Computation of cross sections for the F+H2(v=0,j=0) → FH(v′j)+H reaction by the hyperspherical method

Summary A quantum mechanical calculation of cross sections for the reaction F+H₂(v=0,j=0) FH(vj)+H has been performed on the T5A semiempirical potential surface using hyperspherical coordinates. State-to-state integral and differential cross sections converge rapidly with the number of components of the total angular momentum projection onto the axis of least inertia. Thev=3 differential cross section has a forward peak whose magnitude increases with energy whereas thev=2 differential cross section has a backward maximum, in qualitative agreement with cross-beam experiments. Thev=2 andv=3 rotational distributions are in rather good agreement with experiment, but not the vibrational branching ratios.     

苯并三氮唑及其羧酸酯衍生物对铜缓蚀机理的分子动力学模拟研究

用分子动力学(MD)方法, 模拟计算了5种铜缓蚀剂[苯并三氮唑(BTA)、苯并三氮唑-5-羧酸甲酯(MBTC)、苯并三氮唑-5-羧酸丁酯(BBTC)、苯并三氮唑-5-羧酸己酯(HBTC)、苯并三氮唑-5-羧酸辛酯(OBTC)]与Cu₂O晶体的相互作用. 结果发现, 中性条件下缓蚀剂分子与Cu₂O晶体的结合能均大于酸性条件下的数值, 但两种条件下结合能的大小排序均为OBTC＞HBTC＞BBTC＞MBTC＞BTA. 对体系各种相互作用以及对关联函数g(r)的分析表明, 体系结合能主要由库仑作用提供, Cu₂O晶体中的Cu原子与缓蚀剂分子中的N原子之间形成了配位键. 在与Cu₂O(001)晶面结合过程中, BTA及其衍生物分子发生了扭曲变形, 但形变能远小于体系的非键相互作用能.     

Molecular dynamics simulations of a nucleoside analogue of 1,4-dihydro-4-oxoquinoline-3-carboxylic acid synthesized as a potential antiviral agent: Conformational studies in vacuum and in water

Conformational analysis of nucleosides may have direct applications to the structure–activity relationship (SAR) studies and in the design of new drug candidates. Although conformational analysis may be accessed in many different ways, in this work it was performed using molecular dynamics (MD) simulation in order to study the dynamic behavior of a nucleoside derivative of 1,4-dihydro-4-oxoquinoline-3-carboxylic acid, synthesized by our group as a potential antiviral agent. The MD simulation was carried out during 10 ns in vacuum and in a box of water at two different temperatures (i.e., 300 and 600 K) using the AMBER force field. The in vacuum MD simulation results are in agreement with the crystallographic structure and with the DFT calculations of the nucleoside, revealing the anti conformer as the more stable one. The simulation in water, however, shows that both conformers may exist at 300 K, the temperature of the in vivo and in vitro assays, revealing that both the syn and anti conformers should be considered in a MD simulation study of the inhibitor–enzyme complex. Simulations are also in agreement with the NOE experiment, which shows that the anti conformer is the preferential one in DMSO-d6 solution at 298 K.     

Determining molecular structures and conformations directly from electron diffraction using a genetic algorithm.

A global optimization strategy, based upon application of a genetic algorithm (GA), is demonstrated as an approach for determining the structures of molecules possessing significant conformational flexibility directly from gas-phase electron diffraction data. In contrast to the common approach to molecular structure determination, based on trial-and-error assessment of structures available from quantum chemical calculations, the GA approach described here does not require expensive quantum mechanical calculations or manual searching of the potential energy surface of the sample molecule, relying instead upon simple comparison between the experimental and calculated diffraction pattern derived from a proposed trial molecular structure. Structures as complex as all-trans retinal and p-coumaric acid, both important chromophores in photosensing processes, may be determined by this approach. In the examples presented here, we find that the GA approach can determine the correct conformation of a flexible molecule described by 11 independent torsion angles. We also demonstrate applications to samples comprising a mixture of two distinct molecular conformations. With these results we conclude that applications of this approach are very promising in elucidating the structures of large molecules directly from electron diffraction data.     

