The role of lone pair and dipolar interactions in the non-planarity of 1,3-dioxolane and 1,3-dioxole

1,3-Dioxole has been shown to be non-planar by infrared and Raman spectroscopy. An MM3 study of this molecule enabled the investigators to suggest that this non-planarity was due to the anomeric effect. Subsequently, an ab initio theoretical study of this molecule was performed, which also concluded that the non-planarity of 1,3-dioxole was due to the anomeric effect and not to dipole-dipole interactions. Neither study used rigorous methods for assessing the role of dipolar interactions in the geometry of 1,3-dioxole. A new study of 1,3-dioxole, 1,3-dioxolane, tetrahydrofuran, cyclopentane, and some related molecules using the new QVBMM (molecular mechanics) force field shows conclusively that the non-planarity of 1,3-dioxole and 1,3-dioxolane is due primarily to torsional and dipolar effects, and not secondary molecular orbital overlap interactions.     

Extension of the GLYCAM06 Biomolecular Force Field to Lipids, Lipid Bilayers and Glycolipids

GLYCAM06 is a generalisable biomolecular force field that is extendible to diverse molecular classes in the spirit of a small-molecule force field. Here we report parameters for lipids, lipid bilayers and glycolipids for use with GLYCAM06. Only three lipid-specific atom types have been introduced, in keeping with the general philosophy of transferable parameter development. Bond stretching, angle bending, and torsional force constants were derived by fitting to quantum mechanical data for a collection of minimal molecular fragments and related small molecules. Partial atomic charges were computed by fitting to ensemble-averaged quantum-computed molecular electrostatic potentials.In addition to reproducing quantum mechanical internal rotational energies and experimental valence geometries for an array of small molecules, condensed-phase simulations employing the new parameters are shown to reproduce the bulk physical properties of a DMPC lipid bilayer. The new parameters allow for molecular dynamics simulations of complex systems containing lipids, lipid bilayers, glycolipids, and carbohydrates, using an internally consistent force field. By combining the AMBER parameters for proteins with the GLYCAM06 parameters, it is also possible to simulate protein-lipid complexes and proteins in biologically relevant membrane-like environments.     

Molecular Dynamics as a Mathematical Mapping. I. Differentiable Force Functions

Abstract

The molecular dynamics technique can be viewed as a deterministic mathematical mapping between, on one side, the force field parameters that describe the potential energy interactions and the input macroscopic conditions, and, on the other, the calculated macroscopic properties of the bulk molecular system.

The differentiability of such a mapping in the conventional molecular dynamics calculations is affected by the discontinuities in particle positions introduced by the periodic boundary conditions and the discontinuities introduced by the minimum image convention and other methods commonly employed to approximate the calculation of interparticle potential and force.

This paper proposes an alternative molecular dynamics framework based on modified force functions which are almost everywhere continuous and differentiable, and exhibit a natural periodicity. These characteristics obviate the need for both the periodic boundary conditions and the minimum image convention, as well as for any corrections for long-range interactions. They also make it possible to apply standard methods of variational calculus for the computation of partial derivatives of the molecular dynamics mapping.

The modified framework is first introduced for the case of simple monoatomic fluids where the nature of the forces exerted between any pair of two particles is identical. A more general model describing the interactions of flexible molecules is then developed. We describe the application of this approach to mixtures of alkane molecules interacting via the NERD force field.     

Determination method of the balance of the secondary-structure-forming tendencies of force fields

We propose a new method of optimisation of backbone torsion-energy parameters in the force field for molecular simulations of protein systems. This method is based on the idea of balancing the secondary-structure-forming tendencies, namely, those of α-helix and β-sheet structures. We perform a minimisation of the backbone dihedral angle-based root-mean-square deviation of the helix and β structure regions in many protein structures. As an example, we optimised the backbone torsion-energy parameters of AMBER parm96 force field using 100 protein molecules from the Protein Data Bank. We then performed folding simulations of α-helical and β-hairpin peptides, using the optimised force field. The results imply that the new force-field parameters give structures more consistent with the experimental implications than the original AMBER parm96 force field.     

Molecular dynamics simulations of structural instability of fullerene family under tension force

Fullerene molecules are cage-like nanoscopic structures with pentagonal and hexagonal faces. In practical applications such as fullerene-reinforced nanocomposites (FRNCs), these structures may be subjected to tension force. In this research, we employ molecular dynamics (MD) simulation to compute the behaviour and deformation of different fullerene molecules, ranging from C₆₀ to C₂₀₀₀, under tension force. To model the interactions between carbon atoms in the MD simulations, the adaptive intermolecular reactive bond order (AIREBO) force field is used. The displacement–force and the displacement–strain energy curves are obtained. It is observed that a new type of structural instability occurs in the fullerene molecules when the applied tension force increases. This abnormal structural instability in the fullerenes is investigated for the first time in the literature. The critical tensile forces and the corresponding mode shapes are determined for different fullerenes. The results indicate that the critical forces and deformations strongly depend upon the number of carbon atoms.     

