Quantum chemical studies on 1 charged forms of nitroglycerine

Semiempirical quantum chemical calculations at the level of AM1 (UHF) method are performed on the neutral as well as 1 charged systems originated from nitroglycerine. The geometry optimized systems standing for 1 charged forms fragmented. All the neutral and charged systems are found to be stable and exothermic with the exception of cationic system which is endothermic in nature. The fragmentation occurs by the cleavage of ester O–N bond of the terminal ester group in the charged forms while in the cationic form also the rapture of C–C bond occurs.     

Analysis and characterisation of nitroglycerine based explosives by proton magnetic resonance spectrometry

It has been shown that by using 500 MHz ¹H NMR it is possible, without prior separation, to quantify individual nitroaromatic compounds present in commercial nitroglycerine based explosives (gelignites). Patterns within the quantitative data provide a good degree of sample batch characterisation; typing of the explosive is achieved via total nitroaromatic content.     

Molecular dynamics simulations and quantum chemical calculations on β-cyclodextrin spironolactone complex

Molecular dynamics simulations on β-cyclodextrin in vacuo, with water and complexed with spironolactone (SP) were performed at a temperature of 300 K over a period of 1 ns. Two different orientations of SP in the cavity were considered. Along with conformational parameters, the formation of hydrogen bonds has been monitored during the whole simulation time. Cyclodextrins have the capability to form hydrogen bonds with the surrounding water molecules or intramolecular ones. The incorporation of ligands into the hydrophobic interior of β-cyclodextrin changes the preference of hydrogen bonds significantly and results in a contribution to the decrease of flexibility. Quantum chemical calculations on SP β-CD inclusion complex were performed to determine the interaction energy and to prove the applicability of various methods. Although all applied methods describe reasonable geometries for the association complex, higher level methods (e.g., B3LYP/6-31G(d,p)) seem to be necessary to determine reliable interaction energies.     

Molecular potential-energy surfaces for chemical reaction dynamics

This paper reviews the construction of molecular potential-energy surfaces by an interpolation method which has been developed over the last several years. The method uses ab initio quantum chemistry calculations of the molecular electronic energy in an automated procedure to construct global potential- energy surfaces which can be used to simulate chemical reactions with either classical or quantum dynamics. The methodology is explained and several applications are presented to illustrate the approach. Received: 22 February 2002 / Accepted: 2 May 2002 / Published online: 6 November 2002 Correspondence to: M. A. Collins e-mail: collins@rsc.anu.edu.au Acknowledgements. The methods described in this overview are the result of collaborations with former members of my group, in particular with Josef Ischtwan, Meredith Jordon, Keiran Thompson and Ryan Bettens. I am also indebted for inspiration gained from many discussions with my colleagues Leo Radom and Donghui Zhang (National University of Singapore). This work has been supported by the Supercomputer Facility of the Australian National University and the Australian Partnership for Advanced Computing.     

Molecular dynamics studies on octadecylammonium chloride at the air/liquid interface

Molecular dynamics simulations on surfactant octadecylammonium chloride at the air/liquid interface were performed. It was found that the alkyl chains of octadecylammonium would change to order with increasing the concentration of octadecylammonium at the air/liquid interface. Some functions, such as the concentration distributions, the radial distribution function and the mean squared displacement (MSD) were evaluated to investigate the structural properties of interface. We found that the salts can affect octadecylammonium aggregate at the interface: (1) univalent ions, such as chloride and sodium ions, affect slightly the structure of monolayer and (2) bivalent ions, such as sulfate or calcium ions, affect greatly, especially for the bivalent negative ions.     

新型二肽类长链状化合物的分子动力学和量子化学研究

用分子动力学方法对5种新型肽类长链状化合物进行了构象研究,所得结果证明我们的构象搜索方法有效。分子L~3内的芳环堆积作用使整个分子具有特殊结构,这种结构特征可能使其具有特殊生物功能,该结果为药物分子设计提供了有用的信息。量子化学计算表明分子内形成的负电荷空穴,将使其易与受体结合。     

Molecular dynamics with quantum statistics: time correlation functions and weakly bound nano-clusters

An account of recent developments in the study of molecular dynamics with the inclusion of quantum exchange effects is presented. Approaches for quantum dynamical calculations are reviewed and the determination of time correlation functions is a special point of focus. It is shown that the exact basis set techniques can be used to perform highly accurate calculations but are restricted to relatively small systems since computational cost scales exponentially with system size. Alternate formulations can be introduced to circumvent this problem, and semi-classical initial value representation and Feynman path centroid approaches are considered. It is then showed that from a practical point of view, for complex bosonic systems such as doped helium clusters, Quantum Monte Carlo techniques can currently be used for the calculation of quantities of experimental interest. A perspective on future prospects for the calculation of real time correlation functions of bosonic nano-scale systems is presented     

