C6H5—H…X分子间氢键的理论计算

利用密度泛函理论B3LYP方法, 在6-311+G(3df,2p)水平上对C6H5—H…X型分子间氢键进行了几何构型优化、氢键相互作用能、电子密度分布等计算. 其中C6H6为质子供体, HCOH、H2O、NH3、CH2NH和HCN为质子受体. 从电荷布居分析、自然键轨道等角度详细地讨论了C6H5—H…X 体系中, 共轭π键、O和N的不同键型结构对氢键形成的影响以及孤电子对与C—H 反键轨道之间的相互作用(n→σ*)等.     

抗坏血酸与腺嘌呤和尿嘧啶的相互作用研究

使用循环伏安法、密度泛函理论及自然键轨道分析,分别研究了抗坏血酸与腺嘌呤、尿嘧啶的相互作用。两种混合体系在水溶液及PBS缓冲溶液中的电化学实验结果表明:腺嘌呤氨基上的氢原子、嘌呤环上的氮及氢原子,尿嘧啶羰基上的氧原子及氮上氢原子,均可与抗坏血酸烯二醇羟基上的氢原子及羰基上的氧原子形成氢键。氢键的形成,使抗坏血酸的电化学氧化过程难以进行。理论计算也进一步证明了上述混合体系中氢键作用的存在。     

阳离子-π体系相互作用的理论研究Ⅱ.铵离子-二苯复合物体系的密度泛函研究

运用密度泛函B3LYP/6-31G*方法对铵离子-二苯复合物体系的可能构型进行了结构优化,得到了复合物的能量最低构型为:铵离子位于两个苯环平面之间分别以两个氢原子和苯环作用,频率计算结果表明该构型为稳定结构.复合物的键长、原子净电荷、分子轨道系数、前沿轨道能量、Mullicken键级等都表明,铵氢原子和与之接近的苯环碳原子之间通过s-π相互作用而实现铵与两个苯环的结合,结合时电子从苯环向铵转移,形成电荷转移复合物.它们之间的结合方式和铵离子-苯复合物及典型氢键的结合方式相似,计算得到的热力学参数证明了这一点.复合物的红外特征振动频率位于230em-1附近,振动方式为铵平行于苯环平面来回振动.     

氨及其氟取代物与氟化氢形成氢键络合物的系列理论研究

采用ａｂ ｉｎｉｔｉｏ方法，在６－３１Ｇ水平上，对ＮＨ３…ＮＦ、ＮＨ２Ｆ…ＨＦ、ＮＦ３…ＨＦ４种氢键络合物的５组构型进行了一系列能量梯度法的构型优化和能量计算，取得到关于这些分子络合物的结构特征，氢键键能与键级，单体电荷迁移量等信息，分析，比较得出了在每种构型下各体系的重要物理量随氟基数的递变规律，并探讨了氟基的诱导效应对上述体系氢键作用的影响。     

取代基对1-甲基尿嘧啶与N-甲基乙酰胺氢键复合物中氢键强度的影响

使用密度泛函理论B3LYP方法和二阶微扰理论MP2方法对由1-甲基尿嘧啶与N-甲基乙酰胺所形成的氢键复合物中的氢键强度进行了理论研究, 探讨了不同取代基取代氢键受体分子1-甲基尿嘧啶中的氢原子对氢键强度的影响和氢键的协同性. 研究表明: 供电子取代基使N－H…O＝C氢键键长r(H…O)缩短, 氢键强度增强; 吸电子取代基使N－H…O＝C氢键键长r(H…O)伸长, 氢键强度减弱. 自然键轨道(NBO)分析表明: 供电子基团使参与形成氢键的氢原子的正电荷增加, 使氧原子的负电荷增加, 使质子供体和受体分子间的电荷转移量增多; 吸电子基团则相反. 供电子基团使N－H…O＝C氢键中氧原子的孤对电子轨道n(O)对N－H的反键轨道σ^*(N－H)的二阶相互作用稳定化能增强, 吸电子基团使这种二阶相互作用稳定化能减弱. 取代基对与其相近的N－H…O＝C氢键影响更大.     

