Applications Of Dl_poly And Dl_multi To Organic Molecular Crystals

Molecular dynamics (MD) simulations are capable of giving considerable insight into the polymorphism of organic molecules, a problem of major concern to the pharmaceutical and other speciality chemicals industries. We illustrate some of the challenges involved in small organic systems, which have complex solid-state phase behaviour, including characterizing rotationally disordered phases, modelling polymorphs with very different hydrogen bonding motifs and explaining the solvent dependence of a polymorphic system. Simulating the dynamics within the organic solid state can be very demanding of the model for the weak forces between the molecules. This has led to the development of DL_MULTI so that a distributed multipole electrostatic model can be used to describe the orientation dependence of hydrogen bonding and π–π stacking more realistically. Once a simulation is correctly reproducing the known crystal structures, there are also considerable system-specific challenges in extracting novel insights from the MD simulations.     

Modelling Metal Complexes of Calixarene Esters and Phosphine Oxides Using Molecular Mechanics

This paper focuses on the molecular modelling of a number of calixarene ester and phosphine oxide metal ion complexes. Monte Carlo conformational searches, in conjunction with the Merck Molecular Force Field, were carried out using Spartan SGI Version 5.0.1. running on Silicon Graphics O2 workstations. In the case of the calix[4]arene tetraesters, the optimised models strongly suggest that the selectivity of these ligands is strongly related to the eight-fold nature of the coordination with the Na⁺ ion, while coordination with the Li⁺ ion, for example, is merely three-fold. This feature of eight-fold coordination is also observed in the models of the complexes formed by the calix[4]arene tetraphosphine oxides with calcium. However, whereas the eight-fold coordination is unique to the model of the TPOL:Ca²⁺ complex among the ions modelled, this mode of coordination occurs for TPOS with sodium and potassium, in addition to calcium. This concurs with the observation that calcium selectivity is obtained with ion selective electrodes based on TPOL but not TPOS. Though the cavity in the calix[5]arenes PPOL and PPOLx and the calix[6]arene HPOL, in their uncomplexed form, are much larger than that of the corresponding calix[4]arenes, the pattern of selectivity is the same – the ligands are selective for calcium. The models of the complexes of these larger calixarenes, such as PPOL:Ca²⁺, strongly suggest that the reason for this similarity is that four of the available phosphine oxide groups complex with the calcium ion, and the others are forced away from the cavity region for steric reasons. The resulting eight-fold coordination, is therefore, similar to that of the calix[4]arenes studied.Electronic Supplementary Material available.     

Computer Simulation by Molecular Dynamics as a Tool for Modelling of Molecular Systems

Abstract

A survey is given of methods for simulation of molecular systems on a computer. The various assumptions, approximations and limitations are discussed and the possibility of making comparisons with experimental quantities is assessed. Finally, a number of practical applications of molecular dynamics simulation techniques in chemistry are reviewed.     

Object-oriented Programming Paradigms for Molecular Modeling

This paper discusses the application of object-oriented programming (OOP) design concepts to the development of molecular simulation code. A number of new languages such as Fortran 90 (F90) have been developed over the last decade that support the OOP design philosophy. We briefly describe the salient features of F90 and some basic object-oriented design principles. As an illustration of the design concepts we implement a general interface in F90 for calculating pairwise interactions that can be extended easily to any number of different forcefield models. The ideas presented here are used in the development of a mu ltipurpose si mulation c ode, named Music. An example of the use of Music for grand canonical Monte Carlo (GCMC) simulations of flexible sorbate molecules in zeolites is given. The example illustrates how OOP allowed existing code for molecular dynamics and GCMC to be easily combined to perform hybrid GCMC simulations with minimal coding effort.     

Adsorption Behavior of Polydisperse Polymeric Systems

Adsorption behavior of polydisperse polymers at interfaces is studied by the Monte Carlo simulation method based on a lattice model. Effects of temperature and adsorption energies on the polymer density profile, cluster distributions and adsorption layer thickness are evaluated in two different polydisperse systems. It is found that adsorption properties are greatly different in these two systems. In normal distribution polydisperse systems, polymers are more sensitive to the excluded volume effects while in average distribution polymers are more inclined to adsorb on adsorbing interfaces. As higher temperature and lower attraction constrain the polymer adsorption, more clusters are found under these conditions. When temperature approaches the critical temperature of monodisperse systems, stable and large clusters exist in these two polydisperse systems. These results suggest that micro phase transition may exist in polydisperse systems. Polydisperse systems take little change of phase transition temperatures but altered the clusters morphology to some extent. The adsorption layer thickness changes are more sensitive to both temperature and polymer–interface interactions in average distribution systems when the whole polymer concentration increases slightly. This work also suggests significant differences between the polydisperse and the monodisperse systems in adsorption behavior. Therefore, quantitative system errors may exist when the monodisperse system models are used in simulation to evaluate polymer adsorption properties.     

