Molecular dynamics simulation of liquid N2O4<-->2NO2 by orientation-sensitive pairwise potential. III. Reaction dynamics

The dissociation and association dynamics of N2O4 [see text] 2NO2 in liquid state are studied by classical molecular dynamics simulations of reactive liquid NO2. An OSPP+LJ potential between NO2 molecules, which is a sum of an orientation-sensitive pairwise potential (OSPP) between N-N atoms proposed in Paper I [J. Chem. Phys. 115, 10852 (2001)] and Lennard-Jones potentials between N-O and O-O atoms, has been used in the simulation. The reaction dynamics is studied as a function of well depth De and anisotropy factors of the OSPP potential: Atheta (0< or =Atheta< or =1) for the rocking angle and Atau (0< or =Atau< or =0.5) for the torsional angle of relative NO2-NO2 orientation. The lifetime tauD of initially prepared NO2 dimers is found to increase as De increases, Atheta increases, and Atau decreases. Dissociation and association dynamics are studied in detail around the extreme limit of pure NO2-dimer liquid: De=0.12 x 10(-18) J, Atheta=0.5, and Atau=0.1, which has been found to reproduce both the observed liquid phase equilibrium properties and Raman band shapes of the dissociation mode very well. The dissociation dynamics from microscopic reaction trajectories is compared with the potential of the mean force (PMF) as a function of the N-N distance R. The PMF of reactive liquid NO2 shows a transition state barrier at R=2.3-2.5 A, and NO2-trimer structure is found to be formed at the barrier. Two types of dissociation of the NO2 dimer-the dissociation by collisional activation of the reactive mode to cross the dissociation limit and the NO2-mediated dissociation via bond transfer-are studied. The latter needs less free energy and is found to be much more probable. The dissociation trajectories and PMF in reactive liquid NO2 are compared with those of a reactive NO2 pair in inert solvent N2O4.     

Molecular dynamics simulation of potassium along the liquid-vapor coexistence curve

The applicability of pair potential functions to liquid alkali metals is questionable. On the one hand, some recent reports in the literature suggest the validity of two-parameter pair-wise additive Lennard-Jones (LJ) potentials for liquid alkali metals. On the other hand, there are some reports suggesting the inaccuracy of pair potential functions for liquid metals. In this work, we have performed extensive molecular dynamics simulations of vapor-liquid phase equilibria in potassium to check the validity of the proposed LJ potentials and to improve their accuracy by changing the LJ exponents and taking into account the temperaturedependencies of the potential parameters. We have calculated the orthobaric liquid and vapor densities of potassium using LJ (12–6), LJ (8.5–4) and LJ (5–4), effective pair potential energy functions. The results show that using an LJ (8.5–4) potential energy function with temperature-independent parameters, ε and σ, is inadequate to account for the vapor-liquid coexistence properties of potassium. Taking into account the temperature-dependencies of the LJ parameters, ε(T) and σ(T), we obtained the densities of coexisting liquid and vapor potassium in a much better agreement with experimental data. Changing the magnitude of repulsive and attractive contributions to the potential energy function shows that a two-parameter LJ (5–4) potential can well reproduce the densities of liquid and vapor potassium. The results show that LJ (5–4) potential with temperature-dependent parameters produces the densities of liquid and vapor potassium more accurately, compared to the results obtained using LJ (12–6) and LJ (8.5–4) potential energy functions.     

Ketene-forming eliminations from aryl phenylacetates promoted by R2NH/R2NH2+ in aqueous MeCN. Mechanistic borderline between E2 and E1cb

Elimination reactions of 2-X-4-NO2C6H3CH2C(O)OC6H3-2-Y-4-NO2 [X = H (1), NO2 (2)] promoted by R2NH/R2NH2+ in 70 mol % MeCN(aq) have been studied kinetically. The base-promoted eliminations from 1 proceeded by the E2 mechanism when Y = Cl, CF3, and NO2. The mechanism changed to the competing E2 and E1cb mechanisms by the poorer leaving groups (Y = H, OMe) and to the E1cb extreme by the strongly electron-withdrawing beta-aryl group (2, X = NO2). The values of beta = 0.14 and beta(lg) = 0.10-0.21 calculated for elimination from 1 (Y = NO2) indicate a reactant-like transition state with small extents of proton transfer and C(alpha)-OAr bond cleavage. The extent of proton transfer increased with a poorer leaving group, and the degree of leaving group bond cleavage increased with a weaker base. Also, the changes in the k(1) and k(-1)/k(2) values with the reactant structure variation are consistent with the E1cb mechanism. From these results, a plausible pathway of the change of the mechanism from E2 to the E1cb extreme is proposed.     

