Energy transfer in reactive and nonreactive collisions of Na with Na2

Stimulated by the experimental finding of vibrationally and rotationally cold dimers in supersonic nozzle molecular beams of sodium, we have studied energy transfer in collisions of Na with Na₂ over a wide range of initial relative translation energies E and impact parameters b by a classical mechanical trajectory method. The vibrational and rotational energies were initialized using Boltzmann distributions characterized by temperatures T_vib = 150 K, T_rot = 50 K. We find that for large values of E the energy transfer in reactive collisions increases with b while it decreases with b for the nonreactive collisions. For low values of E, energy transfer is a decreasing function of b for both reactive and nonreactive encounters. Both the reactive and nonreactive mechanisms are very efficient in effecting transfer, between 40–70% of the initial relative translational energy is converted into internal energy of the diatom, leading to the conclusion that the reverse collisions would result in the rapid relaxation observed in experiment.     

Semiclassical Trajectory Studies of Reactive and Nonreactive Scattering of OH(A 2Σ+) by H2 Based on an Improved Full-Dimensional Ab Initio Diabatic Potential Energy Matrix

We present a new full-dimensional diabatic potential energy matrix (DPEM) for electronically nonadiabatic collisions of OH(A ²Σ⁺) with H₂, and we calculate the probabilities of electronically adiabatic inelastic collisions, nonreactive quenching, and reactive quenching to form H₂O+H. The DPEM was fitted using a many-body expansion with permutationally invariant polynomials in bond-order functions to represent the many-body part. The dynamics calculations were carried out with the fewest-switches with time uncertainty and stochastic decoherence (FSTU/SD) semiclassical trajectory method. We present results both for head-on collisions (impact parameter b equal to zero) and for a full range of impact parameters. The results are compared to experiment and to earlier FSTU/SD and quantum dynamics calculations with a previously published DPEM. The various theoretical results all agree that nonreactive quenching dominates reactive quenching, but there are quantitative differences between the two DPEMs and between the b=0 results and the all-b results, especially for the probability of reactive quenching.     

State(R)-state(TS)-state(P) theoretical study of H + H<Subscript>2</Subscript> system

The calculation of H + H₂ system by symplectic quasiclassical trajectory (SQCT) shows that there are two types of collision trajectories A and B, i.e., type A trajectory passes the saddle point of transition state (TS), whereas type B trajectory does not pass the saddle point of transition state. Not all the reactants of type A trajectory are reactive, while not all of type B trajectory are nonreactive. The partition and reactivity of these two types of trajectories are affected by reactant state(R), furthermore, the types of trajectories affect the state and angle distributions of products. Not only the rudiment framework for theoretical study on state(R)-state(TS)-state(P) is established, but also the further understanding of transition state theory (TST) of Eyring is investigated in this paper.     

Pseudo-bimolecular [2+2] cycloaddition studied by time-resolved photoelectron spectroscopy

The first study of pseudo‐bimolecular cycloaddition reaction dynamics in the gas phase is presented. We used femtosecond time‐resolved photoelectron spectroscopy (TRPES) to study the [2+2] photocycloaddition in the model system pseudo‐gem‐divinyl[2.2]paracyclophane. From X‐ray crystal diffraction measurements we found that the ground‐state molecule can exist in two conformers; a reactive one in which the vinyl groups are immediately situated for [2+2] cycloaddition and a nonreactive conformer in which they point in opposite directions. From the measured S₁ lifetimes we assigned a clear relation between the conformation and the excited‐state reactivity; the reactive conformer has a lifetime of 13 ps, populating the ground state through a conical intersection leading to [2+2] cycloaddition, whereas the nonreactive conformer has a lifetime of 400 ps. Ab initio calculations were performed to locate the relevant conical intersection (CI) and calculate an excited‐state [2+2] cycloaddition reaction path. The interpretation of the results is supported by experimental results on the similar but nonreactive pseudo‐para‐divinyl[2.2]paracyclophane, which has a lifetime of more than 500 ps in the S₁ state.     