Calculation of affinities of peptides for proteins

Several methodologies were employed to calculate the Gibbs standard free energy of binding for a collection of protein-ligand complexes, where the ligand is a peptide and the protein is representative for various protein families. Almost 40 protein-ligand complexes were employed for a continuum approach, which considers the protein and the peptide at the atomic level, but includes solvent as a polarizable continuum. Five protein-ligand complexes were employed for an all-atom approach that relies on a combination of the double decoupling method with thermodynamic integration and molecular dynamics. These affinities were also computed by means of the linear interaction energy method. Although it generally proved rather difficult to predict the absolute free energies correctly, for some protein families the experimental ranking order was correctly reproduced by the continuum and all-atom approach. Considerable attention has also been given to correctly analyze the affinities of charged peptides, where it is required to judge the effect of one or more ions that are being decoupled in an all-atom approach to preserve electroneutrality. The various methods are further judged upon their merits.     

Dielectric relaxation of electrolyte solutions in acetonitrile

Complex permittivity spectra in the frequency range 0.95v (GHz)89 for acetonitrile and its solutions of LiBr, NaI, NaClO₄, and Bu₄NBr at 25°C show one Debye equation for the neat solvent whereas the superposition of a Debye process for the solute and a Cole-Cole distribution for the solvent is necessary to account for the dielectric relaxation behavior of the solutions. The reorientation of bulk acetonitrile is diffusive and only weakly coupled to viscosity. The number of solvent molecules irrotationally bound to the electrolyte is in good agreement with conventional solvation numbers for all electrolytes, when kinetic depolarization is assumed to be negligible. The solute relaxation process is dominated by the formation kinetics and reorientation of contact ion pairs. There is evidence for solvent-shared ion pairs in dilute NaClO₄ solutions.     

I NQR and spectroscopic investigation of impurity-doped and mixed lithium iodate Li1−xHxIO3 crystals

The ¹²⁷I NQR, IR absorption and Raman spectra of impurity-doped and mixed lithium iodate Li_1−xH_xIO₃ crystals grown from water solutions with different LiIO₃/HIO₃ ratios were investigated depending on the content of the impurity hydrogen x. The NQR results suggested that, at small concentration of doping iodic acid x<0.22, the lattice dynamics of the crystal grown from water solution changes significantly though the crystal retains hexagonal symmetry. Spectroscopic studies are compatible with average hexagonal symmetry of the grown doped crystals. From the results of Raman studies at room temperature and 100 K, the concentration range of hydrogen dopant 0.22<x<0.36 was found where disordered solid solution crystals Li_1−xH_xIO₃ are formed.     

First principles and experimental 1H NMR signatures of solvated ions: The case of HCl(aq).

A combined experimental and ab initio study is presented of the 1H NMR chemical shift distribution of aqueous hydrogen chloride solution as a function of acid concentration, based on Car-Parrinello molecular dynamics simulations and fully periodic NMR chemical-shift calculations. The agreement of computed and experimental spectra is very good. From first-principles calculations, we can show that the individual contributions of Eigen and Zundel ions, regular water molecules, and the chlorine solvation shell to the NMR line are very distinct and almost independent of the acid concentration. From the computed instantaneous NMR distributions, it is further possible to characterize the average variation in hydrogen-bond strength of the different complexes.     

The photoisomerization mechanism of azobenzene: a semiclassical simulation of nonadiabatic dynamics

We have simulated the photoisomerization dynamics of azobenzene, taking into account internal conversion and geometrical relaxation processes, by means of a semiclassical surface hopping approach. Both n-->pi* and pi-->pi* excitations and both cis-->trans and trans-->cis conversions have been considered. We show that in all cases the torsion around the N==N double bond is the preferred mechanism. The quantum yields measured are correctly reproduced and the observed differences are explained as a result of the competition between the inertia of the torsional motion and the premature deactivation of the excited state. Recent time-resolved spectroscopic experiments are interpreted in the light of the simulated dynamics.