The MM3 force field for amides,polypeptides and proteins

The potential functions for simple amides, several peptides and a small protein have been worked out for the MM3 force field. Structures and energies were fit as previously with MM2, but additionally, we fit the vibrational spectra of the simple amides (average rms error over four compounds, 34 cm^?1), and examined more carefully electrostatic interactions, including charge-charge and charge-dipole interactions. The parameters were obtained and tested by examining four simple amides, five electrostatic model complexes, two dipeptides, six crystalline cyclic peptides, and the protein Crambin. The average root-mean-square deviation from the X-ray structures for the six cyclic peptide crystals was only 0.10 Å for the nonhydrogen atomic positions, and 0.011 Å, 1.0°, and 4.9° for bond lengths, bond angles, and torsional angles, respectively. The parameter set was then further tested by minimizing the high resolution crystal structure of the hydrophobic protein Crambin. The resultant root-mean-square deviations for the non-hydrogen atomic data, in the presence of the crystal lattice, are 0.22 Å, 0.023 Å, 2.0°, and 6.4° for coordinates, bond lengths, bond angles, and torsional angles, respectively.     

Crystal structure of a liquid crystal non‐symmetric dimer: cholesteryl 4‐[4‐(4‐n‐butylphenylethynyl)phenoxy]butanoate

The crystal structure of cholesteryl 4‐[4‐(4‐n‐butylphenylethynyl)phenoxy]butanoate [phase sequence: Cr 155°C (46.1?J?g^?1) SmA 186.8°C (1.5?J?g^?1) TGB‐N* 204.7 (6?J?g^?1) I] has been solved from single crystal X‐ray diffraction data. The compound crystallizes in the monoclinic space group P2₁ with unit cell parameters: a?=?13.129(2), b?=?9.3904(10), c?=?17.4121(8)?Å, β?=?92.790(7)°, Z?=?2. The structure has been solved by direct methods and refined to R?=?0.0606 for 3?250 observed reflections. The bond distances and angles are in good agreement with the corresponding values for compounds containing phenyl and cholesterol moieties. The phenyl rings A and B are planar. The dihedral angle between the least‐squares planes of the two phenyl rings is 28°. The cholesterol moiety has the usual structure: the C and E rings have chair conformations, and the D and F rings adopt half‐chair conformations. The molecules in the unit cell are arranged in an antiparallel manner. The crystal structure is stabilized by an intermolecular C–H…O contact of 2.989(10)?Å.     

The application of molecular mechanics to the structures of carbohydrates

A study is reported of the accuracy with which the geometries of pyranose and methyl pyranoside molecules are predicted by molecular mechanics. Calculations of the conformational energies of the model compounds dihydroxymethane, methoxymethanol, and dimethoxymethane, made with the program MMI, produced results that compare well with previous ab initio molecular orbital calculations. This indicates that MMI gives a satisfactory account of the energetic and conformational aspects of the anomeric effect, a conclusion further supported by calculations on 2-methoxytetrahydropyran. The prediction of the observed preferred conformations of the primary alcohol group in aldohexopyranoses appears to be less satisfactory. MMI-CARB, a version of MMI with changes in some of the equilibrium C? O bond lengths of the program, has been used to calculate the geometries of 13 pyranose and methyl pyranoside molecules, the crystal structures of which have been studied by neutron diffraction. When the C? C? O? H torsion angles are constrained to approximately the values observed in the crystal structures, good agreement is obtained between the theoretical and experimental molecular geometries. The rms deviation for C? C and C? O bonds, excluding those significantly affected by thermal motion in the crystal structure determinations, is 0.005 Å. Corresponding figures for the valence angles that do not involve hydrogen atoms and for the ring torsion angles are 1.2° and 2.0°, respectively. The Cremer and Pople puckering parameters for the pyranose rings are reproduced within 0.026 Å in Q and 5.4° in θ.     

Crystal and Molecular Structure of the bis-Ethyl Urethane of 5,7-Dodecadiyn-1,12,diol (ETCD)

Grown from ethyl acetate solution, the bis-ethylurethane of 5,7-dodecadiyn-1,12-diol is a monoclinic crystal, a = 16.9740(16), b = 4.9770(5), c = 11.0874(11) Å; β = 101.869(6)°; Z = 2; V = 916.63(16) ų. The crystal structure contains two N─H…O hydrogen bonds per molecule and has nearly ideal parameters (d = 4.977 Å, ? = 45.8°, R = 3.477 Å) for solid-state polymerization.     

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.     

