Implementation and performance of the artificial force induced reaction method in the GRRM17 program

This article reports implementation and performance of the artificial force induced reaction (AFIR) method in the upcoming 2017 version of GRRM program (GRRM17). The AFIR method, which is one of automated reaction path search methods, induces geometrical deformations in a system by pushing or pulling fragments defined in the system by an artificial force. In GRRM17, three different algorithms, that is, multicomponent algorithm (MC‐AFIR), single‐component algorithm (SC‐AFIR), and double‐sphere algorithm (DS‐AFIR), are available, where the MC‐AFIR was the only algorithm which has been available in the previous 2014 version. The MC‐AFIR does automated sampling of reaction pathways between two or more reactant molecules. The SC‐AFIR performs automated generation of global or semiglobal reaction path network. The DS‐AFIR finds a single path between given two structures. Exploration of minimum energy structures within the hypersurface in which two different electronic states degenerate, and an interface with the quantum mechanics/molecular mechanics method, are also described. A code termed SAFIRE will also be available, as a visualization software for complicated reaction path networks. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Improving the Q2MM method for transition state force field modeling

The Quantum‐to‐molecular mechanics method (Q2MM) for converting quantum mechanical transition states (TSs) to molecular mechanical minima has been modified to allow a fit to the “natural” reaction mode eigenvalue. The resulting force field gives an improved representation of the energy curvature at the TS, but can potentially give false responses to steric interactions. Ways to address this problem while staying close to the “natural” TS force field are discussed. © 2014 Wiley Periodicals, Inc.     

Variational transition state theory without the minimum-energy path

In this paper we propose a method for carrying out variational transition state theory calculations without first obtaining a converged minimum-energy path (MEP). We illustrate the method in two ways, first of all by employing an unconverged MEP and secondly by using a dynamically optimized distinguished reaction path. Preliminary tests of the algorithm for the reactions OH+H₂→H₂O+H and C₂H₅→C₂H₄+H are very encouraging. Received: 22 January 1997 / Accepted: 11 March 1997     

Theoretical study of the dehydrogenate reaction of H2S by Sc+(1D)

The reaction Sc⁺(¹D)+H₂S→Sc⁺S+H₂ is theoretically investigated by ab initio MO methods. Two possible reaction channels on the singlet potential surface (PES) and the reaction mechanism are examined and discussed. Three regions of the potential surface were studied, the molecular complex, the S‐H insertion products and the transition states for the reaction. In addition the singlet and triplet PESs of this reaction system are compared in an investigation the chemistry of excited electronic state. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 82: 60–64, 2001     

Photo-excited intramolecular charge transfer and excited state intramolecular proton transfer behaviors for HPIBT system: A theoretical investigation

Given facile synthetic route and excellent photo stability, excited state intramolecular proton transfer (ESIPT)-active luminous materials have gained more and more attention. Here, we focus on photo-induced excitation process and the ESIPT reaction process for the novel 5-benzothiazol-2-yl-6-hydroxy-2-methyl-isoindole-1,3-dione (HPIBT) molecule. On the level of chemical geometries and infrared spectra, we verify that O─H⋯N of HPIBT should be enhanced. We find that a proton is likely to be attracted by enhanced electronic densities around N, that is, charge transfer impetus ESIPT trend. Combing potential energy curves and searching for transition state, we clarify the ultrafast ESIPT mechanism of HPIBT due to a low barrier, which legitimately explains previous experimental characteristics.     

Geometric analysis of anharmonic downward distortion following paths

A mathematical aspect of the anharmonic downward distortion following (ADDF) path is discussed. The ADDF method is utilized as an automated reaction path search method, which can explore transition state geometries on a potential energy surface from a potential minimum. We show that the maximum number of the ADD stationary paths intersecting the potential minimum is 2^{f + 1} ? 2 , where f denotes the degree of freedom of the system. We also show that the bifurcation of the ADD stationary path is essential to detect all the transition states connected from a given minimum. The ADDF computation is demonstrated for a H₂O molecule in which pitchfork bifurcation is observed.     

Theoretical investigation of the formation of the tropylium ion from the toluene radical cation

The formation of the tropylium ion, C₇H₇⁺, in the mass spectrum of toluene is a chemical process that has been extensively studied. There is, however, still debate as to the structure of the moieties and the reaction pathways involved. This work presents the first computationally complete reaction schemes for the formation of tropylium from toluene to be reported. The calculations were performed at the HF/6‐31G(d, p) and the DFT/B3LYP/6‐311++G(2d) levels of theory using Gaussian 03W. The previously unreported optimized structures and energies for a transition state and an intermediate in one scheme and a transition state in the other have been determined. These results are consistent with the previously reported literature and the available experimental data. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

CH3CH2,CH3CHCl,CH3CCl2与NO2反应微观动力学理论研究

运用量子化学密度泛函理论UB3LYP/6-311+G*和高级电子相关校正的偶合簇(CCSD(T)/6-311+G*)方法,对CH3CH2,CH3CHCl和CH3CCl2自由基与NO2反应的机理和动力学进行了理论研究,得到了体系的势能面信息和可能的反应机理.根据计算得到的各反应热力学参数及反应能垒,采用传统过渡态理论计算了各反应在温度T=298 K和T=700 K时的速率常数.研究结果表明,该类反应均通过1个中间体和1个过渡态生成产物,产物分别为CH3CHO+HNO,CH3CHO+ClNO和CH3CClO+ClNO.     

