Mass connectivity index,a new molecular parameter for the estimation of ionic liquid properties

A new concept named mass connectivity index (MCI) to encode bond contributions and to allow quantifying the extent of branching in a molecule, especially of ionic liquids, is proposed. The concept is based on the molecular connectivity concept first introduced by Randic in 1975 and modified in different forms by several authors. The proposed concept is much easier to calculate than any of the connectivity indexes available in the literature. Thus the only data required for determining the MCI are the groups forming the molecule and the mass of the groups. The groups forming the molecule are defined as commonly done in group contribution methods. The index is used as a variable in generalized correlations to accurately estimate the density and the heat capacity of ionic liquids.     

Molecular alignment as a penalized permutation Procrustes problem

Molecular alignment is viewed as a permutation Procrustes problem, where the goal is to find the best assignment of points (or functional groups) in one molecule to the points in another molecule. A penalty function ensures that the optimal alignment respects the underlying connectivity between atoms/points. This method helps reveal why molecular alignment suffers from the curse of dimension.     

Rotational viscosity of fluids composed of linear molecules: an equilibrium molecular dynamics study

In this paper, we investigate the rotational viscosity for a chlorine fluid and for a fluid composed of small linear molecules by using equilibrium molecular dynamics simulations. The rotational viscosity is calculated over a large range of state points. It is found that the rotational viscosity is almost independent of temperature in the range studied here but exhibits a power-law dependency on density. The rotational viscosity also shows a power-law relationship with the molecular length, and the ratio between the shear and rotational viscosities approaches 0.5 for the longest molecule studied here. By changing the number of atoms or united atomic units per molecule and by keeping the molecule length fixed, we show that fluids composed of molecules which have a rodlike shape have a lower rotational viscosity. We argue that this phenomenon is due to the reduction in intermolecular connectivity, which leads to larger fluctuations around the values possessed by the fluid on average. The conclusions here can be extended to fluids composed of uniaxial molecules of arbitrary length.     

Putting molecular similarity into context: asymmetric indices for field-based similarity measures

Some of the most widely used indices in molecular similarity searching are intrinsically symmetric in nature, meaning that each molecule under comparison contributes equally to the similarity index. For example, the Carbó and the Hodgkin–Richards similarity indices are respectively, related to the geometric and arithmetic averages of the molecular self-similarities. This work introduces the asymmetric forms of an entire family of field-based molecular similarity indices. By incorporating a weighted contribution of each molecule into the similarity index, the newly obtained asymmetric forms allow for measuring and modulating the similarity of one molecule in the context of another and thus have the potential of alleviating the size dependency often observed in chemical similarity searching     

抗流感病毒抑制剂Nucleozin衍生物的设计合成及抗病毒活性评价

小分子化合物Nucleozin作为靶向流感病毒核蛋白的抑制剂具有良好的抑制活性。本文围绕Nucleozin分子中与哌嗪环直接相连的芳环部分进行研究。通过钯催化偶联反应合成了一系列Nucleozin衍生物,通过检测所合成化合物对流感病毒H1N1的抑制活性,明确了Nucleozin分子中该部分的构效关系。利用甲基在药物分子设计中的作用,设计将分子中的氯原子替换为甲基,发现与原型分子Nucleozin相比其抑制活性有了明显的提高。本文的结果对该类分子成药性的提高具有积极意义。     

Retrosynthetic fragmentation in the fast atom bombardment mass spectra of eserine and some related compounds

The positive-ion fast atom bombardment (FAB) mass spectra of eserine and some carbamate analogues were recorded and showed a partially different fragmentation process, with respect to that of the corresponding chemical ionization (Cl) fragmentation. This unexpected behaviour could be explained by taking into account the known solution chemical behaviour of the protonated species, and assigning to the molecular species observed under FAB a different–yet related–molecular connectivity. This may be considered as evidence that the sputtered species under FAB closely reflect the chemical behaviour of the analysed molecule in the solution environment.     

QSBR Study on the Anaerobic Biodegradation of Chlorophenols

1 INTRODUCTION Chlorophenols (CPs) have been widely applied in such industries[1] as wood preservative, antitrust, bactericide and herbicide since 1930s. Due to the existence of phenol ring structure and chloro-atom, chlorophenols have strong toxicity and high anti- degradation ability. Previous reports show that[2, 3] chlorophenols are difficult to oxidize under aerobic condition, whereas anaerobic biological treatment can effectively reduce the toxicity towards microor- ganism so as to …     

Neutral,Cationic, and Anionic Alkyl Derivatives of Tungsten Bonded to a Calix[4]arene Oxo Surface

The chemically reversible reduction of [(Me)₂W(calix)] to the diamagnetic [(Me)₂W(calix)Na₂] [Eq. (1)], without major changes in the connectivity of the molecule, illustrates the flexibility of the calixarene ligand and stresses its potential as a molecular functional model of heterogeneous oxo surfaces.     

Algorithmically compressed data and the topological conjecture for the inner-core electrons

Eight different properties of three classes of compounds, metal halides, halomethanes, and chlorofluorocarbons, have been modeled with the aim to check the validity of the odd complete graph conjecture suggested for encoding the contribution of the inner-core electrons to the molecular connectivity indices. Modeling using this conjecture is compared with modeling using connectivity indices derived by other well-known algorithms. The conjecture of odd complete graph for the inner-core electrons achieves to improve the modeling quality of the molecular connectivity indices and/or of the molecular connectivity terms. The importance of the recently introduced dual molecular connectivity indices and pseudoindices in further refining the modeling quality of the higher-order terms has also been stressed.     

