Identifying potential binding modes and explaining partitioning behavior using flexible alignments and multidimensional scaling

A method is described for the rapid and automatic analysis of flexible molecular alignments using multidimensional scaling and a normalized scoring scheme. A projection scheme was devised to separate orientational and conformational effects. It is shown that the approach can be utilized for the identification of common binding orientations or to the study of differences in partioning behavior. It is suggested that the method can be employed as a novel approach exploring molecular similarity as a dynamic property, so that it includes aspects of motion (by way of mutual orientations), conformations and molecular properties.     

Predicting properties of molecules using graph invariants

Topological indices (TIs) have been used to study structure-activity relationships (SAR) with respect to the physical, chemical, and biological properties of congeneric sets of molecules. Since there are many TIs and many are correlated, it is important that we identify redundancies and extract useful information from TIs into a smaller number of parameters. Moreover, it is important to determine if TIs, or parameters derived from TIs, can be used for global SAR models of diverse sets of chemicals. We calculated seventy-one TIs for three groups of molecules of increasing complexity and diversity: (a) 74 alkanes, (b) 29 alkylbenzenes, and (c) 37 polycyclic aromatic hydrocarbons (PAHs). Principal components analysis (PCA) revealed that a few principal components (PCs) could extract most of the information encoded by the seventy-one TIs. The structural basis of the first few PCs could be derived from their pattern of correlation with individual TIs. For the three sets of molecules, viz. alkanes, alkylbenzenes and PAHs, PCs were able to predict the boiling points reasonably well. Also, for the combined set of 140 chemicals consisting of the alkanes, alkylbenzenes and PAHs, the derived PCs were not as effective in predicting properties as in the case of individual classes of compounds.     

偏最小二乘和量子化学参数预测酯类物质的闪点

基于化合物定量结构与性质的关系,对其中88个酯类化合物进行了B3LYP/6-31G*水平上的结构优化,并在优化结构基础上进行了量子化学结构参数的计算。应用偏最小二乘(PLS)方法对酯类化合物闪点温度这个理化性质与量子化学参数进行了关联。结果表明,分子热力学自由能(ΔG)结合偶极距(μ)可以很好地表达酯类化合物闪点温度与量子化学参数间的定量关系。所建立的QSPR模型具有较强的稳健性和预测能力。     

Atomic walk counts of negative order

Atomic walk counts (awc's) of order k (k > or = 1) are the number of all possible walks of length k which start at a specified vertex (atom) i and end at any vertex j separated by m (0 < or = m < or = k) edges from vertex i. The sum of atomic walk counts of order k is the molecular walk count (mwc) of order k. The concept of atomic and molecular walk counts was extended to zero and negative orders by using a backward algorithm based on the usual procedure used to obtain the values of mwc's. The procedure can also be used in cases in which the adjacency matrix A related to the actual structure is singular and therefore A(-1) does not exist. awc's and mwc's of negative order may assume noninteger and even negative values. If matrix A is singular, atomic walk counts of zero order may not be equal to one.     

Dithiolodithiole as a Building Block for Conjugated Materials

The development of new conjugated organic materials for dyes, sensors, imaging, and flexible light emitting diodes, field‐effect transistors, and photovoltaics has largely relied upon assembling π‐conjugated molecules and polymers from a limited number of building blocks. The use of the dithiolodithiole heterocycle as a conjugated building block for organic materials is described. The resulting materials exhibit complimentary properties to widely used thiophene analogues, such as stronger donor characteristics, high crystallinity, and a decreased HOMO–LUMO gap. The dithiolodithiole (C₄S₄) motif is readily synthetically accessible using catalytic processes, and both the molecular and bulk properties of materials based on this building block can be tuned by judicious choice of substituents.     