Multiconformer transition state theory rate constants for the reaction between OH and -dimethoxyfluoropolyethers

In this work, we have calculated rate constants for the tropospheric reaction between the OH radical and -dimethoxyfluoropolyethers. The latter are a specific class of the hydrofluoropolyethers family with the general formula , from which we have selected three case studies: , , and . The calculations were performed by applying a cost-effective protocol developed for bimolecular hydrogen-abstraction reactions and based on multiconformer transition state theory relying on computationally accessible M08-HX/apcseg-2//M08-HX/pcseg-1 calculations. Within the protocol's uncertainties and approximations, the results show that (1) the calculated rate constants have the same order of magnitude and (2) if observed together with previous experimental and theoretical investigations, the chain length (that varies with q and p) is seen to have a small effect on the rate constant, which is consistent with the “no discernible effect” reported in the experimental work.     

C2H3和NO2反应势能面的理论研究

在CCSD(T)／6—311G(d，p)／／B3LYP／6—3llG(d，p)水平上给出了反应C2H3 NO2的详细势能面信息，并列出了中间体和过渡态的几何构型．通过深入分析反应路径及反应机理，得到5个能量可行的产物和6条反应通道，其中产物C2H3O NO的形成又有利，而产物CH2CO HNO则是次要产物，其他产物在通常条件下可以忽略．     

Automated reaction path searches for spin‐forbidden reactions

Many catalytic and biomolecular reactions containing transition metals involve changes in the electronic spin state. These processes are referred to as “spin‐forbidden” reactions within nonrelativistic quantum mechanics framework. To understand detailed reaction mechanisms of spin‐forbidden reactions, one must characterize reaction pathways on potential energy surfaces with different spin states and then identify crossing points. Here we propose a practical computational scheme, where only the lowest mixed‐spin eigenstate obtained from the diagonalization of the spin‐coupled Hamiltonian matrix is used in reaction path search calculations. We applied this method to the ^6,4FeO⁺ + H₂ → ^6,4Fe⁺ + H₂O, ^6,4FeO⁺ + CH₄ → ^6,4Fe⁺ + CH₃OH, and ⁷Mn⁺ + OCS → ⁵MnS⁺ + CO reactions, for which crossings between the different spin states are known to play essential roles in the overall reaction kinetics. © 2018 Wiley Periodicals, Inc.     

A comment to the nudged elastic band method

The minimum energy path (MEP) is an important reaction path concept of theoretical chemistry, and the nudged elastic band (NEB) method with its many facets is a central method to determine the MEP. We demonstrate in this comment that the NEB does not have to lead to a steepest descent pathway (as always assumed). In contrast, as long as it is used without spring forces, it can lead to a gradient extremal. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Kinetic calculation for the reaction of H with Si_2H_6 using the variational transition state theory

The reaction of disilane with atomic hydrogen has been studied. This reaction involves both substitution and abstraction. Calculations show that the hydrogen abstraction is the strongest competing channel. The canonical variational transition state theory with a small curvature tunneling correction (SCT) has been used for the kinetic calculation. The theoretical results are in good agreement with the available experimental data. Comparing the reactions of atomic hydrogen with disilane and silane, it can be seen that the reactivity of the Si-H bond is higher in Si2H6than that in SiH4.     

Finding the transition state without initial guess: the growing string method for Newton trajectory to isomerization and enantiomerization reaction of alanine dipeptide and poly(15)alanine

We report a new, high-dimensional application of a method for finding a transition state (TS) between a reactant and a product on the potential energy surface: the search of a growing string along a reaction path defined by any Newton trajectory in combination with the Berny method (Quapp, J Chem Phys (2005), 122, 174106; we have provided this algorithm on a web page). Two given minima are connected by a one-dimensional, but usually curvilinear reaction coordinate. It leads to the TS region. The application of the method to alanine dipeptide finds the TS of the isomerisation C(7 ax) --> C(5), some TSs of the enantiomerisation of C(7 ax) from L-form to quasi-D-form, and it finds the TS region of a transition of a partly unfolded, bent structure which turns back into a mainly alpha-helix in the Ac(Ala)(15)NHMe polyalanine (all at the quantum mechanical level B3LYP/6-31G: the growing string calculation is interfaced with the Gaussian03 package). The formation or dissolvation of some alpha- or 3(10)-hydrogen bonds of the helix are discussed along the TS pathway, as well as the case of an enantiomer at the central residue of the helix.     

