Single‐ended transition state finding with the growing string method

Reaction path finding and transition state (TS) searching are important tasks in computational chemistry. Methods that seek to optimize an evenly distributed set of structures to represent a chemical reaction path are known as double‐ended string methods. Such methods can be highly reliable because the endpoints of the string are fixed, which effectively lowers the dimensionality of the reaction path search. String methods, however, require that the reactant and product structures are known beforehand, which limits their ability for systematic exploration of reactive steps. In this article, a single‐ended growing string method (GSM) is introduced which allows for reaction path searches starting from a single structure. The method works by sequentially adding nodes along coordinates that drive bonds, angles, and/or torsions to a desired reactive outcome. After the string is grown and an approximate reaction path through the TS is found, string optimization commences and the exact TS is located along with the reaction path. Fast convergence of the string is achieved through use of internal coordinates and eigenvector optimization schemes combined with Hessian estimates. Comparison to the double‐ended GSM shows that single‐ended method can be even more computationally efficient than the already rapid double‐ended method. Examples, including transition metal reactivity and a systematic, automated search for unknown reactivity, demonstrate the efficacy of the new method. This automated reaction search is able to find 165 reaction paths from 333 searches for the reaction of NH₃BH₃ and (LiH)₄, all without guidance from user intuition. © 2015 Wiley Periodicals, Inc.     

Rate constants of elementary steps of the reversible chain reaction of N-phenyl-1,4-benzoquinonemonoimine with 2,5-dichlorohydroquinone

The kinetics of reversible chain reactions in quinoneimine-hydroquinone systems has first been studied for the reaction of N-phenyl-1,4-benzoquinonemonoimine with 2,5-dichloro-hydroquinone used as an example. The dependences of the reaction rate on the concentration of the initial reactants, initiator, and each product were studied. The reliable estimates of the rate constants of 11 (of 12) elementary steps of this reaction were obtained from the experimental data using the earlier derived formulas and the method of equal concentrations developed in the present work. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 849–855, May, 2007.     

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 dimensionless reaction coordinate for quantifying the lateness of transition states

The Hammond‐Leffler postulate asserts that transition states of exothermic reactions are reactant‐like (early), whereas transition states of endothermic reactions are product‐like (late). Related postulates have been proposed to describe the sensitivity of activation barriers for reactions occurring on catalytic surfaces to the catalyst structure. To evaluate the validity of these postulates for different chemical reactions, a general method for classifying transition states as either early or late is needed. One can envision a dimensionless reaction coordinate that changes continuously and monotonically from 0 to 1 along a minimum energy reaction pathway. The value of the dimensionless reaction coordinate for the transition state (W_TS) classifies transition states as (a) early when W_TS < 0.5, (b) late when W_TS > 0.5, and (c) equidistant between reactants and products when W_TS = 0.5. In this article, we derive such a dimensionless reaction coordinate and illustrate its usefulness for several different chemical reactions. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Theoretical study of the thermolysis reaction of β‐hydroxynitriles in the gas phase

The gas‐phase thermal decomposition of 3‐hydroxypropionitrile, 3‐hydroxybutyronitrile, and 3‐hydroxy‐3‐methylbutyronitrile has been studied at the MP2/6‐31G(d) level of theory at 683.15 K and 0.06 atm. Results based both in energy and structure data seem to indicate a favorable route of decomposition via a six‐membered cyclic transition state (similar to those suggested for thermal decomposition of other related compounds, such as β‐hydroxyketones, β‐hydroxyalkenes, and β‐hydroxyalkynes) rather than a four‐membered cyclic transition state or even a quasiheterolytic pathway. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

甲醛光催化降解反应机理的量子化学研究

分别采用B3LYP,MP2方法在6-311++G(2df,pd)水平研究了甲醛光催化降解反应的微观机理,找到了可能的反应通道,预测反应产物为HCOOH与H2O.并得到了各反应通道的反应物、中间体、过渡态和产物的优化构型、谐振频率.成功地解释了实验结论.从键长和能量的变化角度,讨论了化学反应过程中化学键的变化规律,整个反应通道中各势能面均较低,从理论角度分析该反应室温下能够进行,为空气中的甲醛降解反应的实验研究提供理论依据.     