聚醚醚酮链结构与反应的模型化合物的量子化学研究

利用ＡＭ１方法对聚醚醚酮模型化合物全优化，结果为：芳环平均相互扭转角为３３．０度，桥键角１１７．０－１１８．０度，其分子结构拓扑图形表明：所有苯环（核）为平面构型，但其内角扭曲；其氢原子对苯环构型无实质性贡献，在更长链的计算中，冻结苯核与氢原子也得出满意结果，根据Ｍｕｌｌｉｋｅｎ键序与电荷讨论了醚交换与磺化反应。     

有机锂化合物中化学键的性质——-反式1,2-二锂代乙烷、1,2-二锂代乙烯和1,2-二锂代乙炔分子中化学键的abinitio研究

用从头计算法计算了电荷密度图和各从是分子轨道的键强参数.结果表明,三个标题化合物的稳定构型都存在双桥式四中心键.追其原因是:这种构型有利于Li的2p轨道的吸电子效应,这种效应可使C-Li键增强.此外,也发现这三个化合物中C-C键的强度大于C=C键,而后者又比C=C键为强,本文亦讨论了这种"反常"的原因.     

有机锂化合物中化学键的性质——-反式1,2-二锂代乙烷、1,2-二锂代乙烯和1,2-二锂代乙炔分子中化学键的abinitio研究

用从头计算法计算了电荷密度图和各价分子轨道的键强参数.结果表明,三个标题化合物的稳定构型都存在双桥式四中心键.追其原因是:这种构型有利于Li的2p轨道的吸电子效应,这种效应可使C—Li键增强.此外,也发现这三个化合物中C—C键的强度大于C=C键,而后者又比C≡C键为强.本文亦讨论了这种“反常”的原因.     

多巴胺盐酸盐与肌醇的相互作用研究

使用电化学循环伏安法、密度泛函理论、分子中的原子理论和自然键轨道理论分析研究了多巴胺盐酸盐(DH)与肌醇的相互作用.结果表明:DH中酚羟基的氢原子和氧原子、-NH_3~+上氢原子以及支链上氢原子,可与肌醇中羟基的氢原子和氧原子、环上的氢原子形成分子间氢键.其中,DH酚羟基上的氢原子是二者作用的主要位点.     

取代苯酚中共振增强的分子内氢键

根据晶体结构资料，计算了59个邻位取代苯酚中分子内氢键的几何．在STO－3G水平上计算了一些分子中原子部分电荷．结果表明，酚基氧与苯环上碳之间的键长，酚基上氢原子的部分电荷，酚基所在位置处的苯环环内角与取代苯酚的酸常数pKa均有近似线性关系，当邻位上存在硝基或羰基时，内氢键由于共振而得到显著的增强，据此可说明这一类酚的显著酸性     

Accurate modeling of the intramolecular electrostatic energy of proteins

The (?, ψ) energy surface of blocked alanine (N-acetyl–N′-methyl alanineamide) was calculated at the Hartree-Fock (HF)/6-31G* level using ab initio molecular orbital theory. A collection of six electrostatic models was constructed, and the term electrostatic model was used to refer to (1) a set of atomic charge densities, each unable to deform with conformation; and (2) a rule for estimating the electrostatic interaction energy between a pair of atomic charge densities. In addition to two partial charge and three multipole electrostatic models, this collection includes one extremely detailed model, which we refer to as nonspherical CPK. For each of these six electrostatic models, parameters—in the form of partial charges, atomic multipoles, or generalized atomic densities—were calculated from the HF/6-31G* wave functions whose energies define the ab initio energy surface. This calculation of parameters was complicated by a problem that was found to originate from the locking in of a set of atomic charge densities, each of which contains a small polarization-induced deformation from its idealized unpolarized state. It was observed that the collective contribution of these small polarization-induced deformations to electrostatic energy differences between conformations can become large relative to ab initio energy differences between conformations. For each of the six electrostatic models, this contribution was reduced by an averaging of atomic charge densities (or electrostatic energy surfaces) over a large collection of conformations. The ab initio energy surface was used as a target with respect to which relative accuracies were determined for the six electrostatic models. A collection of 42 more complete molecular mechanics models was created by combining each of our six electrostatic models with a collection of seven models of repulsion + dispersion + intrinsic torsional energy, chosen to provide a representative sample of functional forms and parameter sets. A measure of distance was defined between model and ab initio energy surfaces; and distances were calculated for each of our 42 molecular mechanics models. For most of our 12 standard molecular mechanics models, the average error between model and ab initio energy surfaces is greater than 1.5 kcal/mol. This error is decreased by (1) careful treatment of the nonspherical nature of atomic charge densities, and (2) accurate representation of electrostatic interaction energies of types 1—2 and 1—3. This result suggests an electrostatic origin for at least part of the error between standard model and ab initio energy surfaces. Given the range of functional forms that is used by the current generation of protein potential functions, these errors cannot be corrected by compensating for errors in other energy components. © 1995 by John Wiley & Sons, Inc.     

