Two-Phase Thermodynamic Model for Efficient and Accurate Absolute Entropy of Water from Molecular Dynamics Simulations

Presented here is the two-phase thermodynamic (2PT) model for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics (MD) simulations. In this method, the density of state (DoS) functions (including the normal modes of translation, rotation, and intramolecular vibration motions) are determined from the Fourier transform of the corresponding velocity autocorrelation functions. A fluidicity parameter (f), extracted from the thermodynamic state of the system derived from the same MD, is used to partition the translation and rotation modes into a diffusive, gas-like component (with 3Nf degrees of freedom) and a nondiffusive, solid-like component. The thermodynamic properties, including the absolute value of entropy, are then obtained by applying quantum statistics to the solid component and applying hard sphere/rigid rotor thermodynamics to the gas component. The 2PT method produces exact thermodynamic properties of the system in two limiting states: the nondiffusive solid state (where the fluidicity is zero) and the ideal gas state (where the fluidicity becomes unity). We examine the 2PT entropy for various water models (F3C, SPC, SPC/E, TIP3P, and TIP4P-Ew) at ambient conditions and find good agreement with literature results obtained based on other simulation techniques. We also validate the entropy of water in the liquid and vapor phases along the vapor-liquid equilibrium curve from the triple point to the critical point. We show that this method produces converged liquid phase entropy in tens of picoseconds, making it an efficient means for extracting thermodynamic properties from MD simulations.

Communication pathways from the anti-codon region to the aminoacylation site in Methionyl tRNA Synthetase: Molecular dynamics simulations and the structure network analysis

The enzymes of the family of tRNA synthetases perform their functions with high precision by synchronously recognizing the anticodon region and the aminoacylation region, which are separated by ?70 in space. This precision in function is brought about by establishing good communication paths between the two regions. We have modeled the structure of the complex consisting of Escherichia coli methionyl-tRNA synthetase (MetRS), tRNA, and the activated methionine. Molecular dynamics simulations have been performed on the modeled structure to obtain the equilibrated structure of the complex and the cross-correlations between the residues in MetRS have been evaluated. Furthermore, the network analysis on these simulated structures has been carried out to elucidate the paths of communication between the activation site and the anticodon recognition site. This study has provided the detailed paths of communication, which are consistent with experimental results. Similar studies also have been carried out on the complexes (MetRS + activated methonine) and (MetRS + tRNA) along with ligand-free native enzyme. A comparison of the paths derived from the four simulations clearly has shown that the communication path is strongly correlated and unique to the enzyme complex, which is bound to both the tRNA and the activated methionine. The details of the method of our investigation and the biological implications of the results are presented in this article. The method developed here also could be used to investigate any protein system where the function takes place through long-distance communication.

Analysis of Hydrogen Bonding and Stability of Protein Secondary Structures in Molecular Dynamics Simulation

Molecular Dynamics (MD) simulations provide an atomic level account of the molecular motions and have proven to be immensely useful in the investigation of the dynamical structure of proteins. Once an MD trajectory is obtained, specific interactions at the molecular level can be directly studied by setting up appropriate combinations of distance and angle monitors. However, if a study of the dynamical behavior of secondary structures in proteins becomes important, this approach can become unwieldy. We present herein a method to study the dynamical stability of secondary structures in proteins, based on a relatively simple analysis of backbone hydrogen bonds. The method was developed for studying the thermal unfolding of beta-lactamases, but can be extended to other systems and adapted to study relevant properties.

Monte Carlo and molecular dynamics simulation of argon clusters andn-alkanes in the confined regions of zeolites

Geometry and energy of argon clusters confined in zeolite NaCaA are compared with those of free clusters. Results indicate the possible existence of magic numbers among the confined clusters. Spectra obtained from instantaneous normal mode analysis of free and confined clusters give a larger percentage of imaginary frequencies for the latter indicating that the confined cluster atoms populate the saddle points of the potential energy surface significantly. The variation of the percentage of imaginary frequencies with temperature during melting is akin to the variation of other properties. It is shown that confined clusters might exhibit inverse surface melting, unlike medium-to-large-sized free clusters that exhibit surface melting. Configurational-bias Monte Carte (CBMC) simulations of n-alkanes in zeolites Y and A are reported. CBMC method gives reliable estimates of the properties relating to the conformation of molecules. Changes in the conformational properties of n-butane and other longer n-alkanes such as n-hexane and n-heptane when they are confined in different zeolites are presented. The changes in the conformational properties of n-butane and n-hexane with temperature and concentration is discussed. In general, in zeolite Y as well as A, there is significant enhancement of the gauche population as compared to the pure unconfined fluid.

Tryptophan-water interaction in Monellin:Hydration patterns from molecular dynamics simulations

Femtosecond spectroscopy carried out earlier on Monellin and some other systems has given insights into the hydration dynamics of the proteins. In the present work, molecular dynamics simulations have been performed on Monellin to study the hydration dynamics. A method has been described to follow up the molecular events of the protein–water interactions in detail. The time constants of the survival correlation function match well with the reported experimental values. This validates the procedure, adapted here for Monellin, to investigate the hydration dynamics in general.

