Binding structures of tri‐N‐acetyl‐β‐glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field

Lysozyme is a well‐studied enzyme that hydrolyzes the β‐(1,4)‐glycosidic linkage of N‐acetyl‐β‐glucosamine (NAG)_n oligomers. The active site of hen egg‐white lysozyme (HEWL) is believed to consist of six subsites, A‐F that can accommodate six sugar residues. We present studies exploring the use of polarizable force fields in conjunction with all‐atom molecular dynamics (MD) simulations to analyze binding structures of complexes of lysozyme and NAG trisaccharide, (NAG)₃. MD trajectories are applied to analyze structures and conformation of the complex as well as protein–ligand interactions, including the hydrogen‐bonding network in the binding pocket. Two binding modes (ABC and BCD) of (NAG)₃ are investigated independently based on a fixed‐charge model and a polarizable model. We also apply molecular mechanics with generalized born and surface area (MM‐GBSA) methods based on MD using both nonpolarizable and polarizable force fields to compute binding free energies. We also study the correlation between root‐mean‐squared deviation and binding free energies of the wildtype and W62Y mutant; we find that for this prototypical system, approaches using the MD trajectories coupled with implicit solvent models are equivalent for polarizable and fixed‐charge models. © 2012 Wiley Periodicals, Inc.     

Polarizable coarse‐grained models for molecular dynamics simulation of liquid cyclohexane

Force field parameters for polarizable coarse‐grained (CG) supra‐atomic models of liquid cyclohexane are proposed. Two different bead sizes were investigated, one representing two fine‐grained (FG) CH₂r united atoms of the cyclohexane ring, and one representing three FG CH₂r united atoms. Electronic polarizability is represented by a massless charge‐on‐spring particle connected to each CG bead. The model parameters were calibrated against the experimental density and heat of vaporization of liquid cyclohexane, and the free energy of cyclohexane hydration. Both models show good agreement with thermodynamic properties of cyclohexane, yet overestimate the self‐diffusion. The dielectric properties of the polarizable models agree very well with experiment. © 2015 Wiley Periodicals, Inc.     

A Computational Approach to the Effects of Solvent on the Structural,Electronic, Spectroscopic (195Pt NMR and IR), and Thermochemical Properties of a Third‐Generation Anticancer Drug: Trans‐Platinum(II) Complex of 3‐Aminoflavone

This study evaluated the structural, electronic and thermochemical properties of an anticancer active molecule, i.e. trans‐bis‐(3‐aminoflavone)dichloridoplatinum(II) (trans‐Pt(3‐af)₂Cl₂; TCAP) in the gas and solution phases. The polarizable continuum model (PCM) model was used to perform the required calculations in five solvents with different polarities. Moreover, the dependencies of energetic aspects, structural, thermodynamic parameters and frontier orbital energies of the complex were also examined. Dependencies of the frequency shifts of u(CO), u(NH) and ¹⁹⁵Pt Chemical shifts on the solvent dielectric were investigated by Kirkwood–Bauer–Magat equation (KBM). The energies of platinum d‐orbitals and formal electron configurations of Pt atom were calculated by natural bond analysis (NBO).     

Peptide free‐energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95

The C96 and AMBER95 force fields were compared with small model peptides Ac‐(Ala)_n‐NMe (Ac = CH₃CO, NMe = NHCH₃, n=2 and 3) in vacuo and in TIP3P water by computing the free‐energy profiles using multicanonical molecular dynamics method. The C96 force field is a modified version of the AMBER95 force field, which was adjusted to reproduce the energy difference between extended β‐ and constrained α‐helical energies for the alanine tetrapeptide, obtained by the high level ab initio MO method. The slight modification resulted in a large difference in the free energy profiles. The C96 force field prefers relatively extended conformers, whereas the AMBER95 force field favors turn conformations. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 748–762, 2000     

Density functional theory study on the reactions of X− with CH3SY (X,Y = F,Cl, Br,I)

