Combined multi-level quantum mechanics theories and molecular mechanics study of water-induced transition state of OH~- + CO_2 reaction in aqueous solution

The presence of a solvent interacting with a system brings about qualitative changes from the corresponding gasphase reactions. A solvent can not only change the energetics along the reaction pathway, but also radically alter the reaction mechanism. Here, we investigated the water-induced transition state of the OH~- + CO_2→ HCO_3~- reaction using a multi-level quantum mechanics and molecular mechanics method with an explicit water model. The solvent energy contribution along the reaction pathway has a maximum value which induces the highest energy point on the potential of mean force. The charge transfer from OH~- to CO_2 results in the breaking of the OH~- solvation shell and the forming of the CO_2 solvation shell. The loss of hydrogen bonds in the OH~-solvation shell without being compensated by the formation of hydrogen bonds in the CO_2 solvation shell induces the transition state in the aqueous solution. The calculated free energy reaction barrier at the CCSD(T)/MM level of theory, 11.8 kcal/mol, agrees very well with the experimental value, 12.1 kcal/mol.     

Quantum mechanical free energy barrier for an enzymatic reaction

We discuss problems related to in silico studies of enzymes and show that accurate and converged free energy changes for complex chemical reactions can be computed if a method based on a thermodynamic cycle is employed. The method combines the sampling speed of molecular mechanics with the accuracy of a high-level quantum mechanics method. We use the method to compute the free energy barrier for a methyl transfer reaction catalyzed by the enzyme catechol O-methyltransferase at the level of density functional theory. The surrounding protein and solvent are found to have a profound effect on the reaction, and we show that energies can be extrapolated easily from one basis set and exchange-correlation functional to another. Using this procedure we calculate a barrier of 69 kJ/mol, in excellent agreement with the experimental value of 75 kJ/mol.     

QM/MM study of hydrolysis of arginine catalysed by arginase

ABSTRACT

In this paper, we have investigated the catalytic mechanism of rat liver arginase using a quantum mechanics/molecular mechanics (QM/MM) approach. The enzyme catalyses the hydrolysis of L-arginine (L-Arg) to generate L-ornithine and urea. The reaction mechanism proposed by the previous experimental studies is well reproduced by the QM/MM computations. The explicit treatment of the protein environment suggests that Glu277 fulfil its role in stabilising and orienting L-Arg before nucleophilic attack by the bridging hydroxide in the first step. We have also found that the proton transfer step involving a hydrogen bond switch is the rate-limiting step. The activation energy is computed to be 9.0 and 5.9 kcal/mol at the UB3LYP-D3/CHARMM22 and UBHandHLYP-D3/CHARMM22 levels, which are comparable to the observed activation barrier of 7.2 kcal/mol.     

Accurate Evaluation on the Interactions of SARS-CoV-2 with Its Receptor ACE2and Antibodies CR3022/CB6

The spread of the coronavirus disease 2019(COVID-19) caused by severe acute respiratory syndrome coronavirus-2(SARS-CoV-2) has become a global health crisis.The binding affinity of SARS-CoV-2(in particular the receptor binding domain,RBD) to its receptor angiotensin converting enzyme 2(ACE2) and the antibodies is of great importance in understanding the infectivity of COVID-19 and evaluating the candidate therapeutic for COVID-19.We propose a new method based on molecular mechanics/Poisson-Boltzmann surface area(MM/PBSA) to accurately calculate the free energy of SARS-CoV-2 RBD binding to ACE2 and antibodies.The calculated binding free energy of SARS-CoV-2 RBD to ACE2 is-13.3 kcal/mol,and that of SARS-CoV RBD to ACE2 is-11.4 kcal/mol,which agree well with the experimental results of-11.3 kcal/mol and-10.1 kcal/mol,respectively.Moreover,we take two recently reported antibodies as examples,and calculate the free energy of antibodies binding to SARS-CoV-2 RBD,which is also consistent with the experimental findings.Further,within the framework of the modified MM/PBSA,we determine the key residues and the main driving forces for the SARS-CoV-2 RBD/CB6 interaction by the computational alanine scanning method.The present study offers a computationally efficient and numerically reliable method to evaluate the free energy of SARS-CoV-2 binding to other proteins,which may stimulate the development of the therapeutics against the COVID-19 disease in real applications.     