Rewiring chemistry: algorithmic discovery and experimental validation of one-pot reactions in the network of organic chemistry

Computational algorithms are used to identify sequences of reactions that can be performed in one pot. These predictions are based on over 86?000 chemical criteria by which the putative sequences are evaluated. The "raw" algorithmic output is then validated experimentally by performing multiple two-, three-, and even four-step sequences. These sequences "rewire" synthetic pathways around popular and/or important small molecules.     

CH2与HNCO反应机理的量子化学研究

异氰酸(HNCO)分解引发的一系列自由基反应是氮氧化物快速消除机理所研究的领域,由于该反应在燃烧化学中讨论氮氧化物NOx的消除过程十分重要,所以获得这些反应准确的位垒就成为实验化学和理论化学所要解决的问题,本文采用量子化学方法,研究了CH2与HNCO体系的反应机理,力求从理论角度给出合理的解释。     

Theoretical study of the mechanism of CH2CO + CN reaction

The potential energy surface information of the CH₂CO + CN reaction is obtained at the B3LYP/6‐311+G(d,p) level. To gain further mechanistic knowledge, higher‐level single‐point calculations for the stationary points are performed at the QCISD(T)/6‐311++G(d,p) level. The CH₂CO + CN reaction proceeds through four possible mechanisms: direct hydrogen abstraction, olefinic carbon addition–elimination, carbonyl carbon addition–elimination, and side oxygen addition–elimination. Our calculations demonstrate that R→IM1→TS3→P3: CH₂CN + CO is the energetically favorable channel; however, channel R→IM2→TS4→P4: CH₂NC + CO is considerably competitive, especially as the temperature increases (R, IM, TS, and P represent reactant, intermediate, transition state, and product, respectively). The present study may be helpful in probing the mechanism of the CH₂CO + CN reaction. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

CH自由基和NO~2反应研究: II.反应的动力学计算

采用MP2(FULL)/6-31G(d)方法从动力学计算上探讨了CH自由基与NO~2反应的可能途径,找到了反应物,中间体及产物之间的能量通道和过渡态,报道了它们的构型、电子态及能量。并通过频率分析和IRC方法对所有的过渡态进行了验证。在此基础上求出了各步反应的活化能。在以前热力学研究的基础上,对于可能的反应通道进一步作了动力学分析,找到了反应主产物通道的分支比,与实验得到的分支比基本吻合。     

Theoretical study on the OH + CH3NHCOOCH3 reaction

The multiple-channel reactions OH + CH3NHC(O)OCH3 --> products are investigated by direct dynamics method. The optimized geometries, frequencies, and minimum energy path are all obtained at the MP2/6-311+G(d,p) level, and energetic information is further refined by the BMC-CCSD (single-point) method. The rate constants for every reaction channels, R1, R2, R3, and R4, are calculated by canonical variational transition state theory with small-curvature tunneling correction over the temperature range 200-1000 K. The total rate constants are in good agreement with the available experimental data and the two-parameter expression k(T) = 3.95 x 10(-12) exp(15.41/T) cm3 molecule(-1) s(-1) over the temperature range 200-1000 K is given. Our calculations indicate that hydrogen abstraction channels R1 and R2 are the major channels due to the smaller barrier height among four channels considered, and the other two channels to yield CH3NC(O)OCH3 + H2O and CH3NHC(O)(OH)OCH3 + H2O are minor channels over the whole temperature range.     