Theory and simulation on the kinetics of protein-ligand binding coupled to conformational change

Conformational change during protein-ligand binding may significantly affect both the binding mechanism and the rate constant. Most earlier theories and simulations treated conformational change as stochastic gating with transition rates between reactive and nonreactive conformations uncoupled to ligand binding. Recently, we introduced a dual-transition-rates model in which the transition rates between reactive and nonreactive conformations depend on the protein-ligand distance [H.-X. Zhou, Biophys. J. 98, L15 (2010)]. Analytical results of that model showed that the apparent binding mechanism switches from conformational selection to induced fit, when the rates of conformational transitions increase from being much slower than the diffusional approach of the protein-ligand pair to being much faster. The conformational-selection limit (k(CS)) and the induced-fit limit (k(IF)) provide lower and upper bounds, respectively, for the binding rate constant. Here we introduce a general model in which the energy surface of the protein in conformational space is coupled to ligand binding, and present a method for calculating the binding rate constant from Brownian dynamics simulations. Analytical and simulation results show that, for an energy surface that switches from favoring the nonreactive conformation while the ligand is away to favoring the reactive conformation while the ligand is near, k(CS) and k(IF) become close and, thus, provide tight bounds to the binding rate constant. This finding has significant mechanistic implications and presents routes for obtaining good estimates of the rate constant at low cost.     

Cl+HCl非反应截面和速率常数的TST-CEQ研究Ⅲ

本文将TST-CEQ方法推广用于计算非反应弛豫速率和平均截面, 并以Cl+HCl反应为例作了计算, 与文献结果比较表明, 这种推广是可行的, 此外, 还给出了该体系反应和非反应一维态态速率常数; 结果发现, 低温时非反应弛豫速率大于反应速率; 高温时两种通道速率相近, 表现了反应的竞争机理。     

Electronic structure of solid state tris(1,3-diphenyl-1,3-propanedionato)aquoeuropium(III)

Single crystal orthoaxial absorption spectra are reported for tris(1,3-diphenyl-1,2-propanedionato)aquoeuropium(III) at ambient temperature and 77 K. The hypersensitive ⁷F_o→⁵D₂ and magnetic/electric dipole forbidden ⁷F_o→⁵D_o transitions are found to be unusually intense. Polarizations and absolute oscillator strengths are determined for all observed transitions from the ground state at 77 K.     

Quantum mechanical study of electronic transitions in collinear atom—diatom collisions

Quantum mechanical calculations are reported for model, nonreactive, collinear collision systems composed of the H₂ diatom and the halogen atom X = F, Cl, Br or I. The model involves two electronic potential energy surfaces, obtained in a diatomics-in-molecules formulation, that correspond asymptotically to the two spin-orbit states of X. On each surface the calculations include as many vibrational states of H₂ as are asymptotically allowed, up to a limiting number of five. The first two collision systems, FH₂ and ClH₂, are characterized by electronic splittings much smaller than any vibrational spacing included in the diatom spectrum, and as a result they show a high degree of vibrational elasticity with essentially all transition activity testricted to spin—orbit switching in the halogen. This pattern is broken for BrH₂ collisions, where the near-equality between electronic and vibrational quanta apparently leads to a resonant exchange of energy between the two modes. The greater spinorbit splitting in iodine (～ 2 vibrational quanta) results in largely elastic behavior in IH₂ collisions for both vibrational and electronic transitions. A modified Massey criterion is exhibited for some of the FH₂ and BrH₂ transitions.     

New insights in the electrocatalytic proton reduction and hydrogen oxidation by bioinspired catalysts: a DFT investigation

In this paper, we present a DFT study of the proton reduction mechanism catalyzed by the complex [Ni(P?(H)N?(H))?](2+), bioinspired from the hydrogenases. A detailed analysis of the reactive isomers is discussed together with the localizations of the transitions states and energy minima. The reactive catalytic species is a biprotonated Ni(0) complex that can show different conformations and that can be protonated on different sites. The energies of the different conformations and biprotonated species have been calculated and discussed. Energy barriers for two different reaction mechanisms have been identified in solvent and in gas phase. Frequency calculations have been performed to check the nature of the energy minima and for the calculations of entropic energetic terms and zero point energies. We show that only one conformation is mostly reactive. All the others species are nonreactive in their original form, and they have to pass through conformational barriers in order to transform in the reactive species.     

A complete decoupling of Faddeev-like equations for three arrangement systems; applications to HH2 collision

A complete decoupling of time-dependent Faddeev-like equations for three identical particles is presented in terms of an operator formalism. No restriction to pairwise additive interaction needs to be made. Our decoupled equations can be looked at as being a generalization of the special decoupled versions of Faddeev and Lovelace in so far as they include all irreducible representations of the permutation group S₃. Thus, the new equations also apply to three composite particles of any spin. An application is made for the system composed of three H-atoms. In particular we show how the cross sections of ortho—para transitions are directly related to the transition operators obtained from the decoupled equations.     