Finding the transition state of quasi-barrierless reactions by a growing string method for newton trajectories: application to the dissociation of methylenecyclopropene and cyclopropane

A method for finding a transition state (TS) between a reactant minimum and a quasi-flat, high dissociation plateau on the potential energy surface is described. The method is based on the search of a growing string (GS) along reaction pathways defined by different Newton trajectories (NT). Searches with the GS-NT method always make it possible to identify the TS region because monotonically increasing NTs cross at the TS or, if not monotonically increasing, possess turning points that are located in the TS region. The GS-NT method is applied to quasi-barrierless and truly barrierless chemical reactions. Examples are the dissociation of methylenecyclopropene to acetylene and vinylidene, for which a small barrier far out in the exit channel is found, and the cycloaddition of singlet methylene and ethene, which is barrierless for a broad reaction channel with Cs-symmetry reminiscent of a mountain cirque formed by a glacier.     

Mechanism and driving force of NO transfer from S-nitrosothiol to cobalt(II) porphyrin: a detailed thermodynamic and kinetic study

The thermodynamics and kinetics of NO transfer from S-nitrosotriphenylmethanethiol (Ph(3)CSNO) to a series of alpha,beta,gamma,delta-tetraphenylporphinatocobalt(II) derivatives [T(G)PPCoII], generating the nitrosyl cobalt atom center adducts [T(G)PPCoIINO], in benzonitrile were investigated using titration calorimetry and stopped-flow UV-vis spectrophotometry, respectively. The estimation of the energy change for each elementary step in the possible NO transfer pathways suggests that the most likely route is a concerted process of the homolytic S-NO bond dissociation and the formation of the Co-NO bond. The kinetic investigation on the NO transfer shows that the second-order rate constants at room temperature cover the range from 0.76 x 10(4) to 4.58 x 10(4) M(-1) s(-1), and the reaction rate was mainly governed by activation enthalpy. Hammett-type linear free-energy analysis indicates that the NO moiety in Ph(3)CSNO is a Lewis acid and the T(G)PPCoII is a Lewis base; the main driving force for the NO transfer is electrostatic charge attraction rather than the spin-spin coupling interaction. The effective charge distribution on the cobalt atom in the cobalt porphyrin at the various stages, the reactant [T(G)PPCoII], the transition-state, and the product [T(G)PPCoIINO], was estimated to show that the cobalt atom carries relative effective positive charges of 2.000 in the reactant [T(G)PPCoII], 2.350 in the transition state, and 2.503 in the product [T(G)PPCoIINO], which indicates that the concerted NO transfer from Ph(3)CSNO to T(G)PPCoII with the release of the Ph(3)CS* radical was actually performed by the initial negative charge (-0.350) transfer from T(G)PPCoII to Ph(3)CSNO to form the transition state and was followed by homolytic S-NO bond dissociation of Ph(3)CSNO with a further negative charge (-0.153) transfer from T(G)PPCoII to the NO group to form the final product T(G)PPCoIINO. It is evident that these important thermodynamic and kinetic results would be helpful in understanding the nature of the interaction between RSNO and metal porphyrins in both chemical and biochemical systems.     

Transition state analysis on regioselectivity in [2+2] photocycloaddition reactions of substituted 2-cyclohexenone with cycloalkenecarboxylates

The experimental results of the triplet [2+2] photocycloaddition reactions of substituted 2-cyclohexenone 1 with cycloalkenylesters 2, 3, 4 have showed remarkable change in the regioselectivity of the products. The ht/hh product ratio increases with increment of the cycle-size. The FMO investigations in addition to the transition state analysis were used to rationalize such regioselectivity. The FMO method with their orbital coefficients and energies could not explain the reaction selectivity since these values of 2-4 showed tendency to form the hh adduct mainly. PM3, PM5, CIS/6-31G, and B3LYP/6-31G methods were used to locate the hh and ht transition states of the three reactions. As the potential energy barriers (TS1) on the first TS surface for the major products were lower than that for the minor products in most of the cases, the real ratio can be explained in terms of TS analysis. The recently improved PM5 and the B3LYP methods were more successful in this debate as partitioning the activation energy at the potential energy barriers into reactant deformation and the interaction (or repulsion) energies is easy and effective. The changes in the ht/hh ratio with the enlargement of the alkene ring size may be due to the increment of the repulsion energy and large changes in the deformation energy of the reactants. In the transition state structures the stabilities of the major products are thought to be due to the existence of some repulsion between the enone carbonyl and esters in the alkenylesters, and some hydrogen bonding between the reactants. The FMO and second transition state (TS2) energy on the biradical intermediates are also thought to play some role in controlling the product selectivity by lowering the closure energy of the biradicals according to the possibility of their overlapping.     

