CALCULATION OF CONFORMATIONAL ENTROPY AND FREE ENERGY OF POLYSILANE CHAIN

The conformational entropy S and free energy F were calculated by exact enumeration of polysilane chain up to 23segments with excluded volume (EV) and long-range van der Waals (VW) interaction. A nonlinear relation between S_(EV+VW)and chain length n was found though S_(EV) was found to vary linearly with n. We found that the second-order transitiontemperature of polysilane chain with VW interaction increases with the increase of chain length, while that of polysilanechain without VW interaction is chain length independent Moreover, the free energies F_(EV+VW) and FEv are both linearlyrelated with n, and F_(EV+VW) 相似文献   

Conformational Behavior of Rigid and Dancing (1,3)(1,4)Cyclophanes

Annelation or substitution of the (1,4)-bridged ring of [2₂](1,3)(1,4)cyclophane 4 , such as in 8 and 9 , respectively, result in two different conformational ground states in each case. Each conformational ground state involves a different destabilizing factor arising from one form of non-bonding interaction. Only the conformers 8b and 9b were isolated experimentally. Their corresponding precursors 11 and 23 were also found to be conformationally rigid. Only the conformers 11a and 23a were isolated indicating an abrupt change in conformational preference going from the dithia[3₂]cyclophanes to the respective [2₂]cyclophanes. The selectively methylated [2₂]cyclophanes 27 , 31 and 32 were, however, found to be conformationally mobile. There is an increase of about 10–15 kJ mol^?1 in conformational energy barrier going from 4 to 27 or 31 . This is consistent with the fact that the presence of the methyl substituents increases the relative conformational ground-state energy more than it would affect the transition-state energy. The conformational barrier of 32 was unexpectedly found to be similar to those of 27 and 31 . This could be explained by a decrease in the transition-state energy due to an inward bending of the (1,4)-bridged ring accompanied by a decrease in conformational ground-state energy due to an outward bending of the methyl groups in 32 .     

Conformation Disturbance of CopC by α-Naphthylamine

It is known that urea and guanidine hydrochloride(GuHCl) induce conformational change of proteins in a certain range of molar ratios. In our research,α-naphthylamine(NA) above 10-4 mol/L at pH 7.0 was discovered to perturb the conformation of CopC,a copper resistant protein with a Greek β-barrel motif; this was reflected by the greater fluorescence quenching and red-shifted emission peak of CopC. The conformation change of CopC was also verified in acrylamide collision experiment by comparing quenching leve...     

Can the conformational flexibility of cis-decalins be modulated through intramolecular O-H?O hydrogen bonding? Profiling the molecular and supramolecular attributes of designer cis-fused polycyclitols

In order to unravel the modalities of hydrogen bonding in conformationally flexible polycyclitols vis-à-vis their conformationally locked siblings, three diastereomeric perhydro-2,3,4a,6,7,8a-naphthalenehexols, all embodying a 4a,8a-dihydroxy-cis-decalin framework, have been synthesized via sequential stereo-controlled oxyfunctionalization of 1,4,5,8-tetrahydronaphthalene. Variable temperature NMR studies on the cis-fused polycyclitols thus obtained suggest that their inherent conformational flexibility in solution is restrained at ambient temperature owing either to the formation of a stable H-bonded molecular solvate or to the presence of strong intramolecular O-H?O H-bonding. Single crystal X-ray diffraction studies on the three hexols reveal an interesting commonality in their gross molecular packing and a ubiquitous presence of the R²₂(10) dimer motif—a supramolecular synthon rarely encountered in the crystal structures of conformationally locked and axially-rich hexols.     

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.     

Beiträge zur Chemie der Pyrrolpigmente, 73. Mitt.