单分子水对CH_2SH+NO_2反应机理影响的理论研究

在B3LYP/6-311++G(2df,p)水平下对单分子水参与下的CH_2SH+NO_2反应的微观机理进行了研究.为了获得更准确的能量信息,采用HL复合方法和CCSD(T)/aug-ccpvtz方法进行单点能校正.结果表明,加入单分子水后的CH_2SH+NO_2反应体系,共经过10条不同的反应路径,得到6种反应产物.与裸反应(CH_2SH+NO_2)相比,水分子在反应中起到了明显的正催化作用.不仅使生成产物trans-HONO的能垒(-52.84kJ·mol~(-1))降低了176.94kJ·mol~(-1),而且不需经过复杂的重排和异构化过程便可得到产物cis-HONO.在生成产物cis-HONO通道(Path3和Path4)中,活化能垒分别为143.65和126.70kJ·mol~(-1),而其裸反应的活化能垒却高达238.34kJ·mol~(-1).生成HNO_2的通道中(Path5和Path6)活化能垒分别为295.23和-42.19kJ·mol~(-1).其中Path6的无势垒过程使HNO_2也成为该反应的主要产物.另外,单分子水还可通过氢迁移的方式直接参与CH_2SH+NO_2的反应,活化能垒(TS7-TS10)分别为-10.62,151.03,186.22和155.10kJ·mol~(-1).除直接抽氢通道中的(Path8-Path10)外,其余反应通道均为放热反应,在热力学上是可行的.     

O~3＋NH→HNO＋O~2反应机理的量子化学研究

用密度泛函(DFT)的B3LYP方法(6－31++G^*^*)研究了臭氧与NH自由基反应的微观机理,优化得到反应途径上的反应物,过渡态,中间体和产物的构型,通过振动分析对过渡态和中间体进行了确认。对单点用QCISD(T)/6－31++G^*^*方法计算能量,同时进行零点能校正。研究结果表明：NH与O~3反应有两条不同的反应通道,且均表现为亲电反应特征,两条不同的反应均为强放热反应。     

化学反应过渡态的结构和动力学

化学反应过渡态决定了包括反应速率和微观反应动力学在内的化学反应的基本特性,而无论是从理论还是实验上研究和观测化学反应过渡态都是极具挑战性的课题.近年来,我国科学家们利用交叉分子束-里德堡氢原子飞行时间谱仪,结合高精度的量子动力学计算,对H＋H2和F＋H2这两个教科书式的典型反应体系进行了全量子态分辨的反应动力学研究,从中得出了关于这两个反应体系的过渡态的结构和动力学性质的结论性的研究成果.     

An investigation on the reaction mechanism of the F2+Cl2→2ClF using the B3LYP method

The reaction mechanism of F₂+Cl₂→2ClF has been investigated with the density functional theory at the B3LYP/6‐311G* level. Six transition states have been found for the three possible reaction paths and verified by the normal mode vibrational and IRC analyses. Ab initio MP2/6‐311G* geometry optimizations and CCSD(T)/6‐311G(2df)//MP2/6‐311G* single‐point energy calculations have been performed for comparison. It is found that when the F₂ (or Cl₂) molecule decomposes into atoms first and then the F (or Cl) atom reacts with the molecule Cl₂ (or F₂) nearly along the molecular axis, the energy barrier is very low. The calculated energy barrier of F attacking Cl₂ is zero and that of Cl attacking F₂ is only 15.57 kJ?mol^?1 at the B3LYP level. However, the calculated dissociation energies of F₂ and Cl₂ are as high as 145.40 and 192.48 kJ?mol^?1, respectively. When the reaction proceeds through a bimolecular reaction mechanism, two four‐center transition states are obtained and the lower energy barrier is 218.69 kJ?mol^?1. Therefore, the title reaction F₂+Cl₂→2ClF is most probably initiated from the atomization of the F₂ molecule and terminated by the reaction of F attacking Cl₂ nearly along the Cl? Cl bond. MP2 calculations lead to the same conclusion, but the geometry of TS and the energy barrier are somewhat different. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2002     