Performance metrics in a hybrid MPI-OpenMP based molecular dynamics simulation with short-range interactions

We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation-intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for parallelizing a generalized MD computation scheme for systems with short range interatomic interactions. The algorithm is discussed in the context of nano-indentation of Chromium films with carbon indenters using the Embedded Atom Method potential for Cr-Cr interaction and the Morse potential for Cr-C interactions. We study the performance of our algorithm for a range of MPI-thread combinations and find the performance to depend strongly on the computational task and load sharing in the multi-core processor. The algorithm scaled poorly with MPI and our hybrid schemes were observed to outperform the pure message passing scheme, despite utilizing the same number of processors or cores in the cluster. Speed-up achieved by our algorithm compared favorably with that achieved by standard MD packages. (C) 2013 Elsevier Inc. All rights reserved.

Estimating successive pK(a) values of polyprotic acids from ab initio molecular dynamics using metadynamics: the dissociation of phthalic acid and its isomers

Estimation of the dissociation constant, or pK(a), of weak acids continues to be a central goal in theoretical chemistry. Here we show that ab initio Car-Parrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free energy profile of the dissociation reaction can provide reasonable estimates of the successive pK(a) values of polyprotic acids. We use the distance-dependent coordination number of the protons bound to the hydroxyl oxygen of the carboxylic group as the collective variable to explore the free energy profile of the dissociation process. Water molecules, sufficient to complete three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. Two distinct minima corresponding to the dissociated and un-dissociated states of the acid are observed and the difference in their free energy values provides the estimate for pK(a), the acid dissociation constant. We show that the method predicts the pK(a) value of benzoic acid in good agreement with experiment and then show using phthalic acid (benzene dicarboxylic acid) as a test system that both the first and second pK(a) values as well, as the subtle difference in their values for different isomers can be predicted in reasonable agreement with experimental data.

Ab Initio Molecular Dynamics Simulations of Amino Acids in Aqueous Solutions: Estimating pK(a) Values from Metadynamics Sampling

Changes in the protonation and deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. Here, we report calculations of the free-energy profile for the protonation deprotonation reaction of the 20 canonical alpha amino acids in aqueous solutions using ab initio Car-Parrinello molecular dynamics simulations coupled with metad-ynamics sampling. We show here that the calculated change in free energy of the dissociation reaction provides estimates of the multiple pK(a) values of the amino acids that are in good agreement with experiment. We use the bond-length-dependent number of the protons coordinated to the hydroxyl oxygen of the carboxylic and the amine groups as the collective variables to explore the free-energy profiles of the Bronsted acid-base chemistry of amino acids in aqueous solutions. We ensure that the amino acid undergoing dissociation is solvated by at least three hydrations shells with all water molecules included in the simulations. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pK(a) values with a mean relative error, with respect to experimental results, of 0.2 pK(a) units.

Stability of Dimeric Interface in Banana Lectin: Insight from Molecular Dynamics Simulations

Banana lectin (Banlec) is a homodimeric non-glycosylated protein. It exhibits the b-prism I structure. High-temperature molecular dynamics simulations have been utilized to monitor and understand early stages of thermally induced unfolding of Banlec. The present study elucidates the behavior of the dimeric protein at four different temperatures and compares the structural and conformational changes to that of the minimized crystal structure. The process of unfolding was monitored by following the radius of gyration, the rms deviation of each residue, change in relative solvent accessibility and the pattern of inter- and intra-subunit interactions. The overall study demonstrates that the Banlec dimer is a highly stable structure, and the stability is mostly contributed by interfacial interactions. It maintains its overall conformation during high-temperature (400–500 K) simulations, with only the unstructured loop regions acquiring greater momentum under such condition. Nevertheless, at still higher temperatures (600 K) the tertiary structure is gradually lost which later extends to loss of secondary structural elements. The pattern of hydrogen bonding within the subunit and at the interface across different stages has been analyzed and has provided rationale for its intrinsic high stability.

NMR studies of molecular dynamics in tetramethylammonium tetrabromo cadmate

Internal motions in a A2BX4 compound (tetramethylammonium tetrabromo cadmate) have been investigated using proton spin—lattice relaxation time (T1) and second moment (M2) measurements in the temperature range 77 to 400 K. T1 measurements at three Larmor frequencies (10, 20 and 30 MHz) show isotropic tumbling of the tetramethylammonium group, random reorientation of methyl groups and spin—rotation interaction, and the corresponding parameters have been computed. The cw spectrum is narrow throughout the temperature range and shows side bands at the lowest temperature. This observation, along with the free-induction-decay behavior at these temperatures, is interpreted as the onset of a coherent motion, e.g. methyl group quantum tunnelling.

