Molecular Tailoring Approach for the Estimation of Intramolecular Hydrogen Bond Energy

Hydrogen bonds (HBs) play a crucial role in many physicochemical and biological processes. Theoretical methods can reliably estimate the intermolecular HB energies. However, the methods for the quantification of intramolecular HB (IHB) energy available in the literature are mostly empirical or indirect and limited only to evaluating the energy of a single HB. During the past decade, the authors have developed a direct procedure for the IHB energy estimation based on the molecular tailoring approach (MTA), a fragmentation method. This MTA-based method can yield a reliable estimate of individual IHB energy in a system containing multiple H-bonds. After explaining and illustrating the methodology of MTA, we present its use for the IHB energy estimation in molecules and clusters. We also discuss the use of this method by other researchers as a standard, state-of-the-art method for estimating IHB energy as well as those of other noncovalent interactions.     

Three-Dimensional Diabatic Potential Energy Surfaces of Thiophenol with Neural Networks

Three-dimensional (3D) diabatic potential energy surfaces (PESs) of thiophenol involving the S\begin{document}$_0$\end{document}, and coupled \begin{document}$^1$\end{document}\begin{document}$\pi\pi^*$\end{document} and \begin{document}$^1$\end{document}\begin{document}$\pi\sigma^*$\end{document} states were constructed by a neural network approach. Specifically, the diabatization of the PESs for the \begin{document}$^1$\end{document}\begin{document}$\pi\pi^*$\end{document} and \begin{document}$^1\pi\sigma^*$\end{document} states was achieved by the fitting approach with neural networks, which was merely based on adiabatic energies but with the correct symmetry constraint on the off-diagonal term in the diabatic potential energy matrix. The root mean square errors (RMSEs) of the neural network fitting for all three states were found to be quite small (\begin{document}$<$\end{document}4 meV), which suggests the high accuracy of the neural network method. The computed low-lying energy levels of the S\begin{document}$_0$\end{document} state and lifetime of the 0\begin{document}$^0$\end{document} state of S\begin{document}$_1$\end{document} on the neural network PESs are found to be in good agreement with those from the earlier diabatic PESs, which validates the accuracy and reliability of the PESs fitted by the neural network approach.     

Sampling Potential Energy Surfaces in the Condensed Phase with Many-Body Electronic Structure Methods

Sampling potential energy surfaces (PES) is pivotal for understanding chemical structure, energetics and reactivity and is of special importance for complex condensed-phase systems. Until recently such simulations based on electronic structure theory have been performed only by density functional theory and semiempirical methods. Many-body electronic structure methods, almost routinely used for molecules, have been practically unavailable for sampling PES in the condensed-phase. This has changed during the last few years, as efficient algorithms and software implementations for the evaluation of electronic energies and forces on atoms have been developed, allowing for geometry optimization, molecular dynamics and Monte-Carlo simulations, which was previously unthinkable. Herein, we introduce the theory and software developments and overview the applications in the field, the most encouraging results being obtained for aqueous chemistry. Requiring state-of-the-art computer resources PES sampling with many-body electronic structure methods in the condensed phase provides high-quality benchmarks and will gradually become more available due to fast progress in reduced scaling algorithms and computational technologies.     

Molecular treatment of charge transfer cross sections in N5+ collisions with H2

We present cross sections for electron capture in N⁵⁺+H₂ collisions in the energy range 100 eV/amu≤E≤6 keV/amu. We employ a model potential aproximation to treat the interaction of the active electron with the cores, and a recently proposed method, which applies the independent particle model to evaluate the Hamiltonian matrix elements. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Embedded,graph-theoretically defined many-body approximations for wavefunction-in-DFT and DFT-in-DFT: Applications to gas- and condensed-phase ab initio molecular dynamics,and potential surfaces for quantum nuclear effects

