Dynamic processes in [16]annulene: Möbius bond-shifting routes to configuration change

Density functional and ab initio methods have been used to study the mechanisms for key dynamic processes of the experimentally known S4-symmetric [16]annulene (1a). Using BH&HLYP/6-311+G** and B3LYP/6-311+G**, we located two viable stepwise pathways with computed energy barriers (Ea = 8-10 kcal/mol) for conformational automerization of 1a, in agreement with experimental data. The transition states connecting these conformational minima have M?bius topology and serve as starting points for non-degenerate pi-bond shifting (configuration change) via M?bius aromatic transition states. The key transition state, TS1-2, that connects the two isomers of [16]annulene (CTCTCTCT, 1 --> CTCTTCTT, 2) has an energy, relative to the S4 isomer, that ranged from 6.9 kcal/mol (B3LYP/6-311+G**) to 16.7 kcal/mol (BH&HLYP/6-311+G**), bracketing the experimental barrier. At our best level of theory, CCSD(T)/cc-pVDZ(est), this barrier is 13.7 kcal/mol. Several other M?bius bond-shifting transition states, as well as M?bius topology conformational minima, were found with BH&HLYP energies within 22 kcal/mol of 1a, indicating that many possibilities exist for facile thermal configuration change in [16]annulene. This bond-shifting mechanism and the corresponding low barriers contrast sharply with those observed for cis/trans isomerization in acyclic polyenes, which occurs via singlet diradical transition states. All M?bius bond-shifting transition states located in [16]- and [12]annulene were found to have RHF --> UHF instabilities with the BH&HLYP method but not with B3LYP. This result appears to be an artifact of the BH&HLYP method. These findings support the idea that facile thermal configuration change in [4n]annulenes can be accounted for by mechanisms involving twist-coupled bond shifting.     

COMPUTER SIMULATIONS ON UNPERTURBED CONFIGURATIONAL DIMENSIONS OF POLY (METHYL ACRYLATE)

A full-relaxation optimization of molecule and the popular MM2 force field are em-ployed to obtain the geometry parameters and the conformational energy surface of a mesoor a racemic dyad of poly(methyl acrylate) (PMA) with a specified carbonyl-bond orien-tation in side-groups. It is found that the conformational energy maps calculated hereconsiderably differ from those calculated with the rigid molecular model as reported in theearlier studies. The g~- state cannot be omitted in the obtained contour maps. Two impor-tant conformers tg~- and g~(-t) with energy minima were newly detected for a racemic dyad.The analysis on the conformations with energy minima confirmed that the ester groupsare not always perpendicular to the plane defined by the two adjacent skeletal bonds andmay change their relative orientations to meet the requirement of lower energies duringthe conformational state transition. Instead of the early way of adjusting the interactionenergy parameters to fit the experimental data, we attempt to predict unperturbed chaindimensions via the reliable force field and the configurational statistical mechanics. Theproposed scheme with three rotational states identified from the contour maps allowed usto satisfactorily reproduce the experimental dimensions of random PMA chains.     

A 3D QSAR approach to the search for geometrical similarity in a series of nonpeptide angiotensin II receptor antagonists

Summary A 3D QSAR methodology based on the combined use of conformational analysis and chemometrics was applied to perform a comparative analysis of the 3D conformational features of 13 nonpeptide angiotensin II receptor antagonists showing different levels of binding affinity. Conformational analysis by using a molecular mechanics MM2 method was carried out for each of these structures to obtain conformational minima. These minima were described by ten interatomic distances which define the relative spatial disposition of five significant atoms belonging to relevant functional groups present in all the 13 molecules. The structure-activity relationship between the interatomic distances and the biological activity was then assessed by using chemometric methods (cluster analysis, principal component analysis, classification methods). With our indirect approach based on the search for geometrical similarity it was possible, even though structural information on the receptor active site was lacking, to identify the 3D geometrical requirements for the binding affinity of nonpeptide angiotensin II receptor inhibitors.     

New insights into the multiple minima problem

Minima distribution of thorough conformational searches of three peptides of different length ranging from five to nine residues, were compared with the density of states of a flexible molecule derived from the rotational isomeric approximation. It is observed that minima distributions generated from the conformational searches exhibit the same characteristics as the density of states derived from the rotational isomeric model: an asymmetric distribution with a maximum. These results together with a more profound understanding of the characteristics of the energy landscapes of polypeptides, provide new insights into the multiple minima problem. The implications in devising more robust conformational search strategies are discussed.     

