Implementation of a graphical user interface for the virtual multifrequency spectrometer: The VMS‐Draw tool

This article presents the setup and implementation of a graphical user interface (VMS‐Draw) for a virtual multifrequency spectrometer. Special attention is paid to ease of use, generality and robustness for a panel of spectroscopic techniques and quantum mechanical approaches. Depending on the kind of data to be analyzed, VMS‐Draw produces different types of graphical representations, including two‐dimensional or three‐dimesional (3D) plots, bar charts, or heat maps. Among other integrated features, one may quote the convolution of stick spectra to obtain realistic line‐shapes. It is also possible to analyze and visualize, together with the structure, the molecular orbitals and/or the vibrational motions of molecular systems thanks to 3D interactive tools. On these grounds, VMS‐Draw could represent a useful additional tool for spectroscopic studies integrating measurements and computer simulations. © 2014 Wiley Periodicals, Inc.     

SurfKin: An ab initio kinetic code for modeling surface reactions

In this article, we describe a C/C++ program called SurfKin (Surface Kinetics) to construct microkinetic mechanisms for modeling gas–surface reactions. Thermodynamic properties of reaction species are estimated based on density functional theory calculations and statistical mechanics. Rate constants for elementary steps (including adsorption, desorption, and chemical reactions on surfaces) are calculated using the classical collision theory and transition state theory. Methane decomposition and water–gas shift reaction on Ni(111) surface were chosen as test cases to validate the code implementations. The good agreement with literature data suggests this is a powerful tool to facilitate the analysis of complex reactions on surfaces, and thus it helps to effectively construct detailed microkinetic mechanisms for such surface reactions. SurfKin also opens a possibility for designing nanoscale model catalysts. © 2014 Wiley Periodicals, Inc.     

Modeling crystal growth from solution with molecular dynamics simulations: approaches to transition rate constants

The feasibility of using the molecular dynamics (MD) simulation technique to study crystal growth from solution quantitatively, as well as to obtain transition rate constants, has been studied. The dynamics of an interface between a solution of Lennard-Jones particles and the (100) face of an fcc lattice comprised of solute particles have been studied using MD simulations, showing that MD is, in principle, capable of following growth behavior over large supersaturation and temperature ranges. Using transition state theory, and a nearest-neighbor approximation growth and dissolution rate constants have been extracted from equilibrium MD simulations at a variety of temperatures. The temperature dependence of the rates agrees well with the expected transition state theory behavior.     

Dynamics and mechanism of the non-adiabatic transitions from the ungerade I2(D0+u) state induced by collisions with rare gas atoms

The stepwise three-photon two-color laser excitation scheme is used for selective population of the first-tier ion-pair D0(+)(u) state of molecular iodine. Collection and analysis of the luminescence after the excitation of the v(D) = 6, 8, 13 and 18 vibronic levels of the D state in the pure iodine vapor and the gas-phase mixtures with He, Ar and Xe provide the total and, whenever possible, partial rate constants for the collision-induced non-adiabatic transitions to the other ion-pair states of the first tier. Comparison with the analogous data obtained previously for the non-adiabatic transitions from the E0(+)(g) state reveals the similarity between two cases. For He, the D ? E transitions are preferable, whereas for Ar and Xe transitions to the D' and β states dominate at v(D) = 6, 8 and 13, in accord with the statistical considerations. Efficient population of the δ state at v(D) = 18 in Ar and Xe is the most prominent non-statistical feature observed. The vibrational product state distributions for the D → E transitions are also obtained. In contrast to the previously studied E → D transition, they show significant positive vibronic energy transfer. The measurements for He and Ar are accompanied by the quantum scattering calculations that reproduce well the main qualitative features of the experimental results.     

A comparative LSER study of the reactivity of 2‐substituted cyclohex‐1‐eneacetic and 2‐substituted phenylacetic acids with diazodiphenylmethane in various solvents

The rate constants for the reaction of 2‐substituted cyclohex‐1‐eneacetic and 2‐substituted phenylacetic acids with diazodiphenylmethane were determined in various aprotic solvents at 30°C. To explain the kinetic results through solvent effects, the second‐order rate constants of the examined acids were correlated using the Kamlet–Taft solvatochromic equation. The correlations of the kinetic data were carried out by means of multiple linear regression analysis, and the solvent effects on the reaction rates were analyzed in terms of initial and transition state contributions. The opposite signs of the electrophilic and the nucleophilic parameters are in agreement with the well‐known mechanism of the reaction of carboxylic acids with diazodiphenylmethane. The quantitative relationship between the molecular structure and the chemical reactivity is discussed, as well as the effect of the molecular geometry on the reactivity of the examined compounds. © 2009 Wiley Periodicals, Inc. Int J Chem Kinet 41: 613–622, 2009     