Crystal structure of poly(dithiotriethylene adipate)

The crystal structure of poly(dithiotriethylene adipate) has been determined through the best fitting of calculated and experimental X‐ray diffraction powder profiles. A triclinic cell was found with dimensions a = 4.942 (7) Å, b = 4.702 (2) Å, c = 20.56 (2) Å, α = 88.9 (2)°, β = 61.0 (1)°, γ = 67.8 (1)°, P‐1 space group, and one chain in the unit cell. A full extended trans conformation of the chain fitted satisfactory the experimental data, yielding to a discrepancy factor R_p = 0.073. A comparison between the crystal structures of poly(dithiotriethylene adipate) and poly (thiodiethylene adipate) is proposed. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 2677–2682, 2005     

Interaction potential models for bulk Zns,Zns nanoparticle,and Zns nanoparticle‐PMMA from first‐principles

An ab initio derived transferable polarizable force‐field has been developed for Zinc sulphide (ZnS) nanoparticle (NP) and ZnS NP‐PMMA nanocomposite. The structure and elastic constants of bulk ZnS using the new force‐field are within a few percent of experimental observables. The new force‐field show remarkable ability to reproduce structures and nucleation energies of nanoclusters (Zn₁S₁‐Zn₁₂S₁₂) as validated with that of the density functional theory calculations. A qualitative agreement of the radial distribution functions of Zn? O, in a ZnS nanocluster‐PMMA system, obtained using molecular mechanics molecular dynamics (MD) and ab initio MD (AIMD) simulations indicates that the ZnS–PMMA interaction through Zn? O bonding is explained satisfactorily by our force‐field. © 2015 Wiley Periodicals, Inc.     

Effect of Cholesteric Liquid Crystalline Compounds on the Radical Polymerization of Methyl Methacrylate

Polymerization of methyl methacrylate was carried out at 55 and 65°C using benzoyl peroxide as initiator in the presence of the fol-lowing additives: (a) cholesteric compounds like cholesterol, cho-lesteryl acetate, cholesteryl caprylate, cholesteryl stearate, choles-teryl chloride, cholesteryl laurate, cholesteryl oleyl carbonate, and cholesteryl 2-ethylhexyl carbonate, (b) a nematic liquid crystal, N-(p-methoxy benzylidene)-p-butyl aniline, and (c) rodlike molecules like 2-butynediol and diacetylene diol. The rates of polymerization, activation energies, molecular weights, and tacticities of the poly-mer are discussed in the light of monomer + additive interactions. It is found that monomer-additive complexes affect the polymerization rates.     

An empirical potential for the O-H ⋯ O hydrogen bond: Part 2. Comparison with observed hydrogen bond geometries

The room temperature distribution of O-H ? O hydrogen bond geometries has been predicted by a Monte Carlo calculation, with an empirical potential energy function for the hydrogen bond. The results are compared with a recent survey of hydrogen bonds in carbohydrate crystal structures. The calculated and observed distributions of the O-H ? O angle have mean values of 165.5° and 167.1° respectively. Both the theoretical and experimental results suggest that short O ? H hydrogen bonds tend to be more linear than long O ? H bonds. The distribution of hydrogen bonding within the lone pair plane of the acceptor oxygen atom is predicted to be broader than the distribution perpendicular to this plane, in agreement with the experimental data. The empirical hydrogen bond function, in conjunction with the molecular mechanics program MMI, has also been used to predict the geometries of inter-residue hydrogen bonds in five disaccharides. The O ? H distances and O-H ? O angles are reproduced with r.m.s. deviations of 0.06 Å and 9° respectively.     

Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics

The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostatic potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1'-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C2-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1 micros MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline-1'-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 micros MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.     

The Periodate‐Based Double Perovskites M2NaIO6 (M = Ca,Sr, and Ba)

The crystal structures of the M₂NaIO₆ series (M = Ca, Sr, Ba), prepared at 650 °C by ceramic methods, were determined from conventional laboratory X‐ray powder diffraction data. Synthesis and crystal growth were made by oxidizing I^– with O₂^(air) to I⁷⁺ followed by crystal growth in the presence of NaF as mineralizator, or by the reaction of the alkali‐metal periodate with the alkaline‐earth metal hydroxide. All three compounds are insoluble and stable in water. The barium compound crystallizes in the cubic space group Fm3m (no. 225) with lattice parameters of a = 8.3384(1) Å, whereas the strontium and calcium compounds crystallize in the monoclinic space group P2₁/c (no. 14) with a = 5.7600(1) Å, b = 5.7759(1) Å, c = 9.9742(1) Å, β = 125.362(1)° and a = 5.5376(1) Å, b = 5.7911(1) Å, c = 9.6055(1) Å, β = 124.300(1)°, respectively. The crystal structure consists of either symmetric (for Ba) or distorted (for Sr and Ca) perovskite superstructures. Ba₂NaIO₆ contains the first perfectly octahedral [IO₆]^5– unit reported. The compounds of the ortho‐periodates are stable up to 800 °C. Spectroscopic measurements as well as DFT calculations show a reasonable agreement between calculated and observed IR‐ and Raman‐active vibrations.     