Insights into enzyme catalysis from QM/MM modelling: transition state stabilization in chorismate mutase

Chorismate mutase provides an important test of theories of enzyme catalysis, and of modelling methods. The Claisen rearrangement of chorismate to prephenate in the enzyme has been modelled here by a combined quantum mechanics/molecular mechanics (QM/MM) method. Several pathways have been calculated. The sensitivity of the results to details of model preparation and pathway calculation is tested, and the results are compared in detail to previous similar studies and experiments. The potential energy barrier for the enzyme reaction is estimated at 24.5—31.6 kcal mol^?1 (AMl/CHARMM), and 2.7—11.9 kcal mol^?1 with corrections (e.g. B3LYP/6-31 + G(d)). In agreement with previous studies, the present analysis of the calculated paths provides unequivocal evidence of significant transition state stabilization by the enzyme, indicating that this is central to catalysis by the enzyme. The active site is exquisitely complementary to the transition state, stabilizing it more than the substrate, so reducing the barrier to reaction. A number of similar pathways for reaction exist in the protein, as expected. Small structural differences give rise to differences in energetic contributions. Major electrostatic contributions to transition state stabilization come in all cases from Arg90, Arg7, one or two water molecules, and Glu78 (Glu78 destabilizes the transition state less than the substrate), while Arg63 contributes significantly in one model.     

过氧硝酸分解势能面的理论研究

使用密度泛函理论B3LYP/6-311+ G(2d,2p)研究了过氧硝酸的最低能量结构．采用耦合簇方法CCSD(T)/aug-cc-pVDZ首次分别扫描了过氧硝酸沿氧-氮和氧-氧键的分解势能面．计算结果表明在氧-氮势能面上,当O3—N4键长是2.82 ?时,对应的疏松过渡态的能垒是25.6 kcal/mol;在氧$-$氧键的势能面上,当O2—O3键长是2.35 ?时,对应的疏松过渡态的能垒是37.4 kcal/mol．这表明过氧硝酸更容易分解为HO₂和NO₂．     

Fe2O3上AsH3催化氧化反应机理的理论研究

本文采用密度泛函理论方法研究了Fe₂O₃上AsH₃的催化氧化反应机理.该反应以Fe₂O₃中的两个Fe原子为不同的活性中心进行研究,每个活性中心均设计了3个步骤. AsH₃分子依次与3个O₂分子在催化剂上相互作用分别形成中间体H₃AsO₂、H₃AsO₄及最终产物H₃AsO₆.研究发现,当氧化反应发生在1号铁原子(Fe1)附近,其速度控制步骤活化自由能垒为49.99 kcal/mol;当氧化反应发生在2号铁原子(Fe2)附近,其活化自由能垒为21.20 kcal/mol,与直接氧化(50.14 kcal/mol)相比大大降低.可见AsH₃在Fe₂O₃上的催化氧化反应更易发生在Fe2附近.     

基于参考势的从头算量子力学/分子力学混合方法研究Parvalbumin B蛋白结合钙、镁离子的选择性

蛋白的离子选择性与蛋白的功能密切相关,而离子选择性本质上来源于蛋白分子与离子结合自由能的差别. 尽管近几十年来分子力场在描述蛋白体系相互作用方面取得了长足的进步,由于缺乏对静电极化和电荷转移效应显式的描述,传统的分子力场依然难以精确地描述金属蛋白体系中蛋白质与金属离子的相互作用. 量子化学方法非常适合于蛋白质与金属离子之间相互作用的描述. 但是在分子模拟中采用量子化学方法则太昂贵了. 近年来发展起来的参考势方法在保证计算精度的前提下兼顾效率,可以有效地解决这个窘境. 在这个方法中,动力学模拟的轨迹是在分子力场的精度下获得的. 随后,通过从分子力场到量子化学方法的矫正,从而获得在量子化学势函数级别下的自由能信息. 本文采用参考势函数方法研究了Parvalbumin B蛋白的结合口袋对钙、镁离子的选择性. 计算结果表明电荷转移效应非常重要,而量子化学方法可以比较精确地预测离子的选择性. 并且,量子化学区域的选择对于结果的可靠性也是非常重要的.     

