Molecular Structure,Vibrational Spectra,Molecular Docking,and ADMET Study of Cellulose Triacetate II

Optics and Spectroscopy - People have started to look for alternative sources because of the health problems created by petrochemical products used in all areas of human life and environmental...     

Vacuum Radiation,Entropy, and Molecular Chaos

Vacuum radiation causes a particle to make a random walk about its dynamical trajectory. In this random walk the root mean square change in spatial coordinate is proportional to t ^1/2, and the fractional changes in momentum and energy are proportional to t ^−1/2, where t is time. Thus the exchange of energy and momentum between a particle and the vacuum tends to zero over time. At the end of a mean free path the fractional change in momentum of a particle in a gas is very small. However, at the end of the mean free path each particle undergoes an interaction that magnifies the preceding change, and the net result is that the momentum distribution of the particles in a gas is randomized in a few collision times. In this way the random action of vacuum radiation and its subsequent magnification by molecular interaction produces entropy increase. This process justifies the assumption of molecular chaos used in the Boltzmann transport equation.     

Molecular spectra, quantum chaos, and scars

Low resolution features in the spectra of classically chaotic atomic and molecular systems are known to be related to recurrences induced by classical periodic motions. In this paper we study how such characteristics reveal in the LiNC/LiCN isomerizing molecular system, and describe how the transition from regularity to classical chaos that takes place in this system shows up at quantum level in the structure of the corresponding wavefunctions in the form of “scars”. To this end we use some projection techniques, based on the propagation of wave packets, which have been developed in our laboratory. In this way some regions at the border of the chaotic region can be detected, in which the systematics of “scar” formation can be studied at a very elementary level, without complications due to the high level density which are customarily used in this type of studies in order to achieve the semiclassical limit. Received: 16 March 1998 / Revised: 23 April 1998 / Accepted: 4 May 1998     

Molecular,metabolic, and genetic control: An introduction

The living cell is a miniature, self-reproducing, biochemical machine. Like all machines, it has a power supply, a set of working components that carry out its necessary tasks, and control systems that ensure the proper coordination of these tasks. In this Special Issue, we focus on the molecular regulatory systems that control cell metabolism, gene expression, environmental responses, development, and reproduction. As for the control systems in human-engineered machines, these regulatory networks can be described by nonlinear dynamical equations, for example, ordinary differential equations, reaction-diffusion equations, stochastic differential equations, or cellular automata. The articles collected here illustrate (i) a range of theoretical problems presented by modern concepts of cellular regulation, (ii) some strategies for converting molecular mechanisms into dynamical systems, (iii) some useful mathematical tools for analyzing and simulating these systems, and (iv) the sort of results that derive from serious interplay between theory and experiment. (c) 2001 American Institute of Physics.     

The Few-Body Approximation in Nuclear,Atomic, and Molecular Physics

The quantum theory of few-body scattering based on Faddeev-Yakubovsky integral and differential equa¬tions is applied to calculations of various processes (elastic, inelastic, atom exchange, and dissociative) in nuclear, atomic, and molecular physics. Analytical solutions of these equations are presented for various limiting cases. The methods used for solving the integral and differential systems of equations are discussed.     

Molecular orbital study of germanium,germanium-gallium and germanium-arsenic clusters

The quasirelativistic INDO/1 method has been used to generate molecular orbitals for some {Ge _x }, doped {Ge _x Ga _y } and {Ge _x As _y } clusters. These one-electron energy levels predefine the density of states (DOS) and/or hole functions. The effect of the cluster size (x=24, 56, 92) and that of dopants on the DOS profiles are discussed. The calculations are compared with those generated by periodic crystal orbitals of the EHT quality.     