Molecular modeling and dynamics of neuropeptide Y

Summary A combination of molecular modeling and molecular dynamics (MD) is used to determine a theoretical structure for neuropeptide Y (NPY). Starting with the X-ray structure for avian pancreatic polypeptide (APP), the substituted amino acids were mutated, the side chains oriented to local potential energy minima, and the entire structure minimized and subjected to an MD simulation. Comparison of the resulting NPY structure with APP X-ray and MD results showed secondary structural elements to be maintained and RMS fluctuations to be similar, although differences in both were observed. The approach presented offers a means to study the structure-function relationships of NPY and other similar polypeptides when combined with pharmacological measurements.Abbreviations NPY Neuropeptide Y - APP Avian pancreatic polypeptide - ABNR Adopted-basis Newton Raphson - MD Molecular dynamics     

Membrane for in situ optical detection of organic nitro compounds based on fluorescence quenching

Fluorescent membrane formulations for detecting organic nitro compounds by fluorescence quenching were evaluated. The most sensitive membrane is prepared by solvent casting from cyclohexanone to incorporate pyrenebutyric acid into cellulose triacetate plasticized with isodecyl diphenylphosphate. The response follows the Stern-Volmer law for 2,4,6-trinitrotoluene (TNT) and 2,4-dinitrotoluene (DNT). The membrane also responds to hexahydro-1,3,5-tri- nitro-1,3,5-triazine (RDX). For a given set of conditions, the primary factor determining sensitivity is the extent to which each nitro compound partitions into the membrane. Detection limits are ca. 2 mg l^?1 for DNT and TNT and 10 mg l^?1 for RDX. Nitrogen purging prior to the measurement enhances the sensitivity and eliminates interference from oxygen. The membrane is designed to be used for remote optical in situ screening of groundwater for contamination by explosives.     

Molecular dynamics on distributed memory (MIMD) parallel computers

Summary Several algorithms are described that have been applied to molecular dynamics simulations and their merits discussed. The subject matter is confined to distributed (MIMD) algorithms. A simple mathematical model is used to illustrate the performance characteristics of a parallel MD algorithm.     

Molecular Recognition of Aromatic Nitro Compounds at Cyclodextrin Dithiocarbamate-modified Electrodes

Silver electrodes were modified by the adsorption of α-, β-, and γ-cyclodextrin dithiocarbamates (2α–γ) and characterized by reductive desorption experiments. Their molecular recognition properties were studied by cyclic voltammetry using three families of positional isomers of aromatic nitro compounds. Electrodes modified with 2α and 2β were selective for meta and para isomers while 2γ showed little selectivity. These observations are explained in terms of cavity sizes and guest structure. Computational studies suggest that the main reason for the observed selectivity is the different position of the NO² group in ortho and para isomers with respect to the CD cavity.     

Non-adiabatic molecular dynamics with quantum solvent effects

Three novel approaches extending quantum-classical non-adiabatic (NA) molecular dynamics (MD) to include quantum effects of solvent environments are described. In a standard NA-MD the solute subsystem is treated quantum mechanically, while the larger solvent part of a system is treated classically. The three novel approaches presented here are based on the Bohmian formulation of quantum mechanics, the stochastic Schrödinger equation for the evolution of open quantum systems and the quantized Hamilton dynamics generalization of classical mechanics. The approaches extend the standard NA-MD to incorporate the following quantum effects of the solvent. (1) Branching, i.e. the ability of solvent quantum wave packets to split and follow asymptotically diverging trajectories correlated with different quantum states of the solute. (2) Decoherence, i.e. loss of quantum interference within the solute subsystem induced by the diverging solvent trajectories. (3) Zero point energy that contributes to NA coupling and must be preserved during the energy exchange between solvent and solute degrees of freedom. The Bohmian quantum-classical mechanics, stochastic mean-field and quantized mean-field approximations incorporate the quantum solvent effects into the standard quantum-classical NA-MD in a straightforward and efficient way that can be easily applied to quantum dynamics of condensed phase chemical systems.     

Molecular dynamics simulation of the water|nitrobenzene interface

The structure and dynamics of the neat water|nitrobenzene liquid|liquid interface are studied at 300 K using molecular dynamics computer simulations. The water is modeled using the flexible SPC potential, and the nitrobenzene is modeled using an empirically determined nitrobenzene potential energy function. Although nitrobenzene is a polar liquid with a large dielectric constant, the structure of the interface is similar to other water|non-polar organic liquid interfaces. Among the main structural features we describe are an enhancement of interfacial water hydrogen bonds, the specific orientation of water dipoles and nitrobenzene molecules, and a rough surface that is locally sharp. Surface roughness is also characterized dynamically. The dynamics of molecular reorientation are shown to be only mildly modified at the interface. The effect due to the polarizable many-body potential energy functions of both liquids is investigated and is found to affect only mildly the above results.     