We present a graph-theoretic approach to adaptively compute many-body approximations in an efficient manner to perform (a) accurate post-Hartree–Fock (HF) ab initio molecular dynamics (AIMD) at density functional theory (DFT) cost for medium- to large-sized molecular clusters, (b) hybrid DFT electronic structure calculations for condensed-phase simulations at the cost of pure density functionals, (c) reduced-cost on-the-fly basis extrapolation for gas-phase AIMD and condensed phase studies, and (d) accurate post-HF-level potential energy surfaces at DFT cost for quantum nuclear effects. The salient features of our approach are ONIOM-like in that (a) the full system (cluster or condensed phase) calculation is performed at a lower level of theory (pure DFT for condensed phase or hybrid DFT for molecular systems), and (b) this approximation is improved through a correction term that captures all many-body interactions up to any given order within a higher level of theory (hybrid DFT for condensed phase; CCSD or MP2 for cluster), combined through graph-theoretic methods. Specifically, a region of chemical interest is coarse-grained into a set of nodes and these nodes are then connected to form edges based on a given definition of local envelope (or threshold) of interactions. The nodes and edges together define a graph, which forms the basis for developing the many-body expansion. The methods are demonstrated through (a) ab initio dynamics studies on protonated water clusters and polypeptide fragments, (b) potential energy surface calculations on one-dimensional water chains such as those found in ion channels, and (c) conformational stabilization and lattice energy studies on homogeneous and heterogeneous surfaces of water with organic adsorbates using two-dimensional periodic boundary conditions.     

电场作用下水表面电势的分子动力学研究

水表面电势在诸多电化学过程与反应中扮演关键角色, 然而实验上直接测量却极具挑战. 本论文提出一套基于平衡态恒定电势分子动力学的模拟-分析-计算方法, 可实现通过保持恒定电势且伴随电荷涨落的电极板将电场作用于附近的水表面, 并以平均探针电势计算方法精确测量空间电势分布. 凭借此套方法, 首次计算了不同电极电势下水表面区域的空间电势分布函数, 并测得了鲜有报道的水表面电势随外电场的变化关系. 发现了阴极附近水的表面电势随外电场增强而降低而阳极附近水的表面电势随外电场增强而增大的非对称性. 同时计算了平衡态水表面分子数密度和偶极矩极化密度分布函数, 展示出逐渐增强的外电场能够强烈改变水表面区域的极化行为也能够使液体水整体微弱的极化. 论文最后提出水表面电势随电场变化的非对称性源自水表面极化行为的非对称性以及液体区域的整体极化.     

亚甲基氰自由基(HCCN)与一氧化氮(NO)反应势能面的理论研究

在CCSD(T)/6-311G(d,p)//B3LYP/6-311G(d,p)+ZPE水平上对反应HCCN+NO的二重态反应势能面进行了计算,得到了4种产物:P1(HCN+NCO),P2(OH+NCCN),P₃[HCN+(CNO)]和P4(HCN+CNO).其中产物P1为主要产物,P2为次要产物,P₃和P4很难得到.在G2(B3LYP/MP2/CC)水平,对产物P1和P2的反应通道的单点能量进行了校正.     

Synthesis of Potential Antiviral Agents for SARS-CoV-2 Using Molecular Hybridization Approach

We synthesized a set of small molecules using a molecular hybridization approach with good yields. The antiviral properties of the synthesized conjugates against the SAR-CoV-2 virus were investigated and their cytotoxicity was also determined. Among all the synthesized conjugates, compound 9f showed potential against SARS-CoV-2 and low cytotoxicity. The conjugates’ selectivity indexes (SIs) were determined to correlate the antiviral properties and cytotoxicity. The observed biological data were further validated using computational studies.     

基态N2O－的势能函数研究

以6-311＋＋G(3df, 3pd)为基函数, 采用密度泛函理论的B3LYP方法对N₂O^－分子体系的结构进行了优化计算. 结果表明N₂O^－分子最稳态为C_s构型, 电子组态为²A', 平衡核间距R_N—N＝0.11873 nm, R_N—O＝0.13012 nm, 键角∠NNO＝133.94448°, 离解能D_e＝10.3857 eV, 基态简正振动频率: 弯曲振动频率ν₁＝656.7488 cm^－1, 对称伸缩振动频率ν₂＝998.1562 cm^－1, 反对称伸缩振动频率ν₃＝1684.3093 cm^－1. 并用多体展式理论方法推导出了基态N₂O^－分子的分析势能函数, 其等值势能图准确地再现了N₂O^－分子的结构特征和离解能.     

基于CASSCF参考函数的块相关耦合簇方法对烷烃中单键解离势能面研究

用以完全活化空间自洽场(CASSCF)波函数为参考波函数的块相关耦合簇(BCCC)方法(简称CAS-BCCC)研究了烷烃(甲烷和乙烷)中的单键解离过程的势能面(PES). 与其它理论方法比较的结果表明, 该方法可以对所研究的整个解离势能面给出定量准确的描述.     