A general approach for atom-type assignment and the interconversion of molecular structure files

In molecular modeling projects which require use of several different computer programs, one encounters problems in sharing data between programs. One difficult problem is the conversion of atom types from one program's definition to another. A second problem is the conversion of a polymer, such as a protein or polynucleotide molecule, from a “general” program, which understands molecules as a collection of atoms, to a “polymer” program, which understands molecules as a collection of molecular fragments stored in some library. We describe here a new method by which atom types are deduced from the environment of each atom. We use the Daylight Chemical Information Systems library of programs to deduce the atom types based only on the atomic symbol, connectivity and formal charge of each atom in the molecule. We also describe a method by which the polypeptide nature and sequence of a molecule can be deduced from minimal information about the atoms in the molecule. We have written a computer program which demonstrates this method. This program deduces atom types for AMBER, GRIN/GRID, CHARMm, and ALOGP. It will also produce input files for the AMBER/PREP fragment library preparation program.     

An improved molecular connectivity index

Through modification of the delta values of the molecular connectivity indexes, and connecting the quantum chemistry with topology method effectively, the molecular connectivity indexes are converted into quantum-topology indexes. The modified indexes not only keep all information obtained from the original molecular connectivity method but also have their own virtue in application, and at the same time make up some disadvantages of the quantum and molecular connectivity methods.     

基于DFT和分子连接性指数方法研究醇类化合物的水溶解度和分配系数

将DFT方法计算得到的量化参数和分子连接性指数联合应用到60个醇类化合物的溶解度和辛醇/水分配系数的QSPR研究中,分别通过逐步回归得到具有显著统计意义的4个参数和5个参数的QSPR方程.以此4个参数和5个参数分别作为输入参数,采用BPNN,RBFNN方法建立了QSPR预测模型,使用Latin-partition交叉验证方法评价模型的预测能力.BPNN,RBFNN模型对溶解度预测的相关系数分别为0.993和0.994,而对辛醇/水分配系数预测的相关系数分别0.990和0.997,结果令人满意.     

A cellular automata model of bond interactions among molecules

The ten types of alkane bonds have been modeled as isolated fragments using cellular automata dynamics. The rules governing the states and the trajectories of the cells simulating the bonds are derived from the bimolecular interaction accessibilites recently described. The sum of cell encounters at unit iteration (time) becomes a parameter associated with the relationship of a molecule with its neighbors. This value is found to correlate very closely with the boiling points of alkanes, pentanes through octanes. The results reinforce the concept that the molecular connectivity indices are describing the interaction possibilities among alkanes. The study introduces a new way of simulating intermolecular bond encounter dynamics among many molecules.     

Overall connectivities/topological complexities: a new powerful tool for QSPR/QSAR

Earlier attempts to assess the complexity of molecules are analyzed and summarized in a number of definitions of general and topological complexity. A concept which specifies topological complexity as overall connectivity, and generalizes the idea of molecular connectivities of Randic, Kier, and Hall, is presented. Two overall connectivity indices, TC and TC1, are defined as the connectivity (the sum of the vertex degrees) of all connected subgraphs in the molecular graph. The contributions to TC and TC1, which originate from all subgraphs having the same number of edges e, form two sets of eth-order overall connectivities, eTC and eTC1. The total number of subgraphs K is also analyzed as a complexity measure, and the vector of its eth-order components, eK, is examined as well. The TC, TC1, and K indices match very well the increase in molecular complexity with the increase in the number of atoms and, at a constant number of atoms, with the increased degree of branching and cyclicity of the molecular skeleton, as well as with the multiplicity of bonds and the presence of heteroatoms. The potential of the three sets of eth-order complexities for applications to QSPR was tested by the modeling of 10 alkane properties (boiling point, critical temperature, critical pressure, critical volume, molar volume, molecular refraction, heat of formation, heat of vaporization, heat of atomization, and surface tension), in parallel with Kier and Hall's molecular connectivity indices (k)chi. The topological complexity indices were shown to outperform molecular connectivity indices in 44 out of the 50 pairs of models compared, including all models with four and five parameters.     

Method and algorithm of obtaining the molecular intrinsic characteristic contours (MICCs) of organic molecules

The molecular intrinsic characteristic contour (MICC) is defined as the set of all the classical turning points of electron movement in a molecule. Studies on the MICCs of some medium organic molecules, such as dimethylether, acetone, and some homologues of alkanes, alkenes, and alkynes, as well as the electron density distributions on the MICCs, are shown for the first time. Results show that the MICC is an intrinsic approach to shape and size of a molecule. Unlike the van der Waals hard-sphere model, the MICC is a smooth contour, and it has a clear physical meaning. Detailed investigations on the cross-sections of MICCs have provided a kind of important information about atomic size changing in the process of forming molecules. Studies on electron density distribution on the MICC not only provide a new insight into molecular shape, but also show that the electron density distribution on the boundary surface relates closely with molecular properties and reactivities. For the homologues of alkanes, Rout(H), Dmin, and Dmax (the minimum and maximum of electron density on the MICC), all have very good linear relationships with minus of the molecular ionization potential. This work may serve as a basis for exploring a new reactivity indicator of chemical reactions and for studying molecular shape properties of large organic and biological molecules.     

醇类化合物气相色谱保留指数的分子拓扑研究

分子中原子i的特征值(ti)定义为tj＝1 ∑hi。并计算了醇类化合物的氢连接性指数，藉助多元线性回归技术分别建立了25个醇类化合物的指数与这些物质的气相色谱保留指数的定量结构／性质相关关系模型。模型具有良好的稳定性和预测能力，氢连接性指数能较好地反映化合物的结构特征。