Thermodynamics of the Dimer Formation of 2I,3I-O-(o-Xylylene)-per-O-Me-γ-cyclodextrin: Fluorescence, Molecular Mechanics and Molecular Dynamics

The thermodynamics of the dimer formation of 2^I,3^I-O-(o-xylylene)-per-O-Me-γ-cyclodextrin (XmγCD) in aqueous solution was studied by fluorescence techniques, Molecular Mechanics and Molecular Dynamics. Lifetime averages á t ñ \left\langle \tau \right\rangle , obtained from fluorescence decay profiles upon excitation of the xylylene appended group, were used as the property sensitive to the association process. The dimerization equilibrium constants (K _D) were obtained from non-linear regression analysis of the plots of á t ñ \left\langle \tau \right\rangle against [XmγCD] at several temperatures and they were compared with the values obtained for the counterparts Xmα- and XmβCDs. The van’t Hoff plot allows us to obtain the ΔH and ΔS showing that the dimerization process was also entropically disfavoured. Molecular Mechanics as well as Molecular Dynamics calculations in the presence of water were also employed to study the conformational behaviour of isolated XmγCDs, the possible structure of the dimers formed and the driving forces involved in such association processes. Results indicate that those conformations where Xy moiety does not block the cavity entrance are favoured. Dimers are preferably formed by head-to-head CD approaching. However, the formation of stable head-to-tail is not dismissed.     

Nanoparticle decoration with surfactants: Molecular interactions,assembly, and applications

Nanostructures of diverse chemical nature are used as biomarkers, therapeutics, catalysts, and structural reinforcements. The decoration with surfactants has a long history and is essential to introduce specific functions. The definition of surfactants in this review is very broad, following its lexical meaning “surface active agents”, and therefore includes traditional alkyl modifiers, biological ligands, polymers, and other surface active molecules. The review systematically covers covalent and non-covalent interactions of such surfactants with various types of nanomaterials, including metals, oxides, layered materials, and polymers as well as their applications. The major themes are (i) molecular recognition and noncovalent assembly mechanisms of surfactants on the nanoparticle and nanocrystal surfaces, (ii) covalent grafting techniques and multi-step surface modification, (iii) dispersion properties and surface reactions, (iv) the use of surfactants to influence crystal growth, as well as (v) the incorporation of biorecognition and other material-targeting functionality. For the diverse materials classes, similarities and differences in surfactant assembly, function, as well as materials performance in specific applications are described in a comparative way. Major factors that lead to differentiation are the surface energy, surface chemistry and pH sensitivity, as well as the degree of surface regularity and defects in the nanoparticle cores and in the surfactant shell. The review covers a broad range of surface modifications and applications in biological recognition and therapeutics, sensors, nanomaterials for catalysis, energy conversion and storage, the dispersion properties of nanoparticles in structural composites and cement, as well as purification systems and classical detergents. Design principles for surfactants to optimize the performance of specific nanostructures are discussed. The review concludes with challenges and opportunities.     

Chemomechanical Coupling of Molecular Motors: Thermodynamics, Network Representations, and Balance Conditions

Molecular motors are considered that convert the chemical energy released from the hydrolysis of adenosine triphosphate (ATP) into mechanical work. Such a motor represents a small system that is coupled to a heat reservoir, a work reservoir, and particle reservoirs for ATP, adenosine diphosphate (ADP), and inorganic phosphate (P). The discrete state space of the motor is defined in terms of the chemical composition of its catalytic domains. Each motor state represents an ensemble of molecular conformations that are thermally equilibrated. The motor states together with the possible transitions between neighboring states define a network representation of the motor. The motor dynamics is described by a continuous-time Markov process (or master equation) on this network. The consistency between thermodynamics and network dynamics implies (i) local and nonlocal balance conditions for the transition rates of the motor and (ii) an underlying landscape of internal energies for the motor states. The local balance conditions can be interpreted in terms of constrained equilibria between neighboring motor states; the nonlocal balance conditions pinpoint chemical and/or mechanical nonequilibrium.     

