Molecular dynamics simulation of acetamide solvation using interaction energy components: Application to structural and energy properties

Molecular dynamics simulation of an aqueous solution of acetamide was performed using Lennard–Jones 12-6-1 potentials to describe the solute–solvent interactions, and TIP3P to describe the water–water interactions. The Morokuma decomposition scheme and the ESIE solute atomic charges were used to reproduce the molecular parameters of the solute–water interaction potential. The results showed that the functions that use the EX-PL-DIS-ES interaction model lead to good values of the structural and energy properties (in particular, the hydration shell and the solvation energies) when they are compared with those from using AMBER-derived parameters, and with the available theoretical and experimental data.     

Molecular dynamics simulation study of superhydrated perdeuterated natrolite using a new interaction potential model

To test a new interaction potential, molecular dynamics simulations of zeolite natrolite were performed for the structures under ambient conditions hydrated by perdeuterated water and at high pressure (1.87 GPa) in the superhydrated phase, which were recently studied by neutron diffraction. The experimental structures were reproduced with reasonable accuracy, and the hydrogen bond features are discussed. As in ordinary natrolite, a flip motion of water molecules around the HOH bisector is found, which, together with translational oscillations, gives rise to transient hydrogen bonds between water molecules, which do not appear from experimental equilibrium coordinates. The dynamics of water molecules can explain some problems encountered in refining the experimental structure. Vibrational spectra of natrolite containing perdeuterated water, which are not yet measured, were simulated, and their qualitative trend is discussed.     

Molecular dynamics simulation of sub-and supercritical water with a new interaction potential

A molecular dynamics experiment was performed for water under sub-and supercritical conditions with a new interaction potential including the nonelectrostatic H-bond component. The internal energy, self-diffusion coefficient, mean number of H-bonds per water molecule, and distributions of molecules according to the number of H-bonds were calculated over a wide temperature range at pressures of 50 and 100 MPa. The temperature dependences of these properties were analyzed.     

Molecular simulation of the hydration Gibbs energy of barbiturates

In the present work, molecular dynamics calculations of the Gibbs energy of hydration of 10 different substituted barbiturates in SPC/E water were performed using thermodynamic integration. Given that experimental determination of the Gibbs hydration energy for this class of compounds is currently unfeasible, computer simulations appear as the only alternative for the estimation of this important quantity. Several simulation parameters are discussed and optimized based on calculations for barbituric acid. It is concluded that accounting for electrostatic interactions with the Reaction-Field method can be up to two times faster than with Particle-Mesh-Ewald method, without loss of accuracy. Different number of solvent molecules and simulation lengths were also tested. Lennard-Jones and electrostatic contributions were scaled down to zero in an independent way. It is shown that the electrostatic contribution is dominant (representing approximately 90% of the total Gibbs energy of hydration) and that barbiturate intra-molecular interactions cannot be neglected. The importance of the electrostatic contribution is attributed to the formation of hydrogen bonds between the barbiturates and water, which play an important role in the solvation process. The influence of the different substituents and their contribution to the Gibbs energy of hydration was assessed. Finally, the Lennard-Jones contributions and the total hydration Gibbs energy can both be correlated against molecular weight or partition coefficient data for mono- and di-substituted barbiturates.     

On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy

Implicit solvent hydration free energy models are an important component of most modern computational methods aimed at protein structure prediction, binding affinity prediction, and modeling of conformational equilibria. The nonpolar component of the hydration free energy, consisting of a repulsive cavity term and an attractive van der Waals solute-solvent interaction term, is often modeled using estimators based on the solvent exposed solute surface area. In this paper, we analyze the accuracy of linear surface area models for predicting the van der Waals solute-solvent interaction energies of native and non-native protein conformations, peptides and small molecules, and the desolvation penalty of protein-protein and protein-ligand binding complexes. The target values are obtained from explicit solvent simulations and from a continuum solvent van der Waals interaction energy model. The results indicate that the standard surface area model, while useful on a coarse-grained scale, may not be accurate or transferable enough for high resolution modeling studies of protein folding and binding. The continuum model constructed in the course of this study provides one path for the development of a computationally efficient implicit solvent nonpolar hydration free energy estimator suitable for high-resolution structural and thermodynamic modeling of biological macromolecules.     

