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.     

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.     

Transiting the molecular potential energy surface along low energy pathways: The TRREAT algorithm

The Transition Rapidly exploring Random Eigenvector Assisted Tree (TRREAT) algorithm is introduced to perform searches along low curvature pathways on a potential energy surface (PES). The method combines local curvature information about the PES with an iterative Rapidly exploring Random Tree algorithm (LaValle, Computer Science Department, Iowa State University, 1998, TR98–11) that quickly searches high‐dimensional spaces for feasible pathways between local minima. Herein, the method is applied to identifying conformational changes of molecular systems using Cartesian coordinates while avoiding a priori definition of collective variables. We analyze the pathway identification problem for alanine dipeptide, cyclohexane and glycine using nonreactive and reactive forcefields. We show how TRREAT‐identified pathways can be used as valuable input guesses for double‐ended methods such as the Nudged Elastic Band when ascertaining transition state energies. This method can be utilized to improve/extend the reaction databases that lie at the core of automatic chemical reaction mechanism generator software currently developed to build kinetic models of chemical reactions. © 2013 Wiley Periodicals, Inc.     

Exploring transition state structures for intramolecular pathways by the artificial force induced reaction method

Finding all required transition state (TS) structures is an important but hard task in theoretical study of complex reaction mechanisms. In the present article, an efficient automated TS search method, artificial force induced reaction (AFIR), was extended to intramolecular reactions. The AFIR method has been developed for intermolecular associative pathways between two or more reactants. Although it has also been applied to intramolecular reactions by dividing molecules manually into fragments, the fragmentation scheme was not automated. In this work, we propose an automated fragmentation scheme. Using this fragmentation scheme and the AFIR method, a fully automated search algorithm for intramolecular pathways is introduced. This version for intramolecular reactions is called single‐component AFIR (SC‐AFIR), to distinguish it from multicomponent AFIR for intermolecular reactions. SC‐AFIR was tested with two reactions, the Claisen rearrangement and the first step of cobalt‐catalyzed hydroformylation, and successfully located all important pathways reported in the literature. © 2013 Wiley Periodicals, Inc.     

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.     

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     

On the ion‐pair dissociation mechanisms in the small NaCl·(H2O)6 cluster: A perspective from reaction path search calculations

We performed reaction path search calculations for the NaCl·(H₂O)₆ cluster using the global reaction route mapping (GRRM) code to understand the atomic‐level mechanisms of the NaCl → Na⁺ + Cl⁻ ionic dissociation induced by water solvents. Low‐lying minima, transition states connecting two local minima and corresponding intrinsic reaction coordinates on the potential energy surface are explored. We found that the Na Cl distances at the transitions states for the dissociation pathways were distributed in a relatively wide range of 2.7–3.7 Å and that the Na Cl distance at the transition state did not correlate with the commonly used solvation coordinates. This suggests that the definition of the transition states with specific structures as well as good reaction coordinate is very difficult for the ionic dissociation process even in a small water cluster. © 2018 Wiley Periodicals, Inc.     

Insights into the excited state intramolecular proton transfer process and mechanism of the novel 3‐hydroxythioflavone system: A theoretical study

It is well known that the molecular excited state dynamical process plays important roles in designing and developing novel applications. In this work, based on density functional theory and time‐dependent density functional theory methods, we theoretically explored a novel 3‐hydroxythioflavone (3HTF). Through calculating the electrostatic potential surface of the 3HTF structure, we confirm the formation of intramolecular hydrogen bonding O2‐H3···O4. Our theoretically obtained dominating bond lengths and bond angles involved in hydrogen bonds demonstrate that the intramolecular hydrogen bonds should be strengthened in the S₁ state. Coupling with the simulated infrared vibrational spectra, we further verify the enhanced hydrogen bonding O2‐H3···O4 in the S₁ state. Upon photoexcitation, we found that the charge transfer characteristics around hydrogen bonding moieties play important roles in facilitating the excited state intramolecular proton transfer (ESIPT) process. Via constructing potential energy curves in both S₀ and S₁ states, we confirm the almost nonbarrier ESIPT reaction should be an ultrafast process that further explains the previous experimental phenomenon. At last, we search the S₁‐state transition state (TS) structure along with ESIPT path, based on which we simulate the intrinsic reaction coordinate path that further confirms the ESIPT mechanism. We hope that our theoretical work could guide novel applications based on the 3HTF system in future.     

Automated Search of Minimum Free‐Energy Path by Umbrella Integration

The free‐energy landscape is an important factor for understanding the conformational equilibria of chemical reactions, and many techniques have been developed to calculate the potential of the mean force. Unfortunately, these methods require a previous knowledge of the system for calculations because the results depend on the reaction coordinates. In this study, we combine the scaled hypersphere search method with the umbrella integration method to obtain the transition states on free‐energy landscapes and minimum‐free‐energy paths (MFEPs). With this approach, the MFEP connections between known and unknown equilibrium points are constructed without the prior knowledge of the free‐energy landscape. The problem of reaction coordinates can be solved by using a multidimensional, fully automated interrogation of MFEPs for acquiring the potential of mean force. The efficiency of the proposed method is demonstrated by applying it to alanine dipeptide and alanine tripeptide. © 2018 Wiley Periodicals, Inc.     