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.     

GRID: A high‐resolution protein structure refinement algorithm

The energy‐based refinement of protein structures generated by fold prediction algorithms to atomic‐level accuracy remains a major challenge in structural biology. Energy‐based refinement is mainly dependent on two components: (1) sufficiently accurate force fields, and (2) efficient conformational space search algorithms. Focusing on the latter, we developed a high‐resolution refinement algorithm called GRID. It takes a three‐dimensional protein structure as input and, using an all‐atom force field, attempts to improve the energy of the structure by systematically perturbing backbone dihedrals and side‐chain rotamer conformations. We compare GRID to Backrub, a stochastic algorithm that has been shown to predict a significant fraction of the conformational changes that occur with point mutations. We applied GRID and Backrub to 10 high‐resolution (≤ 2.8 Å) crystal structures from the Protein Data Bank and measured the energy improvements obtained and the computation times required to achieve them. GRID resulted in energy improvements that were significantly better than those attained by Backrub while expending about the same amount of computational resources. GRID resulted in relaxed structures that had slightly higher backbone RMSDs compared to Backrub relative to the starting crystal structures. The average RMSD was 0.25 ± 0.02 Å for GRID versus 0.14 ± 0.04 Å for Backrub. These relatively minor deviations indicate that both algorithms generate structures that retain their original topologies, as expected given the nature of the algorithms. © 2012 Wiley Periodicals, Inc.     

A new method for empirical force field calculations on localized and delocalized carbocations

A new empirical force field method for localized and delocalized carbocations is described. Additional geometry parameters for carbocations were added to Allinger's MMP2 molecular mechanics program, which can treat delocalized π-systems. The effect of hyperconjugation in carbocations is introduced via a quantum chemical term into force field calculations for the first time. The calculated heats of formation are in excellent agreement with a wide range of experimental data; the largest deviations are about 3.5 kcal/mol. The calculated structures agree very well with those computed at correlated ab initio levels (MP2(full)/6-31G*). The relative energies and geometries of different conformations of representative carbocations also were in good agreement with MP4/6-31G*//MP2(full)/6-31G* results. © 1996 by John Wiley & Sons, Inc.     

United atom force field for phospholipid membranes: Constant pressure molecular dynamics simulation of dipalmitoylphosphatidicholine/water system

We refined the united atom field for the simulations of phospholipid membranes. To validate this potential we performed 1000-ps constant pressure simulation of a dipalmitoylphosphatidicholine (DPPC) bilayer at T=50° C. The average area per head group (61.6±0.6) Ų obtained in our simulation agrees well with the measured one of (62.9±1.3) Ų. The calculated S_CD order parameters for the Sn-2 hydrocarbon tail also display a good agreement with the experiment. The conformations of head groups in our simulations of the liquid crystal phase are different than the ones observed in the crystal structure. ©1999 John Wiley & Sons, Inc. J Comput Chem 20, 531–545, 1999     

Crystalline Behavior and Structure of a Liquid Crystal Compound, 5‐{[4′‐(((Pentyl)oxy)‐4‐biphenylyl)carbonyl]oxy}‐1‐pentyne

Single crystals of two liquid crystal compounds, 5‐{[4′‐(((pentyl)oxy)‐4‐biphenylyl)carbonyl]oxy}‐1‐pentyne (A3EO5) and 5‐{[(4′‐nonyloxy‐4‐biphenylyl)carbonyl]oxy}‐1‐pentyne (A3EO9), have been prepared by solution growth technique. The morphologies and structures of A3EO5 and A3EO9 crystals were investigated by wide angle X‐ray diffraction (WXRD), atom force microscope (AFM) and transmission electron microscope (TEM). In contrast to the same series of compounds which have a longer alkyl tail, 5‐{[(4′‐heptoxy‐4‐biphenylyl)carbonyl]oxy}‐1‐pentyne (A3EO7), 5‐{[(4′‐heptoxy‐4‐biphenylyl)oxy]carbonyl}‐1‐pentyne (A3E′O7) and A3EO9, A3EO5 shows strikingly different crystalline behavior. The former three compounds have only one crystal form, whereas A3EO5 exhibits polymorphism. Specifically, A3EO5 crystals grown from toluene solution show two crystal forms. The first one is crystal I which adopts a monoclinic P112/m space group with unit cell parameters of a?5.79 Å, b?8.34 Å, c?43.92 Å, γ?96°, and the other one is crystal II which adopts a monoclinic P112 space group with unit cell parameters of a?5.55 Å, b?7.38 Å, c?31.75 Å, γ?94°. When using dioxane as the solvent to grow A3EO5 crystal, we can selectively obtain crystal I. A3EO5 melt‐grown crystals also have two crystal forms which derive from crystal I and crystal II, respectively. The different crystalline behavior of the compounds should correlate with their different electron dipole moment resulting from the different length of alkyl tail.     

