A study of the mode-selective trans--cis isomerization in HONO using ab initio methodology

Ab initio calculations on the six-dimensional cis--trans double minimum potential energy surface of the electronic ground state of the HONO molecule were performed using a coupled cluster approach. An analytic fit to the data points was established. The interconversion barrier was calculated to be 4105 cm(-1). The nuclear motion problem was solved variationally using a full six-dimensional Hamiltonian in internal coordinates. The eigenstates up to about 3650 cm(-1) were tentatively assigned by harmonic quantum numbers. The assignment was based on the mean values of the internal coordinates of the six-dimensional eigenfunctions and on a comparison of the eigenenergies with those calculated by second-order perturbation theory from a full quartic force field in dimensionless normal coordinates. In cold matrices the trans- and the cis-OH nu(1) stretching modes and the first trans- and cis-NO 2nu(2) stretching overtones lead to isomerization. In the isolated molecule these modes (J=0) were found to be entirely localized. However, several overtones of the nu(4) ONO bending and nu(5) N-O stretching, which are close in energy to the OH stretch and combined with the torsional mode, were found to be strongly cis-trans delocalized.     

Chemical promenades: Exploring potential-energy surfaces with immersive virtual reality

The virtual-reality framework AVATAR (Advanced Virtual Approach to Topological Analysis of Reactivity) for the immersive exploration of potential-energy landscapes is presented. AVATAR is based on modern consumer-grade virtual-reality technology and builds on two key concepts: (a) the reduction of the dimensionality of the potential-energy surface to two process-tailored, physically meaningful generalized coordinates, and (b) the analogy between the evolution of a chemical process and a pathway through valleys (potential wells) and mountain passes (saddle points) of the associated potential energy landscape. Examples including the discovery of competitive reaction paths in simple A + BC collisional systems and the interconversion between conformers in ring-puckering motions of flexible rings highlight the innovation potential that augmented and virtual reality convey for teaching, training, and supporting research in chemistry.     

Isomerization study of C5H5NO molecules

The complex potential energy surface (PES) for the isomerization of C₅H₅NO species, including 18 isomers and 23 interconversion transition states, is probed theoretically at the B3LYP/6‐311++G(d,p) and MP2//B3LYP/6‐311++G(d,p) levels of theory. The geometries and relative energies for various stationary points were determined. The zero‐point vibrational energy (ZPVE) corrections have been made to calculate the reliable energy. We predicted a six‐membered ring structure as a global minima isomer I, which is 118.49 and 131.48 kcal · mol^?1 more stable than the least stable, four‐ and three‐membered ring isomer VIII at B3LYP and MP2//B3LYP levels of theory, respectively. The isomers and interconversion transition states have verified by frequency calculation. The intrinsic reaction coordinates (IRC) calculations have been performed to confirm that each transition state is linked by the desired reactants and products. The isomer stability has been studied using relative energies, chemical hardness, and chemical potential. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Tork: Conformational analysis method for molecules and complexes

A conformational search method for organic molecules and bimolecular complexes is presented. The method, termed Tork, uses normal-mode analysis in bond-angle-torsion coordinates and focuses on a key subset of torsional coordinates to identify natural molecular motions that lead the initial conformation to new energy minima. New conformations are generated via distortion along these modes and their pairwise combinations, followed by energy minimization. For complexes, special treatment is accorded to the six coordinates that specify the position and orientation of one molecule relative to the other. Tests described here show that Tork is highly efficient for cyclic, acyclic, and mixed single molecules, as well as for host-guest complexes.     

Vibrational stimulation of the coherent tunneling transition in the cyclopentanone molecule

The tunneling interconversion of the cyclopentanone molecule, which leads to the appearance of tunneling doublets in the microwave spectrum of the system, is studied. The dynamics of interconversion is described by two generalized coordinates, one of which corresponds to bending (non-tunneling promoting mode), while the other of which corresponds to twisting of the molecular plane (tunneling coordinate). The coupling between two coordinates is symmetric. A method for quasi-classical calculation of the wave functions in the tunneling region and of the tunneling splittings of the vibrationally excited states in a two-dimensional potential with symmetric coupling is proposed. The tunneling spectrum of cyclopentanone is calculated. It agrees well with the experimental one, and the tunneling splitting increases by 140 times when the transverse quantum number goes from 0 to 6. The dynamic effect of the vibrationally assisted tunneling is shown to be due to the increase in the width of the tunneling channel with the quantum number of bending mode, as well as to the simultaneous shortening of the tunneling distance. The transition state geometry is found using the wave function at the dividing line of the potential.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2098–2105, December, 1994.This work was supported by the Russian Foundation for Basic Research (Project 94-03-08863). The authors express their gratitude to W. Miller for helpful discussions and to H. Nakamura for a preprint of their work.     

