Theoretical study of the interaction between pyridine derivatives and atomic chlorine. Substituent effect and nature of the bonding

The interaction of pyridine derivatives (H, 4-NH₂, 4-CH₃, 4-F, 4-CN, 4-NO₂) with atomic chlorine is investigated theoretically by the density functional theory (DFT)-based LC-BLYP/aug-cc-pVDZ method. Pyridines and Cl° are held together by a (2c--3e) bond and the intermolecular distances range from 2.313 to 2.343 Å. The existence of a N…Cl bond is confirmed by the atom-in-molecule analysis of the systems. The binding energies of the adducts, ranging from ?42.08 to ?53.96 kJ mol^?1, are linearly correlated to the proton affinity of the pyridines. The charge transfer from pyridine to Cl° varies between 0.222 and 0.277 e. The spin density analysis shows that the strongest complex has the highest (2c–3e) character. The CH bonds are contracted and the ν(CH) vibrations are blueshifted owing to the decrease in σ*(CH) occupation. This decrease results not only from the classical anomeric effect but also from the σ(CC) and σ(CN) → σ*(CH) delocalisation in the heteroaromatic ring.     

Association of mono- and dimethyl ethers of chlorine 6 in ethanol-water solutions

The association of γ-mono- and 6,γ-dimethyl ethers of chlorin e₆ (I and II) in mixtures of a phosphate buffer and ethanol is studied. The number of molecules in associates and the dimerization constants are determined. The formation of the dimers of compound I and dimers and associates of a higher order for II is established. It is found that, unlike I, the shift of the Q absorption band of the dimer toward larger wavelengths is rather great as compared to the monomer band for II; it exceeds 30 nm, which is uncommon for porphyrins. This difference of spectral changes in association of I and II is attributed to the dissimilar character of interaction of their molecules with each other and with the molecules of the surroundings, and also to the structural features of the dimers. Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 67, No. 4, pp. 440–444, July–August, 2000.     

甘氨酸与水分子间相互作用的理论研究

在密度泛函(DFT)B3LYP/6_311++G(3d,3p)水平,对中性甘氨酸的最小点结构Ip和H2O分子间可能存在的氢键复合物进行全自由度能量梯度优化,发现了三个氢键极小结构A、C和E,其中结构A为最稳定结构,它是H2O与甘氨酸的羧基(-COOH)形成两个氢键的结构,具有C1对称性.分别采用密度泛函理论(DFT)和MP2方法,在6-311++G(3d,3p)水平,对结构A的结构和结合能进行了比较计算,得到结合能ΔEDFT为-41.88 kJ/mol,ΔEMP2为-40.34 kJ/mol.     

Molecular interaction of silybin with hyaluronidase: A spectroscopic and molecular docking study

In this study, the molecular interaction of silybin with hyaluronidase was investigated by spectroscopic methods and molecular docking. It was found that silybin had strong ability to quench the intrinsic fluorescence of hyaluronidase by a static quenching procedure. The binding constants were obtained at three temperatures (293, 298, and 310 K). The results of synchronous fluorescence and three-dimensional fluorescence and molecular docking showed that silybin bound into the hyaluronidase cavity site and the binding of silybin to hyaluronidase could induce micro-environmental and conformational changes in hyaluronidase, which resulted in the reduced hyaluronidase activity. The thermodynamic parameter analysis and molecular docking experiments revealed that all types of non-covalent interaction, including hydrogen bonding interaction, van der Waals forces, hydrophobic interaction, and electrostatic interaction were present in the binding process of silybin with hyaluronidase. The results obtained here will provide direct evidence at a molecular level to understand the mechanism of the inhibitory effect of silybin against hyaluronidase.     

Multiscale modelling strategies and experimental insights for the solvation of cellulose and hemicellulose in ionic liquids

ABSTRACT

The present study investigates the dissolution behaviour of cellulose and hemicellulose in potential ionic liquids (ILs) using both the quantum chemical and experimental validation. For converging upon the recommended IL, 1428 ILs consisting of 42 cations and 34 anions were studied with the conductor like screening model for real solvents (COSMO-RS) model. Based on the infinite dilution activity coefficient of the components in IL, the selected anions and cations were visualised by observing their interactions with cellulose and hemicellulose using interaction energies, natural bonding orbital analysis and molecular dynamics simulations. The dissolution order of cellulose and hemicellulose in ILs was primarily determined by the evaluation of hydrogen bonds between the oxygen atom of anion and hydroxyl proton of cellulose/hemicellulose. From this discernible fact, the anion of the IL was observed to play a leading role in the solvation process as compared to the cation. Eventually, acetate [OAc]^– anion and 1-ethyl-3-methylimidazolium [EMIM]⁺ cation were found to be good candidates for the dissolution of cellulose and hemicellulose. This was further confirmed by the measurement of solid-liquid equilibria with cellulose and hemicellulose. The regenerated cellulose powder was then characterised by Fourier transform spectroscopy(FTIR), X-ray diffraction (XRD) and Thermal gravimetric analysis (TGA).     

