Conformational study of halogen- and hydrogen-substituted polythionylphosphazenes using density functional theory method

The structure and conformational stability of polythionylphosphazenes is investigated by modeling single polymer chains with small mimics. The model compounds are composed of repeat units of the corresponding polythionylphosphazenes. Two of the model compounds have hydrogens and two have chlorines as substituents on phosphorus atoms. The substituents on sulfur may be either fluorine or chlorine. Fully geometry-optimized structures and energies of the stable conformations involving rotations around the P? N bond near the sulfur are obtained using the density functional theory method. The structural and conformational analyses indicate that the rotation around the N? P bond leads to variations in the bond lengths, the SNP bond angle openings, as well as couplings between dihedral angles in different conformations in all model compounds. In addition, the conformational analysis suggests that the minima on the conformational potential energy surface in these compounds may be located in the vicinity of the following values of the NP? NS dihedral angle: -50°, 90° (or 60°), 180°, and 240°. It was found that the values of the conformational energy differences range between less than 1 to 5 kcal/mol. A comparison is made between the structural results obtained using the density functional theory and the ab initio molecular orbital theory for the global minimum structures. © 1995 John Wiley & Sons, Inc.     

Spannungsenergie und konformation sterisch gehinderter olefine berechnungen von überbrückten derivaten des tetra-tert-butylethylens

Strain energy relaxation by in plane bending is not eflective in tetra-tert-butylethyethylene 1 because of the repulsions between geminal tert-butyl groups. When rings are closed between the geminal tert-butyl groups, the repulsions across the double bond are relieved. The strain energies and conformations of such molecules have been evaluated by empirical force field calculations (molecular mechanics) A close correlation is found between ring size and strain energy: strain increases stepwise with ringsize. In the most stable conformations, the methyl groups adopt a “staggered” arrangement across the double bond. In compounds containing a six-membered ring this can be achieved only in (strongly preferred) twist-boat conformations. The double bond in such molecules is nearly planar when the rings are smaller than 6-membered, but exhibits a torsion of up to 16.5° when 6-membered rings are present.     

Homolytic C-H and N-H bond dissociation energies of strained organic compounds

High-level computations at G3, CBS-Q, and G3B3 levels were conducted, and good-quality C-H and N-H bond dissociation energies (BDEs) were obtained for a variety of saturated and unsaturated strained hydrocarbons and amines for the first time. From detailed NBO analyses, we found that the C-H BDEs of hydrocarbons are determined mainly by the hybridization of the parent compound, the hybridization of the radical, and the extent of spin delocalization of the radical. The ring strain has a significant effect on the C-H BDE because it forces the parent compound and radical to adopt certain undesirable hybridization. A structure-activity relationship equation (i.e., BDE (C-H) = 61.1-227.8 (p(parent)% - 0.75)(2) + 152.9 (p(radical)% - 1.00)(2) + 40.4 spin) was established, and it can predict the C-H BDEs of a variety of saturated and unsaturated strained hydrocarbons fairly well. For the C-H BDEs associated with the bridgehead carbons of the highly rigid strained compounds, we found that the strength of the C-H bond can also be predicted from the H-C-C bond angles of the bridgehead carbon. Finally, we found that N-H BDEs show less dependence on the ring strain than C-H BDEs.     

Preparation of strained axially chiral (1,5)naphthalenophanes by photo-dehydro-Diels-Alder reaction

The preparation of 10 (1,5)naphthalenophanes (10a-j) by photo-dehydro-Diels-Alder (PDDA) reaction is described. Owing to hindered rotation around the biaryl axis, compounds 10 are axially chiral and the separation of enantiomers by chiral HPLC was demonstrated in three cases (10a,b,e). The absolute configuration of the isolated enantiomers could be unambiguously determined by comparison of calculated and measured circular dichroism (CD) spectra. Furthermore, we analyzed ring strain phenomena of (1,5)naphthalenophanes 10. Depending on the length of the linker units, one can distinguish three classes of naphthalenophanes. Compounds 10a-c are highly strained (E(STR) = 7-31 kcal/mol), and the strain is caused by small bond angles in the linker unit and deformation of the naphthalene moiety. Another type of strain is observed if the linker unit becomes relatively long (10g,h) originating from transannular interactions and is comparable with the well-known strain of medium sized rings. The naphthalenophanes 10d-f with a linker length of 10-14 atoms are only marginally strained. To clearly discriminate the different sources of strain, we defined two geometrical parameters (average central dihedral angle δ(C) and naphthalene thickness D(N)) and demonstrated that they are well-suited to indicate naphthalene deformation of our naphthalenophanes 10 as well as of ten model naphthalenophanes (I-X) with different linker lengths and linking positions.     

