Using fractal to solve the multiple minima problem in molecular mechanics calculation

This article presents an approach using fractal to solve the multiple minima problem. We use the Newton–Raphson method of the MM3 molecular mechanics program to scan the conformational spaces of a model molecule and a real molecule. The results show each energy minimum, maximum point, and saddle point has a basin of initial points converging to it in conformational spaces. Points converging to different extrema are mixed, and form fractal structures around basin boundaries. Singular points seem to involve in the formation of fractal. When searching within a small region of fractal basin boundaries, the self‐similarity of fractal makes it possible to find all energy minima, maxima, and saddle points from which global minimum may be extracted. Compared with other methods, this approach is efficient, accurate, conceptually simple, and easy to implement. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1101–1108, 2000     

1-Chloro-1-(trichlorovinyl)cyclopropane : Molecular structure and conformation in the gaseous phase as determined by electron diffraction

A gas phase electron diffraction investigation of 1-chloro-1-(trichlorovinyl)cyclopropane at 65° showed the existence of one conformer having a perpendicular arrangement of the cyclopropyl- and the trichlorovinylgroup, with torsional angle τ = 91(3)° relative to τ = 180° for the antiperiplanar conformer (CCl-CClanti arrangement). Both the experimental data and a molecular mechanics calculation indicate the lower barrier toward the antiperiplanar form,less than 40 kJ · mol^-1. The second barrier was by molecular mechanics calculated to 60 kJ · mol^-1.     

Accurate predictions of water cluster formation, (H₂O)(n=2-10)

An efficient mixed molecular dynamics/quantum mechanics model has been applied to the water cluster system. The use of the MP2 method and correlation consistent basis sets, with appropriate correction for BSSE, allows for the accurate calculation of electronic and free energies for the formation of clusters of 2-10 water molecules. This approach reveals new low energy conformers for (H(2)O)(n=7,9,10). The water heptamer conformers comprise five different structural motifs ranging from a three-dimensional prism to a quasi-planar book structure. A prism-like structure is favored energetically at low temperatures, but a chair-like structure is the global Gibbs free energy minimum past 200 K. The water nonamers exhibit less complexity with all the low energy structures shaped like a prism. The decamer has 30 conformers that are within 2 kcal/mol of the Gibbs free energy minimum structure at 298 K. These structures are categorized into four conformer classes, and a pentagonal prism is the most stable structure from 0 to 320 K. Results can be used as benchmark values for empirical water models and density functionals, and the method can be applied to larger water clusters.     

Conformations of methylcyclooctane. A combined iterative force field—CNDO approach

A combined iterative force field—CNDO molecular orbital approach to conformations of methylcyclooctane is described. This hybrid method involves a full relaxation force-field calculation of conformer structures, followed by a single CNDO calculation on each structure.     

Molecular structure and conformations of benzenesulfonamide: gas electron diffraction and quantum chemical calculations

The molecular structure and conformational properties of benzenesulfonamide, C6H5SO2NH2, were studied by gas electron diffraction (GED) and quantum chemical methods (MP2 and B3LYP with different basis sets). The calculations predict the presence of two stable conformers with the NH2 group eclipsing or staggering the SO2 group. The eclipsed form is predicted to be favored by about 0.5 kcal/mol. According to GED, the saturated vapor over solid benzenesulfonamide at a temperature of 150(5) degrees C consists of the eclipsed conformer. The GED intensities, however, possess a very low sensitivity toward the vapor composition, and contributions of the anti conformer of up to 75% (at the 0.05 level of significance) or up to 55% (at the 0.25 level of significance) cannot be excluded. The molecule possesses C(sS) symmetry with the S-N bond perpendicular to the ring plane.     