气体-表面相互作用中动量和能量分量间转化机制的分子动力学研究

气体分子与壁面之间的相互作用是影响稀薄气体流动状态的主要因素,但是由于其物理上的复杂性和微观性,这一过程的机理并没有得到充分揭示.本文利用分子束法对Ar分子在金属Pt表面的碰撞过程进行了分子动力学模拟,并探究了入射速度、角度和壁面粗糙度对动量、能量转化机制的影响.结果表明,当气体分子以5°的极角入射时,分子的法向速度分...     

苯与PtH分子间电子相互作用的理论研究

采用从头算法在B3LYP水平分别对苯和PtH分子单体及其分子复合物体系(苯-PtH)进行了几何结构优化和振动频率计算,得到了3种苯-PtH分子复合物构型,研究了苯与PtH分子间相互作用对Pt-H键振动频率的影响,并得出了苯与PtH分子之间的相互作用能.     

Cl~–…苯氰…H_2O中阴离子氢键协同效应与芳香性理论研究

本文采用DFT-B3LYP和MP2(full)方法对三聚体Cl–…苯氰…H2O中O/C–H…Cl–阴离子氢键与传统氢键O–H…N和C–H…O之间的协同效应、热力学性质以及芳香性进行了研究.结果表明阴离子氢键O/C–H…Cl–对O–H…N或C–H…O相互作用的影响更显著.在线性结构中发生正协同效应,熵变是促进热力学协同效应的主要因素,而在环状结构中发生反协同效应,焓变成为主要因素.在三聚体形成过程中,苯氰环的芳香性是减弱的,而苯氰中π→π*共轭效应是增强的.结果表明,协同效应能Ecoop.分别与Rc(NICS(1)ternary/NICS(1)binary),ΔΔδ(Δδternary-Δδbinary),Rc'((NICS(1)ternary-NICS(1)binary)/NICS(1)binary)和RBDE(C–CN)(BDE(C–CN)ternary/BDE(C–CN)binary)均具有良好的线性关系.同时,AIM的分析也佐证了协同效应的存在.     

He原子与O2分子相互作用势及碰撞微分截面的研究

本文用量子力学从头算方法深入研究了He原子与O2分子的相互作用势,选定CCSD(T)/6-311++G(3df,2pd)方法和基组,同时采用了Boys和Bernardi提出的Full Couterpoise方法消除了计算中的基组重叠误差(BSSE),得出了该体系的各向异性相互作用势的单点能数据,通过拟合得到了较为准确的He-O2体系相互作用势的解析表达式.采用精确度较高的密耦(Close-Coupling)近似方法,计算了He-O2碰撞体系的碰撞激发微分截面,计算得到的微分截面数据与实验值符合较好,并得出了不同碰撞能量时He原子与O2分子的碰撞的微分截面的规律.     

Analysis of the binding mechanism between o-phenylenediamine and bovine hemoglobin by molecular spectroscopy and molecular modeling methods

Abstract

This study was aimed to reveal the binding mechanism between bovine hemoglobin and o-phenylenediamine by using molecular spectroscopy techniques and molecular modeling methods. The experimental results revealed that the fluorescence quenching mechanism was a combined dynamic and static quenching. The binding constant was (1.17?±?0.02)×10⁴ L/mol, and only a single binding site exists. The binding distance was 2.46?nm. The binding process was a spontaneous reaction, dominated by hydrophobic forces. The molecular docking simulations have also confirmed the results of the spectroscopic methods. The results reported here may significantly help understanding the interaction mechanism of o-phenylenediamine and hemoglobin.     