A local friction model to develop microscopic transport parameters for membrane-soluble ions in bilayer membranes

Charged membrane-soluble ions in bilayer membranes move between opposing interfacial states on application of an electric field. The kinetics of this transition is modeled as discrete state electrophoresis using a Langevin formulation that focuses on local velocities at points along the spatial trajectory of the ion. These local velocities are used to establish both the decay time for the transition and the activation energy profile along the trajectory. The local velocities depend on local frictional coefficients. These coefficients are developed from the molecular structure along the trajectory by introducing a microscopic frictional force. This frictional force is produced by the lateral displacement of segments of the surrounding membrane molecules as the ion passes. The displaced molecular chains produce a non-linear resistive force that translates into a frictional force directly proportional to both ion radius and velocity.     

COMPASS II: extended coverage for polymer and drug-like molecule databases

The COMPASS II force field has been developed by extending the coverage of the COMPASS force field (J Phys Chem B 102(38):7338–7364, 1998) to polymer and drug-like molecules found in popular databases. Using a fragmentation method to systematically construct small molecules that exhibit key functional groups found in these databases, parameters applicable to database compounds were efficiently obtained. Based on the same parameterization paradigm as used in the development of the COMPASS force field, new parameters were derived by a combination of fits to quantum mechanical data for valence parameters and experimental liquid and crystal data for nonbond parameters. To preserve the quality of the original COMPASS parameters, a quality assurance suite was used and updated to ensure that additional atom-types and parameters do not interfere with the existing ones. Validation against molecular properties, liquid and crystal densities, and enthalpies, demonstrates that the quality of COMPASS is preserved and the same quality of prediction is achieved for the additional coverage.     

On the molecular mechanisms implicated in the bipolar cancellation of membrane electroporation

Bipolar cancellation is the phenomenon in which the permeability of cell membranes subjected to high intensity short pulsed electric field (ns-μs range) is reduced or eliminated when the system is subjected to bipolar instead of monopolar pulses. Although several studies have tried to explain bipolar cancellation, the underlying mechanisms remain unclear. Very few articles study bipolar cancellation by means of molecular dynamics (MD) simulation. In this paper, we investigated the molecular mechanisms underlying the difference in electroporation induced by bipolar and monopolar picosecond electric pulses (EPs) using MD simulation. The electric field gradients and electric forces on water molecules of the two pulses were analyzed in detail for the first time. For a certain pulse width, when the field intensity is relatively small, the direction of bipolar electric force on the interfacial water molecule reverses as the bipolar EPs reverse, while the electric force on interfacial water molecules of the cathode side remains in the same direction as that of applied monopolar EPs. The bipolar electric force reversal delays the water protrusion and increases the pore formation time. Therefore, this phenomenon could correspond to bipolar cancellation. When the field intensity is relatively large, although the bipolar electric force direction still reverses, half of the total time of the monopolar EPs has no electric fields. The electric forces of monopolar no-field half-cycles are much smaller than those of the bipolar EPs. Therefore, the pore formation time of bipolar EPs reduces, and this phenomenon is called bipolar enhancement. The occurrence of bipolar cancellation or bipolar enhancement depends on conditions such as the width and intensity of the pulse.     

Conformational analysis of single DNA molecules undergoing entropically induced motion in nanochannels

We have used the interface between a nanochannel and a microchannel as a tool for applying controlled forces on a DNA molecule. A molecule, with a radius of gyration larger than the nanochannel width, that straddles such an interface is subject to an essentially constant entropic force, which can be balanced against other forces such as the electrophoretic force from an applied electric field. By controlling the applied field we can position the molecule as desired and observe the conformation of the molecule as it stretches, relaxes, and recoils from the nanochannel. We quantify and present models for the molecular motion in response to the entropic, electrophoretic, and frictional forces acting on it. By determining the magnitude of the drag coefficients for DNA molecules in the nanostructure, we are able to estimate the confinement-induced recoil force. Finally, we demonstrate that we can use a controlled applied field and the entropic interfacial forces to unfold molecules, which can then be manipulated and positioned in their simple extended morphology.     