Conformational analysis and flexibility of carbohydrates using the CICADA approach with MM3

The potential energy hypersurfaces (PES) of several carbohydrate molecules were studied with a new algorithm for conformational searches, CICADA (Channels in Conformational Space Analyzed by Driver Approach) interfaced with the molecular mechanics program MM3(92). The method requires (1) one or a few low-energy conformations as starting points; and (2) designation of the torsion angles important for understanding the conformational behavior of the molecule. The PES is explored by driving separately each selected torsion angle (in both directions) with a concomitant full-geometry optimization at each increment (except for the driven angle). When a minimum has been detected, the molecule is freely optimized, and the minima so detected are then stored if not encountered previously. The new minima serve as starting structures for further explorations. The results from CICADA permit prediction of relative and absolute flexibility and conformational softness for both the entire molecule as well as for individual group rotations and local minima. The carbohydrates analyzed were Me-α-D -glucopyranoside, β-D -GlcNAc(1-2)α-D -Man, and α-D -GalNAc(1-3)[α-L -Fuc(1-2)]Gal-O-Me. All the low-energy conformers along with the transition states and flexibilities features were characterized. CICADA found all minima and low-energy conversion pathways for the disaccharide that were found by a traditional grid search. In contrast to the grid search method, CICADA concentrates mostly on the exploration of the low-energy regions of the PES, thereby saving a significant amount of computational time. The performance of the method opens new routes for exploring conformational space of larger molecules, such as oligosaccharides. © 1995 by John Wiley & Sons, Inc.     

联吡啶构象异构的理论研究

采用HF/6-31G*方法,对6种联吡啶构造异构体进行了构象分析.之后采用B3LYP/6-311G**方法对处于势能面上的能量极小构象异构体进行全自由度几何优化和频率分析,并且寻找构象异构化过渡态.采用自洽反应场极化导体模型溶剂理论,探讨了水溶剂对优势构象异构体的几何结构和能量的影响.     

Ab initio studies of conformational properties of dimethyl diphosphate dianion and its complex with magnesium

The conformational properties of the diphosphate linkage have been studied with ab initio methods using the dimethyl diphosphate dianion (1) and magnesium dimethyl diphosphate (2) as models. The ab initio energy and geometry of the conformers around the P-O bonds have been determined at the self-consistent-field (SCF) using the 6-31G* and the tzp basis sets; whereas, the 6-31G* basis set alone has been used for 2. In addition, the adiabatic connection method (ACM) of density functional theory (DFT) using the dzvp basis set has been employed for 1. The optimization of all possible staggered conformers assumed for the four P-O bonds, led to nine minima for 1. In agreement with the general anomeric effect, the sc conformation about the P-O bonds is clearly preferred over the ap one. Vibrational frequencies were calculated at the SCF level using the 6-31G* basis set and used to evaluate zero-point energies, thermal energies, and entropies for all minima of 1. The effect of zero-point energies and thermal energies is quite small. However, the effect of entropies, mainly resulting from a multiplicity contribution, changes the stability of the conformers. For each minimum of 1, up to six different arrangements of the Mg²⁺ were used to determine minima of 2. This procedure led to 21 distinct minima. The presence of the magnesium counter-ion appeared to completely change the structure and relative energy of the conformers. The preferred structures of the complex exhibit the (sc, ap) orientation around the two central P–O bonds and an arrangement in which the magnesium cation is coordinated by three phosphoryl oxygen atoms. The results of this work clearly demonstrate that interactions with the metal counter-ion can induce conformational changes in the overall 3D-shape adopted by molecules containing diphosphate linkages. The PM3 and MNDO quantum semi-empirical methods and molecular mechanics methods using the CVFF force field were tested and large differences in the minimum structures, as well as in the conformational energies between these and ab initio methods, are discussed.     