二静电体系相互作用力与相互作用能一般关系的正确表达式

指出二静电体系的相互作用力的普遍表达式F=-↓△w1=-↓△w并不恰当。正确的表达式应当是Fj=δW1/δqj=-δW1/δqj，其中Fj是沿广义坐标qj方向的广义力，W1是静电场总能量，W1是二静电体系的相互作用能，qj为表征二静电体系相对位移的某一广义坐标。     

dsDNA与TiO2 (110)在溶液中相互作用的动力学行为和机制

金红石型TiO2 (110)在DNA传感领域具有广阔的应用前景,然而其与DNA在溶液中相互作用的动力学行为和机制尚不清楚。利用分子动力学模拟,深入研究了双链DNA (dsDNA)在初始时沿轴向平行或垂直于金红石型TiO2 (110)表面时二者在溶液中的相互作用。通过分析dsDNA在吸附后的稳定构型、吸附动力学过程和结构稳定性发现,与一些典型二维纳米材料不同,dsDNA倾向于水平吸附到TiO2 (110)表面。水平吸附不仅使得dsDNA的四种碱基均吸附到TiO2 (110)表面,增加了吸附稳定性,而且不破坏dsDNA的结构稳定性。进而,通过分析dsDNA与TiO2 (110)表面的相互作用能和水分子密度/数量发现,dsDNA的平行吸附可能源于二者之间的短程范德华和长程静电相互作用。此外,纳米级脱湿也增强了dsDNA的吸附。对dsDNA与TiO2 (110)在溶液中的相互作用研究有助于实现TiO2 (110)在DNA传感中的应用。     

Enthalpies of formation and isomerization of aromatic hydrocarbons and ethers by G3(MP2)//B3LYP calculations

A computational method for estimation of the gas‐phase enthalpies of formation of aromatic hydrocarbons and ethers has been developed. The method is based on high‐level G3(MP2)//B3LYP calculations, atomization reactions, and structure‐dependent correction terms. By this method, enthalpies of formation Δ_fH_m°(g, 298.15 K) of 86 aromatic compounds were evaluated. The calculated enthalpies of formation raise questions of the reliability of several experimental enthalpies of formation reported in the literature. As an application of the computational enthalpies of formation, reaction enthalpies for several types of isomerization reactions of aromatic compounds were calculated. In cases in which experimental reaction enthalpies were available for comparison, the agreement between the computational and experimental data proved to be excellent. Copyright © 2008 John Wiley & Sons, Ltd.     

A natural bond orbital analysis of aryl‐substituted polyfluorinated carbanions: negative hyperconjugation

Aryl‐substituted polyfluorinated carbanions, ArCHR_f^? where R_f = CF₃ ( 1 ), C₂F₅ ( 2 ), i‐C₃F₇ ( 3 ), and t‐C₄F₉ ( 4 ), were analyzed by means of the natural bond orbital (NBO) theory at the B3LYP/6‐311+G(d,p) computational level. A lone pair NBO at the formal anionic center carbon (Cα) was not found in the Lewis structure. Instead, significant donor/acceptor NBO interactions between π(Cα‐C1) and σ*(Cβ‐F) or σ*(Cβ‐Cγ) were observed for 1 , 2 , 3a (strong electron‐withdrawing substituent, from p‐CF₃ to p‐NO₂), and 4 . Their second‐order donor/acceptor perturbation interaction energy, E(2), values decreased with the increase of the stability of carbanions. A larger E(2) value corresponds to longer Cβ‐F and Cβ‐Cγ bonds and a shorter Cα‐Cβ bond, indicating that the E(2) values can be associated with the negative hyperconjugation of the Cβ‐F and Cβ‐Cγ bonds. In accordance with this, the E(2) values for π(Cα‐C1) → σ*(Cβ‐F) were linearly correlated with the ΔG^o_β‐F values (an empirical measure of β‐fluorine negative hyperconjugation obtained from an increased acidity). In 3b (weak electron‐withdrawing substituents, from H to m‐NO₂) very large E(2) values for LP(Fβ) → π*(Cα‐Cβ) were obtained. This was attributed to the Cβ‐F bond cleavage and the Cα‐Cβ double bond formation in the Lewis structure that is caused by the extremely strong negative hyperconjugation of the Cβ‐F bond.     

O3与O3分子间相互作用的理论研究

采用从头算方法,在B3LYP水平下对O3分子单体及其二聚体进行了几何结构优化,得到四种O3分子二聚体的稳定构型,并经MP2法、均衡法(Massage)分别校正了电子相关和基组叠加误差(BSSE),通过对分子中原子间的最短距离,分子间质心距离与各构型相互作用能的关系进行了分析、比较,得到了最稳定的构型,其对应的O3分子二聚体相互作用能为:-8.788 kJ/mol.     