Torsional anharmonicity in the conformational analysis of tryptamine

In this paper we calculate the relative conformer populations of the tryptamine molecule. Our approach combines high level electronic structure conformer energies with harmonic frequencies and an anharmonic treatment of the torsional motions using the torsional path integral Monte Carlo method. We have developed a 3-D potential energy surface as a function of the torsional coordinates at the B3LYP/6-31+G(d) level using 2535 grid points. Eight conformers of tryptamine were found to be significantly populated at 430 K as opposed to the experimental observation of seven. This, along with further comparisons with various experimental data, leads us to suppose that conformer interconversion occurs during the cooling phases of many of the experiments. The ordering of the calculated populations fits well with available experimental data. Torsional anharmonicity is found to affect conformer populations more significantly at 430 K than at 100 K (although overall the effects are small), while quantum mechanical effects are not important at either temperature.     

Theoretical study of the V(4F)?+?NO(2��r)?��?VO(4��?)?+?N(4S��) reaction compared with the Sc(2D) and Ti(3F) cases

To understand the title reaction, the MRCI, CCSD, CCSD(T), and DFT calculations have been done. A large domain of the ground-state potential energy surface has been explored including the activation energy barrier to form the triatomic complex, two stable intermediate complexes, V[NO] and NVO, the transition state connecting these two conformers, and the detachment of the nitrogen atom. We compared this reaction with the similar ones involving the Sc and Ti atoms. The activation barrier to form the VNO complex made from the ionic-covalent coupling decreases to approach the experimental data when the electron correlation effect is better included as in the Sc and Ti systems. The transition state connecting the two conformers was calculated to be higher than in the Sc and Ti cases probably due to larger number of nonbonding valence electrons and is probably too high with respect to the reactant energy level to allow the interconversion between the two conformers in the VNO. The direct concerted substitution (abstraction) reaction is improbable because this process will have to overcome a too high potential barrier. We have also found the transition state connecting two conformers of ScNO.     

Quantum-chemical study of 1,3-dioxane complexes with two water molecules

Methods PM3, RHF/6-31G(d), and MP2/6-31G(d)//RHF/6-31G(d) were used in calculation of the energy of formation of five 1,3-dioxane complexes with two water molecules formed through hydrogen bonds. The study of the conformational properties of the most stable associate revealed two routes of the chair-chair conformation isomerization. It was shown that the difference between the minima on the potential energy surface in this gase increased, and the barriersto the interconversion decreased as compared to the calculated values for the isolated molecule of 1,3-dioxane.     

Shape and symmetry of heptacoordinate transition-metal complexes: structural trends

The stereochemistries of heptacoordinate transition-metal complexes are analyzed by using continuous symmetry and shape measures of their coordination spheres. The distribution of heptacoordination through the transition-metal series is presented based on structural database searches including organometallic and Werner-type molecular complexes, metalloproteins, and extended solids. The most common polyhedron seems to be the pentagonal bipyramid, while different preferences are found for specific families of compounds, as in the complexes with three or four carbonyl or phosphine ligands, which prefer the capped octahedron or the capped trigonal prism rather than the pentagonal bipyramid. The symmetry maps for heptacoordination are presented and shown to be helpful for detecting stereochemical trends. The maximal symmetry interconversion pathways between the three most common polyhedra are defined in terms of symmetry constants and a large number of experimental structures are seen to fall along those paths.     

Theoretical study of the N---H tautomerism in free base porphyrin

The N---H tautomerism of free base porphyrin is investigated at the semiempirical spin-unrestricted AM1 (UAM1) and ab initio RHF/3-21G levels. The UAM1 method provides delocalized geometries for all stationary structures without imposing any symmetry constraint. RHF/3-21G geometry optimizations have to be performed under symmetry restrictions to ensure that realistic delocalized structures are obtained. Both the semiempirical and the ab initio calculations predict that the interconversion between trans tautomers proceeds in an asynchronous two-step process via intermediate cis tautomers. The cis tautomers are characterized as minima in the potential energy surface and are 8–10 kcal mol⁻¹ higher in energy. The activation energy for the trans → cis interconversion is calculated to be approximately 23 kcal mol⁻¹ at the 3-21G level. The activation energy for the synchronous trans → trans interconversion is higher and has a value of 30.5 kcal mol⁻¹. The activation energies obtained at the semiempirical UAM1 level are twice as large as the ab initio values.     