Constraint methods for determining pathways and free energy of activated processes

Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and rate-determining barrier regions are not sufficiently sampled by usual simulation techniques. Constraints on a reaction coordinate r have turned out to be a suitable means to explore difficult pathways without changing potential function, energy or temperature. For a dense sequence of values of r, the corresponding sequence of simulations provides a pathway for the process. As only one coordinate among thousands is fixed during each simulation, the pathway essentially reflects the system’s internal dynamics. From mean forces the free energy profile can be calculated to obtain reaction rates and and insight in the reaction mechanism. In the last decade, theoretical tools and computing capacity have been developed to a degree where simulations give impressive qualitative insight in the processes at quantitative agreement with experiments. Here, we give an introduction to reaction pathways and coordinates, and develop the theory of free energy as the potential of mean force. We clarify the connection between mean force and constraint force which is the central quantity evaluated, and discuss the mass metric tensor correction. Well-behaved coordinates without tensor correction are considered. We discuss the theoretical background and practical implementation on the example of the reaction coordinate of targeted molecular dynamics simulation. Finally, we compare applications of constraint methods and other techniques developed for the same purpose, and discuss the limits of the approach.     

基态和单态第一激发态的联氨单分子分解反应的密度泛函研究

本文运用密度泛函B3LYP/6-311+G(3df,2p)方法研究了联氨分子的电子结构和能量,并系统分析了联氨分子的分解反应,计算绘制了单分子联氨在基态和单态第一激发态下沿N-N分解反应的势能曲线。本文计算发现联氨分子在这两种电子态下的离解能分别是：基态58.8 kcal/mol,单态第一激发态495.5 kcal/mol。基态分子分解反应是吸热反应,而单态第一激发态分解反应是放热反应。计算发现单态第一激发态的激发能是554.2 kcal/mol。结合这两种电子态下联氨分子的红外振动频率分析,本文认为,在非强制断键的情况下,联氨分子沿N-N键均裂而生成两个NH2自由基的可能性很小。     

基态和单态第一激发态的联氨单分子分解反应的密度泛函研究

本文运用密度泛函B3LYP/6-311+G(3df,2p)方法研究了联氨分子的电子结构和能量,并系统分析了联氨分子的分解反应,计算绘制了单分子联氨在基态和单态第一激发态下沿N-N分解反应的势能曲线。本文计算发现联氨分子在这两种电子态下的离解能分别是：基态58.8 kcal/mol,单态第一激发态495.5 kcal/mol。基态分子分解反应是吸热反应,而单态第一激发态分解反应是放热反应。计算发现单态第一激发态的激发能是554.2 kcal/mol。结合这两种电子态下联氨分子的红外振动频率分析,本文认为,在非强制断键的情况下,联氨分子沿N-N键均裂而生成两个NH2自由基的可能性很小。     

PdCl2催化芳基硼酸与溴代芳烃Suzuki-Miyaura偶联反应的机理研究

:采用密度泛函理论(DFT)中的M06方法, 以二甲基甲酰胺(DMF)溶剂, 研究了无催化剂、PdCl2为催化剂催化芳基硼酸与溴代芳烃的交叉偶联反应的反应机理. 使用6-311+G*基组 (Pd采用赝势基组LanL2DZ) 对芳基硼酸与溴代芳烃Suzuki-Miyaura偶联反应过程中所有反应物、中间体、过渡态和产物的几何构型进行了优化, 同时进行了频率计算, 各过渡态都有唯一虚频, 确认了中间体和过渡态的合理性; 通过自然键轨道(NBO)理论和AIM理论分析了分子轨道间的相互作用. 结果发现: 在没有催化剂的条件下, Suzuki-Miyaura偶联反应形成的反应速控步骤活化能为49.70 kcal/mol, 在PdCl2催化作用下, 反应速控步骤活化能为31.08 kcal/mol, 比较研究结果, PdCl2能有效催化该反应的进行, 我们的研究结果与实验结果相吻合.     