Molecular dynamics simulation and linear interaction energy study of d-Glu-based inhibitors of the MurD ligase

The biosynthetic pathway of the bacterial peptidoglycan, where MurD is an enzyme involved at the intracellular stage of its construction, represents a collection of highly selective macromolecular targets for novel antibacterial drug design. In this study as part of our investigation of the MurD bacterial target two recently discovered classes of the MurD ligase inhibitors were investigated resulting from the lead optimization phases of the N-sulfonamide d-Glu MurD inhibitors. Molecular dynamics simulations, based on novel structural data, in conjunction with the linear interaction energy (LIE) method suggested the transferability of our previously obtained LIE coefficients to further d-Glu based classes of MurD inhibitors. Analysis of the observed dynamical behavior of these compounds in the MurD active site was supported by static drug design techniques. These results complement the current knowledge of the MurD inhibitory mechanism and provide valuable support for the d-Glu paradigm of the inhibitor design.     

Molecular simulation of the hydration of ethene to ethanol using ab initio potentials and free energy curves

Molecular dynamics simulations of aqueous solutions at infinite dilution of the reaction of water with ethene: H2O + CH2CH2 --> CH3CH2OH were performed using Lennard-Jones 12-6-1 potentials to describe the solute-solvent interactions, and TIP3P to describe the water-water interactions. The Morokuma decomposition scheme of ab initio interaction energies at the SCF level and the dispersion component at the MP2 level were used to reproduce the molecular parameters of the solute-water interaction potentials. The results show that the functions that use the EX-PL-DIS-ES interaction model to describe the solvation of the reactant, transition state, and product systems lead to good values of the reaction (Delta G) and acceptable values of the activation (Delta G#) free energy as compared with those from using AMBER-derived parameters, using the available theoretical and experimental data as referents.     

Finding reaction paths using the potential energy as reaction coordinate

The intrinsic reaction coordinate curve (IRC), normally proposed as a representation of a reaction path, is parametrized as a function of the potential energy rather than the arc-length. This change in the parametrization of the curve implies that the values of the energy of the potential energy surface points, where the IRC curve is located, play the role of reaction coordinate. We use Caratheodory's relation to derive in a rigorous manner the proposed parametrization of the IRC path. Since this Caratheodory's relation is the basis of the theory of calculus of variations, then this fact permits to reformulate the IRC model from this mathematical theory. In this mathematical theory, the character of the variational solution (either maximum or minimum) is given through the Weierstrass E-function. As proposed by Crehuet and Bofill [J. Chem. Phys. 122, 234105 (2005)], we use the minimization of the Weierstrass E-function, as a function of the potential energy, to locate an IRC path between two minima from an arbitrary curve on the potential energy surface, and then join these two minima. We also prove, from the analysis of the Weierstrass E-function, the mathematical bases for the algorithms proposed to locate the IRC path. The proposed algorithm is applied to a set of examples. Finally, the algorithm is used to locate a discontinuous, or broken, IRC path, namely, when the path connects two first order saddle points through a valley-ridged inflection point.     

Molecular dynamics study of hydration in ethanol-water mixtures using a polarizable force field

The abnormal physicochemical characteristics of ethanol solvation in water are commonly attributed to the phenomenon of hydrophobic hydration. To investigate the structural organization of hydrophobic hydration in water-ethanol mixtures, we use molecular dynamics simulations based on detailed atomic models. Induced polarization is incorporated into the potential function on the basis of the classical Drude oscillator model. Water-ethanol mixtures are simulated at 11 ethanol molar fractions, from 0.05 to 0.9. Although the water and ethanol models are parametrized separately to reproduce the vaporization enthalpy, static dielectric constant, and self-diffusion constant of neat liquids at ambient conditions, they also reproduce the energetic and dynamical properties of the mixtures accurately. Furthermore, the calculated dielectric constant for the various water-alcohol mixtures is in excellent agreement with experimental data. The simulations provide a detailed structural characterization of the mixtures. A depletion of water-water hydrogen bonding in the first hydration shell of ethanol is compensated by an enhancement in the second hydration shell. The structuring effect from the second solvation shell gives rise to a net positive hydrogen-bonding excess for ethanol molar fractions up to approximately 0.5. For larger molar fractions, the second hydration shell is not sufficiently populated to overcome the net H-bond depletion from the first shell.     

