The vibrational spectra, molecular structure and conformation of organic azides : Part IV. An ab initio study of hydrazoic acid, azidomethane, azidoethane, azidoethene and azidomethanal

Fully optimized geometries have been calculated for the title compounds at the Hartree—Fock SCF level and compared with existing experimental data. A basis set of double zeta quality has been employed. For hydrazoic acid, a calculation with a larger basis set, expected to give results near the Hartree—Fock limit, has also been performed. All of the calculations show the azide group to be slightly bent with a trans configuration around the central NN bond. Azidoethane is predicted to exist in two conformations, gauche (71°) and anti, with a negligible energy difference of 0.26 kJ mol⁻¹ between them. Azidoethene and azidomethanal both prefer the syn orientation of the azide group with respect to the C---C or C---O bonds, the computed energy difference between the anti and syn conformations being 3.31 and 30.3 kJ mol⁻¹ respectively.

The barrier to rotation around the C---N bond has been calculated to be 3.75 kJ mol⁻¹ in azidomethane while in azidoethane it was 3.30 and 9.40 kJ mol⁻¹ in the eclipsed anti-clinal (120°) and syn positions, respectively.

Complete harmonic force fields and dipole moment derivatives have been calculated for hydrazoic acid, azidomethane and for the two stable conformations of azidoethane. For azidoethane and azidomethanal only the azide part of the harmonic force field has been calculated. The theoretical harmonic force fields have been modified through scaling by a least squares refinement to the observed wavenumbers of hydrazoic acid, azidomethane and azidoethane (anti and gauche). Infrared vapour phase intensities have been calculated and theoretical spectra are presented for azidomethane and azidoethane.     

Molecular dynamics simulation of surface morphology and thermodynamic properties of polyaniline nanostructured film

To develop predictive models in nanostructured films, there is an ongoing research to validate molecular dynamics (MD) simulation results with experimental data. The morphology and surface topography of polyaniline (PANI) nanostructured film coated on a TiO₂ nanocrystalline surface were investigated by scanning electron microscopy and atomic force microscopy, respectively. The atomistic model of the simulated PANI was generated using energy minimization with a condensed‐phase optimized molecular potential for atomistic studies force field function to reach a thermodynamic equilibrium state. Various parameters of PANI such as density, energy, cavity size, and free volume distributions are calculated. MD simulation has also been used to obtain specific volume (V) as a function of temperature (T). It is demonstrated that this V–T curve can be used to determinate glass transition temperature T_g, reliably. Although experimental data available for the PANI film are very limited, simulation results such as density and T_g are in good agreement with the experimental values reported in the literature. Comparison of the surface topography of PANI demonstrates a reasonable trend between atomic force microscopy image analysis and the MD simulation results at various temperatures. Copyright © 2014 John Wiley & Sons, Ltd.     

Molecular dynamics simulation studies of the influence of imidazolium structure on the properties of imidazolium/azide ionic liquids

Atomistic molecular dynamics simulations were performed on 1-butyl-3-methyl-imidazolium azide [bmim][N(3)], 1-butyl-2,3-dimethylimidazolium azide [bmmim][N(3)], and 1-butynyl-3-methyl-imidazolium azide [bumim][N(3)] ionic liquids. The many-body polarizable APPLE&P force field was augmented with parameters for the azide anion and the bumim cation. Good agreement between the experimentally determined and simulated crystal structure of [bumim][N(3)] as well as the liquid-state density and ionic conductivity of [bmmim][N(3)] were found. Methylation of bmim (yielding bmmim) resulted in dramatic changes in ion structuring in the liquid and slowing of ion motion. Conversely, replacing the butyl group of bmim with the smaller 2-butynyl group resulted in an increase of ion dynamics.     

Nitrile and thiocyanate IR probes: molecular dynamics simulation studies

Nitrile- and thiocyanate-derivatized amino acids have been found to be useful IR probes for investigating their local electrostatic environments in proteins. To shed light on the CN stretch frequency shift and spectral lineshape change induced by interactions with hydrogen-bonding solvent molecules, we carried out both classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations for MeCN and MeSCN in water. These QM/MM and conventional force field MD simulation results were found to be inconsistent with the experimental results as well as with the high-level ab initio calculation results of MeCN-water and MeSCN-water potential energies. Thus, a new set of atomic partial charges of MeCN and MeSCN is obtained. By using the MD simulation trajectories and the electrostatic potential model recently developed, the CN and SCN stretching mode frequency trajectories were obtained and used to simulate the IR spectra. The C[Triple Bond]N frequency blueshifts of MeCN and MeSCN in water are estimated to be 9.0 and 1.9 cm(-1), respectively, in comparison with those of gas phase values. These values are found to be in reasonable agreement with the experimentally measured IR spectra of MeCN, MeSCN, beta-cyano-L-alanine, and cyanylated cysteine in water and other polar solvents.     