On-flow gas chromatographic method for the determination of the enantiomer interconversion energy barrier

A novel on-flow gas chromatographic (GC) method is developed for the determination of the kinetic rate constants and interconversion energy barrier of thermally labile enantiomers. The validity of the developed method is approved by the study of interconversion of 1-chloro-2,2-dimethylaziridine enantiomers on an achiral column. The overall experiments are performed in a series of three columns placed in two independently heated GC ovens. The racemate of the 1-chloro-2,2-dimethylaziridine is injected and separated in the first chiral column at 60 degrees C in which the interconversion of enantiomers is suppressed. Separated enantiomers are then transferred into the achiral column, where the enantiomers are interconverted at a selected temperature under the current carrier gas flow. Effluent from this column is transferred into the second chiral column, where the native enantiomers and those originated by the on-flow interconversion on an achiral column are again separated at 60 degrees C. Chromatograms obtained by monitoring the effluents from the second chiral column are used to determine the peak areas of the original and the newly interconverted enantiomers. The corresponding peak areas and the interconversion times are used to calculate the interconversion rate constants and energy barriers of the 1-chloro-2,2-dimethylaziridine enantiomers. The apparent energy barriers of the enantiomers of 1-chloro-2,2-dimethylaziridine are equal for both enantiomers within a 95% confidence interval and independent of the polarity of the stationary phase of the column in which the interconversion of enantiomers occur.     

Vibrational energy levels with arbitrary potentials using the Eckart-Watson Hamiltonians and the discrete variable representation

An effective and general algorithm is suggested for variational vibrational calculations of N-atomic molecules using orthogonal, rectilinear internal coordinates. The protocol has three essential parts. First, it advocates the use of the Eckart-Watson Hamiltonians of nonlinear or linear reference configuration. Second, with the help of an exact expression of curvilinear internal coordinates (e.g., valence coordinates) in terms of orthogonal, rectilinear internal coordinates (e.g., normal coordinates), any high-accuracy potential or force field expressed in curvilinear internal coordinates can be used in the calculations. Third, the matrix representation of the appropriate Eckart-Watson Hamiltonian is constructed in a discrete variable representation, in which the matrix of the potential energy operator is always diagonal, whatever complicated form the potential function assumes, and the matrix of the kinetic energy operator is a sparse matrix of special structure. Details of the suggested algorithm as well as results obtained for linear and nonlinear test cases including H(2)O, H(3) (+), CO(2), HCNHNC, and CH(4) are presented.     

IR Spectra of N,N′-Ethylene-Bis(salicylaldiminates) and N,N′-ethylene-Bis(acetylacetoniminates) of Ni(II), Cu(II), and Zn(II)

Vibrational spectra of N,N′-ethylene-Bis(salicylaldiminaates) and N,N′-ethylene-Bis(acetylacetoniminates) of nickel (II), copper (II), and zinc (II) are studied experimentally (IR spectroscopy, 400–4000 cm⁻¹) and theoretically (B3LYP), band assignment is given, and the distribution of potential energy of normal vibrations in internal coordinates is studied. Differences between vibrational spectra of the complexes are discussed. Thermodynamic functions of gas-phase complexes corresponding to temperatures of 298 and 800 K are calculated.     

Multistep conformational interconversion mechanism of cyclododecane. A simple and fast analysis using potential energy curves

An ab initio and Density Functional Theory (DFT) study of the conformational properties of cyclododecane was carried out. The energetically preferred equilibrium structures, their relative stability, and some of the transition state (TS) structures involved in the conformational interconversion pathways were analyzed from RHF/6‐31G(d), B3LYP/6‐31G(d,p) and B3LYP/6311++G(d,p) calculations. Aug‐cc‐pVDZ//B3LYP/6311++G(d,p) single point calculations predict that the multistep conformational interconversion mechanism requires 11.07 kcal/mol, which is in agreement with the available experimental data. These results allow us to form a concise idea about the internal intricacies of the preferred forms of cyclododecane, describing the conformations as well as the conformational interconversion processes in the conformational potential energy hypersurface. Our results indicated that performing an exhaustive analysis of the potential energy curves connecting the most representative conformations is a valid alternate tool to determine the principal conformational interconversion paths for cyclododecane. This methodology represents a satisfactory first approximation for the conformational analysis of medium‐ and large‐size flexible cyclic compounds. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Determination of the 2,3-pentadienedioic acid enantiomer interconversion energy barrier 1. Classical kinetic approach

