance energies and the resonant wave function patterns of π* states. As for the lowest three π* states, the energetic values predicted in this work are also compared with the theoretical and experimental results available in the literature.

Molecular dynamics study of solvation differences between cis- and transplatin molecules in water

The classical molecular dynamics (MD) simulations for the solvation properties of cis- and transplatins in water are performed with the Lennard-Jones plus Coulomb electrostatic potential parameters that are optimized with ab initio potential energies of the water-platin systems. Two hydration shells are found both for cis- and transplatins. The first shell of water molecules is closer to transplatin than cisplatin. The average number and lifetime of the intermolecular hydrogen bonds (HBs) estimated from the MD trajectories indicate that the Cl and NH(3) ligands are the main groups involved in the intermolecular HBs with water. In comparison with cisplatin, there are more HBs around transplatin and these HBs show the longer lifetime. The distinctly different solvation structures between cis- and transplatins are further revealed with the spatially anisotropic distributions of the first hydration shells.

Monoanion BH4(-) can stabilize zwitterionic glycine with dihydrogen bonds.

Unusual strength: In the complex glycine-BH(4)(-), unconventional dihydrogen bonds are predicted. An ultrashort dihydrogen bond B-H...H-N and a very strong interaction of about -41 kcal mol(-1)) are found in complex 3 (see structures), in which the zwitterionic glycine is stabilized with a big margin.

Orientation effect in the low-energy electron attachment to the apolar carbon tetrafluoride molecule.

Stereodynamics of the molecular fragmentation by energetic particle impact provides essential information about the interaction between the projectile and target, which has been the central topic of chemical reactions. Versatile information on the collision stereodynamics may degrade seriously by measuring the spherically averaged cross-sections because of the randomly oriented target molecules, but can benefit from the oriented target molecules that are prepared prior to the collision. Up to date, the polar molecules in gas phase can be oriented or aligned by an electrostatic field or in a linearpolarized laser field. Except for some sophisticated methods (e.g., the stimulated Raman pumping), the alignment or orientation of apolar molecules (without permanent dipole moment) is still a challenge in experiments. For the randomly oriented molecules in some cases, a similar effect of alignment or orientation could be derived from the significant anisotropy of the polar-angle-resolved differential cross-sections (DCS). However, the orientation effect is scarcely observed in slow collision reactions. During the slow approaching of the projectile, the spatial anisotropy of the projectile–target interaction potential is usually believed to be averaged out because of the molecular rotations of the target. In contrast to the above-mentioned conventional wisdom, the orientation effect in the low-energy electron attachment to the apolar molecule CF4 is observed in our anion velocity image mapping experiments. The CF4 molecule is randomly oriented in a field-free environment during attachment. Up to now, only some simple linear apolar molecules (H2, D2, N2, and CO2) were investigated for the orientation effect in medium(dozens of electronvolts) or high-energy (several hundreds to more one thousand electronvolts) electron collisions. In this work, the low-energy (no more than 6 eV) electron attachment to CF4 shows that electron capture can be strongly influenced by the target molecular orientation, leading to specific distributions of the fragment momenta. In the impulsive dissociation, the axial-recoil approximation has been well validated. The intermediate state of the dissociative precursor usually follows the fragment trajectories parallel or perpendicular to the initial molecular axis. A temporary negative ion CF4 formed by electron attachment is just this type of dissociative precursor and may decay through two complementary dissociation pathways, CF4 !F + CF3 (channel a) and F + CF3 (channel b) with appearance energies of 3.7 and 4.4 eV, respectively. The yield efficiency curves of the F and CF3 fragments produced in these two dissociative electron attachment (DEA) processes were recorded and a broad band in each curve was found. At the lower energies of about 6 eV, channels a and b were suspected to experience the common resonance state T2 of CF4 , while the lower resonance state A1 was mainly responsible for the autodetachment CF4 !e + CF4. Although the DEA dynamics has been partly revealed by angular distributions (at 6.7 eV for F and 6.1 eV for CF3 ) of the anionic fragments, there are a lot of uncertainties because those measurements were performed in the small angular q range of 15 to 1108. Such limitation is due to the spatial restriction of the rotating ion detector used in their turn-table arrangement. The full picture of DEA dynamics should be promising by using more advanced experimental techniques. The state-of-the-art anion velocity image mapping method recently developed in our group and by others can realize measurements of both the DCS of the anionic fragment in a full angular range (q = 0–3608) and the kinetic energy distributions simultaneously. The time-sliced images (azimuth angle f of about 08) of the F velocity were recorded at electron energies of 5.3, 5.5, 6.0, and 7.0 eV (Figure 1); while the images of CF3 were recorded at 5.5, 6.0, 6.5, and 7.0 eV (Figure 2). Because of the different kinetic energies of the anionic fragments and the small size of the detector (its effective diameter is 40 mm), the images were contracted or enlarged by biasing the electrode voltages for the faster F and the slower CF3 anions. The kinetic energies or velocities obtained from the images were calibrated with values available in the literature. As shown in Figure 1, the central higher intensity of F indicates that most anions have low kinetic energies (0– 0.5 eV, increasing slightly at higher attachment energies) and the larger image size implies a higher kinetic energy or a larger velocity of the F ion. At the outer ring, which corresponds to kinetic energies higher than 0.8 eV, a remarkable anisotropy of the F distribution is observed although the ion intensities are much weaker (less than 10 % of the central intensity). The high-momentum distribution appears partially on the image recorded at 6.0 eV but completely disappears at 7.0 eV. The distribution is suspected to be located outside the detector, which is due to its large momentum value or another dissociation channel. The images of the CF3 momentum are distinctly different from those of F . As shown in Figure 2, the low kinetic-energy components are not observed for the CF3 [*] L. Xia, X.-J. Zeng, H.-K. Li, B. Wu, Prof. Dr. S. X. Tian Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemical Physics University of Science and Technology of China Hefei, Anhui 230026 (China) E-mail: sxtian@ustc.edu.cn

An investigation of electron momentum spectroscopy for ethane

The binding energies and electron momentum distributions of the five valence orbitals of have been measured at high momentum resolution. The measured binding energy spectrum has been compared favourably with the results of previously published experimental data, theoretical calculations and outer-valence Green function method calculation of this work. The measured momentum profiles have been quantitatively compared with momentum distributions predicted by Snyder and Basch molecular wavefunctions, self consistent field (SCF) wavefunctions up to the near-Hartree-Fock limit, density functional theory calculations and experimental data (Dey et al 1976 J. Electron Spectrosc. Relat. Phenom. 9 397). They are found to be in excellent agreement with Snyder and Basch molecular wavefunctions and density functional theory calculations, especially for the orbital. The density maps for oriented molecule in position and momentum space are presented.