去质子化精氨酸分子的稳定结构和化学性质

采用从头算方法系统研究了气相去质子化精氨酸的势能面,在B3LYP/6-31G(d)水平,找到了一系列新的稳定构型,其中能量最低的构型比之前报道的低了6.56 kJ/mol. 精氨酸的去质子化发生在羧基端,存在两种同分异构体. 这两种异构体之间存在很高的能垒,因此有着非常不同的红外光谱特征. 理论计算得到的精氨酸的质子解离能和气相酸性与实验值符合很好.     

N-甲替甲酰胺-水的氢键团簇的从头计算研究

利用从头计算方法在MP2 / 6 31+G 和MP2 / 6 311++G(d ,p)水平上对N 甲替甲酰胺 (NMF) 水氢键团簇进行了研究 .计算给出了所有中性和离子化NMF H2 O团簇的优化结构、解离通道以及解离能 .对于N 甲替甲酰胺 ,顺式结构比反式结构具有更低的能量 .对于质子化的NMF ,质子倾向于连接在甲替甲酰胺的氧原子上 .计算结果表明 ,NMF的顺式和反式构型都可以与水分子形成线型的氢键结构 .尽管NMF反式结构比顺式结构能量高 ,但由于反式结构能与水分子形成双氢键 ,因此能更稳定的存在 .N 甲替甲酰胺 水团簇电离后 ,无论顺式和反式结构均有质子化产物生成 .     

质子化丙酮分子团簇的结构和振动光谱

用密度泛函B3LYP/ 6 3 1G(d)方法 ,对质子化丙酮分子团簇 (CH3COCH3) nH+ (n =1～ 7)弱相互作用体系进行了全自由度能量梯度优化 ,得到了该系列团簇的稳定结构及其对应的体系能量 .通过对构型的分析得出了质子化丙酮分子团簇 (CH3COCH3) nH+ (n =1～ 7)的生长规律 .计算了中性丙酮分子团簇体系的质子亲合能并总结出其变化趋势 .分析讨论了质子化团簇的红外振动光谱 ,发现质子化团簇的振动光谱普遍较中性环型团簇的振动光谱复杂 ,最强的振动峰来源于质子在溶剂壳中两个氧原子之间的振动 ,而且随着团簇尺寸的增加羰基的伸缩振动峰的数目也随之增多     

355 nm激光作用下质子化丙酮-水团簇的多光子电离质谱

为研究由氢键形成的超分子体系内的质子化构型,利用355 nm多光子电离(MPI)技术结合飞行时间质谱（TOF-MS）得到丙酮和水的系列团簇质谱.实验观察到的主要产物是质子化的丙酮水团簇.其团簇构型归纳为(CH3COCH3)n(H2O)n－2H+,(CH3COCH3)n(H2O)n－1H+和(CH3COCH3)n(H2O)nH+.利用Gaussian 98程序优化了团簇的离子态构型,通过频率验证了构型的稳定性,并给出了相关能量和零点修正能.     

密度泛函方法研究气相胞嘧啶的互变异构化

分别采用7种基组、3种理论方法对胞嘧啶异构体Cyt1的结构进行优化,通过与Cyt1的实验结果进行比较,选取了适合研究胞嘧啶分子的B3LYP/6311+G方法.用该方法对胞嘧啶分子的8种异构体构型进行了充分优化,研究了其中能量较低的6种胞嘧啶异构体的互变异构化过程.对于得到的所有优化构型都进行了频率分析.对于基态构型,所有的频率都是正的;对于过渡态构型,只有一个虚频.同时,做了详尽的内禀反应坐标计算,以保证所得到的过渡态连接相应的始末异构体.所有给出的能量都已做了零点能校正.理论研究结果可以对已有的实验结果给予合理解释.     

DFT Calculation of Glycine with Methanols Clusters

应用DFT计算方法研究了中性和离子甘氨酸-甲醇氢键团簇Glycine-(CH3OH)n (n=1～6). 对中性和离子的甘氨酸与1～6个甲醇分子组成系列团簇的初始构型在B3LYP/6-13＋G*水平下进行全优化,确定最低能量稳定构型,并对其氢键结构进行分析. 理论预测表明,当n≤3时,在最稳定的中性构型中,所有甲醇分子优先聚集在羧酸基团附近;而在离子构型中,甲醇分子可在氨基和羧酸基团之间形成键桥,且该构型为最稳定构型. 当团簇中的甲醇数量达到5和6时,两种最稳定构型(中性和离子)的能量趋向等同.     