Conformational inversion-topomerization processes of ethylcyclohexane and 1,2-dimethylcyclohexane: A computational investigation

To deeply reveal the impact of the substituents and their special orientations in ring on conformational behaviors for substituted cyclohexanes, a comprehensive study of ethylcyclohexane, cis-, and trans-1,2-dimethylcyclohexanes has been carried out. All conformational structures for them were captured by the accurate ab intio method, that is, B3LYP/6-311++G(d,p) method was used for geometry optimizations, and MP2/6-311++G(d,p), G4, and CCSD(T)/6-311++G(d,p) methods were applied for the high-level single point energy refinements. Based on CCSD(T)/6-311++G(d,p) quantum results, the conformational populations of minima for these three substituted cyclohexanes were calculated by Boltzmann distribution over 300-2500 K. Additionally, the conformational inversion-topomerization pathways for them were thoroughly investigated. The complete characterization involved in their potential energy surfaces are clearly presented by three or two-dimensional schemes.     

Phase behavior, conformations, thermodynamic properties, and molecular motion of multicomponent paraffin waxes: A Raman spectroscopy study

Variable-temperature (72–20 °C) studies of Raman spectra (3100–800 cm⁻¹) and thermal analysis of multicomponent paraffin wax have been carried out. The disorder–order transition under liquid–solid transition was observed and their temperature ranges were obtained through the S_lateral order parameter as a function of temperature. From 56 to 43 °C, the paraffin undergoes a conformational state transition of non-extended chain state (NECS) to extended chain state (ECS). The enthalpy and entropy change for the transition obtained by van’t Hoff analysis were 214.286 ± 21 kJ/mol and 0.661 ± 0.066 kJ/mol/K, respectively. The enthalpy determined by differential scanning calorimetry (DSC) was 52.165 ± 5.2 kJ/mol, which is smaller than the van’t Hoff enthalpy due to larger effective non-extended chain state. The variation of Raman spectra with decreasing temperature presents the structure evolution and molecular motion during the crystallization of paraffin wax.     

Exploring the similarities between potential smoothing and simulated annealing

Simulated annealing and potential function smoothing are two widely used approaches for global energy optimization of molecular systems. Potential smoothing as implemented in the diffusion equation method has been applied to study partitioning of the potential energy surface (PES) for N‐Acetyl‐Ala‐Ala‐N‐Methylamide (CDAP) and the clustering of conformations on deformed surfaces. A deformable version of the united‐atom OPLS force field is described, and used to locate all local minima and conformational transition states on the CDAP surface. It is shown that the smoothing process clusters conformations in a manner consistent with the inherent structure of the undeformed PES. Smoothing deforms the original surface in three ways: structural shifting of individual minima, merging of adjacent minima, and energy crossings between unrelated minima. A master equation approach and explicit molecular dynamics trajectories are used to uncover similar features in the equilibrium probability distribution of CDAP minima as a function of temperature. Qualitative and quantitative correlations between the simulated annealing and potential smoothing approaches to enhanced conformational sampling are established. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 531–552, 2000     

Multiple pathways in conformational transitions of the alanine dipeptide: an application of dynamic importance sampling

We present multiple dynamic transition pathways on the two-dimensional dihedral plane between conformational states of the alanine dipeptide. The method used in this study is dynamic importance sampling (DIMS). To perform DIMS, unbiased molecular dynamic simulations are used to generate equilibrium ensembles for the alanine dipeptide within different states. Free energy surfaces on the dihedral plane are calculated from the equilibrium simulations, and four energy minima defined from the surface are used as the starting and ending points for DIMS dynamics. The DIMS method represents an important step towards finding multiple transition pathways within complex biomolecular systems.     

Simulation of conformational transitions

Conformational transitions are essential for the functioning of many proteins, and understanding this dynamical behavior is a central goal in molecular biology. Computer simulations are playing an important role towards this aim by providing insights into how the conformational changes are induced, propagated and used. Popular methods for the simulation of conformational transitions will be reviewed, with a focus on atomistic molecular dynamics techniques for the calculation of transition pathways     

Conformational analysis of the complex of 2-methyl-1,3,2-dioxaborinane with hydroxyl anion

Studies of the conformationsl transformations of the complex of 2-methyl-1,3,2-dioxaborinane with the hydroxyl anion performed by the quantum-chemical method HF/6-31+G(d) showed that they are more versatile than those in the initial boric ester, include the existence of six minima, five transition states, and are close to the conformational behavior of 1,3-dioxanes.     