邻位吡啶自由基多通道分解反应的动力学和反应机理研究

Utilizing Gaussian94 program package, all species involved in decomposition reactions of o-pyridyl radical were optimized fully at B3LYP/6-311＋＋G^＊＊ level. Intrinsic reaction coordinate calculations were employed to confirm the connections of the transition states and products, and transition states were ascertained by the number of imaginary frequency （0 or 1）. The reaction mechanism was elucidated by the vibrational mode analysis and electronic population analysis, and the reaction rate constants were calculated with transition state theory.     

Ab initio Calculation and Kinetic Study for the Abstraction Reaction of H with Sihcl3

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Excited state properties of the chromophore of the asFP595 chromoprotein: 2D and 3D theoretical analyses

The ground and excited state properties (e.g., the intramolecular charge and energy transfer, and electron‐hole coherence) of the chromophore of the asFP595 chromoprotein from Anemonia sulcata in the neutral and anionic forms are theoretically studied with quantum chemistry methods. The ground‐state properties of the asFP595 in the neutral and anionic forms, such as the alternations of the bond lengths and the Mulliken charge distributions, are compared. The calculated transition energies of the asFP595 in the neutral and anionic form are consistent with the experimental results. To study the excited state properties of the asFP595 chromophore, the energies and densities of highest occupied molecular orbitals (HOMOs) and lowest unoccupied molecular orbitals (LUMOs), as well as the CI main coefficients, are compared between the two forms. The intramolecular charge and energy transfer in the neutral and anionic forms are investigated and compared with the three‐dimensional (3D) real‐space analysis methods, including the strength and orientation of the transition dipoles with transition density, and the orientation and result of the intramolecular charge transfer with charge difference density. The electron‐hole coherence and delocalization on the excitation are studied with the 2D real‐space analysis method of the transition density matrix. In all, the calculated results are remain in good agreement with the experimental data, and the theoretical analysis results supported the proposed models in the experiment. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Direct dynamic study on the hydrogen abstraction reaction CH3CN + OH-->CH2CN + H2O

The reaction of acetonitrile with hydroxyl has been studied using the direct ab initio dynamics methods. The geometries, vibrational frequencies of the stationary points, as well as the minimum energy paths were computed at the BHandHLYP and MP2 levels of theory with the 6-311G(d, p) basis set. The energies were further refined at the PMP4/6-311+G(2df, 2pd) and QCISD(T)/6-311+G(2df, 2pd) levels of theory based on the structures optimized at BHandHLYP/6-311G(d, p) and MP2/6-311G(d, p) levels of theory. The Polyrate 8.2 program was employed to predict the thermal rate constants using the canonical variational transition state theory incorporating a small-curvature tunneling correction. The computed rate constants are in good agreement with the available experimental data.     

Eyringpy: A program for computing rate constants in the gas phase and in solution

Eyringpy is a modular program for calculating thermochemical properties and rate constants for reactions in the gas phase and in solution. The code is written in Python and it has a user-friendly interface and a simple input format. Unimolecular and bimolecular reactions with one and two products are supported. Thermochemical properties are estimated through canonical ensemble and rate constants are computed according to the transition state theory. One-dimensional Wigner and Eckart tunneling corrections are also available. Rate constants of bimolecular reactions involving the formation of pre-reactive complexes are also estimated. To compute rate constants in solution, Eyringpy uses the Collins–Kimball theory to include the diffusion-limit, the Marcus theory for electron transfer processes, and the molar fractions to account for the solvent pH effect.     

Implementation of a microcanonical variational transition state theory for direct dynamics calculations of rate constants

Calculation of microcanonical rate constants has been an important field in chemical dy-namic studies for many years because it can be used not only to give good prediction of rate con-stants in microcanonical assembly, but also to calculate rate constants with certain conserved quantum numbers such as the total angular momentum, and in turn, can be easily converted into thermal rate constants[1—3]. The widely used method for calculating microcanonical rate constants of unimolecular reac-tions…     

Theoretical Studies on the Electronic Structures and Spectral Properties of 4,4′-（Ethane-1,2-diylbis-（oxy））dibenzaldehyde and Its Polymorph

The ground state geometries, frontier molecular orbital properties, and absorption properties of 4,4′-(ethane-1,2-diylbis(oxy))dibenzaldehyde (EDO-DBDHD) and its polymorph have been studied theoretically. The density functional theory (DFT) method was employed to optimize the ground state geometries, and theoretical data reveal that EDO-DBDHD features the planar molecular conformations, in contrast to V-shaped structures of its polymorph, which agrees with the experimental data. Additionally, the absorption spectra of both compounds were predicted using time-dependent density functional theory (TDDFT). The calculated results show that the lowest lying absorption bands of these compounds have the transition configurations of HOMO → LUMO, resulting in the transition character of π→π*/n→π*. The transition of HOMO → LUMO+3 mainly contributes to the highest lying absorption bands of two compounds at 225 nm with the character of π→π*/n→π*.     