峨山褐煤的分子结构和分子模拟

作为重要的化石能源，褐煤资源潜力巨大、分布广泛但综合利用率低。研究褐煤的分子结构模型，有助于预测褐煤在热解、液化和气化过程中的化学反应机理及反应路径，进而提高褐煤的综合应用水平。以云南峨山褐煤为研究对象，利用傅里叶变换红外光谱、13C核磁共振波谱及X射线光电子能谱等分析测试方法，获取了峨山褐煤的含碳、含氧及含氮结构参数。在此基础上，借助Gaussian 09计算平台，采用量子化学建模的方法构建并优化了峨山褐煤的分子结构模型。研究结果表明：峨山褐煤的芳碳率为39.20%，芳香碳结构主要为苯和萘，且芳香桥头碳与周边碳的比值χ_b为0.07；脂碳率为49.51%，脂肪碳结构主要为亚甲基，季碳和氧接脂碳；氧原子主要存在于羟基、醚氧、羰基和羧基结构中；含氮结构则以吡啶为主。基于元素分析、13C 核磁共振波谱分析，又经过热重实验消除褐煤中残余水分的影响后，计算出峨山褐煤的分子式为C₁₅₃H₁₃₇O₃₅N₂。依据分子式及分析结果计算出峨山褐煤的结构单元含量并构建出其初始结构模型，采用半经验法PM 3基组及密度泛函理论M06-2X/3-21G基组对初始分子构型进行优化。优化后的分子模型具有明显的三维立体特征，芳香环之间较为分散且在空间中排列不规则，芳香簇主要通过亚甲基、醚氧基、羰基、酯基和脂肪环连接，含氧官能团主要分布在分子边缘，脂肪族侧链较多。对优化后的分子模型进行振动频率计算进而获得了分子模型的模拟红外光谱，其与实验红外谱图吻合度良好，证明了峨山褐煤分子结构模型的准确性、合理性。分子结构模型的构建有利于直观地了解峨山褐煤的分子结构特征，从而有助于从微观分子角度研究峨山褐煤的宏观性质。同时，峨山褐煤分子结构模型可为其在热解、液化和气化等领域研究中提供理论指导。     

FTIR Emission Spectra, Molecular Constants, and Potential Curve of Ground State GeO

Extensive new high-temperature, high-resolution FTIR emission spectroscopy measurements for the five common isotopomers of GeO are combined with previous diode laser and microwave measurements in combined isotopomer analyses. New Dunham expansion parameters and an accurate analytical potential energy function are determined for the ground X1Sigma+ state. Copyright 1999 Academic Press.     

Molecular gases as a source of coherent,tunable XUV radiation

Coherent and broadly tunable over 3500 cm^-1 extreme ultraviolet (XUV) radiation from 935 to 967 Å has been generated by frequency tripling the second harmonic output of a rhodamine 590 pulsed dye laser in molecular nitrogen and carbon monoxide. The scheme exploits high lying Rydberg and valence states of these gases and leads to the production of about 5 × 10⁹ XUV photons per pulse corresponding to a conversion efficiency of 5 × 10^-6.     

Mechanical,Thermal, and Surface Properties of Ultrahigh Molecular Weight Polyethylene/Polypropylene Blends

Various compositions of ultrahigh molecular weight polyethylene/polypropylene (UHMWPE/PP) blends were prepared in decalin, with the rheological, mechanical, thermal, and surface properties of the blends being determined using the solution cast film. Viscosity and mechanical properties of the blends decreased below the additivity value with increasing PP content implying that PP molecules disturb the entanglement of UHMWPE. Contact angle of the blend films with a water drop increased with increasing content of PP. The atomic force microscope (AFM) images showed that the surface of cast UHMWPE was very smooth whereas that of cast PP was very uneven. For blends, the surface became rough and uneven with increasing content of PP. The melting temperature of PP (T _mP) decreased in the blends with increasing UHMWPE content while that of UHMWPE (T _mU) remained almost constant in blends.