Four new topological indices based on the molecular path code

The sequence of all paths pi of lengths i = 1 to the maximum possible length in a hydrogen-depleted molecular graph (which sequence is also called the molecular path code) contains significant information on the molecular topology, and as such it is a reasonable choice to be selected as the basis of topological indices (TIs). Four new (or five partly new) TIs with progressively improved performance (judged by correctly reflecting branching, centricity, and cyclicity of graphs, ordering of alkanes, and low degeneracy) have been explored. (i) By summing the squares of all numbers in the sequence one obtains Sigmaipi(2), and by dividing this sum by one plus the cyclomatic number, a Quadratic TI is obtained: Q = Sigmaipi(2)/(mu+1). (ii) On summing the Square roots of all numbers in the sequence one obtains Sigmaipi(1/2), and by dividing this sum by one plus the cyclomatic number, the TI denoted by S is obtained: S = Sigmaipi(1/2)/(mu+1). (iii) On dividing terms in this sum by the corresponding topological distances, one obtains the Distance-reduced index D = Sigmai{pi(1/2)/[i(mu+1)]}. Two similar formulas define the next two indices, the first one with no square roots: (iv) distance-Attenuated index: A = Sigmai{pi/[i(mu + 1)]}; and (v) the last TI with two square roots: Path-count index: P = Sigmai{pi(1/2)/[i(1/2)(mu + 1)]}. These five TIs are compared for their degeneracy, ordering of alkanes, and performance in QSPR (for all alkanes with 3-12 carbon atoms and for all possible chemical cyclic or acyclic graphs with 4-6 carbon atoms) in correlations with six physical properties and one chemical property.     

Quantitative structure-activity relationship studies of boron-containing dipeptide proteasome inhibitors using calculated mathematical descriptors

Topological indices (TIs) and atom pairs (APs) were used to develop quantitative structure-activity relationship (QSAR) models of a set of 58 dipeptide boronic acids which are potent inhibitors of proteasome and have found applications in the treatment of various types of cancers. Of the three linear regression methods used for QSAR development, viz., principal components regression (PCR), partial least square (PLS), and ridge regression (RR), the last method gave the most satisfactory models whereas the remaining two methods yielded poor models. RR results obtained in this paper using TIs and APs are comparable to the CoMFA and CoMSIA results reported in the literature with the same set of compounds.     

Quantitative molecular similarity analysis (QMSA) methods for property estimation: a comparison of property-based,arbitrary, and tailored similarity spaces

Three classes of arbitrary quantitative molecular similarity analysis (QMSA) methods have been computed using atom pairs, topological indices, and physicochemical properties. Tailored QMSA models have been developed using a selected number of TIs chosen by ridge regression. The methods have been applied to the K-nearest neighbor based estimation of log P of two sets of chemicals. Results show that the property-based and tailored QMSA methods are superior to the arbitrary similarity methods in estimating log P of both sets of chemicals     

IMiCMO: a new integrated ab initio multicenter molecular orbitals method for molecular dynamics calculations in solvent cluster systems

A new computational scheme integrating ab initio multicenter molecular orbitals for determining forces of individual atoms in large cluster systems is presented. This method can be used to treat systems of many molecules, such as solvents by quantum mechanics. The geometry parameters obtained for three models of water clusters by the present method are compared with those obtained by the full ab initio MO method. The results agree very well. The scheme proposed in this article also intended for use in modeling cluster systems using parallel algorithms. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1107–1112, 2001     

DNA碱基(对)及其Zn2+复合物对CO2,N2,H2小分子的吸附

用M062X/6-31+G^*方法探讨了腺嘌呤(A)、 胸腺嘧啶(T)、 鸟嘌呤(G)、 胞嘧啶(C)及其碱基对(AT, GC)以及Zn²⁺复合物(AAA-Zn²⁺, AAT-Zn²⁺和GGC-Zn²⁺)对混合小分子H₂, N₂, CO₂的吸附情况, 系统研究了其相互作用模式及吸附强度, 预测了常见混合气体分子与碱基(对)及复合物的吸附位置. 研究表明, CO₂倾向于以氢键的形式结合到碱基(对)的氨基氢或亚氨基氢上, 而N₂和H₂分子则倾向于结合到这些碱基(对)的平面π电子上, 以堆垛的形式存在. 根据吸附强度大小, 预测了由这些碱基为骨架合成的金属有机骨架(MOF)吸附材料对小分子的选择性吸附顺序为H₂22. 研究表明, 以AT对结合金属Zn²⁺为节点的纯天然碱基对构成的MOF要比实验合成的AA碱基对与Zn²⁺结合的MOF具备更好的吸附和分离性能.     