乙烯和丙烯自由基共聚反应的多尺度模拟模型

结合量子化学和传统过渡态理论计算了乙烯和丙烯自由基聚合反应的速率常数.利用速率常数定义了聚合反应几率(Pijl),构造了乙烯和丙烯共聚合反应的粗粒化动力学模拟模型,并利用该模型研究了不同组成比的乙烯和丙烯的共聚合反应.发现反应速率常数和链端自由基周围的单体浓度都影响链上组分的序列分布.     

Implementation of empirical dispersion corrections to density functional theory for periodic systems

A recently developed empirical dispersion correction (Grimme et al., J. Chem. Phys. 2010, 132, 154104) to standard density functional theory (DFT‐D3) is implemented in the plane‐wave program package VASP. The DFT‐D3 implementation is compared with an implementation of the earlier DFT‐D2 version (Grimme, J. Comput. Chem. 2004, 25, 1463; Grimme, J. Comput. Chem. 2006, 27, 1787). Summation of empirical pair potential terms is performed over all atom pairs in the reference cell and over atoms in shells of neighboring cells until convergence of the dispersion energy is obtained. For DFT‐D3, the definition of coordination numbers has to be modified with respect to the molecular version to ensure convergence. The effect of three‐center terms as implemented in the original molecular DFT‐D3 version is investigated. The empirical parameters are taken from the original DFT‐D3 version where they had been optimized for a reference set of small molecules. As the coordination numbers of atoms in bulk and surfaces are much larger than in the reference compounds, this effect has to be discussed. The results of test calculations for bulk properties of metals, metal oxides, benzene, and graphite indicate that the original parameters are also suitable for solid‐state systems. In particular, the interlayer distance in bulk graphite and lattice constants of molecular crystals is considerably improved over standard functionals. With the molecular standard parameters (Grimme et al., J. Chem. Phys. 2010, 132, 154104; Grimme, J. Comput. Chem. 2006, 27, 1787) a slight overbinding is observed for ionic oxides where dispersion should not contribute to the bond. For simple adsorbate systems, such as Xe atoms and benzene on Ag(111), the DFT‐D implementations reproduce experimental results with a similar accuracy as more sophisticated approaches based on perturbation theory (Rohlfing and Bredow, Phys. Rev. Lett. 2008, 101, 266106). © 2012 Wiley Periodicals, Inc.     

Solvent and structural effects on the kinetics of the reactions of 2‐substituted cyclohex‐1‐enylcarboxylic and 2‐substituted benzoic acids with diazodiphenylmethane

The rate constants for the reaction of 2‐methyl‐cyclohex‐1‐enylcarboxylic, 2‐phenylcyclohex‐1‐enylcarboxylic, and 2‐methylbenzoic and 2‐phenylbenzoic acids with diazodiphenyl‐methane were determined in 14 various solvents at 30°C. To explain the kinetic results through solvent effects, the second‐order rate constants of the examined acids were correlated using the Kamlet–Taft solvatochromic equation. The correlations of the kinetic data were carried out by means of multiple linear regression analysis, and the solvent effects on the reaction rates were analyzed in terms of initial and transition state contributions. The quantitative relationship between the molecular structure and the chemical reactivity has been discussed, as well as the effect of geometry on the reactivity of the examined molecules. The geometric data of all the examined compounds corresponding to the energy minima in solvent, simulated as dielectric continuum, obtained using semiempirical MNDO‐PM3 energy calculations. © 2007 Wiley Periodicals, Inc. Int J Chem Kinet 39: 664–671, 2007     