Phase transitions in the crystals of L- and DL-cysteine on cooling: intermolecular hydrogen bonds distortions and the side-chain motions of thiol-groups. 1. L-cysteine

The role of the distortion of the hydrogen bond network and of the motions of the -CH 2SH side chains in the phase transition in the orthorhombic L-cysteine ( (+)NH 3-CH(CH 2SH)-COO (-)) on cooling and the reverse transformation on heating is discussed. The extended character of the phase transition, which was recently discovered by adiabatic calorimetry [ J. Phys. Chem. B 2007, 111, 9186 ], and its very high sensitivity to the thermal prehistory of the sample could be interpreted based on the changes in the polarized Raman spectra measured for the single-crystals in several orientations in the temperature range 3-300 K and precise diffraction data on the changes in intramolecular conformations and intermolecular hydrogen bonding. In the low-temperature phase the SH...S hydrogen bonds dominate as compared to the weaker SH...O contacts, and at ambient temperature the situation is inverse. The transition from one phase to another goes via a series of states differing in conformations of the cysteine zwitterions and the intermolecular contacts of the thiol-group. Motions of different molecular fragments (NH 3 (+), CH 2, CH, SH) are activated at different temperatures. Structural strain on cooling involves several dynamic processes, such as a rigid rotation of the molecule in the lattice, a rigid rotation of the NH 3 group with respect to NH 3-CH bond, and the rotation of the thiol side chain resulting in the switching of S-H hydrogen bonding from one type to another. Different NH...O hydrogen bonds forming the framework in the L-cysteine crystal structure are distorted to a different extent, and this provokes the rotation of the -CH 2SH side chains within the cavities of this framework resulting in a change in the coordination from SH...O to SH...S at low temperatures. The results are interesting for understanding the polymorphism of molecular crystals and the factors determining their dynamics and structural instability, and also for biophysical chemistry, since the properties of the hydrogen bonded thiole-groups in biomolecules can be mimicked using L-cysteine in the crystalline state, variations in temperature and pressure serving as powerful tools, to modify the intramolecular conformations and the intermolecular hydrogen bonding.     

Towards an Understanding of the Carbon-Carbon Bond

In this essay, the classical question of “the influence of the number and kind of substituents on the strength of the C? C bond”, is pursued with the modern tools of contemporary physical organic chemistry. Based on the work of Karl Ziegler, the products and kinetics of thermolysis of a large number of highly branched aliphatic hydrocarbons and phenyl- or cyano-substituted derivatives were investigated. For each class of compounds, a linear relationship was found between the free enthalpy of activation of the homolytic cleavage of the weakest C? C bond and the strain energy in the ground state. These relationships permitted a quantitative separation of steric and electronic effects on the cleavage of C? C bonds. The influence of the size of the substituent groups on bond angles, bond lengths, and the conformational behavior of model compounds was studied by means of experimental structure determinations and force field calculations. C? C bond lengths up to 164 pm, bond angles at tetracoordinate carbon as large as 126°, and unusual eclipsed and gauche preferred conformations were found.     

Monte Carlo Simulation of Uniaxial Deformation of Polyethylene‐Like Polymer Glass: Role of Constraints and Deformation Protocol

The deformation of a glassy amorphous polymer has been simulated by Monte Carlo. A molecular model with constrained chemical bonds (rigid‐bond model) and one with chemical bonds represented by Gaussian springs (flexible‐bond model) have been compared. Furthermore, two different deformation protocols have been tested. Comparisons on the basis of stress–strain behavior, contributions of various interactions to stress and energy, evolution of density and distribution of dihedral angles, and of pair correlation functions show that both the introduction of constrained bonds and the deformation protocol influence the results dramatically. The results obtained using the flexible‐bond model, employing a deformation protocol in which all the monomers are displaced affinely with the box size, show the best agreement with experimental facts.