Exploring Potential Energy Surfaces for Aggregation‐Induced Emission—From Solution to Crystal

Aggregation‐induced emission (AIE) is a phenomenon where non‐luminescent compounds in solution become strongly luminescent in aggregate and solid phase. It provides a fertile ground for luminescent applications that has rapidly developed in the last 15 years. In this review, we focus on the contributions of theory and computations to understanding the molecular mechanism behind it. Starting from initial models, such as restriction of intramolecular rotations (RIR), and the calculation of non‐radiative rates with Fermi's golden rule (FGR), we center on studies of the global excited‐state potential energy surfaces that have provided the basis for the restricted access to a conical intersection (RACI) model. In this model, which has been shown to apply for a diverse group of AIEgens, the lack of fluorescence in solution comes from radiationless decay at a CI in solution that is hindered in the aggregate state. We also highlight how intermolecular interactions modulate the photophysics in the aggregate phase, in terms of fluorescence quantum yield and emission color.     

Ne-HCl势能面和振转光谱的理论研究

利用量子化学计算方法CCSD(T)和大基组aug-cc-pVTZ加键函数3_s3_p2_d对Ne-HCl体系的分子间势能面进行了理论研究.结果表明,势能面上有两个势阱,分别对应于线性Ne-ClH和Ne-HCl构型.通过精确求解核运动方程发现,该从头算势能面分别支持5个(对Ne-HCl)和7个(Ne-DCl)振动束缚态.计算得到的振转跃迁频率与实值值吻合.     

复合物Kr-CS2的一个新的四维的势能面及其红外光谱的预测

用高精度的量子化学从头算方法构建了Kr-CS₂体系的精确的四维势能面.对该势能面不仅考虑了分子间的振动方式,而且考虑了单体CS₂分子内的ν₁对称伸缩和ν₃反对称伸缩.采用了量子化学超分子方法在[CCSD（T）]-F12水平上构建了从头算势能面.将得到的四维势能面作积分,便得到CS₂处于振动基态和激发态的复合物平均势能面,这两个态的势能面均有一个T型的全局最小值和两个相等的线性极小值.还通过径向部分采用离散变量表象法（DVR）和角度部分采用有限基组表象法（FBR）结合Lanczos循环算法对Kr-CS₂复合物的振转能级进行了计算,对光谱常数进行了预测.另外,也预测了Kr-CS₂复合物的带心位移（-1.2357 cm^-1）.     

First Principles Neural Network Potentials for Reactive Simulations of Large Molecular and Condensed Systems

Modern simulation techniques have reached a level of maturity which allows a wide range of problems in chemistry and materials science to be addressed. Unfortunately, the application of first principles methods with predictive power is still limited to rather small systems, and despite the rapid evolution of computer hardware no fundamental change in this situation can be expected. Consequently, the development of more efficient but equally reliable atomistic potentials to reach an atomic level understanding of complex systems has received considerable attention in recent years. A promising new development has been the introduction of machine learning (ML) methods to describe the atomic interactions. Once trained with electronic structure data, ML potentials can accelerate computer simulations by several orders of magnitude, while preserving quantum mechanical accuracy. This Review considers the methodology of an important class of ML potentials that employs artificial neural networks.     

Composite Correlated Molecular Orbital Theory Calculations of Ring Strain for Use in Predicting Polymerization Reactions

Strained ring systems play an important role in synthesis and can be characterized by the ring strain energy (RSE). The RSE of 3, 4, 5, and 6 membered saturated and unsaturated ring systems containing N, O, P, and S heteroatoms and H, F, SiMe₃, and SO₂Me substituents were calculated at the G3(MP2) composite correlated molecular orbital theory level using up to 5 models to predict the RSE. Generally, the RSE decreased as ring size increased with a substantial decrease from 4 to 5 membered rings. Replacement of a ring CH₂ with P or S reduced the RSE, consistent with less angle strain. The RSE for unsaturated systems were generally greater than for saturated systems due to increased angle strain. No general trends were found with respect to substituent effects. The RSE values suggest that 3-pyrroline and 2-pyrroline and their derivatives may be able to support ring opening metathesis polymerization and warrant further study.     

分子拓扑学方法估算多环芳香烃类化合物的电离能

It was found that the ionization potentials (Ip) is related with the polarizability effect index (PEI) for the fragments CH, CH2, and CH3 of polycyclic aromatic hydrocarbon. Therefore a kind of adjacent matrix of molecular graph was constructed, in which the characteristics of the diagonal elements were expressed with the PEI of the fragments C, CH, CH2, and CH3 in molecular graph. The research result shows that there is a good correlation between the eigenvalue of the matrix and the ionization potential for the title compounds: Ipi=4.756+2.870OMOi, R=0.9853, s=0.1765, n=446. This new calculation method has only one parameter for calculating ionization potentials of polycyclic aromatic hydrocarbon. The obtained result shows that the topologic molecular method is convenient and reliable.     

