QSAR modeling of large heterogeneous sets of molecules

In aquatic toxicology, QSAR models are generally designed for chemicals presenting the same mode of toxic action. Their proper use provides good simulation results. Problems arise when the mechanism of toxicity of a chemical is not clearly identified. Indeed, in that case, the inappropriate application of a specific QSAR model can lead to a dramatic error in the toxicity estimation. With the advent of powerful computers and easy access to them, and the introduction of soft modeling and artificial intelligence in SAR and QSAR, radically different models, designed from large noncongeneric sets of chemicals have been proposed. Some of these new QSAR models are reviewed and their originality, advantages, and limitations are stressed.     

Computer-aided molecular modeling and design of DNA-inserting molecules

Summary Intercalators are molecules capable of sliding between base pairs without disturbing the overall stacking pattern. In addition, there may exist molecules capable of inserting into a base pair thereby disrupting the hydrogen bonds and replacing them with new hydrogen bonds. A molecule probably capable of inserting, i.e., an insertor, is the diketopiperazine cyclo-[Gly-Gly] (1). A barbiturate (2), alloxan (3), a pyrimidine derivative (4) and a hydantoin (5) were also studied as possible insertors. Furthermore, molecules such as ethyleneurea (6), succinimide (7), as well as a malonamide derivative (8) and oxamide derivatives (9–11) were studied in order to investigate the arrangement and the number of hydrogen bonds necessary for insertion. Molecules 12–14 were designed and studied for their capacity to act as bisinsertors and/or bisintercalators. These molecules feature two diketopiperazine moieties which are connected via a diphenyl(thio)ether, i.e., 12 and 13, or a bisphenol A spacer, i.e., 14. The latter molecule (14) seems a promising candidate as a bisinsertor.     

Covalent interaction and semiempirical modeling of small molecules

The use of sophisticated methods for modeling complex systems is gaining ever more importance recently because they allow the design of material with properties tailored to specific applications. However, problems may arise from conflicts between different reaction pathways inherent in the wide variety of chemical elements used. This is reflected by the impossibility of exactly solving the Schroedinger equation or of exactly describing the exchange interaction in density functional theory when the system complexity increases. An alternative is offered by the application of semiempirical methods because they strongly reduce system complexity. Normally, this is accomplished by increasing the degree of the approximations to the detriment of the formalism generality. This work is aimed to improve the semiempirical electronegativity equalization method. This is accomplished by modifying the point charge Madelung potential with the introduction of covalent interaction to better describe the chemical bonds.     

Macromodel—an integrated software system for modeling organic and bioorganic molecules using molecular mechanics

An integrated molecular modeling system for designing and studying organic and bioorganic molecules and their molecular complexes using molecular mechanics is described. The graphically controlled, atom-based system allows the construction, display and manipulation of molecules and complexes having as many as 10,000 atoms and provides interactive, state-of-the-art molecular mechanics on any subset of up to 1,000 atoms. The system semiautomates the graphical construction and analysis of complex structures ranging from polycyclic organic molecules to biopolymers to mixed molecular complexes. We have placed emphasis on providing effective searches of conformational space by a number of different methods and on highly optimized molecular mechanics energy calculations using widely used force fields which are supplied as external files. Little experience is required to operate the system effectively and even novices can use it to carry out sophisticated modeling operations. The software has been designed to run on Digital Equipment Corporation VAX computers interfaced to a variety of graphics devices ranging from inexpensive monochrome terminals to the sophisticated graphics displays of the Evans & Sutherland PS300 series.     

Hydrodynamic modeling of diffusion tensor properties of flexible molecules

We present a computationally efficient implementation of hydrodynamic modeling for the evaluation of diffusion tensors of molecules with internal degrees of freedom, adapted to take into account information from linear scaling computations of solvent accessible surfaces implemented in the framework of last generation continuum solvent models. Torsional angles are taken also explicitly into account, while retaining correct hydrodynamic interactions. A comparison with literature data is presented to prove the effectiveness of the approach for a wide range of molecular dimensions and solvent environments.     