Solvent dependence on conformational transition, dipole moment, and molecular geometry of 1,2-dichloroethane: insight from Car-Parrinello molecular dynamics calculations

We have investigated the molecular geometry and dipole moment distribution for the major conformational states of 1,2-dichloroethane (DCE) in three different solvents under ambient conditions using the Car-Parrinello mixed quantum mechanics/molecular mechanics method. The solvents studied were water, DCE, and chloroform. Within the time scale investigated, we find a conformational equilibrium existing between the gauche and trans forms of DCE in all three solvents. In the chloroform solvent, the conformational transition occurs more frequently than in water solvent and in liquid DCE (i.e., DCE solute in DCE solvent). The population of gauche conformer is more in the case of water solvent, while the trans conformer dominates in chloroform solvent. We report a bimodal nature of the dipole moment distribution for DCE in all three solute-solvents studied, where the peaks are attributed to the trans and gauche conformational states. The dipole moments of both of the conformational states increase with increasing polarity of the solvent. Also, with an increase in solvent polarity, an increase in the C-Cl bond length and magnitude of atomic charges in DCE has been observed. The increase in atomic charges of DCE is almost twice when the solvent is changed from chloroform to water.     

Theoretical study of the relative stability of rotational conformers of alpha and beta-D-glucopyranose in gas phase and aqueous solution

The alpha-beta anomer energy difference and the stability of 10 rotamers of counterclockwise D-glucopyranose were studied in vacuo and in aqueous solution at the B3LYP/6-31+G(d,p) level. To obtain the solute charge distribution and the solvent structure around it, we used the averaged solvent electrostatic potential from molecular dynamics method, ASEP/MD, which alternates molecular dynamics and quantum mechanics calculations in an iterative procedure. The main characteristics of the anomeric equilibrium, both in vacuo and in solution, are well reproduced. The relative stability of the different anomers is related to the availability of the free pairs of electrons in the anomeric oxygen to interact with the water molecules. The influence of solvation in the conformer equilibrium is also analyzed.     

Peak deconvolution in high-field asymmetric waveform ion mobility spectrometry (FAIMS) to characterize macromolecular conformations

Protonated poly(ethylene glycol), produced by electrospray ionization (ESI), with molecular weights ranging from 0.3 to 5 kDa and charge states from 1+ to 7+ were characterized using high-field asymmetric waveform ion mobility spectrometry (FAIMS). Results for all but some of the 3+ and 4+ charge states are consistent with a single gas-phase conformer or family of unresolved conformers for each of these charge states. The FAIMS compensation voltage scans resulted in peaks that could be accurately fit with a single Gaussian for each peak. The peak widths increase linearly with compensation voltage for maximum ion transmission but do not depend on m/z or molecular weight. Fitting parameters obtained from the poly(ethylene glycol) data were used to analyze conformations of oxidized and reduced lysozyme formed from different solutions. For oxidized lysozyme formed from a buffered aqueous solution, a single conformer (or group of unresolved conformers) was observed for the 7+ and 8+ charge states. Two conformers were observed for the 9+ and 10+ charge states formed from more denaturing solutions. Data for the fully reduced form indicate the existence of up to three different conformers for each charge state produced directly by ESI and a general progression from a more extended to a more folded structure with decreasing charge state. These results are consistent with those obtained previously by proton-transfer reactivity and drift tube ion mobility experiments, although more conformers were identified for the fully reduced form of lysozyme using FAIMS.     

Does the boat-like conformer exist for 1,8,8-trimethylbicyclo[3.2.1]Octan-3-one?

Neither molecular mechanics (MM2 and MM2′) nor molecular orbital (MNDO and $\text{ab}$$\text{initio}$) calculations confirmed the existence of a boat-like conformer for the title compound, recently proposed to exist up to 20% in hydrocarbon solvents based on the CD spectra.     

分子模拟技术在高分子科学实验中的应用

分子模拟技术是一项成熟的、有潜力的计算机实验技术,计算机具备高速稳定的图形处理能力,可以将实验结果以数据和图形的形式呈现出来,数据库技术可以方便的提取和存储各种分子模型和聚合物片段,通过可视化的三维图形的让学生更容易理解高分子科学的抽象概念,分子动力学的计算方法以牛顿力学为基础,在一定力场下建立周期性边界条件模型,通过几何构型优化和动力学运算,直观地了解到高分子的近程结构和聚集态结构,计算得出普通高分子实验无法得到微观相态结构,丰富了实验内容,开拓了高分子科学实验的新领域。     

Empirical relationship between structure and molecular optical rotation in six-membered cyclic compounds

The molecular optical rotation of a six-membered series of cyclic compounds has been calculated with a simple method which relates the sign and magnitude of the molecular optical rotation to the geometry, conformation and absolute configuration of the studied compounds. The optimised geometry of each conformer was calculated by molecular mechanics calculations. The values obtained seem to confirm the existence of a close relationship between the value of molecular optical rotation of a compound and its geometry.     