Gas‐phase anionic reactions X^? + CH₃SY (X, Y = F, Cl, Br, I) have been investigated at the level of B3LYP/6‐311+G (2df,p). Results show that the potential energy surface (PES) of gas‐phase reactions X^? + CH₃SY (X, Y = Cl, Br, I) has a quadruple‐well structure, indicating an addition–elimination (A–E) pathway. The fluorine behaves differently in many respects from the other halogens and the reactions F^? + CH₃SY (Y = F, Cl, Br, I) correspond to deprotonation instead of substitution. The gas‐phase reactions X^? + CH₃SF (X = Cl, Br, I), however, follow an A–E pathway other than the last two out going steps (COM2 and PR) that proceeds via a deprotonation. The polarizable continuum model (PCM) has been used to evaluate the solvent effects on the energetics of the reactions X^? + CH₃SY (X, Y = Cl, Br, I). The PES is predicted to be unimodal in the solvents of high polarity. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Excess enthalpies and molecular interactions in solutions of 1-fluoroalkanes in alkanes,benzene or tetrachloromethane. A group contribution (DISQUAC) study

Molar excess enthalpies H ^E at 298.15 K and atmospheric pressure were determined for 12 binary liquid mixtures, 1-fluoropentane, 1-fluorohexane, or 1-fluorononane + a non-polar solvent (hexane, cyclohexane, benzene, or tetrachloromethane) and were interpreted by the DISQUAC group contribution model. 1-Fluoroalkane + n-alkane mixtures are characterized by two types of groups or contact surfaces, fluorine (F) and alkane (CH₃, CH₂), the remaining mixtures by the additional contact surfaces of the solvents (C₆H₁₂ C₆H₆, or CCl₄). The interchange energies, entirely dispersive, of the alkane-solvent contacts were determined independently from the study of solvent-alkane mixtures. The dispersive F-alkane parameters were assumed to equal the parameters of perfluoroalkanes + n-alkanes. The shape of the H ^E curves of 1-fluorolkane + polarizable solvent (C₆H₆, CCl₄) mixtures are best reproduced by the model when the quasi-chemical F-solvent parameters are assumed to equal zero. The quasi-chemical F-alkane (the same for n-alkanes and cyclohexane) and the dispersive F-solvent parameters were estimated in this work. The 1-fluoroalkane solutions in C₆H₆ or CCl₄ exhibit the characteristic features of polar solute + polarizable solvent mixtures, viz., the deviations from the ideality are less positive than in alkanes and the experimental H ^E curves are strongly asymmetrical.     

Polarizable empirical force field for sulfur‐containing compounds based on the classical Drude oscillator model

Condensed‐phase computational studies of molecules using molecular mechanics approaches require the use of force fields to describe the energetics of the systems as a function of structure. The advantage of polarizable force fields over nonpolarizable (or additive) models lies in their ability to vary their electronic distribution as a function of the environment. Toward development of a polarizable force field for biological molecules, parameters for a series of sulfur‐containing molecules are presented. Parameter optimization was performed to reproduce quantum mechanical and experimental data for gas phase properties including geometries, conformational energies, vibrational spectra, and dipole moments as well as for condensed phase properties such as heats of vaporization, molecular volumes, and free energies of hydration. Compounds in the training set include methanethiol, ethanethiol, propanethiol, ethyl methyl sulfide, and dimethyl disulfide. The molecular volumes and heats of vaporization are in good accordance with experimental values, with the polarizable model performing better than the CHARMM22 nonpolarizable force field. Improvements with the polarizable model were also obtained for molecular dipole moments and in the treatment of intermolecular interactions as a function of orientation, in part due to the presence of lone pairs and anisotropic atomic polarizability on the sulfur atoms. Significant advantage of the polarizable model was reflected in calculation of the dielectric constants, a property that CHARMM22 systematically underestimates. The ability of this polarizable model to accurately describe a range of gas and condensed phase properties paves the way for more accurate simulation studies of sulfur‐containing molecules including cysteine and methionine residues in proteins. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Dissociation constants of 2‐azidoethanamines in aqueous solution