Quantum dynamics study on multichannel dissociation and isomerization reactions of formaldehyde

We study quantum dynamics of the multichannel reactions of H(2)CO including the molecular and radical dissociation channels as well as the isomerization ones, H(2)CO-->trans-HCOH and trans-HCOH-->cis-HCOH. For this purpose, the previously developed potential energy function [T. Yonehara and S. Kato, J. Chem. Phys. 117, 11131 (2002)] is refined to give accurate transition state energies and to describe the radical dissociation channel. The cumulative reaction probabilities for the molecular dissociation and two isomerization channels are calculated by using the full Watson Hamiltonian. We also carry out wave packet dynamics calculations starting from the transition state region for the molecular dissociation. A contracted basis set for the angular coordinates is constructed to reduce the size of dynamics calculations. The intramolecular vibrational relaxation dynamics is found to be fast and almost complete within 300 fs. Using the energy filtered wave functions, the time propagation of HCOH population is obtained in the energy range from 81 to 94 kcal/mol. The branching ratio of the radical product is estimated by calculating the time dependent reactive fluxes to the molecular and radical dissociation products.     

Theoretical evidence for enhanced NO dimerization in aromatic hosts: implications for the role of the electrophile (NO)(2) in nitric oxide chemistry

Nitric oxide dimerization in gas phase and aromatic hosts (benzene) has been investigated with ab initio quantum mechanics. Using the (RO)MP2-aug-cc-pVDZ method, the computed bond dissociation energy (ON...NO) and geometry of (NO)2 in the gas phase are consistent with the reported spectroscopic data. A relatively strong interaction (-5.4 kcal/mol) between (NO)2 and benzene indicates that aromatic surrounding enhances the NO dimerization. Calculations on reactions of phosphine and methanethiol with NO and (NO)2 show that the dimer is much more reactive. This explains reactions of NO with phosphines and thiols.     

State(R)-state(TS)-state(P) theoretical study of H+H_2 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.     

Diphtheria toxin catalyzed hydrolysis of NAD(+): molecular dynamics study of enzyme-bound substrate, transition state, and inhibitor.

The mechanism of the diphtheria toxin-catalyzed hydrolysis of NAD(+) was investigated by quantum chemical calculations and molecular dynamics simulations. Several effects that could explain the 6000-fold rate acceleration (Delta Delta G(++) approximately 5 kcal/mol) by the enzyme were considered. First, the carboxamide arm of the enzyme-bound NAD(+) adopts a trans conformation while the most stable conformation is cis. The most stable conformation for the nicotinamide product has the amide carbonyl trans. The activation energy for the cleavage of the ribosidic bond is reduced by 2 kcal/mol due to the relaxation of this ground state conformational stress in the transition state. Second, molecular dynamics simulations to the nanosecond time range revealed that the carboxylate of Glu148 forms a hydrogen bond to the substrate's 2' hydroxyl group in E.S (approximately 17% of the time) and E.TS (approximately 57% of the time) complexes. This interaction is not seen in crystal structures. The ApUp inhibitor is held more tightly by the enzyme than the transition state and the substrate. Analysis of correlated motions reveals differences in the pattern of anticorrelated motions for protein backbone atoms when the transition state occupies the active site as compared to the E.NAD(+) complex.     

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.     

Transition state theory with Tsallis statistics

We discuss the rate of an elementary chemical reaction. We use the reaction path and especially its saddle point on the potential energy surface. The reaction path connects reactant and product of a reaction over the transition state (TS). Usually, the TS is assumed near or at the single saddle point of the reaction path. By means of comparison of the statistics of states at the reactant and at the TS, one can estimate the reaction rate by the Eyring theory. We propose to use the Tsallis statistics at the TS, a statistics of seldom accidents. Thus, we propose to generalize the well‐known Boltzmann–Gibbs statistics, which is the limiting case of the Tsallis statistics. We use features of this nonextensive thermostatistics. The basic properties of the statistics are used to derive (approximated) partition functions, and they are applied on reaction rates. The approximation includes a factorization of the partition functions. The theory is applied to HCN isomerization to HNC, and to the reaction H₂ + CN → H + HCN. It allows an accordance with experimental estimations of the reaction rates. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Revision of the dissociation energies of mercury chalcogenides--unusual types of mercury bonding.