基态S3分子的结构与解析势能函数

本文采用Gaussian03 B3P86方法,在6-311 G(3d2f)基组水平上,对S3分子进行几何优化理论计算,计算结果表明S3分子基态1A1最稳定的构型为C2V构型,其离解能为10.8372 eV,能量最小值为-1193.19946 a.u.,计算还得到了谐振频率、力常数,计算结果与实验值符合得很好.在此基础上利用多体展式理论方法得到了S3分子的解析势能函数和等值势能图,势能函数正确反映了S3分子的构型与能量变化.     

Ab initio Study on Structures and Isomerization of Magnesium Fluorosilylenoid H2SiFMgF

采用从头算分子轨道理论对镁氟类硅烯H2SiFMgF的构型及异构化进行了研究. 在B3LYP/6-31G(d,p)和G3MP2B3水平上找出四种构型及三种过渡态，并进行了全优化. 在B3LYP/6-31G(d,p)的优化参数基础上，得到了各构型的振动频率，计算了e29Si的化学位移.在B3LYP/6-31G(d,p)水平上，以四氢呋喃为溶剂，采用可极化连续模型研究了溶剂化效应. 并采用内察反应坐标方法对过渡态进行了验证. 研究结果表明，四面体结构具有最低的能量，最稳定. 四面体、三元环和p-络合物结构为实验可探测结构，σ-络合物结构具有最高能量，也是不能存在的构型     

苯二聚体的密度泛函和分子力场的理论研究

针对苯二聚体中的六种重要构象的相互作用,对四种新的密度泛函方法(B97-D、BLYP-D3、M06-2X、XYG3)和常用的分子力场(CHARMM、AMBER、MM3、AMOEBA)进行了系统的评测.研究结果不仅突出了这些新型密度泛函方法,特别是XYG3泛函在 描述- 相互作用体系的实用性,同时也为进一步发展适合描述相互作用体系的分子力场奠定了基础.     

NH4+离子的结构和振动光谱

用Gaussian 03W 程序中的密度泛函B3LYP/6-31+G(d)方法对氨分子的质子化产物NH4+离子的可能几何构型进行了结构优化和频率计算，得到了它的稳定结构和红外振动光谱. 通过对计算结果的分析发现，NH4+的稳定构型为正四面体结构，属Td分子点群；它的红外振动光谱中共有两个位于3390 cm-1和1478 cm-1处的三重简并振动峰，分别对应着N-H键的反对称伸缩振动和弯曲振动.     

Vibrational spectroscopy and DFT calculations of di‐amino acid peptides: α‐ and β‐N‐acetyl‐L‐Asp‐L‐Glu in the solid state

Experimental vibrational spectroscopic studies and density functional theory (DFT) calculations of the di‐amino acid peptide derivatives α‐ and β‐N‐acetyl‐L‐Asp‐L‐Glu have been undertaken. Raman and infrared spectra have been recorded for samples in the solid state. DFT simulations were conducted using the B3‐LYP correlation functional and the cc‐pVDZ basis set to determine energy minimized/geometry optimized structures (based on a single isolated molecule in the gaseous state). Normal coordinate calculations have provided vibrational assignments for fundamental modes, including their potential energy distributions. Significant differences are observed between α‐ and β‐N‐acetyl‐L‐Asp‐L‐Glu both in the computed structures and in the vibrational spectra. The combination of experimental and calculated spectra provide an insight into the structural and vibrational spectroscopic properties of di‐amino acid peptide derivatives. Copyright © 2009 John Wiley & Sons, Ltd.     