Several 10-arylbilatrienes-abc substituted with various substituents in position 4 of the phenyl residue were prepared. Configurational and conformational analysis using NOE-measurements, UV-VIS spectra together withPPP-SCF-LCAO-MO-CI-calculations, ring current effects andpK _a -determinations showed the bilin chromophor to adopt a more or less undisturbed (Z,Z,Z)-sp,sp,sp-geometry, compared to bilatrienes-abc. The plane of the aryl moiety is, however, heavily twisted against the mean plane of the bilin chromophor—the torsional angle is estimated to be about 60°.

Herrn Prof. Dr.F. Asinger mit den besten Wünschen zum 80. Geburtstag gewidmet.     

Anab initio SCF molecular orbital study of acetylcholine

A standard ab initio (STO 3 G) study indicates, in distinction to theab initio molecular fragment results, that the preferred conformation of acetylcholin is gauche.     

谷氨酰胺与碱金属及碱土金属离子络合物的构象和金属离子亲和势：第一性原理研究

Conformations and reaction energetics are important for understanding the interactions be-tween biomolecules and metal ions. In this work, we report a systematic ab initio study on the conformations and metal ion affinities of glutamine (Gln) binding with alkali and alkaline earth metal ions. An efficient and reliable method of searching low energy conformations of metalated Gln is proposed and applied to the complexes of Gln.M^+/++ (M^+/++=Li⁺、Na⁺、K⁺、Rb⁺、Cs⁺、Be⁺⁺、Mg⁺⁺、Ca⁺⁺、Sr⁺⁺和Ba⁺⁺). In addition to all conformers known in literatures, many new important conformations are located, demonstrating the power of the new method and the necessity of the conformational search performed here. The metal coordination modes, relative energies, dipole moments, and equilibrium distribu-tions of all important conformations of Gln.M^+/++ are calculated by the methods of B3LYP, BHandHLYP, and MP2. IR spectra and metalation enthalpies and free energies are also pre-sented and compared with the available experiments. The results form an extensive database for systematic examination of the metalation properties of Gln.     

Computer simulation of conformational movement based on interconversion phenomena

A computer method has been developed which is an alternative to molecular dynamics in the sense that it pictures conformational motion. It simulates propagation in conformational movement based on conformational interconversion phenomena. The method starts with the knowledge of the topology of the conformational potential energy hyper-surface, which is described by the minima and the transition states. The topology is obtained by the recently described software . The simulation of conformational motion is based on the Boltzmann statistics of movement between the minima and the transition states at a given temperature. The method is illustrated for methyl--glucopyranoside and - -galNAc(1-3)[- -Fuc(1-2)]Gal-O-Me molecules. Conformational transitions of hydroxyl groups as well as glycosidic linkages are discussed.     

Solution conformation of tripeptides by NMR spectroscopy and force-field calculations

The solution conformation of three linear tripeptides Boc-Ala-Val-Val-OMe1, Boc-Ala-Pro-Val-OMe2, and Boc-Ala-(D)Pro-Val-OMe3 was studied by NMR spectroscopy and accompanying force-field calculations. In one case,2, as preferred conformation the-turnall trans conformer was found.     

Flexibases: A way to enhance the use of molecular docking methods

Summary Specially expanded databases containing three-dimensional structures are created to enhance the utility of docking methods to find new leads, i.e., active compounds of pharmacological interest. The expansion is based on the automatic generation of a set of maximally dissimilar conformations. The ligand receptor system of methotrexate and dihydrofolate reductase is used to demonstrate the feasibility of creating flexibases and their utility in docking studies.     

Synthesis of (thia)calix[4]arene oligomers: towards calixarene-based dendrimers

Thiacalix[4]arenes bearing two or four carboxylic functions on the lower rim served as starting compounds for the synthesis of novel calixarene oligomers connected by amidic functions. The cone conformers react smoothly with four molecules of 5-amino-calix[4]arene to yield the corresponding pentakis-calixarenes. On the other hand, because steric hindrance, the 1,3-alternate condenses only with two molecules leading thus to tris-calixarene, possessing a novel type of inherent chirality based on the 25,26-substitution pattern. The title compounds, which connect together ‘classical’ calixarene and thiacalixarene building blocks, represent a first step towards calixarene-based dendritic structures.     