Catalytic reaction mechanism of L-lactate dehydrogenase: an ab initio study

Studies on the catalytic reaction mechanism of L-lactate dehydrogenase have been carried out by using quantum chemical ab initio calculation at HF/6-31G* level. It is found that the interconversion reaction of pyruvate to L-lactate is dominated by the hydride ion H_r transfer, and the transfers of the hydride ionH _r and protonH _r are a quasi-coupled process, in which the energy barrier of the transition state is about 168.37 kJ/mol. It is shown that the reactant complex is 87.61 kJ/mol lower, in energy, than the product complex. The most striking features in our calculated results are that pyridine ring of the model cofactor is a quasi-boat-like configuration in the transited state, which differs from a planar conformation in some previous semiempirical quantum chemical studies. On the other hand, the similarity in the structure and charge between theH _r transfer process and the hydrogen bonding with lower barrier indicates that the H_r transfer process occurs by means of an unusual manner. In addition, in the transition state the electrostatic interaction between the substrate and the active site of LDH is quite strong and the polarization of the carbonyl in the substrate is gradually enhanced accompanying the formation of the transition state. These calculated results are well in accord with the previous experimental studies, and indicate that the charge on the hydride ion H_r is only +0.13e in the transition state, which is in agreement with the reported semiempirical quantum chemical calculations.     

Theoretical study on the reaction of SiH(CH(3))(3) with SiH(3) radical

The multiple-channel reactions SiH(3) + SiH(CH(3))(3) --> products are investigated by direct dynamics method. The minimum energy path (MEP) is calculated at the MP2/6-31+G(d,p) level, and energetic information is further refined by the MC-QCISD (single-point) method. The rate constants for individual reaction channels are calculated by the improved canonical variational transition state theory with small-curvature tunneling correction over the temperature range of 200-2400 K. The theoretical three-parameter expression k(T) = 2.44 x 10(-23)T(3.94) exp(-4309.55/T) cm(3)/(molecule s) is given. Our calculations indicate that hydrogen abstraction channel R1 from SiH group is the major channel because of the smaller barrier height among five channels considered.     

Theoretical study on the reaction CX3 + SiH(CH3)3 (X = H, F)

Theoretical investigations are carried out on the multiple-channel reactions, CH(3) + SiH(CH(3))(3) → products and CF(3) + SiH(CH(3))(3) → products. The minimum energy paths (MEP) are calculated at the MP2/6-311 + G(d,p) level, and energetic information is further refined by the MC-QCISD (single point) method. The rate constants for major reaction channels are calculated by the canonical variational transition state theory (CVT) with small-curvature tunneling (SCT) correction over the temperature range 200-1500 K. The theoretical rate constants are in good agreement with the available experimental data and are found to be k(1a)(T) = 1.93 × 10(-24) T(3.15) exp(-1214.59/T) and k(2a)(T) = 1.33 × 10(-25) T(4.13) exp(-397.94/T) (in unit of cm(3) molecule(-1) s(-1)). Our calculations indicate that hydrogen abstraction channel from SiH group is the major channel due to the smaller barrier height among five channels considered.     

锗烯与异硫氰酸反应机理的量子化学研究

采用密度泛函理论B3LYP方法研究了GeH2自由基与HNCS的反应机理,并在B3LYP/6-311++G**水平上对反应物,中间体,过渡态进行了全几何参数优化,通过频率分析和IRC确定中间体和过渡态。为了得到更精确的能量值,用QCISD(T)/6-311++G**方法计算了各个驻点的单点能,计算结果表明单重态的锗烯与异硫氰酸的反应有抽提硫、插入N-H键、抽提亚氨基的路径,而经由三元环中间体的抽提硫反应GeH2+HNCS→IM3→TS2→IM4→TS3→IM5→GeH2S+HNC(P1),反应能垒最低,为主反应通道,甲锗硫醛和异氰氢酸为主产物。锗烯经由四元环中间体抽提硫的反应为竞争反应通道。