The production of prop-2-ynylideneamine by thermolysis of N-chloropropargylamine,N-fluoropropargylamine and N-hydroxypropargylamine: a computational study

Ab initio molecular orbital calculations using MP2 and DFT/B3LYP methods at the 6-311++G(d,p) and aug-cc-pvdz basis sets were applied to characterise the kinetics of the thermal dissociation of HC≡CCH₂NHX [where X = OH(I), F(II) and Cl(III)] to produce Z- and E-prop-2-ynylideneamines (HC≡CCH=NH) (IV and V, respectively), which tautomerise to vinyl cyanide (CH₂=CHC≡N) (VI). The optimised geometries and electronic energies of reactants, transition states and products were estimated and discussed. A concerted proton migration and HX abstraction mechanism was proposed for the imine formation. The reliance of these properties on the elected levels of theory was discussed. The activation energies and barrier heights for the Z- and E-forms and their vinyl cyanide tautomers were estimated and analysed. The Z-form was computed to be more stable than the E-form. Using natural bond orbital calculations, the origin of the preference of the Z-form was attributed mainly to the N lone pair delocalisations. Vinyl cyanide was located to have a lower energy (33–35 kcal/mol) than prop-2-ynylideneamine. The provenance of the preference of the former and its tautomerisation mechanism will be addressed in a separate publication.     

PH, PD和PT分子常数理论研究

采用内收缩多参考组态相互作用(MRCI)方法和包含Davidson修正(+Q) 的MRCI方法结合相关一致基aug-cc-pV5Z研究了PH (X³Σ^-, a¹Δ和A³∏)分子的势能曲线. 在同位素质量识别的基础上对势能曲线进行拟合, 得到PH, PD和PT分子各个电子态的光谱常数(T_e, R_e, ω_e, ω_ex_e, α_e和 B_e). 通过与已有实验数据的比较发现, 本文的结果与实验结果非常一致. 对于PH, PD和PT分子的Σ^-电子态, 计算得到了J = 0时的前12个振动态. 对于每一个振动态, 还分别计算了它的振动能级、惯性转动常数和离心畸变常数. 与其他理论结果和实验数据进行比较可知, 本文的结果更精确、更完整. 文中PD和PT分子的光谱常数和分子常数均属首次报导.     

Basicity of the polydentate captodative aminoenones. Ab initio,DFT, and FTIR study

Electron donating ability of the oxygen, nitrogen, and carbon atoms of captodative aminoenones R'CH = C(NR₂)EWG, EWG = CHO, C(O)Me, C(O)CF₃, C(O)Ph was investigated using ab initio and Density Functional Theory (DFT) calculations, Natural Bond Analysis (NBO) analysis, and Fourier Transform InfraRed (FTIR) spectroscopy. The influence of both electron withdrawing group (EWG) and double bond substituents on the proton affinity of the basic centers, orbital interaction, as well as resonance stabilization energies between heteroatoms and double bonds are discussed. The results obtained are critically compared with the push–pull aminoenones. The comparison of experimental values ΔνOH and theoretical values of H‐bonding energy was used to determine the H‐complex type of aminoenone with phenol and the H‐bond strength. Copyright © 2016 John Wiley & Sons, Ltd.     

切伦柯夫相互作用中分段式慢波结构与均匀慢波结构的比较研究

 分析了切伦柯夫束波相互作用中使用单段慢波结构的缺点。指出在分段式慢波结构中，漂移段及其两端的慢波结构组成一Bragg谐振腔，当漂移段长度合适时，根据渡越时间效应理论，这种结构能减小调制束中电子的速度分散，提高束波转化效率。通过粒子模拟方法，比较了均匀慢波结构与分段式慢波结构中束波相互作用的物理图像，验证了理论分析结果，并说明了后者有束密度群聚充分，束电子速度分散小，产生微波功率高、频谱质量好，最佳工作电流大，输入电功率高等优点。     

石墨烯-纳米探针相互作用有限元准静态计算

纳米尺度探针是研究纳米薄膜材料的重要工具.针对纳米探针和石墨烯相互作用有限元模型静态计算中难以收敛的困难,应用动态显式算法通过间歇式探针进给方式进行能量耗散,得出静态计算结果.模型中界面作用力由界面黏结能和原子间作用势导出并植入Abaqus软件中界面作用子程序,实现对石墨烯、探针,基体系统内相互作用的仿真计算.通过对比计算结果和实验数据,对实验结果给出了一致性解释.