Molecular modelling of poly(aryl ether ketones). I. Aryl··aryl interactions in crystal structures

Summary Non-bonded potentials for the aryl interaction have been derived using crystal structure data of a number of small aromatic molecules. The potentials, based on atom-centred interactions, give an accurate reproduction of the benzene crystal geometry and sublimation energy when used in conjunction with coulombic energies evaluated using point atomic charges. An examination of the charge distribution on benzene suggested values of 0.13e (H) and -0.13e (C) to be suitable. The transferability of the potentials has been shown by prediction of crystal geometries and sublimation energies of other hydrocarbon molecules and, with additional interactions for the oxygen atom included, preliminary polymer crystal structure calculations have been carried out. These demonstrate the validity of the derived parameters by successfully predicting crystallographic unit cell dimensions and ring conformations in the poly(phenylene oxide) and poly(aryl ether ketone) crystals.     

Analysis of the transferability of atomic multipoles for amino acids in modeling macromolecular charge distribution from fragments

Cumulative Atomic Multipole Moments were calculated for all natural amino acids and symmetric cyclic hexapeptides within Self‐Consisted Field (SCF) and Density Functional Theory (DFT) approaches using a standard 6‐31G(d,p) basis set. These data were used to analyze in detail the quality and the conformational and the intermolecular transferability of molecular charge distributions expressed in the atomic multipole form. Intermolecular interaction energies were reproduced reasonably by CAMM transformed from other conformations. Good transferability of CAMM based model was also achieved between similar molecular environments, which opens a route to modeling electrostatic effects in highly symmetric (e.g., crystalline) systems. Transferability deficiencies of various charge distribution models were analyzed and attributed to different levels of multipole expansion. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1082–1097, 2001     

N?H···S and S?H···N intramolecular hydrogen bond in β‐thioaminoacrolein: A quantum chemical study

The conformational study of β‐thioaminoacrolein was performed at various theoretical levels, HF, B3LYP, and MP2 with 6‐311++G(d,p) basis set, and the equilibrium conformations were determined. To have more reliable energies, the total energies of all conformers were recomputed at high‐level ab initio methods, G2MP2, G3, and CBS‐QB3. According to these calculations, the intramolecular hydrogen bond is accepted as the origin of conformational preference in thialamine (TAA) and thiolimine groups. The hydrogen bond strength in various resonance‐assisted hydrogen bond systems was evaluated by HB energy, geometrical parameters, topological parameters, and charge transfers corresponding to orbital interactions. Furthermore, our results reveal that the TAA tautomer has extra stability with respect to the other tautomers. The population analyses of the possible conformations by NBO predict that the origin of this preference is mainly due to the π‐electron delocalization in framework of TAA forms, especially usual π_C?C → π*_C?S and Lp (N) → π*_C?C charge transfers. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Conformational analysis—133: 3,3-dimethyl-2,4-pentanedione. The importance of induction and solvationTetrahedron 34, 3385 (1978).

The conformations of the title compound have been analyzed in detail with respect to steric interaction energies, charge interaction energies, and solvation energies in heptane and benzene. Using previously developed methods, which include induction by dipoles in polarizable bonds, and the solvation of molecular dipoles and quadrupoles, predictions regarding the conformational equilibrium are made. These were tested by experimental determination of the dipole moment of the molecule in heptane and benzene, and are in agreement with the predictions. More simplified calculations lead to qualitatively erroneous results.     