     

A stable silicon congener of highly strained bicyclo[3.2.0]hepta-1,3,6-triene

A silicon-containing fused bicyclic compound with a highly strained bridgehead double bond, 2,3,6,7-tetra-tert-butyl-4-(tert-butyldimethylsilyl)-5-(tert-butyldimethylsiloxy)-5-silabicyclo[3.2.0]hepta-1,3,6-triene (2), was synthesized quantitatively by the reaction of 1,2-bis-tert-butyl-4,4-bis(tert-butyldimethylsilyl)-4-silatriafulvene (3) with di-tert-butylcyclopropenone (4) at 80 degrees C. An X-ray crystallographic analysis for 2 not only confirmed a bicyclic structure having a silacyclopentadiene (silole) ring fused with a silacyclobutene ring but also the remarkable deformation around the double bonds; the sum of the bond angles around the unsaturated bridgehead carbon was 333 degrees . The strain energy of a model 5-silabicyclo[3.2.0]hepta-1,3,6-triene was calculated at the MP2/6-31+G(d,p)//B3LYP/6-31+G(d) level (30.2 kcal/mol) to be comparable to that for parent bicyclo[3.2.0]hepta-1,3,6-triene (30.7 kcal/mol). Despite the high steric strain, 2 was stable enough to be kept intact for several months in the air. The high stability is ascribed to the effective steric protection of the ring system by the bulky substituents.     

Computer simulations of molecular motion in liquid crystals by the method of Brownian dynamics

Computer simulations of the molecular motion of polymer chains in the presence of a strong nematic field were carried out by the method of Brownian dynamics. Two models were studied: the first model (linear liquid crystal) is a freely jointed chain with rigid bonds, the second model (comb-like liquid crystal) is a chain with fixed bond angles and rigid side groups. The influence of ordering on chain conformations, orientational and translational mobility and spectra of relaxation times was investigated.     

Relative Configuration and Conformation of 5-(Dimethoxyphosphoryl)-2-methoxy-1,2λ5-oxaphospholan-2-ones by Multinuclear NMR Spectroscopy

Information on the hitherto unknown relative configuration and on the conformation of the title compounds in solution can be derived from nuclear Overhauser effects and coupling constants. Whereas the bridged 5-(dimethoxyphosphoryl)-2-methoxy-1,2λ⁵-oxaphospholan-2-ones 6 and 7 are sterically strained and, therefore, conformationally rigid, the C(3)-unsubstituted compound 1 does not show a preferred solution conformation. Phenyl substituents at C(3) (compounds 2 – 5 ) tend to adopt a pseudoequatorial position, this way leading to a definite conformation of the respective compounds. The influence of the conformation on the NMR spectra is discussed. ³¹P-NMR Spectroscopy is ideally suited for the characterization and quantification of the isomers 2 – 5 present in the reaction mixture.     

高分子熔体和浓溶液流变性能的研究

基于多重缠结网络结构模型和高分子链上缠结点在流动中可进行动态解缠和再缠结的多重蠕动机理,用统计力学和动力学相结合的方法,分别计算出了缠结链组的末端距分布函数;处于缠结状态下高分子链构象统计分布函数;受力下聚合物熔体粘弹性形变自由能和解除外力下高分子挤出体可回复性粘弹性形变自由能,提出了高分子挤出体可回复形变的粘弹性分子理论。推导出的高分子熔体的回忆函数、简单剪切流下的本构方程和物料函数,并采用一种新的方法测定出物料的四种参数： η0、 GN0、 n′和 a。对于高分子挤出体,可回复性粘弹性形变由快速弹性形变和慢速粘弹性形变两者组成,当把两种形变量的复合结构参数－分子链的反式构象分数引入两种形变自由能表达式后,就从理论上得到了可回复形变量同挤出胀大比间的定量表达式,从而建立起一个具有分子链结构参数的新的挤出胀大比方程,可回复形变量同挤出条件（温度、挤出速率和量以及口模长径比不同的挤出机）和树脂结构特征（分子量及分布）的关系式以及在特殊情形下的简化表达式,并用几种高分子熔融体系的挤出胀大比和可回复性形变量的实验数据对理论进行验证,理论方程同实验数据较好的符合。     

Thermodynamic analysis of strain in the five-membered oxygen and nitrogen heterocyclic compounds