Role of etch products in polysilicon etching in a high-density chlorine discharge

For low-pressure, high-density plasma systems, etch products can play a significant role in affecting plasma parameters such a.s species concentration and electron temperature. The residence time of etch products in the chamber can he long, hence depleting the concentration of the reactants, and leading to a decrease in etch rate. We use a spatially averaged global model including both gas phase and surface chemistry to study Cl₂ etching of polvsilicon. Etch products leaving the wafer surface are assioned to he SiCL₂ and SiCl₄. These species can be fragmented and ionized by collisions with energetic electrons, generating neutral and charged SiCl, products (x=0–4). Two limiting cases of the etch mechanism are found. an ion flux-limited regime and a neutral reactant-limited regime. The high degree of dissociation in high-density plasmas leads to the formation of elemental silicon, which can deposit on the chamber walls and wafer surface. We include surface models for both the wall and the wafer to better understand the role of etch products as a function of flowrate, pressure, and input pwer. A phenomenological model for the surface chemistry is based on available experimental data. We consider the two limiting conditions of nonreactive and reactive walls. These models are perfectly reflective walls, where all silicon-containing species are reflected; and reactive walls, which act as reactive sites for the formation of SiCl₂ and SiCl₄ etch products. The two limiting conditions give significantly different results. A decrease in the absolute atomic silicon density and a weaker dependence of etch rate on flowrate are observed for the reactive wall.     

The approximate conservation of P-helicity in rotational excitation: A new decoupling scheme

A new decoupling scheme for atom — rigid-rotor scattering based on Jacob and Wick's helicity formalism is suggested and found to be satisfactory for a wide range of systems of chemical interest. The number of coupled equations which needs to be solved simultaneously is greatly reduced. Conditions for the validity of this approximation are explored. Very accurate results are obtained for the opacity functions of the individual transitions.     

Product branching between reactive and nonreactive pathways in the collisional quenching of OH A 2Sigma+ radicals by H2

The collisional quenching of OH radicals in their excited A 2Sigma+ electronic state by molecular hydrogen is examined to determine the partitioning between reactive and nonreactive pathways. This is achieved using a pump-probe laser technique to compare the population prepared in the excited OH A 2Sigma+ state with that produced in the OH X 2Pi ground state from nonreactive quenching. Only a small fraction of the products, less than 15%, arise from nonreactive quenching; reactive quenching is the dominant product channel. The branching between the product channels provides a new dynamical signature of the conical intersection region(s) that couple the excited state potential for OH A 2Sigma++H2 with OH X 2Pi+H2 and H2O+H products.     

Collision dynamics of O(3P) + DMMP using a specific reaction parameters potential form

Starting from previous benchmark CBS-QB3 electronic structure calculations (Conforti, P. F.; Braunstein, M.; Dodd, J. A. J. Phys. Chem. A 2009, 113, 13752), we develop two global potential energy surfaces for O((3)P) + DMMP collisions, using the specific reaction parameters approach. Each surface is simultaneously fit along the three major reaction pathways: hydrogen abstraction, hydrogen elimination, and methyl elimination. We then use these surfaces in classical dynamics simulations and compute reactive cross sections from 4 to 10 km s(-1) collision velocity. We examine the energy disposal and angular distributions of the reactive and nonreactive products. We find that for reactive collisions, an unusually large amount of the initial collision energy is transformed into internal energy. We analyze the nonreactive and reactive product internal energy distributions, many of which fit Boltzmann temperatures up to ~2000 K.     

Amide I vibrational frequencies of alpha-helical peptides based upon ONIOM and density functional theory (DFT) studies

We present ONIOM and pure DFT calculations on infrared spectra of alpha-helical-capped polyalanines. The calculations used two-layer ONIOM (B3LYP/D95**:AM1) calculations of the amide I vibrational frequencies for acetyl(ala)NNH2 (N=8, 10, 12-18) whose structures have been previously completely optimized by the same method. These are the first such calculations based upon structures of alpha-helical peptides that are completely optimized using DFT or molecular orbital methods. As the peptide becomes longer, the amide I band becomes both more intense and more red shifted. However, the individual absorptions that contribute most to the band vary between three patterns: one very intense absorption, two absorptions of similar intensity, and two strong absorptions where one is roughly twice as intense as the other. This pattern appears to be related to the relative number of H bonds in the individual H-bonding chains; however, there is one exception. Using 14C=O's to selectively decouple specific C=O's, we found that the couplings between the C=O's within each of the three individual H-bonding chains within the helices follow the same pattern previously reported for planar H-bonding chains of formamides. The coupling between the H-bonding chains appears to involve through-space coupling between the H-bonding chains. While decoupling individual C=O's always decreases the intensity of the amide I band, it leads to complex changes in the individual amide I absorptions that contribute to the band. Depending upon the position of the 14C=O, the amide I band can either red or blue shift. Moreover, the individual absorptions that contribute to the band can increase or decrease in intensity as well as shift. The patterns of the individual absorptions (mentioned above) also change. Using the C=O stretch of acetamide as a reference, we calculate the red shifts for the most intense absorptions to be much greater than predicted by the transition dipole method.     