Condensed-phase properties of n-alkyl-amines from molecular dynamics simulations using charge equilibration force fields

Charge equilibration force fields are applied to molecular dynamics simulations of liquid straight-chain alkyl-amine systems—methylamine, ethylamine, and n-propylamine. The models used are based on the CHARMM charge equilibration force field developed for methylamine and applied here to simulations for larger n-alkyl amines. The effects of the parameter set used for extension to larger systems, and the importance of defining the extent of molecular charge transfer via judicious selection of charge normalization units are considered and evaluated. Condensed-phase properties including molecular volumes, enthalpy of vaporization, isothermal compressibility, isobaric heat capacity, dielectric constants, and self-diffusion constants are calculated for each system. Molecular volumes are predicted to within 2.3–18.0% of the experimental values, where the error increases with the size of the molecule. Enthalpy of vaporization is predicted to be within 2.5–24.4% of experiment. Dielectric constants are calculated within 0.5–17.3% of experimental values. Properties of ethylamine and n-propylamine (to which the original charge equilibration force field was not calibrated/fitted) calculated using parameters from an alkane model outperformed those from a lysine model in most cases by up to a 16% reduction in error from experiment. Compared to previous MD simulations [T. Kosztolanyi, I. Bako, and G. Palinkas, Hydrogen Bonding in Liquid Methanol, Methylamine, and Methanethiol Studied by Molecular-Dynamics Simulations. Journal of Chemical Physics, 2003. 118(10): 4546–4555.], the radial distribution functions (RDF) of methylamine showed reduced values of the first maximum and minimum position by up to 8.2% for N–N and 12.4% for N–H. The need for careful treatment of charge transfer schemes is suggested by the significant difference in condensed-phase and single-molecule properties when charge transfer was normalized in a partitioned n-propylamine molecule as opposed to normalization over the whole molecule. The partitioned normalization reduced the error from experiment nearly 15% for molecular volume and 10% for enthalpy of vaporization. The influence of various applied normalization schemes on condensed-phase and select gas-phase properties (gas-phase dipole moment) was greater than the effects of different parameterizations, indicating the importance of a proper selection of charge normalization unit in the application and parameterization of charge equilibration force fields for small molecules to larger biological assemblies.     

Shell sources of stationary axisymmetric gravitational fields

A number of solutions for material shell sources of stationary axisymmetric gravitational fields are presented. Explicit solutions are found for shells lying on equipotential hypersurfaces (g _tt = const) and generating static monopole fields in prolate and oblate spheroidal coordinates (Zipoy-Voorhees fields). Numerical solutions are found for shells lying on hypersurfaces of constantg /g and generating Kerr- and Tomimatsu-Sato ( = 2) fields. The shells have minimum areas allowed by the energy conditions of Hawking and Ellis.     

The effect of a magnetic field on Jahn-Teller ordering in the monoclinic crystal RbDy(WO4)2

This paper presents the results of a study of the thermal properties of monoclinic single-crystal RbDy(WO₄)₂ at temperatures of 2–15 K and in magnetic fields up to 6 T. From the results of measurements of the heat capacity and thermograms, two structural phase transitions are detected, at T _c1=4.9 K and T _c2=9.0 K. The transformation from the high-temperature phase to the low-temperature phase occurs via an intermediate phase. The field dependences of the critical temperatures are found for various magnetic-field orientations. H-T phase diagrams are constructed for H‖a and H‖c. An anomalous increase (by almost an order of magnitude) of the relaxation time of the system, associated with structural instability of the crystal lattice, is detected in the region of the structural phase transitions. A symmetry analysis is carried out, and possible crystal structures of the low-temperature phase are indicated. Fiz. Tverd. Tela (St. Petersburg) 40, 2221–2225 (December 1998)     

Experimental and theoretical structure and vibrational analysis of ethyl trifluoroacetate,CF3CO2CH2CH3

The molecular structure and conformational properties of ethyl trifluoroacetate, CF₃CO₂CH₂CH₃, were determined in the gas phase by electron diffraction, and vibrational spectroscopy (IR and Raman). The experimental investigations were supplemented by ab initio (MP2) and DFT quantum chemical calculations at different levels of theory. Experimental and theoretical methods result in two structures with C_s (anti–anti) and C₁ (anti–gauche) symmetries, the former being slightly more stable than the latter. The electron‐diffraction data are best fitted with a mixture of 56% anti–gauche and 44% anti–anti conformers. The conformational preference was also studied using the total energy scheme, and the natural bond orbital scheme. Also, the infrared spectra of CF₃CO₂CH₂CH₃ are reported for the gas, liquid and solid states, as is the Raman spectrum of the liquid. The comparison of experimental averaged IR spectra of C_s and C₁ conformers provides evidence for the predicted conformations in the IR spectra. Harmonic vibrational wavenumbers and scaled force fields have been calculated for both conformers. Copyright © 2009 John Wiley & Sons, Ltd.     