PdCl_2催化芳基硼酸与溴代芳烃Suzuki-Miyaura偶联反应的机理研究

采用密度泛函理论(DFT)中的M06方法,以二甲基甲酰胺(DMF)溶剂,研究了无催化剂、PdCl_2为催化剂催化芳基硼酸与溴代芳烃的交叉偶联反应的反应机理.使用6-311+G*基组(Pd采用赝势基组Lan L2DZ)对芳基硼酸与溴代芳烃Suzuki-Miyaura偶联反应过程中所有反应物、中间体、过渡态和产物的几何构型进行了优化,同时进行了频率计算,各过渡态都有唯一虚频,确认了中间体和过渡态的合理性;通过自然键轨道(NBO)理论和分子内原子理论(AIM)理论分析了分子轨道间的相互作用.结果发现:在没有催化剂的条件下,Suzuki-Miyaura偶联反应形成的反应速控步骤活化能为49.70 kcal/mol,在PdCl_2催化作用下,反应速控步骤活化能为31.08 kcal/mol,比较研究结果,PdCl_2能有效催化该反应的进行,我们的研究结果与实验结果相吻合.     

Theoretical investigation on the excited‐state intramolecular proton transfer mechanism of 2‐(2′‐benzofuryl)‐3‐hydroxychromone

Spectroscopic studies on excited‐state proton transfer of a new chromophore 2‐(2′‐benzofuryl)‐3‐hydroxychromone (BFHC) have been reported recently. In the present work, based on the time‐dependent density functional theory (TD‐DFT), the excited‐state intramolecular proton transfer (ESIPT) of BFHC is investigated theoretically. The calculated primary bond lengths and angles involved in hydrogen bond demonstrate that the intramolecular hydrogen bond is strengthened. In addition, the phenomenon of hydrogen bond reinforce has also been testified based on infrared (IR) vibrational spectra as well as the calculated hydrogen bonding energies. Further, hydrogen bonding strengthening manifests the tendency of excited state proton transfer. Our calculated results reproduced absorbance and fluorescence emission spectra of experiment, which verifies that the TD‐DFT theory we used is reasonable and effective. The calculated Frontier Molecular Orbitals (MOs) further demonstrate that the excited state proton transfer is likely to occur. According to the calculated results of potential energy curves along O―H coordinate, the potential energy barrier of about 14.5 kcal/mol is discovered in the S₀ state. However, a lower potential energy barrier of 5.4 kcal/mol is found in the S₁ state, which demonstrates that the proton transfer process is more likely to happen in the S₁ state than the S₀ state. In other words, the proton transfer reaction can be facilitated based on the photo‐excitation effectively. Moreover, the phenomenon of fluorescence quenching could be explained based on the ESIPT mechanism. Copyright © 2015 John Wiley & Sons, Ltd.     

Microhydration of oxalic acid leading to dissociation

The effect of microhydration on the simplest dicarboxylic acid, namely oxalic acid, leading to the dissociation of its proton, is studied using first principle-based electronic structure calculations. The geometry of the hydrated clusters of oxalic acid considering up to seven water molecules is determined at ωB97X-D/aug-cc-pVDZ level of theory. Solvent stabilisation and interaction energy parameters are calculated applying CCSD(T) level of theory. The calculated free energy of formation shows that the hydrated oxalic acid clusters are stable only at low temperature and pressure. Though the solvent stabilisation energy increases linearly with an increase in the size of the hydrated cluster, the calculated interaction energy, acidic O–H bond dipole moment and hydrogen bond energy show characteristic features of ion pair formation. The spectral manifestation of the weakening hydroxyl bond is observed as red shift in its stretching frequency. A rigid potential energy scan, altering the dissociating O–H bond length of the oxalic acid molecule, shows an energy barrier for acid to water proton transfer in all cases except hepta-hydrate of oxalic acid, where a barrier-less proton transfer occurs. The number of water molecules (n) needed for dissociation of oxalic acid molecule is consistent with the value obtained from recently reported emperical correlation between n and pKa.     

POX(X=1,2)的光谱常数与从头算势能曲线

采用从头算的多种方法对PO、PO₂自由基的基态结构进行优化计算，结果表明：使用密度泛函（DFT）方法计算的结果最接近实验值.对PO双原子分子优选6-311G（3df）基组进行计算、扫描并拟合.对PO₂三原子分子优选出6-311+G（3df）方法计算结构参数、谐振频率、离解能及力常数，借助多体项展式理论导出PO₂自由基的势能函数并绘制等值势能图.发现：PO₂自由基的对称伸缩振动和旋转势能图中，在O+PO→OPO反应通道上都有鞍点出现，O原子需要越过0.55 eV的能量才能生成稳定的PO₂自由基.要形成PO₂自由基只能通过两等价的通道越过势垒才能形成.     

