Ab initio conformational analysis of 1,3-propanedithiol

By carrying out Hartree-Fock full, symmetry unconstrained geometry optimizations on the 25 symmetrically unique staggered conformers, using the 4-31+G^* basis set it was found that, on the Hartree-Fock level, gTTg and gTTg′ are the lowest energy rotamers in 1,3-propanedithiol. We also found a number of clear conformational trends. Intramolecular hydrogen bonding was found to be of minor importance. The introduction of electron correlation yields a stabilization of the rotamers with one or two gauche SCCC arrangements relative to those with less gauche SCCC arrangements. Consistent with this, we find that on the MP2 level the most stable conformers are gGGg′ and gGGg.     

Conformational analysis of the antimalarial agent quinine

Quinine, an active antimalarial compound, is one of the most abundant constituents extracted from the bark ofCinchona trees. The activity differences among structurally related molecules appear to depend on the absolute stereochemistry of some functional groups, a result that has stimulated a detailed conformational analysis of these molecules of biological interest. In the present study the potential energy surface (PES) for the antimalarial agent quinine (C₂₀H₂₄O₂N₂) has been comprehensively investigated using the molecular mechanics (MM) and quantum mechanical semiem-pirical AM1 and PM3 methods. Six distinct minimum-energy structures are located on the multidimensional PES and also characterized as true minima through harmonic frequency analysis. The relative stabilities and thermodynamic properties are reported. The coexistence of different conformers is discussed for the first time in the literature based on the calculated transition-state (TS) structures connecting the six minima located on the PES for the quinine molecule. The theoretical results reported in the present study are in agreement with the experimental proposal, based on NMR data, that there are two possible forms for the quinine molecule in solution.     

WIZARD: AI in conformational analysis

Summary A program which utilizes the techniques of Artificial Intelligence and Expert Systems to solve problems in the area of Conformational Analysis is described. The program searches conformational space in a systematic fashion, based on the technique known as heuristic state-space search. The program proceeds by recognizingconformational units, assigning one or moreconformational templates to each unit, andjoining them to form conformational suggestions. These suggestions arecriticized to discover logical inconsistencies, and any resulting stresses areresolved. The resulting conformational suggestions are sometimes accurate enough for immediate use, or may be further refined by a numerical program. The latter combination is shown to be quite efficient compared to purely numerical conformational search techniques.     

Molecular mechanics-based conformational analysis of previtamin D and its A-ring analogues

Summary The ground-state conformational analysis of previtamin D and analogues with different substituents at C-3, C-1, and C-10 have been performed by force-field calculations. Differences in the photochemistry of these analogues are discussed in view of the concept of ground-state conformational control in photochemical reactions. The effect of complexes of previtamin D with silanol derivatives, formedvia hydrogen bonds, on their conformational equilibrium has been calculated. An increase in the population ofcZc conformers with increasing size of the silanol molecules (as a model for a heterogeneous silica surface) was observed.

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Konformationsanalyse von Previtamin D und seiner A-Ring-Analogen mit Hilfe von Kraftfeldrechnungen

Zusammenfassung Eine Konformationsanalyse des Grundzustandes von Previtamin D and von an C-1, C-3 und C-10 substituierten Analogen wurde mit Hilfe von Kraftfeldrechnungen durchgeführt. Unterschiedliches Reaktionsverhalten bei den photochemischen Umsetzungen dieser Verbindungen werden unter dem Gesichtspunkt der Grundzustandskontrolle von photochemischen Reaktionen diskutiert. Der Einfluß von Komplexbildung über Wasserstoffbrücken von Previtamin D mit Silanolen wurde berechnet. Eine Zunahme der Population dercZc-Konformeren mit zunehmender Größe des Silanols (ein Modell für eine heterogene Kieselgeloberfläche) wurde dabei beobachtet.

     

Comparative conformational analysis of peptide T analogs

A series of peptide T analogs were investigated within the molecular mechanics framework. In order to determine the role of the aminoacid residues in spatial formation of peptide T the conformational peculiarities of the glycine-substituted analogs were investigated. The conformational profiles of some biologically tested analogs of this peptide were determined independently. The received data permit to assess the active form of this peptide. It is characterized by β-turn at the C-terminal physiologically active pentapeptide fragment of peptide molecule. The received results are important for the investigation of the structure-activity relationship and may be used at design of a rigid-molecule drug against HIV.     