Coarse-grained representation of beta-helical protein building blocks

A general strategy to develop coarse-grained models of beta-helical protein fragments is presented. The procedure has been applied to a building block formed by a two-turn repeat motif from E. coli galactoside acetyltransferase, which is able to provide a very stable self-assembled tubular nanoconstruct upon stacking of its replicas. For this purpose, first, we have developed a computational scheme to sample very efficiently the configurational space of the building block. This method, which is inspired by a strategy recently designed to study amorphous polymers and by an advanced Monte Carlo algorithm, provides a large ensemble of uncorrelated configurations at a very reasonable computational cost. The atomistic configurations provided by this method have been used to obtain a coarse-grained model that describes the amino acids with fewer particles than those required for full atomistic detail, i.e., two, three, or four depending on the chemical nature of the amino acid. Coarse-grained potentials have been developed considering the following types of interactions: (i) electrostatic and van der Waals interactions between residues i and i + n with n >/= 2; (ii) interactions between residues i and i + 1; and (c) intra-residue interactions. The reliability of the proposed model has been tested by comparing the atomistic and coarse-grained energies calculated for a large number of independent configurations of the beta-helical building block.     

Optimal neighbor selection in molecular similarity: comparison of arbitrary versus tailored prediction spaces

Three classes of arbitrary quantitative molecular similarity analysis (QMSA) methods have been computed using atom pairs (APs), topological indices (TIs), and principal components (PCs) derived from topological indices. Tailored QMSA models have been developed from TIs selected through ridge regression. K-nearest neighbor (kNN) based estimation has been applied to all of the methods to estimate normal vapor pressure (p(vap)) and water solubility (sol) for a set of 194 chemicals. Results show that the tailored QMSA methods are superior to arbitrary similarity methods in estimating both of these properties for the given set of chemicals.     

Quantitative molecular similarity analysis (QMSA) methods for property estimation: A comparison of property-based,arbitrary, and tailored similarity spaces

Three classes of arbitrary quantitative molecular similarity analysis (QMSA) methods have been computed using atom pairs, topological indices, and physicochemical properties. Tailored QMSA models have been developed using a selected number of TIs chosen by ridge regression. The methods have been applied to the K -nearest neighbor based estimation of log P of two sets of chemicals. Results show that the property-based and tailored QMSA methods are superior to the arbitrary similarity methods in estimating log P of both sets of chemicals     

Ab initio integrated multi-center molecular orbitals method for large cluster systems: total energy and normal vibration

A new computational scheme integrating multi-center ab initio molecular orbitals for determining total energy and normal vibration of large cluster systems is presented. This method can be used to treat large cluster systems such as solvents by quantum mechanics. The geometry parameters, the total energies, the relative energies, and the normal vibrations for four models of water cluster, the hydrated hydronium ion complex, and the transition state of proton transfer are calculated by the present method and are compared with those obtained by the full ab initio MO method. The results agree very well. The scheme proposed in this article is also intended to be used in modeling computer cluster systems using parallel algorithms.     

用定量结构性质关系预测表面活性剂的Krafft点

以空间、电子、热力学等方面的微观性质作为描述符,建立了阴离子表面活性剂Krafft点与微观结构参数之间的关系。这些描述符包括:辛醇/水分配系数LogP、分子能量Energy、最高占据轨道能量HOMO、分子体积V和偶极距Dipole-z等。通过阴离子表面活性剂的Krafft点和5个结构性质参数之间的关系式,可以预测和计算阴离子和其它离子型表面活性剂的Krafft点。