Influence of electrostatic interactions on the properties of cyanobiphenyl liquid crystals predicted from atomistic molecular dynamics simulations

The influence of force field details in all-atom molecular dynamics (MD) simulations on the predicted thermodynamic, structural, and dynamic properties of bulk 4-cyano-4?-pentylbiphenyl (5CB) systems have been investigated in the 292–368 K temperature range. The effect of the molecular dipole moment and the details of dihedral potential for biphenyl unit were investigated using both polarisable (POL) and non-polarisable (NP) versions of the quantum chemistry-based force field. The predicted densities for the nematic and isotropic phases of bulk 5CB were found to be in excellent agreement with available experimental data. The nematic-isotropic transition temperature (T_NI) showed strong sensitivity to the force field details, MD simulations with partial atomic charge distributions and molecular dipole moment corresponding to high-level quantum chemistry calculations predicted an overestimation of the T_NI by about 30 K. Rescaling the charges to allow the molecular dipole to be closer to experimentally reported values of 5CB dipole in condensed phases, significantly improved the prediction of T_NI as well as other thermodynamic and dynamic properties of 5CB. We also discuss how the structural, thermodynamic, and dynamic properties of bulk 5CB are affected by the flexibility of the central biphenyl dihedral and the inclusion of induced polarisation effects.     

Molecular dynamics simulations of the melting of 1,3,3-trinitroazetidine

Physical properties of condensed-phase 1,3,3-trinitroazetidine (TNAZ) have been computed with molecular dynamics (MD) and a nonreactive, fully flexible force field formulated by combining the intramolecular interactions obtained from the Generalized AMBER Force Field and the rigid-molecule force field developed by Sorescu-Rice-Thompson [J. Phys. Chem. B 1997, 101, 798] (AMBER-SRT). The results are compared with MD calculations, using the AMBER force field. The predicted densities of crystalline TNAZ from both force fields are about 10% lower than the experimental value. The calculated thermodynamic melting point at 1 atm from the AMBER-SRT force field is 390 K, in good agreement with the measured value of 374 K, while the AMBER force field predicts a thermodynamic melting point of 462 K. The lattice parameters and the molecular and crystal structures calculated with the AMBER-SRT force field are in excellent agreement with experiment. Simulations with the AMBER-SRT force field were also used to generate the isotherm of TNAZ up to 4 GPa and the bulk modulus and its pressure derivative.     

Molecular simulation of guanidinium-based ionic liquids

A new systematic all-atom force field was developed for cyclic guanidinium-based ionic liquids (ILs) based on the AMBER force field. Optimized molecular geometries and equilibrium bond lengths and angles were obtained by ab initio calculations, and charges were allocated to each atom center by fitting the ab initio electrostatic potential. Molecular dynamics simulations were performed for eleven kinds of ILs that are comprised of NO3(-) anions and cyclic guanidinium-based cations. Validation was carried out by comparing our simulated densities with experimental and calculated data from the literature. Transport properties such as self-diffusion coefficients, viscosities, and conductivities were calculated by molecular dynamic simulation, and their dependence on the length of the alkyl chains of cyclic guanidinium-based cations are discussed. Radial distribution functions and spatial distribution functions were investigated to depict the microscopic structures of the ILs, and the relationship between their properties and microstructures is also discussed.     

Using spectroscopic data on imidazolium cation conformations to test a molecular force field for ionic liquids

A molecular force field for the computer simulation of ionic liquids is evaluated a posteriori by confrontation against Raman spectroscopic data, published after the force field had been formulated. Specifically, the terms in the force field describing the conformational aspects of dialkylimidazolium cations, which were specifically developed for these compounds using high level ab initio calculations, are those affecting the distribution of conformers in simulated ionic liquids. Those distributions are compared with analyses of the liquid-phase Raman spectra, and the features of a series of dihedral torsions along the alkyl side chains in 1-alkyl-3-methylimidazolium cations in several ionic liquids are discussed.     