Vibrational spectrum at a water surface: a hybrid quantum mechanics/molecular mechanics molecular dynamics approach

A hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation is applied to the calculation of surface orientational structure and vibrational spectrum (second-order nonlinear susceptibility) at the vapor/water interface for the first time. The surface orientational structure of the QM water molecules is consistent with the previous MD studies, and the calculated susceptibility reproduces the experimentally reported one, supporting the previous results using the classical force field MD simulation. The present QM/MM MD simulation also demonstrates that the positive sign of the imaginary part of the second-order nonlinear susceptibility at the lower hydrogen bonding OH frequency region originates not from individual molecular orientational structure, but from cooperative electronic structure through the hydrogen bonding network.     

Oxidation pathways in the reaction of diacetylene with OH radicals

We present a portion of the potential energy surface of the reaction of diacetylene with OH radicals, calculated using RQCISD(T) and two basis set extrapolation schemes. Based on this surface, we performed calculations of the rate coefficients using an RRKM/master-equation formalism. After a small (1 kcal/mol) adjustment to the energy barrier of the association reaction, our calculated rate coefficients of the high-pressure limit agree very well with previous direct measurements. However, our calculations at high temperatures are considerably smaller than the values inferred in previous studies. The non-Arrhenius behavior and significant pressure dependence of the rate coefficients above 800 K is due to the competition between stabilization, abstraction and addition-elimination channels. At low temperatures, the reaction proceeds mostly to the addition products, as well as to CO and propargyl. Above 1200 K, direct hydrogen abstraction and production of H atoms become important.     

Interaction of Ga<Subscript>3</Subscript> cluster with molecular hydrogen: combined DFT and CCSD(T) theoretical study

We have explored the lowest doublet and quartet potential energy surfaces (PES) for the reaction of gallium trimer with H₂. This reaction was studied experimentally by Margrave and co-workers in a noble gas matrix. The detailed reaction paths ending up with the low-energy Ga₃H₂ hydride isomers have been predicted based on the high level ab initio coupled-cluster calculations (CCSD(T)) with large basis set. We have found that the reaction occuring on the lowest doublet PES is described by the activation barrier for H₂ cleavage of about 15 kcal/mol, consistent with experiment. In the most stable Ga₃H₂ hydride structure, whose formation is exothermic by 15 kcal/mol, both H atoms assume three-fold bridged positions. The diterminal planar structure of Ga₃H₂, proposed experimentally from the observed IR spectra, is found to be only 1 kcal/mol less stable than the dibridged form.     

The ESIPT mechanism of dibenzimidazolo diimine sensor: a detailed TDDFT study

Spectroscopic investigations on excited state proton transfer of a new dibenzimidazolo diimine sensor (DDS) were reported by Goswami et al. recently. In our present work, based on the time‐dependent density functional theory (TDDFT), the excited‐state intramolecular proton transfer (ESIPT) mechanism of DDS is studied theoretically. Our calculated results reproduced absorption and fluorescence emission spectra of the previous experiment, which verifies that the TDDFT method we adopted is reasonable and effective. The calculated dominating bond lengths and bond angles involved in hydrogen bond demonstrate that the intramolecular hydrogen bond is strengthened. In addition, the phenomenon of hydrogen bond reinforce has also been testified based on infrared vibrational spectra. Further, hydrogen bonding strengthening manifests the tendency of ESIPT process. The calculated frontier molecular orbitals further demonstrate that the excited state proton transfer is likely to occur. According to the calculated results of potential energy curves along O–H coordinate, the potential energy barrier of about 5.02 kcal/mol is discovered in the S₀ state. However, a lower potential energy barrier of 0.195 kcal/mol is found in the S₁ state, which demonstrates that the proton transfer process is more likely to happen in the S₁ state than the S₀ state. In other words, the proton transfer reaction can be facilitated based on the photo‐excitation effectively. Moreover, the phenomenon of fluorescence quenching could be explained based on the ESIPT mechanism. Copyright © 2015 John Wiley & Sons, Ltd.