Cyclopentane is conventionally strained. Replacement of a carbon atom by a heteroatom obviously impacts angular strain in the five-membered ring compounds. Changes of strains in the five-membered cycles are also caused by a double bond or atttached benzene rings. We studied the thermochemical properties of Indane, 2,3-dihydrobenzofuran, indoline, N-methyl-indoline, carbazole, and N-ethyl-carbazole to obtain a better quantitative understanding of the energetics associated with these compounds containing five-membered ring units. We used combustion calorimetry, transpiration method, and high-level first-principles calculations to derive gaseous enthalpies of formation of the five-membered heterocyclic compounds. Our new values together with the selected values for parent heterocyclic compounds, available from the literature, were used for calculation of the strain energies H(S) of five-membered C-, N-, and O-containing cycles. Quantitative analysis of the resulting stabilization or destabilization of a molecule due to interaction of benzene rings with the heteroatom has been performed.     

Molecular structure of 2-Amino-5-(1-methyl-5-nitro-2-imidazolyl)-1,3,4-thiadiazol (Megazol) and related compounds: A concerted study using X-ray crystallography,molecular mechanics,and semiempirical methods

A structural study of three nitroimidazoles was carried out using molecular mechanics, semiempirical methods, and X-ray crystallography. Structural features which might account for the high efficiency of1 (Megazol) as an antiparasitic drug and its opposite, the inactivity of its regiomers2 and3 were examined, i.e., coplanarity of the two rings, preferred conformations, and rotational barriers around the pivot bond between the two rings. For the three compounds an antiperiplanar conformation is preferred for the N(CH₃) and C-S bonds. For compounds1 and3, the rings are coplanar, with2 being somewhat twisted. The geometry obtained by molecular mechanics for compound1 is in excellent agreement with the X-ray structure, and greater confidence can be placed in this method than in semiempirical ones. Similarities observed on the LUMO positions, as well as rotational barriers lead to the conclusion that the differences in biological activity of these compounds do not rely on their ground state properties but rather on their subsequent reactions with oxygen. In addition, the calculations revealed significant structural information of a family of biological importance (nitroimidazoles) and constitute a comparative test for the MM2, AM1, and PM3 methods.     

Structural factors controlling tensile yield deformation of semi‐crystalline polymers

In this work, a molecular model is proposed to account for the stress‐strain relationships of spherulitic polymers. To describe the yielding behavior of spherulitic polymers, we introduced a new structural unit, i.e. the lamellar cluster, which is represented by several stacked lamellae bound by some tie molecules. It was shown that the tie molecules between the adjacent lamellar clusters produce the concentrated load acting on the cluster surface, leading to bending deformation of the lamellar cluster. The yielding behavior was explained by the disintegration of lamellar cluster due to the bending deformation.     

Absolute on-line molecular mass analysis of basic fibroblast growth factor and its multimers by reversed-phase liquid chromatography with multi-angle laser light scattering detection

The multi-angle laser light scattering (MALLS) detection method was combined with reversed-phase high-performance liquid chromatography to analyze multimerization of basic fibroblast growth factor (bFGF) formed by oxidation of bFGF with air or with 5,5′-dithio-bis(2-nitrobenzoic acid) (DTNB). This analysis provided the absolute molecular mass and the mean square radius for each eluted protein fraction of each slice of the chromatogram. It was shown that depending on the oxidation conditions, bFGF forms different multimetric forms, from dimers to hexamers. It was found that these multimers have varied conformations of the same molecular mass, but different structure. Molecular mass and size analyses provided molecular conformation of the aggregates; the results indicated the formation of rod-like rigid structures. The MALLS analysis confirmed that, during oxidation, each bFGF monomer bound sequentially to form the extended multimer. The proposed scheme of bFGF oxidation with DTNB revealed that the difference in the aggregate structural forms was probably due either to the presence of covalently bound residues of nitrobenzoic acid in the products of oxidation, or to the participation of sulfhydryl groups in disulfide bond formation.     