Comparison of Force Fields on the Basis of Various Model Approaches—How To Design the Best Model for the [CnMIM][NTf2] Family of Ionic Liquids

In this contribution, we present two new united‐atom force fields (UA‐FFs) for 1‐alkyl‐3‐methylimidazolium bis(trifluoromethylsulfonyl)imide [C_nMIM][NTf₂] (n=1, 2, 4, 6, 8) ionic liquids (ILs). One is parametrized manually, and the other is developed with the gradient‐based optimization workflow (GROW). By doing so, we wanted to perform a hard test to determine how researchers could benefit from semiautomated optimization procedures. As with our already published all‐atom force field (AA‐FF) for [C_nMIM][NTf₂] (T. Köddermann, D. Paschek, R. Ludwig, ChemPhysChem­ 2007, 8, 2464 ), the new force fields were derived to fit experimental densities, self‐diffusion coefficients, and NMR rotational correlation times for the IL cation and for water molecules dissolved in [C₂MIM][NTf₂]. In the manual force field, the alkyl chains of the cation and the CF₃ groups of the anion were treated as united atoms. In the GROW force field, only the alkyl chains of the cation were united. All other parts of the structures of the ions remained unchanged to prevent any loss of physical information. Structural, dynamic, and thermodynamic properties such as viscosity, cation rotational correlation times, and heats of vaporization calculated with the new force fields were compared with values simulated with the previous AA‐FF and the experimental data. All simulated properties were in excellent agreement with the experimental values. Altogether, the UA‐FFs are slightly superior for speed‐up reasons. The UA‐FF speeds up the simulation by about 100 % and reduces the demanded disk space by about 78 %. More importantly, real time and efforts to generate force fields could be significantly reduced by utilizing GROW. The real time for the GROW parametrization in this work was 2 months. Manual parametrization, in contrast, may take up to 12 months, and this is, therefore, a significant increase in speed, though it is difficult to estimate the duration of manual parametrization.     

A force field for molecular simulation of tetrabutylphosphonium amino acid ionic liquids

An all-atom force field was set up for a new class of ionic liquids (ILs), tetrabutylphosphonium amino acid, on the basis of the AMBER force field with determining parameters related to the phosphorus atom and modifying several parameters. Ab initio quantum chemical calculations were employed to obtain molecular geometries, infrared frequencies, and torsion energy profiles. Atom partial charges were obtained by using the one-conformation, two-step restraint electrostatic potential approach. Molecular dynamics simulation was carried out in the isothermal-isobaric ensemble for 14 tetrabutylphosphonium amino acid ILs at two temperatures to validate the force field against the experimental densities and heat capacities at constant pressure. Computed thermodynamic properties are in good agreement with available experimental values. Moreover, radial distribution functions were investigated to depict the microscopic structures of these ILs.     

Surface relaxation in water clusters: evidence from theoretical analysis of the oxygen 1s photoelectron spectrum

We present a theoretical interpretation of the oxygen 1s photoelectron spectrum published by Ohrwall et al. [J. Chem. Phys. 123, 054310 (2005)]. A water cluster that contains 200 molecules was simulated at 215 K using the polarizable AMOEBA force field. The force field predicts longer O...O distances at the cluster surface than in the bulk. Comparisons to ab initio molecular dynamics (MD) simulations indicate that the force field underestimates the degree of surface relaxation. By comparing cluster lineshape models, computed from MD simulations, to the experimental spectrum we find further evidence of surface relaxation.     

Crosslinking PMMA: Molecular dynamics investigation of the shear response

Crosslinking can fundamentally change the mechanical properties of a linear glassy polymer. It has been experimentally observed that when lightly crosslinked, poly(methyl‐methacrylate) (PMMA) has a characteristically more ductile response to mechanical loading than does linear PMMA despite having a higher glass transition temperature. Here, molecular dynamics (MD) simulations are used to investigate conformational and energetic differences between linear PMMA and lightly crosslinked PMMA under shear deformation. As consistent with experiments, crosslinked PMMA is found to have a reduced yield stress relative to linear PMMA. Using the probing capabilities of our explicit atom MD approach, it is observed that while the crosslinks have a minimal direct energy contribution to the total system, they can alter how the main chains conform to macroscopic loading. In crosslinked PMMA, the backbone aligns more with the direction of external loading, thereby reducing the force applied to (and associated deformation of) the polymer bonds. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014 , 52, 444–449     

Parametrization, molecular dynamics simulation, and calculation of electron spin resonance spectra of a nitroxide spin label on a polyalanine alpha-helix

The nitroxide spin label 1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl-methanethiosulfonate (MTSSL), commonly used in site-directed spin labeling of proteins, is studied with molecular dynamics (MD) simulations. After developing force field parameters for the nitroxide moiety and the spin label linker, we simulate MTSSL attached to a polyalanine alpha-helix in explicit solvent to elucidate the factors affecting its conformational dynamics. Electron spin resonance spectra at 9 and 250 GHz are simulated in the time domain using the MD trajectories and including global rotational diffusion appropriate for the tumbling of T4 Lysozyme in solution. Analysis of the MD simulations reveals the presence of significant hydrophobic interactions of the spin label with the alanine side chains.     