Characterization of cellulose molecules in bio-system studied by modeling methods

Cellulose chains in bio-system were examined. A model system, in which molecular chains were fixed at one end in an aqueous environment, was analyzed as a model bio-system of cellulose. Five cellulose chains (DP = 40), whose one end was fixed (like a cantilever), were placed in 20.0 × 2.8 × 2.8 nm³ cell which was filled up with water molecules. This model cell was thoroughly annealed and then piled up three-dimensionally. The molecular dynamics simulation was applied to this model system at room temperature (298 K) with time step of 1.0 femto-second in AMBER force field with parameter sets for carbohydrates. The molecular motion of cellulose chains in cantilever condition was found to be more moderate compared with case of free chains. The water molecules around the cellulose chains were interrupted directly forming hydrogen bondings among the cellulose chains. This result suggests that degree of crystallinity of cellulose in bio-system is low. The result also reminds us that the cellulose chains are originally able to hold water molecules giving them a gel property, although dried cellulose is not soluble in water. Conformational and Packing Analysis of Polysaccharides, Part 4. Presented at 22nd International Carbohydrate Symposium, July 23–27, 2004.     

Molecular modeling of phosphonate molecules onto barium sulfate terraced surfaces

The adsorption of phosphonate molecules onto mineral surfaces is of interest due to their use as scale inhibitors. Molecular modeling is an important tool that can aid the fundamental understanding of how these inhibitors operate. This paper presents an empirical molecular mechanics study of the adsorption of a series of straight chain phosphonate molecules onto barium sulfate. It has been found that inhibition can be predicted for this straight chain series of molecules, which differ by the number of phosphonate groups present as well as by the chain length. Even more importantly, the modeling results can predict which faces will be preferred, and this has been verified by scanning and transmission electron microscopy on the resultant barite particles. It has been found that, in general, lattice matching results in the lowest replacement energy for all of the organic molecules investigated. The agreement between the experiment and the model confirms that the dominant mechanism of interaction for the additives on barium sulfate is via the deprotonated phosphonate groups with the barium ions on the surface.     

Synthesis of heterocycles using amphoteric molecules

Amphoteric molecules contain functional groups that are normally regarded as incompatible. We have shown that reagents of this class, particularly unprotected aziridine aldehydes and alpha-boryl aldehydes, enable rapid synthesis of complex heterocycles and facilitate the development of new synthetic processes that are characterized by high bond-forming efficiency.     

Side Chain Functionalization of Lanosterol by Hydroboration and Allylboration: Synthesis of a Ganoderic Acid Analog

A convenient method for the introduction of 23-keto and 26-carboxyl groups (Synthesis of a genoderic acid analog) into lanosterol side chain by use of hydroboration and allylboration as key reactions is described.     

Chain length effects in the second virial coefficient of linear polymer molecules

A generalized perturbation theory is presented for the second virial coefficient of linear and branched polymer systems. Results have been computed for linear chains having two to five hundred statistical segments. These are found to differ significantly from the long-chain asymptotic results of Zimm. A semi-empirical modification of the Flory--Orofino theory is also suggested.     

Hybrid classical quantum force field for modeling very large molecules

A coherent computational scheme on a very large molecule in which the subsystem that undergoes the most important electronic changes is treated by a semiempirical quantum chemical method, though the rest of the molecule is described by a classical force field, has been proposed recently. The continuity between the two subsystems is obtained by a strictly localized bond orbital, which is assumed to have transferable properties determined on model molecules. The computation of the forces acting on the atoms is now operating, giving rise to a hybrid classical quantum force field (CQFF ) which allows full energy minimization and modeling chemical changes in large biomolecules. As an illustrative example, we study the short hydrogen bonds and the proton-exchange process in the histidine-aspartic acid system of the catalytic triad of human neutrophil elastase. The CQFF approach reproduces the crystallographic data quite well, in opposition to a classical force field. The method also offers the possibility of switching off the electrostatic interaction between the quantum and the classical subsystems, allowing us to analyze the various components of the perturbation exerted by the macromolecule in the reactive part. Molecular dynamics confirm a fast proton exchange between the three possible energy wells. The method appears to be quite powerful and applicable to other cases of chemical interest such as surface reactivity of nonmetallic solids. © 1996 John Wiley & Sons, Inc.     