Aqueous‐phase dissociation constants (K_a) for the conjugate acids of a series of 2‐azidoethanamine bases: R¹N(R²)CH₂CH₂N₃ ( 1 , R¹ = CH₃, R² = H; 2 , R¹ = CH₃, R² = CH₃; 3 , R¹ = CH₂CH₃, R² = CH₂CH₃; 4 , R¹/R² =  CH₂CH₂CH₂CH₂ ; 5 , R¹/R² =  CH₂CH₂OCH₂CH₂ ; 6 , R¹ = CH₂CH₃, R² = CH₂CH₂N₃) were measured and found to fall between those for analogous unfunctionalized and cyano‐functionalized ethanamines. To explore the possibility of a relationship existing between the constants and molecular geometry, a theoretically based study was conducted. In it, the Gibbs free energies of aqueous‐phase (equilibrium) conformers of the bases and their conjugate acids were determined via a density functional theory/polarizable continuum model method. The results indicate that an attractive interaction between the amine and azide groups that underlies the lowest‐energy gas‐phase conformer of 2 is negated in an aqueous environment by solvent–solute interactions. The magnitudes of the free energy changes of solvation and −TS (entropic) energies of the conformers of the 2‐azidoethanamines and their conjugate acids are observed to correlate with the magnitude of the separation between the conformers' amine and azide groups. However, those correlations are not by themselves sufficient to predict the relative free energies of a molecule's conformers in an aqueous environment. That insufficiency is due to the influence of the correlations being mitigated by three other parameters that arise within the thermodynamic framework employed to compute the observable. The nature of those parameters is discussed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Continuum treatment of electronic polarization effect

A continuum treatment of electronic polarization has been explored for in molecular mechanics simulations in implicit solvents. The dielectric constant for molecule interior is the only parameter in the continuum polarizable model. A value of 4 is found to yield optimal agreement with high-level ab initio quantum mechanical calculations for the tested molecular systems. Interestingly, its performance is not sensitive to the definition of molecular volume, in which the continuum electronic polarization is defined. In this model, quantum mechanical electrostatic field in different dielectric environments from vacuum, low-dielectric organic solvent, and water can be used simultaneously in atomic charge fitting to achieve consistent treatment of electrostatic interactions. The tests show that a single set of atomic charges can be used consistently in different dielectric environments and different molecular conformations, and the atomic charges transfer well from training monomers to tested dimers. The preliminary study gives us the hope of developing a continuum polarizable force field for more consistent simulations of proteins and nucleic acids in implicit solvents.     

Polarizable empirical force field for alkanes based on the classical Drude oscillator model

Recent extensions of potential energy functions used in empirical force field calculations have involved the inclusion of electronic polarizability. To properly include this extension into a potential energy function it is necessary to systematically and rigorously optimize the associated parameters based on model compounds for which extensive experimental data are available. In the present work, optimization of parameters for alkanes in a polarizable empirical force field based on a classical Drude oscillator is presented. Emphasis is placed on the development of parameters for CH3, CH2, and CH moieties that are directly transferable to long chain alkanes, as required for lipids and other biomolecules. It is shown that a variety of quantum mechanical and experimental target data are reproduced by the polarizable model. Notable is the proper treatment of the dielectric constant of pure alkanes by the polarizable force field, a property essential for the accurate treatment of, for example, hydrophobic solvation in lipid bilayers. The present alkane force field will act as the basis for the aliphatic moieties in an extensive empirical force field for biomolecules that includes the explicit treatment of electronic polarizability.     

Synthesis of polyacetals with various main‐chain structures by the self‐polyaddition of vinyl ethers with a hydroxyl function

To establish the optimum conditions for obtaining high molecular weight polyacetals by the self‐polyaddition of vinyl ethers with a hydroxyl group, we performed the polymerization of 4‐hydroxybutyl vinyl ether (CH₂?CH? O? CH₂CH₂CH₂CH₂? OH) with various acidic catalysts [p‐toluene sulfonic acid monohydrate, p‐toluene sulfonic anhydride (TSAA), pyridinium p‐toluene sulfonate, HCl, and BF₃OEt₂] in different solvents (tetrahydrofuran and toluene) at 0 °C. All the polymerizations proceeded exclusively via the polyaddition mechanism to give polyacetals of the structure [? CH(CH₃)? O? CH₂CH₂CH₂CH₂? O? ]_n quantitatively. The reaction with TSAA in tetrahydrofuran led to the highest molecular weight polymers (number‐average molecular weight = 110,000, weight‐average molecular weight/number‐average molecular weight = 1.59). 2‐Hydroxyethyl vinyl ether, diethylene glycol monovinyl ether, cyclohexane dimethanol monovinyl ether, and tricyclodecane dimethanol monovinyl ether were also employed as monomers, and polyacetals with various main‐chain structures were obtained. This structural variety of the main chain changed the glass‐transition temperature of the polyacetals from approximately ?70 °C to room temperature. These polyacetals were thermally stable but exhibited smooth degradation with a treatment of aqueous acid to give the corresponding diol compounds in quantitative yields. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 4053–4064, 2002     