GAFF-IC: realistic viscosities for isocyanate molecules with a GAFF-based force field

Aliphatic diisocyanates and their derivatives are key liquid components in the industrial processing of polyurethane materials. In particular, for the synthesis of crosslinked polyurethane materials, the higher functionality molecules obtained by reacting three -or more- diisocyanates are of interest. However, despite their widespread application, the relation between molecular structure and macroscopic physical properties, in particular viscosity, is poorly understood in these systems. In this work, we introduce a new force field parameter set, GAFF-IC, based on the widely-used and versatile GAFF force field, meant for accurate predictions of physical properties of isocyanate-based molecular liquids. The new parameters allow to predict the vaporization enthalpies and densities of several isocyanate-based molecules, which are found in excellent agreement with the available experimental data. The effectiveness and transferability of the improved parameters is verified by calculating the viscosities of several isocyanates, isocyanate dimers (uretdiones) and isocyanate trimers (isocyanurates), resulting in accurate viscosity predictions in excellent agreement with experimental values.     

Molecular Mechanics: The Conjugate Nitro Group Parameters in the MM2 Force Field

The conjugated nitro group has been included in the π system calculation within the MM2 force field. New parameters have been estimated by a statistical process from X-ray molecular structures recorded in the C.S.D.S. Comparison of the corresponding results with those given by the MM2(91) force field parameters show a clear improvement for dihedral and bond angles. For N-O and C-N bond lengths a slight global improvement is also observed. A closer examination of the results for the latter bond shows that sometimes MM2(91) gives better results for six membered ring nitro compounds. By contrast the parameters proposed here are more adapted to five membered ring derivatives. The derived linear relations permit the study of molecules over a wider range of π indices. The introduction of a correction factor to the calculated molecular π dipole moment in conjunction with a necessary reestimation of some σ-bond dipole moments also leads to improved total molecular dipole moments.     

Molecular Mechanics: The Conjugate Nitro Group Parameters in the MM2 Force Field

The conjugated nitro group has been included in the π system calculation within the MM2 force field. New parameters have been estimated by a statistical process from X-ray molecular structures recorded in the C.S.D.S. Comparison of the corresponding results with those given by the MM2(91) force field parameters show a clear improvement for dihedral and bond angles. For N-O and C-N bond lengths a slight global improvement is also observed. A closer examination of the results for the latter bond shows that sometimes MM2(91) gives better results for six membered ring nitro compounds. By contrast the parameters proposed here are more adapted to five membered ring derivatives. The derived linear relations permit the study of molecules over a wider range of π indices. The introduction of a correction factor to the calculated molecular π dipole moment in conjunction with a necessary reestimation of some σ-bond dipole moments also leads to improved total molecular dipole moments.     

A molecular mechanical force field for the conformational analysis of oligosaccharides: comparison of theoretical and crystal structures of Man alpha 1-3Man beta 1-4GlcNAc

A molecular mechanical force field is described for the conformational analysis of oligosaccharides. This force field has been derived by the addition of new parameters to the AMBER force field and is compatible with simulations of proteins. This new parametrization is assessed by comparison of the theoretically predicted conformations of Man alpha 1-3Man beta 1-4GlcNAc with the corresponding crystal structure. Molecular dynamics simulation data are presented for this structure both in vacuo and with the explicit inclusion of water molecules. While the former demonstrate significant torsional oscillations about glycosidic linkages at physiological temperature, in the latter these oscillations are highly damped due to the stabilizing influence of a "cage" of solvent-solvent and solvent-solute hydrogen bonds.     

MD simulation of subtilisin BPN' in a crystal environment.

In this paper we present a molecular dynamics (MD) simulation of subtilisin BPN' in a crystalline environment containing four protein molecules and solvent. Conformational and dynamic properties of the molecules are compared with each other and with respect to the X-ray structure to test the validity of the force field. The agreement between simulated and experimental structure using the GROMOS force field is better than that obtained in the literature using other force fields for protein crystals. The overall shape of the molecule is well preserved, as is the conformation of alpha-helices and beta-strands. Structural differences are mainly found in loop regions. Solvent networks found in the X-ray structure were reproduced by the simulation, which was unbiased with respect to the crystalline hydration structure. These networks seem to play an important role in the stability of the protein; evidence of this is found in the structure of the active site. The weak ion binding site in the X-ray structure of subtilisin BPN' is occupied by a monovalent ion. When a calcium ion is placed in the initial structure, three peptide ligands are replaced by 5 water ligands, whereas a potassium ion retains (in part) its original ligands. Existing force fields yield a reliable method to probe local structure and short-time dynamics of proteins, providing an accuracy of about 0.1 nm.     