A string model for the chemical reaction coordinate in static external fields

A theoretical method for estimating the effects of a static external field upon a reaction path is proposed. The reaction path is defined as the intrinsic reaction coordinate (IRC) which is treated as a string. The string is deformed by the external static force field. We project the external force onto the normal modes orthogonal and parallel to the string. The string is dragged along each direction of the normal mode. The cell structure [10b] attached to the string is also deformed; the transition state (TS) is shifted, and the internal structure of the reaction system is expanded or compressed in configuration space. A min-max relationship of the external effect on the string is found: the smaller the magnitude of the force constant of the normal mode orthogonal to the string, the larger the deformation of the string in the direction of the normal mode. As an example, the effects of one water molecule for hydrogen-migrating isomerization of formaldehyde and fluoroformaldehyde are considered.     

几种过渡态结构的有效优化方法

通过双桥反应机理、电环合反应和催化反应三个不同类型的过渡态优化，说明当标准方法难以给出结果时，对物理问题本身的分析有助于给出过渡态优化的线索．第一个例子根据化学问题给出限制条件，通过平衡几何构型优化方法优化得到过渡态；第二个例子是在使用标准过渡态优化方法失败后，根据物理问题从反应途径上用平衡几何构型优化方法选择过渡态优化的初始结构；第三个例子通过Gaussian 98程序中的标准方法QST2直接得到过渡态．     

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.     

Reactivity Tracers of the Hydrolysis of Fe(II)‐Bis(salicylidene) Complexes: Initial–Transition States Analysis and Enhanced Impact of Tensides on the Kinetic Trends

The kinetics of the acid hydrolysis reaction of Fe(II)‐bis(salicylidene) complexes were followed under pseudo–first‐order conditions ([H⁺] >> [complex]) at 298 K. The ligands of the studied azomethine complexes were derived from the condensation of salicylaldehyde with different five α‐amino acids. The hydrolysis reactions were studied in acidic medium at different ratios (v/v) of aqua–organic mixtures. The decrease in the dielectric constant values of the reaction mixture enhances the reactivity of the reaction. The transfer chemical potentials of the initial and transition states (IS–TS) from water into mixed solvents were determined from the solubility measurements combined with the kinetic data. Nonlinear plots of logk_obs versus 1/D (the reciprocal of the dielectric constant) suggest the influence of the solvation of IS–TS on the reaction reactivity. Furthermore, the acid hydrolysis reactions were screened in the presence of different concentrations of cationic and anionic tensides. The addition of surfactants to the reaction mixture accelerates the reaction reactivity. The obtained kinetic data were used to determine the values of δ_mΔG^# (the change in the activation barrier) for the studied complexes when transferred from “water to various ratios (v/v) of water–co‐organic binary mixtures” and from “water to water containing different [surfactant].” It was found that the reactivity of the acid hydrolysis reaction was controlled by the hydrophobicity of the studied chelates.     

Theoretical studies of mechanisms of cycloaddition reaction between difluoromethylene carbene and acetone

Mechanisms of the cycloaddition reaction between singlet difluoromethylene carbene and acetone have been investigated with the second‐order Møller–Plesset (MP2)/6‐31G* method, including geometry optimization and vibrational analysis. Energies for the involved stationary points on the potential energy surface (PES) are corrected by zero‐point energy (ZPE) and CCSD(T)/6‐31G* single‐point calculations. From the PES obtained with the CCSD(T)//MP2/6‐31G* method for the cycloaddition reaction between singlet difluoromethylene carbene and acetone, it can be predicted that path B of reactions 2 and 3 should be two competitive leading channels of the cycloaddition reaction between difluoromethylene carbene and acetone. The former consists of two steps: (i) the two reactants first form a four‐membered ring intermediate, INT2, which is a barrier‐free exothermic reaction of 97.8 kJ/mol; (ii) the intermediate INT2 isomerizes to a four‐membered product P_2b via a transition state TS2b with an energy barrier of 24.9 kJ/mol, which results from the methyl group transfer. The latter proceeds in three steps: (i) the two reactants first form an intermediate, INT1c, through a barrier‐free exothermic reaction of 199.4 kJ/mol; (ii) the intermediate INT1c further reacts with acetone to form a polycyclic intermediate, INT3, which is also a barrier‐free exothermic reaction of 27.4 kJ/mol; and (iii) INT3 isomerizes to a polycyclic product P₃ via a transition state TS3 with an energy barrier of 25.8 kJ/mol. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Gas‐Phase Synthesis of 1‐Silacyclopenta‐2,4‐diene

Silole (1‐silacyclopenta‐2,4‐diene) was synthesized for the first time by the bimolecular reaction of the simplest silicon‐bearing radical, silylidyne (SiH), with 1,3‐butadiene (C₄H₆) in the gas phase under single‐collision conditions. The absence of consecutive collisions of the primary reaction product prevents successive reactions of the silole by Diels–Alder dimerization, thus enabling the clean gas‐phase synthesis of this hitherto elusive cyclic species from acyclic precursors in a single‐collision event. Our method opens up a versatile and unconventional path to access a previously rather obscure class of organosilicon molecules (substituted siloles), which have been difficult to access through classical synthetic methods.     