Y220C突变体影响p53C蛋白质构象转换的分子动力学模拟

p53是迄今发现突变频率最高的一种肿瘤抑制蛋白质,突变会导致p53抑癌功能丧失并诱导癌症的发生。绝大多数的突变发生在p53的核心DNA结合区域（p53C）,其中Y220C是研究较多的一种突变体。虽然已有研究表明该突变能够降低p53C的结构稳定性,但其影响p53C构象转换的分子机制尚不清晰。本文利用分子动力学（MD）模拟方法研究了p53C突变体Y220C（p53C-Y220C）的结构变化,发现Y220C突变主要影响Y220C cluster区域（包括残基138-164和215-238）,且Y220C突变减少了Y220C cluster的β-折叠含量。进一步分析发现,Y220C突变不仅直接破坏突变氨基酸与周围氨基酸Leu145和Thr155之间的氢键,而且降低了Y220C cluster区域的折叠片S3和S8之间的氢键数量,使Y220C突变所形成的亲水性空腔变大,加速了水分子进入该蛋白质内部,并最终导致了p53C-Y220C变性。MD模拟结果揭示了Y220C突变影响p53C结构转换的分子机制,该研究对p53C-Y220C突变体高效稳定剂的筛选和设计具有重要意义。     

Novel algorithms for searching conformational space

Summary The modelling of biological molecules by molecular dynamics is beset by a range of problems. The most important of these is the multiple-minima problem. The deep metastable minima can cause difficulties in proper equilibration of a molecular system and result in the simulated system being trapped in a long-lived metastable state. One way to overcome these problems is to re-engineer the Newtonian Rules in order to more efficiently search conformational space. Re-engineering of the Newtonian Rules implies a redesign of the physical laws arising from them. This is done in various ways by the RUSH, Hybrid Monte Carlo and PEACS algorithms. This paper explores applications of these algorithms, and compares them to a traditional molecular dynamics method.     

Localized states in polymeric molecules. II. Applications to chemical and biological processes

We present a simple real space method, based on the Green's function formalism, which is convenient for the calculation of the electronic structure of polymers with broken translational symmetry. The method is applied to the study of a model Hamiltonian which may describe conformational modifications of polymeric molecules. The possible role of localized states in chemical and biophysical processes is discussed.This work has been partially supported by the Brazilian Agencies FINEP and CNPq.     

Theoretical Study on Photoisomerization of 2-Methylfuran to 3-Methylfuran

1 INTRODUCTION 2-Methylfuran belongs to the basic heteroaromatic compounds relevant to many fields of modern che- mistry, ranging from the study of natural products and biologically active substances to the develop- ment of building blocks for organic synthesis and conducting polymers[1]. Since the photochemistry ofR-furan was gradually recognized in 1960s[2～7], lots of interest has been aroused. Herein we only study one branch of photoche- mistry of R-furan: the isomerization of 2-methy…     

Influence of the basis set on the calculation of the absolute 13C shieldings of methyl derivatives (CH3X with X?=?CH3, CN, NH2, NO2, OH, F) with special emphasis in the cases of X?=?Cl, Br, SH, SeH, and PH2

A theoretical B3LYP/6-311++G(d,p) study of four derivatives of cyclooctadiene bearing two aromatic or heteroaromatic rings is reported. The conformational analysis reproduces well the experimental results (minima and transition states). The GIAO calculated ¹H and ¹³C chemical shifts proved useful in solving some stereochemical questions.     

Conformational analysis and vibrational assignments of 2,2,3,3-tetrafluoro-1-propanol CHF2CF2CH2OH as three-rotors system

The conformational stability of 2,2,3,3-tetrafluoro-1-propanol was investigated by DFT-B3LYP/6-311+G** and ab initio MP2/6-311+G** calculations. The calculated potential energy curves of the molecule at DFT-B3LYP level were consistent with five distinct minima that correspond to gauche(-)-gauche-gauche (G1gg), trans-trans-gauche (Ttg), trans-gauche-gauche (Tgg), trans-gauche-gauche(-) (Tgg1) and gauche(-)-gauche-trans (G1gt) conformers in the order of decreasing relative stability. The equilibrium constants for the conformational interconversion of 2,2,3,3-tetrafluoro-1-propanol were calculated and found to correspond to an equilibrium mixture of about 38% G1gg, 28% Ttg, 13% Tgg, 11% Tggt and 10% G1gt conformations at 298.15K. The vibrational frequencies of 2,2,3,3,-tetrafluoro-1-propanol in its five stable forms were computed at B3LYP level and complete vibrational assignments were made based on normal coordinate calculations and comparison with experimental data of the molecule.