New diagnostic of the most populated conformer of tetrahydrofuran in the gas phase

The most populated conformer of tetrahydrofuran (C(4)H(8)O) has been diagnosed as the Cs conformer in the present study, jointly using experimental electron momentum spectroscopy (EMS) and quantum mechanics. Our B3LYP/6-311++G** model indicates that the C1 conformation, which is one of the three possible conformations of tetrahydrofuran produced by pseudorotation in the gas phase, is a transition state due to its imaginary frequencies, in agreement with the prediction from a recent ab initio MP2/aug-cc-pVTZ study (J. Chem. Phys. 2005, 122, 204303). The study has identified the fingerprint of the highest occupied molecular orbital (HOMO) of the C(s) (12a') conformer as the most populated conformer. The identification of the C(s) structure, therefore, leads to the orbital-based assignment of the ionization binding energy spectra of tetrahydrofuran for the first time, on the basis of the outer valence Green function OVGF/6-31G* model and the density functional theory (DFT) SAOP/ET-PVQZ model. The present study explores an innovative approach to study molecular stabilities. It also indicates that energetic properties are not always the most appropriate means to study conformer-rich biological systems.     

Spontaneous formation of super water-repellent fractal surfaces in mixed wax systems

Alkylketene dimers (AKDs) and triglyceride waxes form fractal surfaces spontaneously and show super water-repellent property. Spontaneous formation of fractal structures on their surfaces takes place when the meta-stable crystalline phase of the waxes transforms to the thermodynamically stable form of crystal. The triglyceride waxes form the meta-stable alpha-phase in whole specimen when solidified from their melt. In the case of AKD, on the other hand, only a small portion of the specimen solidifies in the meta-stable form of crystal. The surface of the AKD, however, becomes fractal in the whole part. We have, thus, examined the fractal structure formation in the mixed wax systems in which one wax forms fractal surfaces and the other one does not. In the stearic acid/tristearin mixed system as a typical one, the super water-repellent fractal surfaces form in the higher composition region of tristearin than that of the eutectic point in their mixture.     

Temperature-induced dynamical conformational disorder in 4-vinyl benzoic acid molecular crystals: a molecular simulation study

Extensive molecular simulations are carried out as a function of temperature to understand and quantify the conformational disorder in molecular crystals of 4-vinyl benzoic acid. The conformational disorder is found to be dynamic and associated with a flip-flop motion of vinyl groups. The population of minor conformer is less than 3% up to 300 K and is 13.2% at 350 K and these results are consistent with the experimental observations. At still higher temperatures, the population of minor conformer increases up to 25%. The evolution of structure at both molecular and unit-cell level of the molecular crystal as a function of temperature has been characterized by various quantities such as radial distribution functions, average cell parameters, volume, and interaction energies. The van't Hoff plot shows a nonlinear behavior at lower temperatures as it has been reported recently by Ogawa and co-workers in the case of stilbene, azobenzene, and N-(4-methylbenzylidene)-4-methylaniline molecular crystals. A set of rigid body simulations were also carried out to quantify the effect of conformational disorder on structural quantities such as unit-cell volume and interaction energy. The anomalous shrinkage of vinyl C=C bond length as a function of temperature has been explained by combining the results of simulations and a set of constrained optimizations using ab initio electronic structure calculations for various molecular structures differing in torsional angle.     

3-羰基吡唑质子转移过程的理论研究

采用密度泛函B3LYP／6—311G^＊＊方法,对3-羰基吡唑几何构型进行了全自由度优化,获得了它们的几何结构和电子结构．计算并考察了3-羰基吡唑的两种构象即syn和anti构象的稳定性以及3-羰基吡唑进行结构互变的质子转移过程的四种可能途径：（a）分子内质子转移;（b）水助质子转移;（C）同种二聚体双质子转移;（d）异种二聚体双质子转移．计算结果表明3-羰基吡唑的syn构象中N2-H型的稳定性大于N1-H型,进行质子转移时途径（C）所需要的活化能最小（52．78kJ／mol）,途径（a）所需要的活化能最大（200．59kJ／mol）;3,羰基吡唑的。anti构象中N1-H型的稳定性大于N2-H型,进行质子转移时途径（d）所需要的活化能最小（61．09kJ／mol）,途径（a）所需要的活化能最大（204．15kJ／mol）．     