A classical kinetic method was used to determine the energy barrier for the inter-conversion of 2,3-pentadienedioic acid enantiomers. Each individual enantiomer was isolated by collecting the appropriate peaks from the HPLC enantiomeric separation, of racemic 2,3-pentadienedioic acid. The isolated enantiomers were racemized at 22 degrees C using various interconversion times. The ratio of enantiomers in each reaction solution was determined by HPLC at 22 degrees C. The corresponding peak areas of the enantiomers and the interconversion times obtained from the HPLC chromatograms were used to calculate both the interconversion rate constants describing (+)--> (-) and (-) --> (+) interconversions as well as the energy barriers. It was confirmed that the interconversion of 2,3-pentadienedioic acid enantiomers is a firstorder kinetic reaction. Both semiempirical and ab initio methods were used to explore the mechanism of the interconversion of 2,3-pentadienedioic acid enantiomers, and to calculate the interconversion energy barrier. Comparison of the interconversion energy barriers found by the ab initio method (deltaG# = 110.7 kJ/mol) and by classical kinetics in the mobile phase solution at 22 degrees C (delta Gapp = 93.9+/-0.2 kJ/mol) shows a difference which may be attributed to the different conditions assumed in the theoretical calculation (i.e., a gaseous state) and the actual experimental conditions (i. e., liquid solution) and a possible catalytic effect of the solution composition.     

Quantum-chemical investigation of conformational characteristics of the complex of 2-methyl-1,3,2-dioxaborinane with dimethyl ether

With the help of the quantum-chemical approximation MP2/6-31G(d)//HF/6-31G(d) conformational characteristics were investigated of donor-acceptor associate of 2-methyl-1,3,2-dioxaborinane with dimethyl ether, 1:1. The character of the conformational isomerization of the adduct differs from that established for the proper cyclic boric ester and involves an interconversion between two conformers nondegenerate by the energy. The stability of the associate under study is comparable with those of the molecular complexes of 2-methyl-1,3,2-dioxaborinane with water and methanol.     

Determination of the interconversion energy barrier of enantiomers by separation methods

Separation methods have become versatile tools for the determination of kinetic activation parameters and energy barriers to interconversion of isomers and enantiomers in the last 20 years. New computer-aided evaluation systems allow the on-line determination of these data after separating minute amount of pure compounds or mixture of isomers or enantiomers, respectively. Both dynamic interconversion during the separation process as well as static stopped-flow techniques have been applied to determine the kinetic activation parameters and interconversion energy barriers by separation methods. The use of (1) combinations of batchwise kinetic studies with enantioselective separations, (2) a continuous flow model, (3) a comparison of real chromatograms with simulated ones, (4) stopped-flow techniques, (5) stochastic methods, (6) approximation functions and (7) deconvolution methods, for the determination of interconversion energy barriers by separation methods is summarized in detail.     

Binding energies of water to sodiated valine and structural isomers in the gas phase: the effect of proton affinity on zwitterion stability

The structures of valine (Val) and methylaminoisobutyric acid (Maiba) bound to a sodium ion, both with and without a water molecule, are investigated using both theory and experiment. Calculations indicate that, without water, sodiated Val forms a charge-solvated structure in which the sodium ion coordinates to the nitrogen and the carbonyl oxygen (NO-coordination), whereas Maiba forms a salt-bridge structure in which the sodium ion coordinates to both carboxylate oxygens (OO-coordination). The addition of a single water molecule does not significantly affect the relative energies or structures of the charge-solvated and salt-bridge forms of either cluster, although in Maiba the mode of sodium ion binding is changed slightly by the water molecule. The preference of Maiba to adopt a zwitterionic form in these complexes is consistent with its higher proton affinity. Experimentally, the rates of water evaporation from clusters of Val.Na(+)(H(2)O) and Maiba.Na(+)(H(2)O) are measured using blackbody infrared radiative dissociation (BIRD). The dissociation rates from the Val and Maiba complexes are compared to water evaporation rates from model complexes of known structure over a wide range of temperatures. Master equation modeling of the BIRD kinetic data yields a threshold dissociation energy for the loss of water from sodiated valine of 15.9 +/- 0.2 kcal/mol and an energy of 15.1 +/- 0.3 kcal/mol for the loss of water from sodiated Maiba. The threshold dissociation energy of water for Val.Na(+)(H(2)O) is the same as that for the charge-solvated model isomers, while the salt-bridge model complex has the same water threshold dissociation energy as Maiba.Na(+)(H(2)O). These results indicate that the threshold dissociation energy for loss of a water molecule from these salt-bridge complexes is approximately 1 kcal/mol less than that for loss of water from the charge-solvated complexes.