Spectroscopy of the polyatomic molecules,excited by an intense IR laser field

Using double IR resonance technique the transformation of the SF₆ linear spectrum while excited by fn intense laser field has been investigated. The saturation intensities for the transitions between excited vibrational states of the SF₆ have been measured. It has been found that the multiplephoton laser excitation is forming two molecular ensembles, one of these two is strongly excited along the ν₃ mode. It is shown that between excited vibrational states a fast collisional relaxation is taking place.     

氢原子共线交换反应的动力学计算 II: 在反应势能面上Cl+HCl(ν)碰撞对的振动去激

本文用一维量子散射方法, 计算了氢原子交换反应Cl+HCl(ν≤3)→ClH(ν'≤3)+Cl,得到了各振动态间反应和非反应非弹性几率。结果表明反应和非反应非弹性几率均呈振荡变化。反应与非反应去激几率相差不大, 预期在Cl原子与HCl(ν=1,2,3,)碰撞去激过程中, 反应和非反应散射都是一种有效的机理; 此与Wilkins的轨迹结果相符。去激几率与始终态振动量子数密切相关, 我们归纳出公式: P~ν~ν~'≈10^ν^+^ν^'^-^2^(^ν^'^'^+^1^)P~ν~ν~'~',(ν>ν'>ν')。与Moor的实验结果符合较好。     

一维精确量子散射研究——H+ClH(u)在反应势能面上的振动去激

HCl化学激光中存在振动激发的HCl及游离的H和Cl,故HCl在H原子和Cl原子碰撞下振动弛豫速率过程的研究很重要。不久前我们报道了Cl原子对HCl碰撞去激的一维精确量子散射研究,本文用类似方法,讨论H原子对激发态的HCl的碰撞去激。     

Calculated optical spectrum of model oxyheme complex

The optical spectrum of a model oxyheme complex has been calculated using a new intermediate neglect of differential overlap (INDO-SCF-CI ) method that allows for the inclusion of configuration interaction and transition metals. In addition to the porphyrin π→π* transitions common to all heme proteins, four weak x,y polarized transitions observed only in oxyheme complexes have been calculated and assigned to excitations involving the lowest-empty highly delocalized (Oπ, dπ) orbital. Two broad z-polarized bands observed in the single-crystal polarized absorption spectra of oxymyoglobin and hemoglobin have also been calculated. Controversy exists over the assignment of these transitions and, in particular, over the extent of involvement of the oxygen ligand. Our calculations assign the weaker near-IR visible band mainly to the d σ dπ→ dπ* excitations and the more intense UV band mainly to a_2u → dσ* excitations. While significant participation (25%) of the highly delocalized (Oπ, dπ) virtual orbital is also found, these z-polarized transitions need not be totally unique to oxyheme complexes, in keeping with experimental observation.     

Structures of gas-phase C2F 7 + ions

In an ion cyclotron resonance spectrometer, less than 96% of the C₇F ₇ ⁺ cation formed on electron ionization of perfluorotoluene reacts with hexamethyldisilazane. In contrast, the C₇F ₇ ⁺ from perfluoronorbornadiene or perfluorobicyclo[3.2.O]hepta-2,6-diene is nonreactive with hexamethyldisilazane. Collision-induced dissociation results support this dichotomy, although the evidence is not as clear-cut. The reactive ion is assigned the benzyl structure and the nonreactive ion the tropyl structure, on the basis of analogy with the protio cases. By AM1 calculations, the perfluorobenzyl ion is 25 kcal/mol more stable than the perfluorotropyl ion, the opposite of the situation for the protio analogs (? 12 kcal/mol). Ab initio calculations at the 3–21G level agree with the semiempirical energy difference to within 0.4 kcal/mol; at the more appropriate 6–31G*/MP2 level, the perfluorobenzyl cation is 9.7 kcal/mol more stable than the perfluorotropyl cation.