Conformational analyses on histamine H2-receptor antagonists

Summary In a series of compounds with H₂-antihistaminic activity, a conformational analysis was performed based on force field calculations. The drugs studied were cimetidine, ranitidine, famotidine, roxatidine and the conformationally more restricted ICI127032. For the compounds containing a flexible chain, the local minima conformations and the global minimum conformation were calculated. These conformations were used for a systematic structural comparison with all energetically allowed conformations of the ICI derivative, with regard to the best fit of the common structural features. In this way a pharmacophore could be developed consisting of four parts: (1) a polar planar group, uncharged at physiological pH; (2) a hydrophobic part formed by aromatic systems or flexible chains; (3) an—under physiological conditions—protonated nitrogen atom; and (4) a substructure, which contains a hydrogen bond donor site and a hydrogen bond acceptor site in a specific spatial arrangement.     

A proposed common spatial pharmacophore and the corresponding active conformations of some peptide leukotriene receptor antagonists

Summary Molecular modeling studies were carried out by a combined use of conformational analysis and 3D-QSAR methods to identify molecular features common to a series of hydroxyacetophenone (HAP) and non-hydroxyacetophenone (non-HAP) peptide leukotriene (pLT) receptor antagonists. In attempts to develop a ligand-binding model for the pLT receptor, the Apex-3D program was used to identify biophoric structural patterns that are common to 13 diverse sets of compounds showing different levels of biological activity. A systematic conformational analysis was carried out to obtain sterically accessible conformations for these flexible compounds. Apex-3D was then utilized to propose common biophoric regions based on the selection of one of several conformations (MOPAC-minimized AM1) from each compound's data set that best fits the biophoric pattern and the resulting superimposition with all the other data-set compounds. Apex-3D identified three common biophoric features important for activity: one as the hydroxyl, acetyl, carbonyl and carboxyl groups, which mimic the acid-binding region of an agonist, the other as the hydrogen-bond donating site, and the third part is represented by a plane in which lipophilic aromatic groups align. The structure-activity relationships were then assessed by using the 3D-QSAR model. A common biophore model is proposed from the Apex-3D analysis which may be useful in designing new pLT antagonists. Molecular volumes and electrostatic potential similarities were also calculated in order to obtain the important structural requirements for the activity.     

丙氨酸二肽分子二级结构与振动光谱特性

利用从头算方法探索蛋白质模型分子——丙氨酸二肽的二级结构布居特性以及体系势能变化. 引入对分子结构敏感的振动探针(酰胺振动吸收带), 借助其光谱表象, 寻求振动光谱参数与分子结构之间的联系. 研究结果表明: 丙氨酸二肽分子处于C_7eq构型(Φ/Ψ=-80°/80°)时具有最低能量值, 且分子易形成β折叠、PP_II、C₅及C₇等能量较低的稳定构型. 通过简正模式分析, 得到分子3N-6 个振动模式的吸收光谱, 并通过势能分布分析方法对分子骨架上酰胺振动吸收带的特征振动模式进行了指认. 重点考察分子骨架上酰胺-I带振动光谱参数与分子构型变化之间的相关性, 建立振动光谱参数与蛋白质二级结构之间的联系, 为在化学键水平上研究蛋白质的结构及其发挥作用的机制提供科学依据.     

群多普利溶液构象的NMR研究

采用1D和2D NMR技术对血管紧张素转化酶抑制剂群多普利在CDCl₃溶液中存在的两种构象进行了结构解析, 并结合分子动力学和密度泛函理论方法对其进行了结构的几何优化和能量计算. 结果表明, 群多普利因分子中酰胺键的旋转而形成反式构象A和顺式构象B, 两种构象的能量差为6.35 kJ/mol, 且顺式构象为该药物的优势构象.     

苯并呋喃／噻吩联二苯类PTP1B抑制剂三维构效关系研究

主要采用比较分子力场分析方法（CoMFA）对苯并呋喃／噻吩联二苯类PTP1B (protein tyrosine phosphatase 1B)抑制剂进行了三维构效关系的研究，考察了 静电场、立体场和氢键场对构效关系的影响，交叉系数q^2的值达到0．58，表明 CoMFA得到的构效关系模型比较理想，同时test set中分子的预测活性也表明，模 型具有较好的预测能力，研究还表明，氢键场的加入不一定有利于模型的改善，通 过对分子场等值面图的分析，可以观察到叠合分子周围立体场和静电场对化合物活 性的影响，为改进原有化合物的结构，提高它们的活性提供了指导，还尝试采用比 较分子相似性指数分析方法（CoMFA）对这一系列化合物作了研究，结果表明虽然 CoMFA中加入了疏水场，但是对于研究的体系，CoMFA的模型质量并没有显著提高。