Mercury chalcogenides HgE (E=O, S, Se, etc.) are described in the literature to possess rather stable bonds with bond dissociation energies between 53 and 30 kcal mol(-1), which is actually difficult to understand in view of the closed-shell electron configuration of the Hg atom in its ground state (...4f(14)5d(10)6s(2)). Based on relativistically corrected many body perturbation theory and coupled-cluster theory [IORAmm/MP4, Feenberg-scaled IORAmm/MP4, IORAmm/CCSD(T)] in connection with IORAmm/B3LYP theory and a [17s14p9d5f]/aug-cc-pVTZ basis set, it is shown that the covalent HgE bond is rather weak (2-7 kcal mol(-1)), the ground state of HgE is a triplet rather than a singlet state, and that the experimental bond dissociation energies have been obtained for dimers (or mixtures of monomers, dimers, and even trimers) Hg2E2 rather than true monomers. The dimers possess association energies of more than 100 kcal mol(-1) due to electrostatic forces between the monomer units. The covalent bond between Hg and E is in so far peculiar as it requires a charge transfer from Hg to E (depending on the electronegativity of E) for the creation of a single bond, which is supported by electrostatic forces. However, a bonding between Hg and E is reduced by strong lone pair-lone pair repulsion to a couple of kcal mol(-1). Since a triplet configuration possesses somewhat lower destabilizing lone pair energies, the triplet state is more stable. In the dimer, there is a Hg-Hg pi bond of bond order 0.66 without any a support. Weak covalent Hg-O interactions are supported by electrostatic bonding. The results for the mercury chalcogenides suggests that all experimental dissociation energies for group-12 chalcogenides have to be revised because of erroneous measurements.     

Density-dependent liquid nitromethane decomposition: molecular dynamics simulations based on ReaxFF

The decomposition mechanism of hot liquid nitromethane at various compressions was studied using reactive force field (ReaxFF) molecular dynamics simulations. A competition between two different initial thermal decomposition schemes is observed, depending on compression. At low densities, unimolecular C-N bond cleavage is the dominant route, producing CH(3) and NO(2) fragments. As density and pressure rise approaching the Chapman-Jouget detonation conditions (～30% compression, >2500 K) the dominant mechanism switches to the formation of the CH(3)NO fragment via H-transfer and/or N-O bond rupture. The change in the decomposition mechanism of hot liquid NM leads to a different kinetic and energetic behavior, as well as products distribution. The calculated density dependence of the enthalpy change correlates with the change in initial decomposition reaction mechanism. It can be used as a convenient and useful global parameter for the detection of reaction dynamics. Atomic averaged local diffusion coefficients are shown to be sensitive to the reactions dynamics, and can be used to distinguish between time periods where chemical reactions occur and diffusion-dominated, nonreactive time periods.     

Selective OD bond dissociation of HOD: photodissociation of vibrationally excited HOD in the 5nu(OD) state

Exclusively selective OD bond dissociation of HOD has been demonstrated by the ultraviolet photodissociation at 243.1 nm through the fourth overtone state of the OD stretching mode (5nu(OD)). Branching ratio between the OH and OD bond dissociation channels has been determined by detecting H and D atoms, utilizing a (2+1) resonance-enhanced multiphoton ionization (REMPI) process. The OD bond dissociation has been solely observed with the branching ratio phi(D+OH)/phi(H+OD)>12, which has been determined by the detection limit for the H atom. Time-dependent wave-packet calculations reveal two important features for the highly selective OD bond dissociation: (1) strong local-mode character of the 5nu(OD) state and (2) limitation of the total excitation energy lower than the saddle point between the OH and OD dissociation channels in the A state. Additionally, the recoil velocity and angular distribution of the nascent D atom are roughly evaluated by analyzing the Doppler-resolved REMPI spectrum. Based on these results, the dynamics of the selective OD dissociation has been discussed in detail.     

Fully state-selected VMI study of the near-threshold photodissociation of NO(2): variation of the angular anisotropy parameter

Velocity-map ion imaging (VMI) has been used to study the angular distribution of the NO fragment generated in the photodissociation of NO(2) at a variety of photolysis wavelengths. Images were recorded for the channels NO (2)Pi(1/2) (v = 0, J= 3/2, 11/2 and 21/2) + O ((3)P(2,1)), for excitation energies ranging from the onset (E(avl)/hc = 0 cm(-1)) to E(avl)/hc approximately 900 cm(-1). The angular anisotropy parameter beta was obtained as a function of available energy. Photofragment multiphoton ionization (PHOMPI) spectra were also recorded in the energy range E(avl)/hc = 0-300 cm(-1) for each of these channels. Large fluctuations of beta as a function of E(avl) were found in all observed dissociation channels. These variations are discussed in terms of the lifetimes of the originally photoexcited overlapping resonances in the A(2)B(2) state of NO(2), the dynamics of which are strongly influenced by nonadiabatic coupling with the X[combining tilde](2)A(1) state. The potential use of this photolysis process for production of cold oxygen atoms is discussed.     