FMO-MD simulations on the hydration of formaldehyde in water solution with constraint dynamics

Full-quantum mechanical fragment molecular orbital-based molecular dynamics (FMO-MD) simulations were applied to the hydration reaction of formaldehyde in water solution under neutral conditions. Two mechanisms, a concerted and a stepwise one, were considered with respect to the nucleophilic addition and the proton transfer. Preliminary molecular orbital calculations by means of polarized continuum model reaction field predicted that the hydration prefers a concerted mechanism. Because the calculated activation barriers were too high for free FMO-MD simulations to give reactive trajectories spontaneously, a More O'Ferrall-Jencks-type diagram was constructed from the statistical analysis of the FMO-MD simulations with constraint dynamics. The diagram showed that the hydration proceeds through a zwitterionic-like (ZW-like) structure. The free energy changes along the reaction coordinate calculated by means of the blue moon ensemble for the hydration and the amination of formaldehyde indicated that the hydration proceeds through a concerted process through the ZW-like structure, whereas the amination goes through a stepwise mechanism with a ZW intermediate. In inspection of the FMO-MD trajectories, water-mediated cyclic proton transfers were observed in both reactions on the way from the ZW-like structure to the product. These proton transfers also have an asynchronous character, in which deprotonation from the nucleophilic oxygen atom (or nitrogen atom for amination) precedes the protonation of the carbonyl oxygen atom. The results showed the strong advantage of the FMO-MD simulations to obtain detailed information at a molecular level for solution reactions.     

Free energy calculation using molecular dynamics simulation combined with the three-dimensional reference interaction site model theory. II. Thermodynamic integration along a spatial reaction coordinate

We propose the thermodynamic integration along a spatial reaction coordinate using the molecular dynamics simulation combined with the three-dimensional reference interaction site model theory. This method provides a free energy calculation in solution along the reaction coordinate defined by the Cartesian coordinates of the solute atoms. The proposed method is based on the blue moon algorithm which can, in principle, handle any reaction coordinate as far as it is defined by the solute atom positions. In this article, we apply the present method to the complex formation process of the crown ether 18-Crown-6 (18C6) with the potassium ion in an aqueous solution. The separation between the geometric centers of these two molecules is taken to be the reaction coordinate for this system. The potential of mean force (PMF) becomes the maximum at the separation between the molecular centers being ～4 A?, which can be identified as the free energy barrier in the process of the molecular recognition. In a separation further than the free energy barrier, the PMF is slightly reduced to exhibit a plateau. In the region closer than the free energy barrier, approach of the potassium ion to the center of 18C6 also decreases the PMF. When the potassium ion is accommodated at the center of 18C6, the free energy is lower by -5.7 ± 0.7 kcal/mol than that at the above mentioned plateau or converged state. By comparing the results with those from the free energy calculation along the coupling parameters obtained in our previous paper [T. Miyata, Y. Ikuta, and F. Hirata, J. Chem. Phys. 133, 044114 (2010)], it is found that the effective interaction in water between 18C6 and the potassium ion vanishes beyond the molecular-center-separation of 10 A?. Furthermore, the conformation of 18C6 is found to be significantly changed depending upon the 18C6-K(+) distance. A proper conformational sampling and an accurate solvent treatment are crucial for realizing the accurate PMF, and we believe that the proposed method is useful to evaluate the PMF in a solution. A discussion upon the PMF in terms of the three-dimensional distribution function for the solvent is also presented.     