Stereoselective Rhodium‐Catalysed [2+2+2] Cycloaddition of Linear Allene–Ene/Yne–Allene Substrates: Reactivity and Theoretical Mechanistic Studies

Allene–ene–allene ( 2 and 5 ) and allene–yne–allene ( 3 and 7 ) N‐tosyl and O‐linked substrates were satisfactorily synthesised. The [2+2+2] cycloaddition reaction catalysed by the Wilkinson catalyst [RhCl(PPh₃)₃] was evaluated. Substrates 2 and 5 , which bear a double bond in the central position, gave a tricyclic structure in a reaction in which four contiguous stereogenic centres were formed as a single diastereomer. The reaction of substrates 3 and 7 , which bear a triple bond in the central position, gave a tricyclic structure with a cyclohexenic ring core, again in a diastereoselective manner. All cycloadducts were formed by a regioselective reaction of the inner allene double bond and, therefore, feature an exocyclic diene motif. A Diels–Alder reaction on N‐tosyl linked cycloadducts 8 and 10 allowed pentacyclic scaffolds to be diastereoselectively constructed. The reactivity of the allenes on [2+2+2] cycloaddition reactions was studied for the first time by density functional theory calculations. This mechanistic study rationalizes the order in which the unsaturations take part in the catalytic cycle, the reactivity of the two double bonds of the allene towards the [2+2+2] cycloaddition reaction, and the diastereoselectivity of the reaction.     

Impedance DNA Biosensor Using Electropolymerized Polypyrrole/Multiwalled Carbon Nanotubes Modified Electrode

In this paper, we present an electrochemical impedance‐based DNA biosensor by using a composite material of polypyrrole (PPy) and multiwalled carbon nanotubes (MWNTs) to modify glassy carbon electrode (GCE). The polymer film was electropolymerized onto GCE by cyclic voltammetry (CV) in the presence of carboxylic groups ended MWNTs (MWNTs‐COOH). Such electrode modification method is new for DNA hybridization sensor. Amino group ended single‐stranded DNA (NH₂‐ssDNA) probe was linked onto the PPy/MWNTs‐COOH/GCE by using EDAC, a widely used water‐soluble carbodiimide for crosslinking amine and carboxylic acid group. The hybridization reaction of this ssDNA/PPy/MWNTs‐COOH/GCE resulted in a decreased impedance, which was attributed to the lower electronic transfer resistance of double‐stranded DNA than single‐stranded DNA. As the result of the PPy/MWNTs modification, the electrode obtained a good electronic transfer property and a large specific surface area. Consequently, the sensitivity and selectivity of this sensor for biosensing DNA hybridization were improved. Complementary DNA sequence as low as 5.0×10^?12 mol L^?1 can be detected without using hybridization marker or intercalator. Additionally, it was found that the electropolymerization scan rate was an important factor for DNA biosensor fabrication. It has been optimized at 20 mV s^?1.     

Full rate constant matrix contraction method for obtaining branching ratio of unimolecular decomposition

The branching ratio of unimolecular decomposition can be evaluated by solving the rate equations. Recent advances in automated reaction path search methods have enabled efficient construction of the rate equations based on quantum chemical calculations. However, it is still difficult to solve the rate equations composed of hundreds or more elementary steps. This problem is especially serious when elementary steps that occur in highly different timescales coexist. In this article, we introduce an efficient approach to obtain the branching ratio from a given set of rate equations. It has been derived from a recently proposed rate constant matrix contraction (RCMC) method, and termed full‐RCMC (f‐RCMC). The f‐RCMC gives the branching ratio without solving the rate equations. Its performance was tested numerically for unimolecular decomposition of C₃H₅ and C₄H₅. Branching ratios obtained by the f‐RCMC precisely reproduced the values obtained by numerically solving the rate equations. It took about 95 h to solve the rate equations of C₄H₅ consisting of 234 elementary steps. In contrast, the f‐RCMC gave the branching ratio in less than 1 s. The f‐RCMC would thus be an efficient alternative of the conventional kinetic simulation approach. © 2016 Wiley Periodicals, Inc.     

CH3NO2异构化反应的理论研究

利用密度泛函和电子密度拓扑分析方法对CH3NO2 (NM)的异构化反应进行了研究。 找到了九种可能的异构体和八个反应通道。通过内禀反应坐标(IRC)分析确认了过渡态与异构体之间的连接关系。计算结果表明,在CH3NO2→CH3ONOt反应过程中,过渡态为紧密结构(在整个反应过程中CH3NO2没有分解为CH3 和NO2 ),与Arenass等人的结论一致。在CH3NOOc→CH2NOOH反应过程中,存在有一个含有四元环→五元环→四元环→五元环变化过程的结构过渡区,这也是在反应过程中首次发现五元环状过渡结构。