Computational simulations of hydrolysis of phosphazene oligomer utilizing atom‐centered density matrix propagation

Density functional theory (DFT) calculations, including the ab initio molecular dynamics method, atom‐centered density matrix propagation (ADMP), were used to investigate the hydrolysis reaction of a dichlorophosphazene trimer. The model trimer, intermediate structures and the product of the first step of hydrolysis, were optimized using DFT with the B3LYP density functional, followed by a 600 fs ADMP simulation. Natural bond order analysis (NBO) was used to determine atomic charges and occupancy of the bond orbitals and the lone pair orbitals of the molecule at various points along the simulation pathway. The simulation successfully shows dissociation of the trimer backbone into two distinct product molecules, shown through both increasing separation of the product units and through the more thorough NBO analysis of the bond orbitals. © 2012 Wiley Periodicals, Inc.     

MO theoretical studies of electron pair decorrelation processes. I. Pair correlation energy and single bond dissociation

The homolytic dissociation of a single bond involves the decorrelation of one electron pair. Thus, the contribution of electron correlation to dissociation energies is large. In the present paper a new procedure is presented which allows the computation of the (within the given basis) complete correlation energy of one optimized electron pair. The method which requires only modest computational effort has been applied to the calculation of dissociation energies of a number of bonds of different types. The results show that the correlation of the electron pair of the bond which is broken contributes about 50–80% to the change of the total correlation energy occuring during the dissociation process which amounts to 20–70 kcal/mol. The fraction of correlation contributed by the bond electron pair as well as the relative importance of the left-right correlation within the bond depend very much on the type of the bond. In the case of CC and CH single bonds our method yields dissociation energies which are low by only about 5 kcal/mol. Thus, the method seems to be well suited for the calculation of potential surfaces of non-concerted organic chemical reactions which involve diradicals as intermediates.     

Electronic state selectivity in dication-molecule single electron transfer reactions: NO(2+) + NO

The single-electron transfer reaction between NO(2+) and NO, which initially forms a pair of NO(+) ions, has been studied using a position-sensitive coincidence technique. The reactivity in this class of collision system, which involves the interaction of a dication with its neutral precursor, provides a sensitive test of recent ideas concerning electronic state selectivity in dicationic single-electron transfer reactions. In stark contrast to the recently observed single-electron transfer reactivity in the analogous CO(2)(2+)/CO(2) and O(2)(2+)/O(2) collision systems, electron transfer between NO(2+) and NO generates two product NO(+) ions which behave in an identical manner, whether the ions are formed from NO(2+) or NO. This observed behaviour is in excellent accord with the recently proposed rationalization of the state selectivity in dication-molecule SET reactions using simple propensity rules involving one-electron transitions.     

Guided ion beam and theoretical study of the reactions of Hf+ with H2, D2, and HD

The kinetic energy dependences of reactions of the third-row transition metal cation Hf(+) with H(2), D(2), and HD were determined using a guided ion beam tandem mass spectrometer. A flow tube ion source produces Hf(+) in its (2)D (6s(2)5d(1)) electronic ground state level. Corresponding state-specific reaction cross sections are obtained. The kinetic energy dependences of the cross sections for the endothermic formation of HfH(+) and HfD(+) are analyzed to give a 0 K bond dissociation energy of D(0)(Hf(+)-H)=2.11±0.08 eV. Quantum chemical calculations at several levels of theory performed here generally overestimate the experimental bond energy but results obtained using the Becke-half-and-half-LYP functional show good agreement. Theory also provides the electronic structures of these species and the reactive potential energy surfaces. Results from the reactions with HD provide insight into the reaction mechanisms and indicates that Hf(+) reacts via a statistical mechanism. We also compare this third-row transition metal system with the first-row and second-row congeners, Ti(+) and Zr(+), and find that Hf(+) has a weaker M(+)-H bond. As most third-row transition metal hydride cation bonds exceed their lighter congeners, this trend is unusual but can be understood using promotion energy arguments.