Molecular Modelling Studies on the Catalytic Mechanism of Candida Rugosa Lipase

Quantum chemical and molecular dynamics investigations have been performed on model systems for Candida rugosa lipase (CRL) to study mechanistic and conformational features of the catalytic hydrolysis. Based on X-ray data, a simplified model of the CRL substrate complex was created for the PM3 and ab initio calculations, including the amino acid residues both of the catalytic triad and the oxyanion hole.The energetic and structural properties of significant species along the pathway of the hydrolysis of the model substrate acetic acid methyl ester have been calculated. By modifications of the residues of the oxyanion hole as well as the catalytic triad, the influence of these parts of the active site on the pathway of the reaction was analysed in more detail.Moreover, molecular dynamics simulations have been carried out on CRL adducts with (±)-cis-4-acetamido-cyclopent-2-ene-1-carboxylic esters with different lengths of their alkyl chain and their absolute configuration as substrates. For the MD simulations using the AMBER program, all amino acid residues and water molecules with a cut-off radius less than 1500 pm from the substrate were taken into account. From the analysis of the trajectories and histograms for significant hydrogen bonds in the active site of the enzyme adducts, some hints were obtained for the enantiodifferentiation and the chain dependence of the esters in catalytic hydrolysis by CRL.Electronic Supplementary Material available.     

Atomistic Monte Carlo Simulations of Liquids of Chain Molecules Confined by Solid Surfaces: Methods and Recent Results

Abstract

The molecular arrangements of liquid tridecane near solid surfaces and in narrow slits have been studied by atomistic Monte Carlo computer simulations. A single surface perturbs the liquid over a distance of 1.5 nm, inducing the formation of progressively less dense and ordered layers of thickness 0.4 nm. Chains with atoms in the first layer tend to run parallel to the surface. The tendency to form layer structures is maintained or destroyed in narrow slits, depending on the slit thickness. For instance, it is slighly increased in slits of thickness 1.2 nm, while it is practically destroyed when the slit thickness is reduced to 1.0 nm. When added in small amounts, shorter-chain components are preferentially adsorbed at the solid surface, making the first layer of liquid in contact with these surfaces much less ordered.     

Molecular Atomistic Simulations of Clay Swelling in Water Dispersions

An atomistic model has been constructed for a dimeric montmorillonite type clay aggregate. The solid was supposed to be dispersed in water. The surrounding aqueous phase was modified from pure water to either salt or polymer solution, and finally represented by a mixed solution containing electrolytes and polyols. A combined energy minimisation procedure followed by a 100 ps real time molecular dynamic simulation was performed on each amorphous cell modelling the solid dispersion. 3D periodic boundary conditions were established to ensure fluid spatial continuity and the calculations proceeded at room temperature. Sodium, potassium and calcium chlorides were tested as shale swelling inhibition additives. The lower hydration energy cation K⁺ was the most effective swelling inhibitor. The adsorption of poly(propylene glyco)s to the ideal smectite surface was also studied. Their tendency to remain adsorbed was associated with the irreversibility of the polymer adsorption process. The conformational changes obtained for organic molecules were responsible for the final orientation of the clay sheets. So it was possible to conclude from qualitative observations that intramolecular interactions may determine a clay dispersion–agglomeration transition by modifying the system entropy. Finally, it was also concluded that specific combinations of additives could enhance their individual capabilities by synergistic effects, determining the effectiveness for some water-based mud formulations. This revised version was published online in June 2006 with corrections to the Cover Date.     