Three-state trajectory surface hopping studies of the photodissociation dynamics of formaldehyde on ab initio potential energy surfaces

Full-dimensional, three-state, surface hopping calculations of the photodissociation dynamics of formaldehyde are reported on ab initio potential energy surfaces (PESs) for electronic states S(1), T(1), and S(0). This is the first such study initiated on S(1) with ab initio-calculated spin-orbit couplings among the three states. We employ previous PESs for S(0) and T(1), and a new PES for S(1), which we describe here, as well as new spin-orbit couplings. The time-dependent electronic state populations and the branching ratio of radical products produced from S(0) and T(1) states and that of total radical products and molecular products at three total energies are calculated. Details of the surface hopping dynamics are described, and a novel pathway for isomerization on T(1) via S(0) is reported. Final translational energy distributions of H + HCO products from S(0) and T(1) are also reported as well as the translational energy distribution and final rovibrational distributions of H(2) products from the molecular channel. The present results are compared to previous trajectory calculations initiated from the global minimum of S(0). The roaming pathway leading to low rotational distribution of CO and high vibrational population of H(2) is observed in the present calculations.     

Molecular dynamics simulation study of the interaction of trehalose with lipid membranes

The interactions of the cryoprotective agent trehalose with a lipid membrane made of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine at 323 K were studied by means of molecular dynamics simulations. It was observed that trehalose binds to the phospholipid headgroups with its main axis parallel to the membrane normal. Trehalose establishes hydrogen bonds with the carbonyl and phosphate groups and replaces water molecules from the lipid headgroup. Notably, the number of hydrogen bonds (HBs) that the membrane made with its environment was conserved after trehalose binding. The HBs between lipid and trehalose have a longer lifetime than those established between lipid and water. The binding of the sugar does not produce changes either in the lipid area or in the lipid order parameter. The effect of trehalose on the dipole potential is in agreement with experimental results. The contribution of the different components to the membrane dipole potential was analyzed. It was observed that the binding of trehalose produces changes in the different components and the sugar itself contributes to the surface potential due to the polarization of its hydroxyl in the interface.     

Molecular dynamics simulation study of interaction between model rough hydrophobic surfaces

We study some aspects of hydrophobic interaction between molecular rough and flexible model surfaces. The model we use in this work is based on a model we used previously (Eun, C.; Berkowitz, M. L. J. Phys. Chem. B 2009, 113, 13222-13228), when we studied the interaction between model patches of lipid membranes. Our original model consisted of two graphene plates with attached polar headgroups; the plates were immersed in a water bath. The interaction between such plates can be considered as an example of a hydrophilic interaction. In the present work, we modify our previous model by removing the charge from the zwitterionic headgroups. As a result of this procedure, the plate character changes: it becomes hydrophobic. By separating the total interaction (or potential of mean force, PMF) between plates into the direct and the water-mediated interactions, we observe that the latter changes from repulsive to attractive, clearly emphasizing the important role of water as a medium. We also investigate the effect of roughness and flexibility of the headgroups on the interaction between plates and observe that roughness enhances the character of the hydrophobic interaction. The presence of a dewetting transition in a confined space between charge-removed plates confirms that the interaction between plates is strongly hydrophobic. In addition, we notice that there is a shallow local minimum in the PMF in the case of the charge-removed plates. We find that this minimum is associated with the configurational changes that flexible headgroups undergo as the two plates are brought together.     

Thickness of the hydration layer of a protein from molecular dynamics simulation

Water molecules around a protein exhibit slow dynamics with respect to that of pure bulk water. One important issue in protein hydration is the thickness of the hydration layer (i.e., the distance from the protein surface up to which the water dynamics is influenced by the protein). Estimation of thickness is crucial to understand better the properties of "biological water" and the role that it plays in guiding the protein's function. We have performed an atomistic molecular dynamics simulation of an aqueous solution of the protein villin headpiece subdomain or HP-36 to estimate the thickness of its hydration water. In particular, several dynamical properties of water around different segments (three alpha-helices) of the protein have been calculated by varying the thickness of the hydration layers. It is found that in general the influence of the helices on water properties extends beyond the first hydration layer. However, the heterogeneous nature of water among the first hydration layers of the three helices diminishes as the thickness is increased. It indicates that, for a small protein such as HP-36, the thickness of "biological water" is uniform for different segments of the protein.     