Synthesis and conformational investigation of tetrapeptide analogues of the fragment B23-B26 of insulin

Tetrapeptides containing one of a set of four different α,α-dialkyl glycines at the C-terminus were synthesized by conventional methods in solution and their conformational behavior investigated by ¹H NMR spectroscopy in connection with molecular mechanics calculations. The results were consistent with conformations stabilized by a γ-turn in the case of compounds with alkyl groups larger than methyl, while the corresponding Aib derivative did not exhibit intramolecular hydrogen bonding.     

Vibrational analysis of a rate-slowing conformational kinetic isotope effect

An enthalpy-entropy approach to analyzing a rate-slowing conformational kinetic isotope effect (CKIE) in a deuterated doubly-bridged biaryl system is described. The computed isotope effect (k_H/k_D?=?1.075, 368?K) agrees well with the measured value (k_H/k_D?=?1.06, 368?K). The rate-slowing (normal isotope effect) nature of the computed CKIE is shown to originate from a vibrational entropy contribution defined by the twenty lowest frequency normal modes in the ground state and transition state structures. This normal entropy contribution is offset by an inverse vibrational enthalpy contribution, which also arises from the twenty lowest frequency normal modes. Zero point vibrational energy contributions are found to be relatively small when all normal modes are considered. Analysis of the H_ZPE, H_vib, and S_vib energy terms arising from the low frequency vibrational modes reveals their signs and magnitudes are determined by larger vibrational energy differences in the labeled and unlabeled ground state structures.     

Automated conformational analysis: Algorithms for the efficient construction of low-energy conformations

Summary The method of constructing low-energy conformations using template joining can provide an efficient means of searching the conformational space of molecules. The simplest algorithm to perform this task would construct each potential conformation from scratch. However, new algorithms, some of which use techniques from Artificial Intelligence, have been developed which can greatly improve the efficiency of this approach.     

A comprehensive conformational analysis of tryptophan,its ionic and dimeric forms

Tryptophan is an essential amino acid, and understanding the conformational preferences of monomer and dimer is a subject of outstanding relevance in biological systems. An exhaustive first principles investigation of tryptophan ( W ) and its ionized counterparts cations (WC) , anions (WA) , and zwitterions (WZ) has been carried out. A comprehensive and systematic study of tryptophan dimer (WD) conformations resulted in about 62 distinct minima on the potential energy surface. The hydrogen bonds and a variety of noncovalent interactions such as OH‐π, NH‐π, CH‐π, CH‐O, and π‐π interactions stabilized different forms of tryptophan and its dimers. Over all in monomeric conformers which have NH‐O, hydrogen bonds showed higher stability than other conformers. A cursory analysis reveal that the most stable dimers stabilized by hydrogen bonding interactions while the less stable dimers showed aromatic side chain interactions. Protein Data Bank analysis of tryptophan dimers reveals that at a larger distance greater than 5 Å, T‐shaped orientations (CH‐π interactions) are more prevalent, while stacked orientations (π‐π interactions) are predominant at a smaller distance. © 2013 Wiley Periodicals, Inc.     

Novel erythromycin A 9-tritylhydrazone: selective 6-O-methylation and conformational analysis

The straightforward synthesis of the novel 9-tritylhydrazone erythromycin A and its highly regioselective O-methylation at C(6)-OH are described. Preliminary conformational data based on X-ray diffraction, ¹H NMR and molecular mechanics is also presented with the aim of understanding the observed high regioselectivity. The facile synthesis of 6,12-O-dimethylerythromycin A, a standard to assess clarithromycin purity in quality control processes, is reported as well.     

Crystallographic and conformational analysis of two novel trans-azo benzene compounds

The molecular and crystal structure of (E)-2-Acetyl-4-(2-bromophenyldiazenyl)phenol (1) and (E)-2-Methyl-4-(o-tolyldiazenyl)phenol (2) were characterized and determined by single crystal X-ray diffraction method besides spectroscopic means. The periodic organization of 1 is stabilized by C–H···O type weak H-bond and Br···O type weak halogen bonding and thus, a two dimensional puckered network is established almost parallel to () the plane. Molecules of 2 are linked into C(7) chains generated by translation along the [1 0 1] direction with the aid of O–H···N type H-bonds, and these chains are strengthened by C–H···π interactions involving o-tolylphenol ring. Quantum chemical studies at B3LYP/6-311 ++G(d,p) level reveal that potential barrier of the compounds around Ar–N torsions is of double minimum character unless it is defected by the presence of o-substituent groups in the vicinity of the azo bridge. The results from crystallographic and quantum chemical studies suggest that azo benzene compounds may adapt non-planar geometry apart from the most stable planar conformation, which is located on the secondary minima of double potential barrier regarding rotational motion around Ar–N bonds.     