Molecular dynamics studies show solvation structure of type III antifreeze protein is disrupted at low pH

Antifreeze proteins are a class of biological molecules of interest in many research and industrial applications due to their highly specialized function, but there is little information of their stability and properties under varied pH derived from computational studies. To gain novel insights in this area, we conducted molecular dynamics (MD) simulations with the antifreeze protein 1KDF at varied temperatures and pH. Water solvation and H-bond formation around specific residues – ASN14, THR18 and GLN44 – involved in its antifreeze activity were extensively studied. We found that at pH1 there was a disruption in water solvation around the basal and the ice binding surfaces of the molecule. This was induced by a small change in the secondary structure propensities of some titrable residues, particularly GLU35. This change explains the experimentally observed reduction in antifreeze activity previously reported for this protein at pH1. We also found that THR18 showed extremely low H-bond formation, and that the three antifreeze residues all had very low average H-bond lifetimes. Our results confirm long-standing assumptions that these small, compact molecules can maintain their antifreeze activity in a wide range of pH, while demonstrating the mechanism that may reduce antifreeze activity at low pH. This aspect is useful when considering industrial and commercial use of antifreeze proteins subject to extreme pH environments, in particular in food industrial applications.     

Molecular dynamics simulation of the aggregation of colloidal particles

The spontaneous time evolution of systems containing N colloidal particles (N = 12, 24, 100) in a spherical cell of volume V at a constant volume fraction φ=0.1 was studied by a molecular dynamics method in the NVT ensemble. The starting velocities of the particles are allocated according to the Maxwell distribution at T=273 K.

Pairwise interaction of the particles was specified by molecular, electrostatic and elastic forces. The changes in the potential energy of the systems were calculated during the establishment of dynamic equilibrium. Coagulation takes place at sufficiently high values of the Hamaker constant. The value of the coefficient of Brownian diffusion, which is calculated from the half-time of coagulation, is found to be close to the known value for aqueous dispersions. The inclusion of electrostatic forces prevents coagulation.

The results obtained are in agreement with those obtained using theories of aggregate formation. Some structural characteristics of aggregates and stable systems are discussed.     

基于分子对接的thanatin与NDM-1分子动力学模拟研究

耐碳青霉烯类抗生素的超级细菌给人类健康带来了严重威胁,其所携带的金属 β-内酰胺酶编码基因是耐药性的主要来源。NDM-1作为其中传播最广、活性最强的 β-内酰胺酶,其抑制剂的研发刻不容缓。具有广谱作用的抗菌肽thanatin对NDM-1展现出了较好的抑制效果,但抑制机理并不清楚。本文使用HPEPDOCK与Rosetta FlexPepDock服务器,将thanatin与NDM-1进行了分子对接,并使用Desmond软件包对对接模型进行了分子动力学模拟。结果表明,thanatin与NDM-1活性中心的Zn2+ 并无直接相互作用,而作为竞争性抑制剂结合于NDM-1的活性口袋,阻止抗生素分子进入活性口袋与Zn2+ 结合,从而抑制NDM-1的水解活性。本文为研发有效的NDM临床抑制剂探索了可行的方法。     

Molecular dynamics study of selective adsorption of PCB on activated carbon

The selectivity of PCB adsorption from fish oil onto activated carbon (AC) was investigated by means of molecular dynamics to determine the importance of molecular planarity. PCB congeners 77 and 118 were selected for comparison purposes due to pronounced differences in mean adsorption efficiency and molecular geometry; triolein, a triacylglycerol of oleic acid (C18:1), was used as the representative fish oil component. Graphitic carbon structure was set up to serve as activated carbon model. Molecular force fields employed in the simulations combined short-range parameters from the OPLS with partial atomic charges obtained via quantum chemical calculations using DFT/B3LYP/6-31**G+ and Solvation Model 6. We modified the dihedral angle potential between the PCB aromatic rings and applied Schrödinger's Jaguar package to evaluate the required force field constants. Our complete system comprised a number of PCB molecules dissolved in triacylglycerol that overlaid and filled the pores of an AC structure. The production run of 4 ns provided strong indications that smaller pores will be conductive to better selectivity though also resulted in certain doubts concerning the estimation and assignment of partial atomic charges on the activated carbon. The majority of PCB molecules trapped in pores were attached via cl-AC “bonding”, leaving the main part of the PCB molecule free to interact with triolein. The cl-AC adsorption energy was found to surpass the energy criteria conventionally used for hydrogen bonds. Planar orientation assumed by a PCB molecule in a very energetically favored position on top of the graphite sheet clearly supported the π-cloud overlap hypothesis.