部分水解聚丙烯酰胺与蠕虫状胶束在微米级毛细管中的驱替粘度

部分水解聚丙烯酰胺(HPAMs)被大量地用作三次采油中驱替液的增稠剂,表面活性剂在一定的条件下可以通过自组装形成蠕虫状胶束,具有与高分子相似的增稠的作用。本文在半径为1–10 μm的毛细管中,分别考察了HPAMs与蠕虫状胶束的微观驱替行为,研究结果表示毛细管内腔的尺寸限制了这些非牛顿流体的增稠作用。随着毛细管半径的减小,聚合物溶液的剪切变稀越剧烈,甚至从非牛顿流体转变为牛顿流体的流体行为。结合驱替研究和超滤、电镜的结果,证明了高分子的缠绕结构在毛细管中已被破坏。通过对比驱替数据,蠕虫状胶束在毛细管中能够更大程度地保留宏观的粘度,我们提出表面活性剂能够通过自组装修复被破坏的缠绕结构,比高分子聚合物在微观有限空间中有更好的增稠能力。     

Bola反离子诱导的高粘弹十六烷基硫酸钠蠕虫胶束溶液

利用稳态和频率扫描研究了十六烷基硫酸钠(SHS)与Bola盐(N,N’-双乙基二甲基-α,ω-乙烷溴化铵(Bola2Et)或N,N’-三甲基-α,ω-丁烷溴化铵(Bola4))混合体系的流变行为.实验结果表明两个体系均在45℃时形成了长蠕虫胶束,溶液呈现出高粘弹性,尤其是SHS/Bola2Et溶液表现出很高的弹性,零剪接粘度高达2520Pa’s,表观上呈现胶状.这些结果归因于在Bola反离子诱导下,表面活性剂SHS与Bola反离子形成了静电吸引的2:1结构复合物.由于这两个Bola反离子的联接链长度均短于季铵离子的静电平衡距离,因此形成的复合物在形状上有利于蠕虫胶束生成.作为对比,添加简单的四甲基铵反离子无法诱导SHS形成蠕虫胶束,溶液仅呈现低粘度.     

Surface modification of ZnO using triethoxysilane-based molecules

Zinc oxide (ZnO) is an important material for hybrid inorganic-organic devices in which the characteristics of the interface can dominate both the structural and electronic properties of the system. These characteristics can be modified through chemical functionalization of the ZnO surface. One of the possible strategies involves covalent bonding of the modifier using silane chemistry. Whereas a significant body of work has been published regarding silane attachments to glass and SiO2, there is less information about the efficacy of this method for controlling the surface of metal oxides. Here we report our investigation of molecular layers attached to polycrystalline ZnO through silane bonding, controlled by an amine catalyst. The catalyst enables us to use triethoxysilane precursors and thereby avoid undesirable multilayer formation. The polycrystalline surface is a practical material, grown by sol-gel processing, that is under active exploration for device applications. Our study included terminations with alkyl and phenyl groups. We used water contact angles, infrared spectroscopy, and X-ray photoemission spectroscopy to evaluate the modified surfaces. Alkyltriethoxysilane functionalization of ZnO produced molecular layers with submonolayer coverage and evidence of disorder. Nevertheless, a very stable hydrophobic surface with contact angles approaching 106 degrees resulted. Phenyltriethoxysilane was found to deposit in a similar manner. The resulting surface, however, exhibited significantly different wetting as a result of the nature of the end group. Molecular layers of this type, with a variety of surface terminations that use the same molecular attachment scheme, should enable interface engineering that optimizes the chemical selectivity of ZnO biosensors or the charge-transfer properties of ZnO-polymer interfaces found in oxide-organic electronics.     

Preparation of donor-sigma-acceptor molecules using arene-ruthenium chemistry

Several donor-sigma acceptor (D-sigma-A) molecules with thioalkyl side chains have been prepared by ruthenium-activated nucleophilic aromatic substition (S(N)Ar) reactions. Selective substitution of chloride from cyclopentadienyl(1,4-dichlorobenzene)ruthenium by using piperazine derivatives as nucleophiles is addressed. This selectivity, in combination with further manipulation of the complexes, allows the preparation of unsymmetrically functionalized tetraalkyl-p-phenylenediamine (TAPD) units which are difficult to synthesize by traditional organic S(N)Ar conditions. Phenanthroline-assisted decomplexation of the product arene-RuCp systems under UV irradiation is described.     

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.