卤代苯和苯酚衍生物的位电荷密度能和1og Kow与-lg LC50的QSAR研究

以简易的量子化学方法计算了二十多种卤代苯和苯酚衍生物的FMO位电荷密度能,并进行定量结构-活性相关(quantiktive struvyitr biodegradability)研究,获得满意的结果.最后从生物酶促反应本质、污染物-生物酶的轨道控制反应角度对QSAR提出新的解释.     

Molecular structure and conformational analysis of chiral alcohols. Application to the enantioselectivity study of lipases

The molecular structures of the chiral compounds 1-phenylethanol, 2-hexanol and 1-phenylethanol acetate have been studied theoretically by ab initio methods. Conformational analysis and electronic structure studies have been carried out with these molecules at STO-3G^* and 6-31G^* basis sets. For the study of the interaction of lipases with substrates, a simplified model of the tetrahedral intermediate has been calculated at the 6-31G^*//4-31G^* level. Molecular mechanics simulations of the interaction of these compounds with the lipases of Candida rugosa, Pseudomonas cepacia and Rhizomucor miehei have been used to study the enantioselectivity of these lipases in the transesterification reaction of the chiral alcohols. The theoretical results have been compared with experimental data and good agreement was observed. It can be concluded that the enantioselectivity of these lipases is controlled by the formation of a tetrahedral intermediate, whereas Michaelis complex formation has a much lower significance.     

基于分子指纹对黄酮类化合物及其抗DPPH自由基活性的QSAR分析

应用定量构效关系（Quantitative structure activity relationship, QSAR）研究阐明黄酮类化合物（Flavonoid compounds, FCs）的子结构指纹（Substructure fingerprint）与1,1-二苯基-2-三硝基苯肼（1,1-Diphenyl-2-picrylhydrazyl, DPPH）自由基清除能力之间的关系,从而指导高效抗氧化物质的设计和发现。在PubMed数据库中收集77个具有明确抗氧化活性的黄酮类化合物,而在ChEMBL数据库中收集86个无抗DPPH活性的黄酮类化合物。这163个黄酮类化合物的子结构指纹由PubChem系统生成,然后通过卡方检验筛选出与黄酮类化合物的抗氧化活性显著相关的分子指纹,最后通过判别分析建立预测QSAR模型,并采用回代法和交叉验证法对已建立的模型进行准确性和稳健性的验证。结果表明,黄酮类化合物抗DPPH自由基活性与ESSSR环的计数、简单相邻原子的类型和简单的SMARTS模式等因素有关。此外,所建立的QSAR模型能较好地预测黄酮类化合物的DPPH自由基清除活性,可用于评价候选抗氧化剂的潜力。     

Constitutional,configurational and conformational analysis of transition metal coordination complexes

Summary A computational approach to conformational analysis is applied to the study of transition metal coordination complexes. The method provides a means of rapidly exploring conformational space without any inherent reliance on energy calculations and is therefore applicable to a wide variety of systems. It has been incorporated into an algorithm which explores the constitutional, configurational and conformational degrees of freedom for a metal ion and a number of potential ligands. The program determines which of the possible coordination complex products could form stable conformations and can therefore be used to rationalise the products obtained from the mixture. The method is illustrated using two cases: the cobalt(III)-triethylenetetramine-glycine system and complexes of diindolopyridine derivatives.Abbreviations en ethylenediamine - trien triethylenetetramine - gly glycine - RMS root mean square - 3D three dimensional     

A QSAR of the toxicity of amino-benzenes and their structures

The quantum chemical parameters and the topological indices have been calculated for the prediction of the toxicity of amino-benzenes in the environment, and work has been done on the multiple regression and neural networks. The combination of CoMFA with formation heat yields greatly improved results. A good model has been obtained which provides a basis for the studies of the toxic action mechanism.