紫杉醇作用的分子机制研究进展

紫杉醇是从紫杉树皮中提取的新型抗肿瘤药物,由于对多种肿瘤有很好的疗效,目前已得到越来越广泛的应用。紫杉醇的细胞学效应是将细胞周期阻断于Ｇ２／Ｍ期,还可诱导多种肿瘤细胞凋亡。紫杉醇结合于微管后如何诱导细胞周期阻断和细胞凋亡,目前仍不清楚。去年我们总结了紫杉醇诱导的与细胞凋亡有关的一些信号转导途径［１］,都是很简单的、推测性的结果。仅仅一年的时间,对于紫杉醇作用的分子机制的研究获得不少进展,如紫杉醇可以改变很多基因的表达,促使一些蛋白激酶活化,包括细胞周期调节分子的改变,促使信号分子激活及增加多种凋…     

MolMod – an open access database of force fields for molecular simulations of fluids

The MolMod database is presented, which is openly accessible at http://molmod.boltzmann-zuse.de and contains intermolecular force fields for over 150 pure fluids at present. It was developed and is maintained by the Boltzmann-Zuse Society for Computational Molecular Engineering (BZS). The set of molecular models in the MolMod database provides a coherent framework for molecular simulations of fluids. The molecular models in the MolMod database consist of Lennard-Jones interaction sites, point charges, and point dipoles and quadrupoles, which can be equivalently represented by multiple point charges. The force fields can be exported as input files for the simulation programmes ms2 and ls1 mardyn, GROMACS, and LAMMPS. To characterise the semantics associated with the numerical database content, a force field nomenclature is introduced that can also be used in other contexts in materials modelling at the atomistic and mesoscopic levels. The models of the pure substances that are included in the database were generally optimised such as to yield good representations of experimental data of the vapour–liquid equilibrium with a focus on the vapour pressure and the saturated liquid density. In many cases, the models also yield good predictions of caloric, transport, and interfacial properties of the pure fluids. For all models, references to the original works in which they were developed are provided. The models can be used straightforwardly for predictions of properties of fluid mixtures using established combination rules. Input errors are a major source of errors in simulations. The MolMod database contributes to reducing such errors.     

Molecular Dynamics Simulations of The Swelling of Terephthalate Containing Anionic Clays

Abstract

We report on molecular simulations of the swelling of terephthalate containing anionic clays. We find good agreement with experimentally derived interlayer spacings, and models for the structure and dynamics of the interlayer water. We predict a swelling profile which suggests that at high water content a sharp increase in interlayer spacing will occur. The corresponding swelling curve for methanol incorporation, however, indicates a more continuous expansion.     

Molecular Modelling of the Mechanism of Action of Borate Retarders on Hydrating Cements at High Temperature

Abstract

We consider the class of borate additives in an attempt to understand, on the basis of molecular modelling techniques, why they are effective high temperature cement setting retarder aids. Borates are known to act as cement retarders under ambient conditions, for which the Billingham-Coveney clock reaction scheme [1] based on a gel → crystalline ettringite transformation provides the basic model. Under conditions of high temperature (above ca. 80°C) ettringite is known to be unstable, so that a modification to this mechanism is then required. However, conceptually (and mathematically) the kinetic scheme remains unchanged: we are concerned with a gel → crystalline silicate transition, which can be inhibited by suitable retarders. Thus the proposed mechanism for the high temperature retardation of hydrating cements by borates is that the latter prevent the growth of polymeric or crystalline calcium silicate hydrates such as tobermorite from the initially formed C ? S ? H gel.

The mechanism which we propose in this paper, which is based on chemisorption of borate species, explains some experimentally observed phenomena relating to the retarding action of both monomeric and polymeric borates in solution. On the basis of this work, we are able to predict vibrational frequencies for the cyclic borosilicate species which is formed, observation of which would confirm the validity of the mechanism proposed here. We can also use our work to explain the effectiveness of different borates. We conclude by suggesting a novel boronate retarder which might be expected to be more potent than those currently in use.     

Computational analyses of virtual proteolytic fragments generated by naphthalene 1,2-dioxygenase. In search of native-like conformation and function

Structural and energetic properties of proteolytic fragments originated from naphthalene 1,2-dioxygenase (NDO) enzyme were investigated through a computational approach. A library of fragments was generated by using an algorithm able to identify specified regions of the primary sequence and simulating cleavages on target sites. Structure of the fragments was optimised by Monte Carlo and molecular dynamics (MD) methods and the conformational and energetic properties were compared with those of the native enzyme. Protonation states of ionizable groups were predicted on the basis of effective pK _a values. Proteolytic fragments structurally similar to NDO were docked to naphthalene and interaction energies were evaluated by using MD computations. Many candidate fragments were able to maintain properties close to those which occur in the native conditions, while structures obtained by cleavages on the β-subunit of the NDO asymmetric unit were found to be rather unstable. Among the investigated structures, owing to comparable energetic and structural characteristics, 146–694 proteolytic fragment may be a promising alternative to NDO enzyme for complexation and biodegradation of naphthalenes.     