Geometry prediction of bridged zirconocene dichlorides by quantum chemical methods

The ab initio Hartree–Fock theory has been demonstrated to give accurate geometry predictions for bridged zirconocene dichlorides. Equilibrium geometries of crystallographically characterized bridged zirconocene dichlorides were optimized by Hartree–Fock, MP2, BLYP, and B3LYP methods, with basis sets ranging from 3‐21G* to 6‐311G**. Selected geometrical parameters were compared with experimental crystal structures. The least expensive HF/3‐21G* method proved to be notably accurate. The accuracy of HF/3‐21G* was verified by a comprehensive data set of 62 bridged zirconocene dichlorides. Furthermore, experimental corrections were applied to the optimized geometry parameters to eliminate systematic deviations. Corrections resulted in considerably improved accuracy for systematically overestimated metal–ligand distances, with maximum deviation falling from 0.081 to 0.039 Å, and absolute average deviations from 0.048 to 0.012 Å. Ligand–metal–ligand angles were predicted accurately with absolute average deviations of 0.7–1.3°. Zirconium–chlorine distances and chlorine–zirconium–chlorine angles are relatively constant in the studied molecules. Zirconium–cyclopentadienyl distances can be influenced mainly by modifying the ligand structure, whereas cyclopentadienyl–zirconium– cyclopentadienyl angles and cyclopentadienyl–cyclopentadienyl plane angles can be controlled by bridge modifications. The HF/3‐21G* method can be applied for the estimation of steric effects in zirconocene catalyzed polymerization reactions, therefore being suitable for the construction of structure–polymerization property correlations. © 2000 John Wiley & Sons, Inc. J Comput Chem 22: 51–64, 2001     

Synthesis of two novel cobalt complexes and their crystal structures

Two new cobalt complexes were successfully synthesized from the reaction of binaphthyl Schiff base 2 with Co(OAc)₂ in the presence of sodium methoxide at 80 °C for 24 h and Co(acac)₃ in toluene under reflux. Their unique crystal structures are unambiguously disclosed by X‐ray analysis. Complex 3 is triclinic, space group P1 , unit cell dimensions a = 10.742(2) Å, b = 11.153(2) Å, c = 12.715 Å, α = 79.865(3) °, β = 76.053 °, γ = 72.532(4) °, volume 1401.3(5) ų, Z = 2. Complex 4 is triclinic, space group P1 , unit cell dimensions a = 10.801(2) Å, b = 12.554(3) Å, c = 15.219(3) Å, α = 105.672(4) °, β = 103.048 °, γ = 104.594(4) °, volume 1824.8(7) ų, Z = 2, calculated density 1.428 Mg m⁻³. Copyright © 2003 John Wiley & Sons, Ltd.     

A molecular dynamics study of the thermal response of crystalline cellulose Iβ

Molecular dynamics simulations were performed to better understand the atomic details of thermal induced transitions in cellulose Iβ. The latest version of the GLYCAM force field series (GLYCAM06) was used for the simulations. The unit cell parameters, density, torsion angles and hydrogen-bonding network of the crystalline polymer were carefully analyzed. The simulated data were validated against the experimental results obtained by X-ray diffraction for the crystal structure of cellulose Iβ at room and high temperatures, as well as against the temperature-dependent IR measurements describing the variation of hydrogen bonding patterns. Distinct low and high temperature structures were identified, with a phase transition temperature of 475–500 K. In the high-temperature structure, all the origin chains rotated around the helix axis by about 30° and the conformation of all hydroxymethyl groups changed from tg to either gt on origin chains or gg on center chains. The hydrogen-bonding network was reorganized along with the phase transition. Compared to the previously employed GROMOS 45a4 force field, GLYCAM06 yields data in much better agreement with experimental observations, which reflects that a cautious parameterization of the nonbonded interaction terms in a force field is critical for the correct prediction of the thermal response in cellulose crystals.