Seven dimensional quantum dynamics study of the H2+NH2-->H+NH3 reaction

Initial state-selected time-dependent wave packet dynamics calculations have been performed for the H2+NH2-->H+NH3 reaction using a seven dimensional model on an analytical potential energy surface based on the one developed by Corchado and Espinosa-Garcia [J. Chem. Phys. 106, 4013 (1997)]. The model assumes that the two spectator NH bonds are fixed at their equilibrium values and nonreactive NH2 group keeps C2v symmetry and the rotation-vibration coupling in NH2 is neglected. The total reaction probabilities are calculated when the two reactants are initially at their ground states, when the NH2 bending mode is excited, and when H2 is on its first vibrational excited state, with total angular momentum J=0. The converged cross sections for the reaction are also reported for these initial states. Thermal rate constants and equilibrium constants are calculated for the temperature range of 200-2000 K and compared with transition state theory results and the available experimental data. The study shows that (a) the reaction is dominated by ground-state reactivity and the main contribution to the thermal rate constants is thought to come from this state, (b) the excitation energy of H2 was used to enhance reactivity while the excitation of the NH2 bending mode hampers the reaction, (c) the calculated thermal rate constants are very close to the experimental data and transition state theory results at high and middle temperature, while they are ten times higher than that of transition state theory at low temperature (T=200 K), and (d) the equilibrium constants results indicate that the approximations applied may have different roles in the forward and reverse reactions.     

Importance of anharmonicity, recrossing effects, and quantum mechanical tunneling in transition state theory with semiclassical tunneling. A test case: the H2 + Cl hydrogen abstraction reaction

The hydrogen abstraction reaction from H2 by the Cl atom is studied by means of the variational transition state theory with semiclassical tunneling coefficients on the BW2 potential energy surface. Vibrational anharmonicity and coupling between the bending modes are taken into account. The occurrence of trajectories that recross the transition state is estimated by means of the canonical unified statistical method and by classical trajectories calculations. Different semiclassical methods for tunneling calculations are tested. Our results show that anharmonicity has a small but nonnegligible effect on the thermal rate constants, recrossing can be neglected, and tunneling is adequately described by the least-action approximation, and less successfully by the large-curvature version 3 approximation. However, the large-curvature version 4 and small-curvature approximations lead to a severe underestimation of tunneling. Thermal rate constants calculated using transition state theory including anharmonicity and tunneling agree very well with accurate quantal thermal rate constants over a wide temperature range, although the improvement over the harmonic transition state theory with the microcanonically optimized semiclassical tunneling approximation (based on version 3 of the large-curvature tunneling method) used in a previous study of this reaction is only marginal.     

Intermolecular Charge‐Transfer Transition Emitter Showing Thermally Activated Delayed Fluorescence for Efficient Non‐Doped OLEDs

A novel molecular model of connecting electron‐donating (D) and electron‐withdrawing (A) moieties via a space‐enough and conjugation‐forbidden linkage (D‐Spacer‐A) is proposed to develop efficient non‐doped thermally activated delayed fluorescence (TADF) emitters. 10‐(4‐(4‐(4,6‐diphenyl‐1,3,5‐triazin‐2‐yl) phenoxy) phenyl)‐9,9‐dimethyl‐9,10‐dihydroacridine (DMAC‐o‐TRZ) was designed and synthesized accordingly. As expected, it exhibits local excited properties in single‐molecule state as D‐Spacer‐A molecular backbone strongly suppress the intramolecular charge‐transfer (CT) transition. And intermolecular CT transition acted as the vital radiation channel for neat DMAC‐o‐TRZ film. As in return, the non‐doped device exhibits a remarkable maximum external quantum efficiency (EQE) of 14.7 %. These results prove the feasibility of D‐Spacer‐A molecules to develop intermolecular CT transition TADF emitters for efficient non‐doped OLEDs.     

Prediction of product branching ratios in the C(3P)+C2H2-->l-C3H+H/c-C3H+H/C3+H2 reaction using ab initio coupled clusters calculations extrapolated to the complete basis set combined with Rice-Ramsperger-Kassel-Marcus and radiationless transition theories

Ab initio CCSD(T) calculations of intermediates and transition states on the singlet and triplet C3H2 potential energy surfaces extrapolated to the complete basis set limit are combined with statistical computations of energy-dependent rate constants of the C(3P)+C2H2 reaction under crossed molecular beam conditions. Rice-Ramsperger-Kassel-Marcus theory is applied for isomerization and dissociation steps within the same multiplicity and radiationless transition and nonadiabatic transition state theories are used for singlet-triplet intersystem crossing rates. The calculated rate constants are utilized to predict product branching ratios. The results demonstrate that, in qualitative agreement with available experimental data, c-C3H+H and C3+H2 are the most probable products at low collision energies, whereas l-C3H+H becomes dominant at higher Ec above approximately 25 kJ/mol.