Parameterization of Coulomb interaction in three-dimensional periodic systems

A simple method is proposed to calculate Coulomb interactions in three-dimensional periodic cubic systems. It is based on the parameterization of the interaction on polynomials and rational functions. The parameterized functions are compared to tabulation methods, to the Ewald calculations and cubic harmonic function fits found in the literature. Our parameterizations are computationally more efficient than, the use of tabulations at all cases and seem to be more efficient than the cubic harmonic parameterizations in the case of simultaneous potential energy and force calculations. In comparison to the Ewald method, it is feasible to use the parameterizations on small systems and on systems, where pair-wise additive short-range interactions are dominant. One also may prefer the parameterizations to the Ewald method for large systems, if limited accuracy is needed. The embedding of the method into existing molecular dynamics and Monte Carlo simulation codes is very simple. The presented investigation contains some numerical experimental data to support the correct theoretical partition of potential energy in periodic systems, as well.     

The Role of Molecular Dynamics Simulations for the Study of Slow Dynamics

Abstract

A two step strategy is proposed to study dynamical properties of a physical system much slower than the time scales accessible by molecular dynamics simulations. The strategy is applied to investigate the slow dynamics of supercooled liquids.     

Molecular simulation of size-selective gas adsorption in idealised carbon nanotubes

Molecular simulations were used to examine the adsorption of diatomic molecules (nitrogen and oxygen) and similarly sized gases (argon and methane) in pores with van der Waals diameters similar in size to the gas diameters. Idealised carbon nanotubes were used to model generic pores, to better understand the effect of pore diameter on guest adsorption in the absence of defects, specific adsorption sites, or variations in pore diameter that often complicate studies of gas adsorption in other porous materials. Molecular dynamics simulations of open nanotubes show that argon and methane are able to enter tubes whose diameters are slightly smaller than the gas diameters. Diatomic gases are able to enter tubes that are significantly smaller than their kinetic diameters with the molecular axis aligned parallel to the nanotube. The results indicate that size-selective adsorption of these gases is theoretically possible, although differences in pore diameters of only a few tenths of an Angstrom are required. Grand canonical Monte Carlo simulations of a 3.38 Å nanotube indicate significant uptake by argon and oxygen, but not nitrogen or methane. The adsorption of nitrogen and methane gradually increases as the nanotube diameter approaches 4.07 Å, and all gases fully saturate a 4.54 Å nanotube. Of the nanotubes studied, the largest adsorption enthalpy for any gas corresponds to the 4.54 Å nanotube, with significantly lower enthalpies seen in the 5.07 Å nanotube. These results suggest an ideal pore diameter for each gas based on the gas–pore van der Waals interaction energies. Trends in the ideal diameter correlate with the minimum tube diameter accessible to each gas.     

小分子酪氨酸激酶抑制剂耐药机制

表皮生长因子受体（epidermal growth factor receptor,EGFR）通路异常在肿瘤发生、发展过程中起到非常重要的作用,特异性抑制该通路的小分子受体酪氨酸激酶抑制剂在肿瘤治疗上取得了显著的效果,但是该药在临床上已经出现耐药现象,现将有关EGFR基因突变、EGFR旁路信号通路的激活、下游信号分子的结构性活化3个方面对EGFR抑制剂耐药机制的研究进展进行综述。     

Effect of Cation Concentration on Molecular Dynamics Simulations of UDP-Glucose

Abstract

Glycosyl esters of nucleoside di or mono-phosphates, generally referred to as “sugar nucleotides”, serve as a sugar donors during the biosynthesis of oligo- and polysaccharides; they are therefore of a primary importance in carbohydrate metabolism in the living world. Molecular dynamics simulations were used to explore the conformational flexibility of one nucleotide sugar, UDP-glucose (UDP-Glc). The AMBER program package was used with some new parameters especially developed for nucleotide sugars. Several simulations on this molecule in aqueous solution, each of 2 ns duration, were carried out for increasing concentrations of monovalent K⁺ and divalent Mg²⁺ ions. For the monovalent ion, it is revealed that its presence and concentration is crucial for the conformational behavior, resulting in the stabilization of the extended conformation. The preferred location of K⁺ is in close proximity to the negatively charged phosphate oxygens, but the ion moves freely and can occupy other sites. Since the size of this cation is close that of the water molecules, the hydration scheme is not perturbed. Completely different results are obtained when the divalent Mg²⁺ cation is introduced in the simulation. A very strong interaction is established between the phosphate group and the cation; as a result the UDP-Glc molecule is locked in a rigid extended geometry. The analyses of the trajectories provide new insight on the role of the metal ion in the catalytic mechanism of glycosyltransferases.