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.     

聚合物链构象的Monte Carlo模拟:单链的构象熵

本工作提出了一种新的直接用Monte Carlo模拟方法计算聚合物链构象熵,我们称这种方法为构象计数法。在本文中首先叙述了这个方法的计算原理,然后将它应用到简单立方格子中的无规自避行走问题上。具体计算了短链(链步数n=7～19)和长链(n～2100)时的熵在短链下所得到的熵数据与准确值相比偏差在0.04％以内(2000个样本)。在长链下所得到的熵数据与重整化群理论的结果相比,误差在0.8％左右(样本数为300)。同时本文还计论了限制在边长为2的立方体内,最大链步数n=26的受限链的构象熵。由本方法所求得的数据和用直接计算构象数得到的熵准确值也符合得很好。偏差在0.6％以内(2000个样本)。本文还对权重因子进行了讨论,提出改进数据准确度的方法。     

Conformational behaviour of dinuclear Rh(I) complexes of the open-chain tetrapyrrolic ligand 2,2′-bidipyrrin (H2BDP)

The reaction of 2,2′-bidipyrrins H₂BDP with the Rh^I complexes [Rh(COD)(μ-OMe)]₂ and [Rh(CO)₂(μ-Cl)]₂ yields the neutral species [{Rh(COD)}₂BDP] (7, 8) and [{Rh(CO)₂}₂BDP] (2, 9), respectively. Treatment of the COD complexes with carbon monoxide results in the exchange of all COD ligands against CO. Ligand exchange studies on the carbonyl complexes 2 and 9 with different phosphane donors reveal the regioselective exchange of one CO per metal ion. In most cases, the reaction is accompanied by a large conformational change of the tetrapyrrole from a syn to an anti conformation. This conformational change was resolved by a combination of NMR spectroscopy and X-ray diffraction studies.     

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.     

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.     

Synthesis of α,α-disubstituted 4-phosphonophenylalanine analogues as conformationally-constrained phosphotyrosyl mimetics

Syntheses of N-Boc (S)-4-(diethylphosphono)-(α-methyl)phenylalanine [Boc-(α-Me)Phe(4-PO₃Et₂)-OH] (9) and N-Boc (S)-2-amino-6-(diethylphosphono)tetralin-2-carboxylic acid [Boc-Atc(6-PO₃Et₂)-OH] (18) are reported as conformationally-constrained phosphotyrosyl mimetics suitably protected for peptide synthesis. Both syntheses proceeded through chiral arylhalides that are converted to arylphosphonates by palladium-catalyzed cross coupling with diethylphosphite. These amino acid analogues may be useful in the study of cellular signal transduction processes.     

Influence of Intra-Molecular Conformational Transitions and some Physico-Chemical Quantities of Liquids on their Thermal Conductivity

It is shown that the thermal conductivity of various liquids can be described adequately by taking into account the influence of intra-molecular conformational transitions on the number of bimolecular collisions in the liquid phase. The proposed equations allow the calculation of this transport property at different temperatures.     

Synthesis of terphenyl oligomers as molecular electronic device candidates

Six functionalized bis(phenylene ethynylene)-p,p-terphenyls (BPETs) have been synthesized as potential molecular electronic devices. The molecules containing mono- and dinitro terphenyl cores, were rationally designed based on the electronic properties recently found in oligo(phenylene ethynylene)s (OPEs). From our understanding of the conductance properties in OPEs, improvement of electronic properties may be possible by using BPETs due to a higher rotational barrier between the central aromatic rings of the compounds prepared here. BPETs cores were functionalized with nitro groups and with different metallic adhesion moieties (alligator clips) to provide new compounds for testing in the nanopore and planar testbed structures.