The molecular structure of 1,1-dichloro-1-silacyclo-hexane and of 1,1-dimethoxy-1-silacyclohexane in the gas phase, an electron diffraction study

The molecular structure of 1,1-dichloro-1-silacyclohexane (DCSC) and of 1,1-dimethoxyl-silacyclohexane (DMSC) has been determined by gas phase electron diffraction. Starting values for the vibrational parameters were obtained from force field calculations.

Both molecules are in the chair conformation with a flattening in the vicinity of the silicon atom, which is most pronounced in the dichloro-compound. Disregarding the substituents the title compounds show C_s-symmetry. In DMSC the gem-dimethoxy grouping is in the sc, sc conformation in accordance with the anomeric effect.

A comparison is made between the experimentally found geometries with predictions of molecular mechanics calculations based on two available force fields.     

Force field dependence of phospholipid headgroup and acyl chain properties: Comparative molecular dynamics simulations of DMPC bilayers

The reliability of molecular simulations largely depends on the quality of the empirical force field parameters. Force fields used in lipid simulations continue to be improved to enhance the agreement with experiments for a number of different properties. In this work, we have carried out molecular dynamics simulations of neat DMPC bilayers using united‐atom Berger force field and three versions of all‐atom CHARMM force fields. Three different systems consisting of 48, 72, and 96 lipids were studied. Both particle mesh Ewald (PME) and spherical cut‐off schemes were used to evaluate the long‐range electrostatic interactions. In total, 21 simulations were carried out and analyzed to find out the dependence of lipid properties on force fields, system size, and schemes to calculate long‐range interactions. The acyl chain order parameters calculated from Berger and the recent versions of CHARMM simulations have shown generally good agreement with the experimental results. However, both sets of force fields deviate significantly from the experimentally observed P‐C dipolar coupling values for the carbon atoms that link the choline and glycerol groups with the phosphate groups. Significant differences are also observed in several headgroup parameters between CHARMM and Berger simulations. Our results demonstrate that when changes were introduced to improve CHARMM force field using PME scheme, all the headgroup parameters have not been reoptimized. The headgroup properties are likely to play a significant role in lipid–lipid, protein–lipid, and ligand–lipid interactions and hence headgroup parameters in phospholipids require refinement for both Berger and CHARMM force fields. © 2009 Wiley Periodicals, Inc.J Comput Chem, 2010     

Structural and phase properties of tetracosane (C24H50) monolayers adsorbed on graphite: an explicit hydrogen molecular dynamics study

We discuss molecular dynamics (MD) computer simulations of a tetracosane (C24H50) monolayer physisorbed onto the basal plane of graphite. The adlayer molecules are simulated with explicit hydrogens, and the graphite substrate is represented as an all-atom structure having six graphene layers. The tetracosane dynamics modeled in the fully atomistic manner agree well with experiment. The low-temperature ordered solid organizes into a rectangularly centered structure that is not commensurate with underlying graphite. Above T=200 K, as the molecules start to lose their translational and orientational order via gauche defect formation a weak smectic mesophase (observed experimentally but never reproduced in united atom (UA) simulations) appears. The phase behavior of the adsorbed layer is critically sensitive to the way the electrostatic interactions are included in the model. If the electrostatic charges are set to zero (as for a UA force field), then the melting temperature increases by approximately 70 K with respect to the experimental value. When the nonbonded 1-4 interaction is not scaled, the melting temperature decreases by approximately 90 K. If the scaling factor is set to 0.5, then melting occurs at T=350 K, in very good agreement with experimental data.     

On achieving experimental accuracy from molecular dynamics simulations of flexible molecules: aqueous glycerol

The rotational isomeric states (RIS) of glycerol at infinite dilution have been characterized in the aqueous phase via a 1 micros conventional molecular dynamics (MD) simulation, a 40 ns enhanced sampling replica exchange molecular dynamics (REMD) simulation, and a reevaluation of the experimental NMR data. The MD and REMD simulations employed the GLYCAM06/AMBER force field with explicit treatment of solvation. The shorter time scale of the REMD sampling method gave rise to RIS and theoretical scalar 3J(HH) coupling constants that were comparable to those from the much longer traditional MD simulation. The 3J(HH) coupling constants computed from the MD methods were in excellent agreement with those observed experimentally. Despite the agreement between the computed and the experimental J-values, there were variations between the rotamer populations computed directly from the MD data and those derived from the experimental NMR data. The experimentally derived populations were determined utilizing limiting J-values from an analysis of NMR data from substituted ethane molecules and may not be completely appropriate for application in more complex molecules, such as glycerol. Here, new limiting J-values have been derived via a combined MD and quantum mechanical approach and were used to decompose the experimental 3J(HH) coupling constants into population distributions for the glycerol RIS.