The molecular structure of N-benzylidene-aniline

The molecular structure of N-benzylidene-aniline has been studied experimentally by the gas electron diffraction method, and also by molecular mechanics calculations. Both approaches gave the same results for the most stable conformer of the free molecule. The phenyl ring bonded to the carbon end of the CN bond was found to be coplanar with this bond, while the other phenyl ring was extensively (ca. 52°) rotated about the NΦ bond.     

Vibrational Circular Dichroism and Theoretical Study of the Conformational Equilibrium in (−)‐S‐Nicotine

We report an extensive study of the molecular and electronic structure of (?)‐S‐nicotine, to deduce the phenomenon that controls its conformational equilibrium and to solve its solution‐state conformer population. Density functional theory, ab initio, and molecular mechanics calculations were used together with vibrational circular dichroism (VCD) and Fourier transform infrared spectroscopies. Calculations and experiments in solution show that the structure and the conformational energy profile of (?)‐S‐nicotine are not strongly dependent on the medium, thus suggesting that the conformational equilibrium is dominated by hyperconjugative interactions rather than repulsive electronic effects. The analysis of the first recorded VCD spectra of (?)‐S‐nicotine confirmed the presence of two main conformers at room temperature. Our results provide further evidence of the hypersensitivity of vibrational optical activity spectroscopies to the three‐dimensional structure of chiral samples and prove their suitability for the elucidation of solution‐state conformer distribution.     

π-Hydrogen bonding wins over conventional hydrogen bonding interaction: a jet-cooled study of indole···furan heterodimer

In this study, we have explored the conformational landscape of the indole···furan dimer in a supersonic jet by using resonant two-photon ionization (R2PI) and IR-UV double-resonance spectroscopic techniques combined with dispersion-corrected density functional theory (DFT) calculations. Only one conformer of the dimer has been observed in the experiment. DFT/B97-D level calculation shows that N-H···π hydrogen-bonded conformer (T') is energetically more stable than the N-H···O hydrogen-bonded conformer (HB). Natural bond orbital (NBO) calculation also shows that the hydrogen-bonding interaction in the HB conformer is very weak. Finally, the structure of the observed dimer has been determined to be tilted T-shaped N-H···π hydrogen-bonded (T') from very excellent agreement between experimental and theoretical N-H stretch frequency. The most significant finding of this study is the first-time observation of a N-H···π bound conformer of a dimer, which wins over a conventional hydrogen-bonded conformer of the dimer.     

Pyrrolizidine alkaloids necine bases: Ab initio,semiempirical, and molecular mechanics approaches to molecular properties

The structural stabilities of endo and exo conformations of retronecine and heliotridine molecules were analyzed using different ab initio, semiempirical, and molecular mechanics methods. All electron and pseudopotential ab initio calculations at the Hartree-Fock level of theory with 6-31G* and CEP-31G* basis sets provided structures in excellent agreement with available experimental results obtained from X-ray crystal structure and ¹H-NMR (nuclear magnetic resonance) studies in D₂O solutions. The exo conformations showed a greater stability for both molecules. The most significant difference between the calculations was found in the ring planarity of heliotridine, whose distortion was associated with the interaction between the O(11)H group and the C(1)-C(2) double bond as well as with a hydrogen bond between O(11)H and N(4). The discrepancy between pseudopotential and all-electron optimized geometries was reduced after inclusion of the innermost electrons of C(1), C(2), and N(4) in the core potential calculation. The MNDO, AM1, and PM3 semiempirical results showed poor agreement with experimental data. The five-membered rings were observed to be planar for AM1 and MNDO calculations. The PM3 calculations for exo-retronecine showed a greater stability than the endo conformer, in agreement with ab initio results. A good agreement was observed between MM3 and ab initio geometries, with small differences probably due to hydrogen bonds. While exo-retronecine was calculated to be more stable than the endo conformer, the MM3 calculations suggested that endo-heliotridine was slightly more stable than the exo form. © 1996 by John Wiley & Sons, Inc.