A Computational Understanding of Solvent Effect on the Structure,Electronic, Thermochemical,and Spectroscopic Properties of Ni(η2‐C6H4)(H2PCH2CH2PH2) Complex

Here we report the density functional calculations of the molecular parameters including the energy, geometries, electric dipole moments, vibrational IR frequencies, and ¹H and ¹³C NMR chemical shifts of Ni(η²‐C₆H₄ )(H₂PCH₂CH₂PH₂ ) (a benzyne complex). Based on the polarizable continuum model (PCM ), the effect of polarity of the solvent on these parameters was explored. The wavenumbers of υ(C1–C2 ) as well as the ¹H and ¹³C NMR chemical shift values of complex in various solvents were calculated and correlated with the Kirkwood–Bauer–Magat equation (KBM ), the solvent acceptor numbers (ANs ), and the linear solvation energy relationship (LSER ). The bonding interaction between the benzyne and Ni(H₂PCH₂CH₂PH₂ ) fragment was analyzed by means of the energy decomposition analysis (EDA ). The character of the Ni–C bonds of the molecules was analyzed by natural bond orbital (NBO ) analysis. Also, Monte Carlo simulations were used for the calculation of the total energy and solvation free energy of the complex in water.     

Amphiphilic polymethacrylates as crosslinked polymer precursors obtained by free‐radical monomethacrylate/dimethacrylate copolymerizations

As an extension of our work on the elucidation of the mechanism and control of 3‐dimensional network formation in the free‐radical crosslinking polymerization and copolymerization of multivinyl compounds with the aim to molecularly design vinyl‐type network polymers, novel amphiphilic polymers were prepared as crosslinked polymer precursors. Thus, benzyl methacrylate, a nonpolar monomer, was copolymerized radically with 5 mol % of triicosaethylene glycol dimethacrylate [CH₂C(CH₃)CO(OCH₂CH₂)₂₃OCOC(CH₃)CH₂], a polar monomer, in the presence of lauryl mercaptan as a chain transfer agent. The resulting prepolymers (i.e., vinyl‐type network‐polymer precursors or amphiphilic polymers) were characterized mainly by viscometry using t‐butylbenzene (t‐BB) and a t‐BB/MeOH (80/20) mixture as solvents. The viscosities in the t‐BB/MeOH (80/20) mixture were quite high compared with those in t‐BB, and completely reversed concentration dependencies were observed in the solvents. These are discussed by considering the difference in conformation and the shrinkage of polar, flexible polyoxyethylene units or the entanglement of nonpolar, rigid primary chains. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 4396–4402, 2000     

Apparent Molar Volume, Heat Capacity, and Conductance of Lithium Bis(trifluoromethylsulfone)imide in Glymes and Other Aprotic Solvents

Lithium bis(trifluoromethylsulfone)imide (LiTFSI) is a promising electrolyte for high-energy lithium batteries due to its high solubility in most solvents and electrochemical stability. To characterize this electrolyte in solution, its conductance and apparent molar volume and heat capacity were measured over a wide range of concentration in glymes, tetraethylsulfamide (TESA), acetonitrile, -butyrolactone, and propylene carbonate at 25°C and were compared with those of LiClO₄ in the same solvents. The glymes or n(ethylene glycol) dimethyl ethers (nEGDME), which have the chemical structure CH₃–O–(CH₂–CH₂–O) _n –CH₃ for n = 1 to 4, are particularly interesting since they are electrochemically stable, have a good redox window, and are analogs of the polyethylene oxides used in polymer-electrolyte batteries. TESA is a good plasticizer for polymer-electrolyte batteries. Whenever required, the following properties of the pure solvents were measured: compressibilities, expansibilities, temperature and pressure dependences of the dielectric constant, acceptor number, and donor number. These data were used in particular to calculate the limiting Debye-Hückel parameters for volumes and heat capacities. The infinite dilution properties of LiTFSI are quite similar to those of other lithium salts. At low concentrations, LiTFSI is strongly associated in the glymes and moderately associated in TESA. At intermediate concentrations, the thermodynamic data suggests that a stable solvate of LiTFSI in EGDME exists in the solution state. At high concentrations, the thermodynamic properties of the two lithium salts approach those of the molten salts. These salts have a reasonably high specific conductivity in most of the solvents. This suggests that the conductance of ions at high concentration in solvents of low dielectric constant is due to a charge transfer process rather than to the migration of free ions.     