In-water gas combustion for thrust production

The paper presents the results of experimental study for hydrodynamic processes occurring during combustion of a stoichiometric mixture propane-oxygen in combustion chambers with different configurations and submerged into water. The pulses of force acting upon a thrust wall were measured for different geometries: cylindrical, conic, hemispherical, including the case of gas combustion near a flat thrust wall. After a single charge of stoichiometric mixture propane-oxygen is burnt near the thrust wall, the process of cyclic generation of force pulses develops. The first pulse is generated due to pressure growth during gas combustion, and the following pulses are the result of hydrodynamic pulsations of the gaseous cavity. Experiments demonstrated that efficient generation of thrust occurs if all bubble pulsations are used during combustion of a single gas combustion. In the series of experiments, the specific impulse on the thrust wall was in the range 10⁴–10⁵ s (10⁵–10⁶ m/s) with account for positive and negative components of impulse.     

Computer simulations and analysis of structural and energetic features of crystalline cage energetic compound: 2, 4, 6, 8, 12‐pentanitro‐10‐(3, 5, 6‐trinitro (2‐pyridyl))‐2, 4, 6, 8, 12‐hexaazatetracyclo [5.5.0.03,11.05,9]dodecane

First principles molecular orbital and plane‐wave ab initio calculations have been used to investigate the structural and energetic properties of a new cage compound 2, 4, 6, 8, 12‐pentanitro‐10‐(3, 5, 6‐trinitro (2‐pyridyl))‐2, 4, 6, 8, 12‐hexaazatetracyclo [5.5.0.0^3,11.0^5,9]dodecane (PNTNPHATCD) in both the gas and solid phases. The molecular orbital calculations using the density functional theory methods at the B3LYP/6‐31G(d,p) level indicate that both the heat of formation and strain energy of PNTNPHATCD are larger than those of 2, 4, 6, 8, 10, 12‐hexanitro‐2, 4, 6, 8, 10, 12‐hexaazatetracyclo [5.5.0.0.0] dodecane (CL‐20). The infrared spectra and the thermodynamic property in gas phase were predicted and discussed. The calculated detonation characteristics of PNTNPHATCD estimated using the Kamlet–Jacobs equation equally matched with those of CL‐20. Bond‐breaking results on the basis of natural bond orbital analysis imply that C–C bond in cage skeleton, C–N bond in pyridine, and N–NO₂ bond in the side chain of cage may be the trigger bonds in the pyrolysis. The structural properties of PNTNPHATCD crystal have been studied by a plane‐wave density functional theory method in the framework of the generalized gradient approximation. The crystal packing predicted using the Condensed‐phase Optimized Molecular Potentials for Atomistic Simulation Studies (COMPASS) force fields belongs to the Pbca space group, with the lattice parameters a = 20.87 Å, b = 24.95 Å, c = 7.48 Å, and Z = 8, respectively. The results of the band gap and density of state suggest that the N–NO₂ bond in PNTNPHATCD may be the initial breaking bond in the pyrolysis step. As the temperature increases, the heat capacity, enthalpy, and entropy of PNTNPHATCD crystal all increase, whereas the free energy decreases. Considering that the cage compound has the better detonation performances and stability, it may be a superior high energy density compound. Copyright © 2015 John Wiley & Sons, Ltd.     

Analysis of the interface configuration and flow characteristics in tanks in a multiphase liquid–gas system using numerical simulation

A multiphase study was conducted using a turbulence model of large eddy simulation to investigate the interaction between the gaseous phase and the interface and its respective behaviour until the liquid phase movement was established, first in the near interface, as well as the presence of turbulent structures in the study of transport between phases. The results are shown for three surface configurations: a surface with waves in which the Reynolds number and friction velocity of the gaseous phase are, respectively, 210 and 0.25 m/s; a surface with small undulations, 86 and 0.10 m/s; and a flat surface, 43 and 0.05 m/s. Coherent structures are detected on both sides of the interface; these are intensified and less elongated for larger Reynolds numbers. Additionally, the interface exhibits distinct behaviour with regard to the examined phases. For the gaseous phase, it behaves like a no-slip surface.