Molecular dynamics simulation study of the water-mediated interaction between zwitterionic and charged surfaces

We calculated the potential of mean force (PMF) for the interaction between a model zwitterionic bilayer and a model charged bilayer. To understand the role of water, we separated the PMF into two components: one due to direct interaction and the other due to water-mediated interaction. In our calculations, we observed that water-mediated interaction is attractive at larger distances and repulsive at shorter. The calculation of the entropic and enthalpic contributions to the solvent-mediated components of the PMF showed that attraction is entropically dominant, while repulsion is dominated by the enthalpy.     

Quasiclassical trajectory study of the Cl+CH4 reaction dynamics on a quadratic configuration interaction with single and double excitation interpolated potential energy surface

An ab initio interpolated potential energy surface (PES) for the Cl+CH(4) reactive system has been constructed using the interpolation method of Collins and co-workers [J. Chem. Phys. 102, 5647 (1995); 108, 8302 (1998); 111, 816 (1999); Theor. Chem. Acc. 108, 313 (2002)]. The ab initio calculations have been performed using quadratic configuration interaction with single and double excitation theory to build the PES. A simple scaling all correlation technique has been used to obtain a PES which yields a barrier height and reaction energy in good agreement with high level ab initio calculations and experimental measurements. Using these interpolated PESs, a detailed quasiclassical trajectory study of integral and differential cross sections, product rovibrational populations, and internal energy distributions has been carried out for the Cl+CH(4) and Cl+CD(4) reactions, and the theoretical results have been compared with the available experimental data. It has been shown that the calculated total reaction cross sections versus collision energy for the Cl+CH(4) and Cl+CD(4) reactions is very sensitive to the barrier height. Besides, due to the zero-point energy (ZPE) leakage of the CH(4) molecule to the reaction coordinate in the quasiclassical trajectory (QCT) calculations, the reaction threshold falls below the barrier height of the PES. The ZPE leakage leads to CH(3) and HCl coproducts with internal energy below its corresponding ZPEs. We have shown that a Gaussian binning (GB) analysis of the trajectories yields excitation functions in somehow better agreement with the experimental determinations. The HCl(v'=0) and DCl(v'=0) rotational distributions are as well very sensitive to the ZPE problem. The GB correction narrows and shifts the rotational distributions to lower values of the rotational quantum numbers. However, the present QCT rotational distributions are still hotter than the experimental distributions. In both reactions the angular distributions shift from backward peaked to sideways peaked as collision energy increases, as seen in the experiments and other theoretical calculations.     

Molecular dynamics investigations of chlorine peroxide dissociation on a neural network ab initio potential energy surface

Molecular dissociation of chlorine peroxide (ClOOCl), which consists of two elementary dissociation channels (of Cl–O and O–O), is investigated using molecular dynamics simulations on a neural network-fitted potential energy surface constructed by MP2 calculations with the 6-311G(d,p) basis set. When relaxed scans of the surface are executed, we observe that Cl–O dissociation is extremely reactive with a low barrier height of 0.1928 eV (18.602 kJ/mol), while O–O bond scission is less reactive (0.7164 eV or 69.122 kJ/mol). By utilizing the “novelty sampling” method, 35,006 data points in the ClOOCl configuration hyperspace are collected, and a 40-neuron feed-forward neural network is employed to fit approximately 90% of the data to produce an analytic potential energy function. The mean absolute error and root mean squared error of this fit are reported as 0.0078 eV (0.753 kJ/mol) and 0.0137 eV (1.322 kJ/mol), respectively. Finally, quasi-classical molecular dynamics is executed at various levels of internal energy (from 0.8 to 1.3 eV) to examine the bond ruptures. The two first-order rate coefficients are computed statistically, and the results range from 5.20 to 22.67 ps⁻¹ for Cl–O dissociation and 3.72–8.35 ps⁻¹ for O–O dissociation. Rice-Ramsperger-Kassel theory is utilized to classically correlate internal energies to rate coefficients in both cases, and the plots exhibit very good linearity, thus can be employed to predict rate coefficients at other internal energy levels with good reliability.