New interpretation of progression bands observed in infrared spectra of nylon‐m/n

A series of progression bands observed in the infrared spectra of nylon‐m/n and their model compounds have been interpreted in a new manner on the basis of simply coupled oscillator models of zigzag alkyl chains. Nylon‐m/n possesses the methylene sequences of (CH₂)_m and (CH₂)_n?2, and so the effective models of m and n ? 2 coupled oscillators, respectively, had previously been assumed for the methylene rocking–twisting mode, for example. However, the spectral patterns of progression bands predicted by this previously proposed model have been found to be inconsistent with those observed for many kinds of nylon samples with various m and n values. It is rather reasonable to assume that the effective numbers of oscillators should be m ? 2 and n ? 4 for the methylene rocking, twisting, and wagging modes of the (CH₂)_m and (CH₂)_n?2 sequences, respectively. In other words, the infrared progression bands observed for methylene local modes of nylon‐m/n may be interpreted reasonably with the data of n‐alkane molecules with the chemical formulae CH₃(CH₂)_m?2CH₃ and CH₃(CH₂)_n?4CH₃. For the C? C stretching modes, the equivalent n‐alkanes are CH₃(CH₂)_m?1CH₃ and CH₃(CH₂)_n?3CH₃, respectively. In the simply coupled oscillator model, the vibrational mode of one methylene group is represented by an oscillator, for example. Our new concept is to isolate the terminal oscillator adjacent to the amide group from the other oscillators in the inner parts of the methylene zigzag sequence. This corresponds to a physical situation in which the methylene group adjacent to the amide group shows a different vibrational behavior of larger amplitude than those of the inner methylene sequence, as supported by broad‐line NMR data and molecular dynamics calculations reported in the literature. Another possibility is a difference in the electron structure of the methylene unit adjacent to the amide group from that of the inner methylene sequence, resulting in a difference in the force constant and giving a vibrational decoupling between these two types of methylene units. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 1294–1307, 2003     

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.     

Understanding the Initial Decomposition Pathways of the n‐Alkane/Nitroalkane Binary Mixture

Addition of nitroalkanes into n‐alkanes can lower the activation barriers of free‐radical production and accelerate the decomposition of n‐alkanes at relatively low temperatures. Four initial decomposition mechanisms of the n‐butane/nitroethane binary mixture were proposed for the promoting effect and considered theoretically at the B3LYP, BB1K, BMK, MPW1K, and M06‐2X levels with MG3S basis set. Energetics above was compared to high‐level CBS‐QB3 and G4 calculations. Calculated results confirm the feasibility of the four initial decomposition pathways: (I) the C? NO₂ bond rupture of nitroethane to produce ethyl and ·NO₂, (II) HONO elimination from nitroethane followed by decomposition to ·OH and ·NO, (III) rearrangement of nitroethane to ethyl nitrite which further dissociates into CH₃CH₂O· and ·NO, and (IV) direct hydrogen‐abstraction of nitroethane with n‐butane.     

Anionic Copolymerization of Carbonyl Sulfide with Epoxides via Alkali Metal Alkoxides

Carbonyl sulfide (COS), an analogue of carbon dioxide (CO₂), can be converted to CO₂ via the carbonic anhydride enzymes widely existing in nature. COS is an ideal monomer for making poly(monothiocarbonate)s, which are difficult to synthesize by traditional methods. Herein, for the first time, we describe an anionic copolymerization of COS with epoxides using alkali metal alkoxides as the catalysts (initiators), affording poly(monothiocarbonate)s with 100% alternating degree, >99% tail‐to‐head (T‐H) content, high number‐average molecular weights (M_ns, up to 90.3 kg/mol) with narrow molecular weight distributions (Đ=M_w/M_n, 1.05—1.31 for COS/propylene oxide copolymers) under solvent‐free and mild conditions. Oxygen‐sulfur exchange reaction (O/S ER), which can result in the production of contaminated dithiocarbonate and carbonate units in the main chain, was nearly completely depressed at 0 ^oC. In addition, in contrast to previously reported salen chromium (iron) complexes that required multiple synthetic steps, this work provides simple, low‐cost, and effective catalysts for making colorless sulfur‐containing polymers.