Molecular Expansion for Constructing Porous Organic Polymers with High Surface Areas and Well-Defined Nanopores

Construction of porous organic polymers (POPs) with high surface areas, well-defined nanopores, and excellent stability remains extremely challenging because of the unmanageable reaction process. Until now, only a few reported POPs have Brunauer-Emmett-Teller (BET) surface areas (S_BET) exceeding 3000 m² g⁻¹. Herein, we demonstrate a molecular expansion strategy to integrate high surface areas, large nanopore sizes, and outstanding stability into POPs. A series of hyper-crosslinked conjugated polymers ( HCCPs ) with exceptional porosity are synthesized through this strategy. Specially, HCCP-6 and HCCP-11 exhibit the highest surface areas (S_BET >3000 m² g⁻¹) and excellent total pore volumes (up to 3.98 cm³ g⁻¹) among these HCCPs . They present decent total CH₄ storage capacities of 491 and 421 mg g⁻¹ at 80 bar and 298 K, respectively. Meanwhile, they are highly stable in harsh environments. The facile and general molecular expansion strategy would lead to improved synthetic routes of POPs for desired functions.     

高电位胶体颗粒强相互作用的近似表达式

When surface potential of the particles, ,is high,sinh y can be approximated by ≈ey/2 in the nonlinear Poisson Boltzmann equation.Thus,we present a simple method of calculating the interaction force and energy per unit area between two dissimilar plates with high potentials at constant surface potential.These formulae could be applicable to the case of repulsive case,in which the derivative of y must vanish at an interior point,and a minimum ymin=u always exists.A turning point at ～kh≈2(1)e－y1/2 for the repulsion or attraction between dissimilar planar surfaces.These formulae are divergent at 阧∞,and zero point at kh≈2 .This means that they can only be used at 阧 < 2 and accurate location is at kh ≤ 4. 　　Agreement of the approximation for force,Eq.（13）,is good with the exact numerical values of the interaction of dissimilar plates given by Devereux [6] for high surface potentials.For y1 ≥5 kh ≤ 3.0 the relative errors of Eq.(13) are less than 5％,and for kh ≤ 3.5 relative errors are less than 10％.For the interaction energy,Eq.(15),the applicable range extends to kh =4.0.Beyond this range the error increases rapidly.The higher surface potential is the better the precision of Eq.（13）and Eq.( 15).The condition of the strong interaction has been satisfied.     

Predicting Accurate Lead Structures for Screening Molecular Libraries: A Quantum Crystallographic Approach

Optimization of lead structures is crucial for drug discovery. However, the accuracy of such a prediction using the traditional molecular docking approach remains a major concern. Our study demonstrates that the employment of quantum crystallographic approach-counterpoise corrected kernel energy method (KEM-CP) can improve the accuracy by and large. We select human aldose reductase at 0.66 Å, cyclin dependent kinase 2 at 2.0 Å and estrogen receptor β at 2.7 Å resolutions with active site environment ranging from highly hydrophilic to moderate to highly hydrophobic and several of their known ligands. Overall, the use of KEM-CP alongside the GoldScore resulted superior prediction than the GoldScore alone. Unlike GoldScore, the KEM-CP approach is neither environment-specific nor structural resolution dependent, which highlights its versatility. Further, the ranking of the ligands based on the KEM-CP results correlated well with that of the experimental IC₅₀ values. This computationally inexpensive yet simple approach is expected to ease the process of virtual screening of potent ligands, and it would advance the drug discovery research.     

Analytical Potential Energy Function for the Ground State(C2V,A1)of LaH2

The present work has derived analytical potential energy function for the ground state(C2V,A1) of LaH2.In the first place,the electronic state and it’s reasonable dissociation limits are correctly determined based on Atomic and Molecular Reaction Statics(AMRS),and then,using the relativisti ccompact effective potential(RCEP)for La,the equilibrium geometry,dissociation energy and harmonic frequencies for LaH2 have been calculated by ab initio method,the reasults show that RLaH=2.1945?,∠HLaH=124.4°and De=5.599eV,and v1,v2 and v3 are 1216.521,1087.417 and 2156.957cm-1,recpectively.Molecular reaction kinetic of La+H2 and La+H based on this potential energy function is under the way.