Molecular dynamics simulation of hen egg white lysozyme: a test of the GROMOS96 force field against nuclear magnetic resonance data

Biomolecular force fields for use in molecular dynamics (MD) simulations of proteins, DNA, or membranes are generally parametrized against ab initio quantum-chemical and experimental data for small molecules. The application of a force field in a simulation of a biomolecular system, such as a protein in solution, may then serve as a test of the quality and transferability of the force field. Here, we compare various properties obtained from two MD simulations of the protein hen egg white lysozyme (HEWL) in aqueous solution using the latest version, GROMOS96, of the GROMOS force field and an earlier version, GROMOS87+, with data derived from nuclear magnetic resonance (NMR) experiments: NOE atom-atom distance bounds, (3)J(HNalpha)-coupling constants, and backbone and side-chain order parameters. The convergence of these quantities over a 2-ns period is considered, and converged values are compared to experimental ones. The GROMOS96 simulation shows better agreement with the NMR data and also with the X-ray crystal structure of HEWL than the GROMOS87+ simulation, which was based on an earlier version of the GROMOS force field.     

AmberFFC, a flexible program to convert AMBER and GLYCAM force fields for use with commercial molecular modeling packages

A program for converting the different existing AMBER and GLYCAM force fields for use with commercial molecular modeling packages is presented, using the Molecular Simulations Inc. (MSI or Accelrys) software package as a case model. Called AmberFFC, the program creates AMBER and GLYCAM force field files suitable for use with the Accelrys molecular mechanics modules by transforming the amino acid, nucleotide, and monosaccharide topology databases and force field parameter files to the Accelrys file format. It is intended for any modeler who is interested in using the current AMBER and GLYCAM force fields with the Accelrys FDiscover and CDiscover programs. AmberFFC has been written entirely with the Perl programming language, making it highly flexible and portable. In order to compare the implementation of the force fields converted by AmberFFC in the Accelrys package with their corresponding execution in the AMBER software, and also to verify the efficiency of the AmberFFC program, results from single point energy calculations for 13 model molecules were obtained with the two programs. It is demonstrated that results obtained with the CDiscover and FDiscover modules compare well to those found using Sander_classic, thus showing that AmberFFC is a highly efficient program. Some energy differences between the AMBER and Accelrys software have been observed, and their origin has been characterized and discussed.     

MolStruc: a force field calculation program allowing interactive modifications of the force field parameters

To analyze the influence of parameters and functions on the energy and geometry obtained through different force field calculations, we have developed program MolStruc. This software allows the user to choose between two sets of functions and parameters, MM2 and AMBER.The MM2 option of the program was developed to compute the coulombic energy in a dipole or monopole approximation. To establish comparisons between the energy values, the coulombic contribution is computed in the same way in the Amber and MM2 options of the program.The force field parameters can be handled interactively (through addition or modification).The program was used to study molecules of a representative sample displaying most of the problems encountered in molecular mechanics (MM).     

A CFF 91-based Continuum Solvation Model: Solvation Free Energies of Small Organic Molecules and Conformations of the Alanine Dipeptide in Solution

Abstract

For molecular mechanics simulations of solvated molecules, it is important to use a consistent approach for calculating both the force field energy and the solvation free energy. A continuum solvation model based upon the atomic charges provided with the CFF91 force field is derived. The electrostatic component of the solvation free energy is described by the Poisson-Bolzmann equation while the nonpolar comonent of the solvation energy is assumed to be proportional to the solvent accessible surface area of the solute. Solute atomic radii used to describe the interface between the solute and solvent are fitted to reproduce the energies of small organic molecules. Data for 140 compounds are presented and compared to experiment and to the results from the well-characterized quantum mechanical solvation model AM1-SM2. In particular, accurate results are obtained for amino acid neutral analogues (mean unsigned error of 0.3 kcal/mol). The conformational energetics of the solvated alanine dipeptide is discussed.     

Adsorption of phenol and aniline on natural and organically modified montmorillonite: experiment and molecular modelling

Natural and intercalated Wyoming montmorillonite (MMT) with the tetramethylammonium (TMA) cations were used for the adsorption of phenol and aniline. Laboratory experiments characterised by adsorption isotherms were compared with the results of molecular modelling simulations. Aniline adsorbed itself strongly on MMT; while using the TMA intercalates (TMA-MMT), its adsorption decreased. On the contrary, the adsorption of phenol on TMA-MMT was moderately higher than on the MMT surface. The MMT surface models were described by empirical force field used in molecular mechanics and dynamics. The Burchart–Universal force field was used in the Cerius² modelling environment. The modelling results revealed the important role of water forming a moderately concentrated layer on the pure MMT surface. Water molecules enable the adsorption of aniline on MMT and, on the contrary, repel phenol molecules from MMT. In the case of TMA-MMT, lower amount of water near a silicate layer caused decrease in the aniline adsorption and, on the contrary, increase in the phenol adsorption.