Quantum trajectory method calculation of collinear collisions in the hydrogen exchange reaction H + ClH′ → HCl + H′

The quantum trajectory method was used to study the collinear reaction H + ClH′ → HCl + H′. The potential energy surface was calculated on the QCISD(T)/6-311++G(3df,3pd) level. The reaction probabilities are in good accord with the results obtained by solving the Schroedinger equation using the finite difference method. Translated from Teoreticheskaya i éksperimental’naya Khimiya, Vol. 45, No. 3, pp. 156-159, May-June, 2009.     

Basis sets for the evaluation of van der Waals complex interaction energies: Ne–N2 intermolecular potential and microwave spectrum

In order to obtain efficient basis sets for the evaluation of van der Waals complex intermolecular potentials, we carry out systematic basis set studies. For this, interaction energies at representative geometries on the potential energy surfaces are evaluated using the CCSD(T) correlation method and large polarized LPol‐n and augmented polarization‐consistent aug‐pc‐2 basis sets extended with different sets of midbond functions. On the basis of the root mean square errors calculated with respect to the values for the most accurate potentials available, basis sets are selected for fitting the corresponding interaction energies and getting analytical potentials. In this work, we study the Ne–N₂ van der Waals complex and after the above procedure, the aug‐pc‐2–3321 and the LPol‐ds‐33221 basis set results are fitted. The obtained potentials are characterized by T‐shaped global minima at distances between the Ne atom and the N₂ center of mass of 3.39 Å, with interaction energies of ?49.36 cm^?1 for the aug‐pc‐2–3321 surface and ?50.28 cm^?1 for the LPol‐ds‐33221 surface. Both sets of results are in excellent agreement with the reference surface. To check the potentials further microwave transition frequencies are calculated that agree well with the experimental and the aV5Z‐33221 values. The success of this study suggests that it is feasible to carry out similar accurate calculations of interaction energies and ro‐vibrational spectra at reduced cost for larger complexes than has been possible hitherto. © 2013 Wiley Periodicals, Inc.     

Reliable and efficient reaction path and transition state finding for surface reactions with the growing string method

The computational challenge of fast and reliable transition state and reaction path optimization requires new methodological strategies to maintain low cost, high accuracy, and systematic searching capabilities. The growing string method using internal coordinates has proven to be highly effective for the study of molecular, gas phase reactions, but difficulties in choosing a suitable coordinate system for periodic systems has prevented its use for surface chemistry. New developments are therefore needed, and presented herein, to handle surface reactions which include atoms with large coordination numbers that cannot be treated using standard internal coordinates. The double‐ended and single‐ended growing string methods are implemented using a hybrid coordinate system, then benchmarked for a test set of 43 elementary reactions occurring on surfaces. These results show that the growing string method is at least 45% faster than the widely used climbing image‐nudged elastic band method, which also fails to converge in several of the test cases. Additionally, the surface growing string method has a unique single‐ended search method which can move outward from an initial structure to find the intermediates, transition states, and reaction paths simultaneously. This powerful explorative feature of single ended‐growing string method is demonstrated to uncover, for the first time, the mechanism for atomic layer deposition of TiN on Cu(111) surface. This reaction is found to proceed through multiple hydrogen‐transfer and ligand‐exchange events, while formation of H‐bonds stabilizes intermediates of the reaction. Purging gaseous products out of the reaction environment is the driving force for these reactions. © 2017 Wiley Periodicals, Inc.     

Spin-inversion mechanisms in the reactions of transition metal cations (Sc+, Ti+, V+, Cr+, Mn+, Fe+, Co+, Ni+, and Cu+) with OCS in the gas phase: A perspective from automated reaction path search calculations

The mechanisms including spin-inversion have been systematically studied for the M⁺ + OCS → MS⁺ + CO/MO⁺ + CS (M denotes a transition metal from Sc to Cu) ion-molecule reactions using the automated reaction path search method. We used the lowest mixed-spin potential energy surface obtained from the diagonalization of the spin-coupled Hamiltonian matrix, whose diagonal elements are taken to be the lowest two spin states. This scheme can effectively locate approximate minimum energy crossing points between the two potential energy surfaces with different spin multiplicities. The spin-orbit couplings at spin-inversion points have been calculated to understand the efficiencies of nonadiabatic transitions. The obtained reaction pathways and the calculated spin-orbit couplings are employed to interpret previous experimental studies.