Interactions of halichondrin B and eribulin with tubulin

Compounds that modulate microtubule dynamics include highly effective anticancer drugs, leading to continuing efforts to identify new agents and improve the activity of established ones. Here, we demonstrate that [(3)H]-labeled halichondrin B (HB), a complex, sponge-derived natural product, is bound to and dissociated from tubulin rapidly at one binding site per αβ-heterodimer, with an apparent K(d) of 0.31 μM. We found no HB-induced aggregation of tubulin by high-performance liquid chromatography, even following column equilibration with HB. Binding of [(3)H]HB was competitively inhibited by a newly approved clinical agent, the truncated HB analogue eribulin (apparent K(i), 0.80 μM) and noncompetitively by dolastatin 10 and vincristine (apparent K(i)'s, 0.35 and 5.4 μM, respectively). Our earlier studies demonstrated that HB inhibits nucleotide exchange on β-tubulin, and this, together with the results presented here, indicated the HB site is located on β-tubulin. Using molecular dynamics simulations, we determined complementary conformations of HB and β-tubulin that delineated in atomic detail binding interactions of HB with only β-tubulin, with no involvement of the α-subunit in the binding interaction. Moreover, the HB model served as a template for an eribulin binding model that furthered our understanding of the properties of eribulin as a drug. Overall, these results established a mechanistic basis for the antimitotic activity of the halichondrin class of compounds.     

Inter- and intramolecular potential for the N-formylglycinamide-water system. A comparison between theoretical modeling and empirical force fields

An intramolecular NEMO potential is presented for the N-formylglycinamide molecule together with an intermolecular potential for the N-formylglycinamide-water system. The intramolecular N-formylglycinamide potential can be used as a building block for the backbone of polypeptides and proteins. Two intramolecular minima have been obtained. One, denoted as C5, is stabilized by a hydrogen bonded five member ring, and the other, denoted as C7, corresponds to a seven membered ring. The interaction between one water molecule and the N-formylglycinamide system is also studied and compared with Hartree-Fock SCF calculations and with the results obtained for some of the more commonly used force fields. The agreement between the NEMO and SCF energies for the complexes is in general superior to that of the other force fields. In the C7 region the surfaces obtained from the intramolecular part of the commonly used force fields are too flat compared to the NEMO potential and the ab initio calculations. We further analyze the possibility of using a charge distribution obtained from one conformation to describe the charge distribution of other conformations. We have found that the use of polarizabilities and generic dipoles can model most of the changes in charge density due to the different geometry of the new conformations, but that one can expect additional errors in the interaction energies that are of the order of 1 kcal/mol.     

Theoretical investigation of the structure and properties of H2B=NH2...Mn+, HB≡NH...Mn+, and Borazine...Mn+ complexes (M = Alkaline and Earth Alkaline Metals)

The nature of H₂B=NH₂...M ⁿ⁺, HB=NH...M ⁿ⁺, and Borazine...M ⁿ⁺ interactions were studied with ab-initio calculations. The interaction energies were calculated at B3LYP/6-31G(d, p) level. The calculations suggest that the size and charge of cation are two influential factors that affect the nature of interaction. The theory of atoms in molecules (AIM) and natural bond orbital (NBO) analysis of complexes indicate that the variation of densities and the extent of charge shifts upon complexation correlate well with the obtained interaction energies.     

Calculation of hydration free energy for a solute with many atomic sites using the RISM theory: A robust and efficient algorithm

We have developed an algorithm for solving the reference interaction site model (RISM) equations for water near a solute molecule with many atomic sites (interaction sites). It is a hybrid of the Newton–Raphson and Picard methods and is judiciously constructed. Various considerations are given so that the computer time can be saved as much as possible. The robustness and high efficiency of the algorithm has been demonstrated for calculating hydration free energies of Met-enkephalin (a peptide with 75 sites) with different conformations. The Jacobian matrix is treated as part of the input data, and it has been found that the same matrix can be used for a considerably large set of different conformations of the solute molecule. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1320–1326, 1997