Conformational Dynamics in Alkyl Chains of an Anchored Bilayer: A Molecular Dynamics Study

Molecular dynamics (MD) simulations are reported for an anchored bilayer formed by the intercalation of cetyl trimethyl ammonium (CTA) and CH3(CH2)15N+(CH3) ions in a layered solid, CdPS3. The intercalated CTA ions are organized with the cationic headgroups tethered to the inorganic sheet and the hydrocarbon tails arranged as bilayers. Simulations were performed at three temperatures, 65, 180, and 298 K, using an isothermal−isobaric ensemble that was subsequently switched once macroscopic parameters had converged to a canonical isothermal−isochoric ensemble. The simulations are able to reproduce the experimental features of this system, including the formation of the bilayer and layer-to-layer separation distance. An analysis of the conformation of the chains showed that at all three temperatures a fraction of the alkyl chains retained a planar all-trans conformation, and that gauche bonds occurred as part of a “kink” (gauche+−trans−gauche−) sequence and not as isolated gauche bonds. Trans−gauche isomerization rates for the alkyl chains in the anchored bilayer are slower than those in lipid bilayers at the same temperature and show a progressive increase as the torsion numbers approach the tail. A two-dimensional periodic Voronoi tessellation analysis was performed to obtain the single-molecular area of an alkyl chain in the bilayer. The single-molecular area relaxation times are an order of magnitude longer than the trans−gauche isomerization times. The results indicate that the trans−gauche isomerization is associated with the creation and annihilation of a kink defect sequence. The results of the present MD simulation explain the apparent conflicting estimates of the gauche disorder in this system as obtained from infrared and 13C nuclear magnetic resonance measurements.

Proton magnetic resonance study of molecular dynamics in (NH4)2CdI4

Proton magnetic resonance and spin-lattice relaxation studies have been carried out on (NH4)2CdI4 as a function of temperature (77–400 K) and Larmor frequency (10, 20 and 30 MHz). The T1 data indicate isotropic tumbling of ammonium ions at equivalent sites till 160 K. There is an indication of a phase transition at 265 K, the activation energy for molecular reorientation increases from 2.8 kcal/mole to 4.6 kcal/mole. The relaxation results and the linewidth data support the presence of two inequivalent sites at low temperatures, one having an environment corresponding to near-rigid-lattice limit and the other undergoing fast reorientations. The behaviour of the free induction decay with temperature below 120 K suggests a coherent motion for the faster species.

Molecular Dynamics in [(CH8)aN]z Cd14 A Proton Magnetic Relaxation Study

second moment measurements are carried out on [(CH,),N], CdI, in the temperature range 77 to 400 K. The results are interpreted based on a molecular dynamical model of randomly reorienting methyl groups and isotropically tumbling tetramethyl ammonium group. The relaxation data show contributions from spin-rotation interaction at high temperatures and presence of inequivalent methyl groups. The correlation times and associated activation energies, connected with this model, are calculated from the data. The structure in the absorption line and in the free-induction decay signal at 77 K indicates the possibility of tunnelling motion of the methyl groups. Im Temperaturbereich 77 bis 400 K werden an [(CH,),N],CdI, Protonen-Spin-Gitter-Relaxationsexperimente (bei Larmorfrequenzen von 10,20 und 30 MHz) und Messungen des zweiten Moments durchgefiihrt. Die Ergebnisse werden an Hand eines molekularen dynamischen Modells sich statistisch umorientierender Methylgruppen und isotrop taumelnder Tetramethyl-Ammoniumgruppen interpretiert. Die Relaxationswerte zeigen Beitriige von Spin-Rotations-Wechselwirkung bei hohen Temperaturen und die Anwesenheit von inaquivalenten Methylgruppen. Die Korrelationszeiten und verknupften Aktivierungsenergien, die mit diesem Model1 verbunden sind, werden am den Werten berechnet. Die Struktur in der Absorptionslinie und im Abklingsignal der freien Induktion bei 77 K zeigt die Moglichkeit einer Tunnelbewegung der Methylgruppen.

Molecular dynamics simulations of sliding in an Fe-Cu tribopair system

Experimental evidence suggests that high strain rates, stresses, strains and temperatures are experienced near sliding interfaces. The associated microstructural changes are due to several dynamic an interacting phenomena. 3D non-equilibrium molecular dynamics (MD) simulations of sliding were conducted with the aim of understanding the dynamic processes taking place in crystalline tribopairs, with a focus on plastic deformation and microstructural evolution. Embedded atom potentials were employed for simulating sliding of an Fe-Cu tribopair. Sliding velocity, crystal orientation and presence of lattice defects were some of the variables in these simulations. Extensive plastic deformation involving dislocation and twin activity, dynamic recrystallization, amorphization and/or nanocrystallization, mechanical mixing and material transfer were observed. Mechanical mixing in the vicinity of the sliding interface was observed even in the Fe-Cu system, which would cluster under equilibrium conditions, hinting at the ballistic nature of the process. Flow localization was observed at high velocities implying the possible role of adiabatic heating. The presence of preexisting defects (such as dislocations and interfaces) played a pivotal role in determining friction and microstructural evolution. The study also shed light on the relationship between adhesion and plastic deformation, and friction. Comparisons with experiments suggest that such simulations can indeed provide valuable insights that are difficult to obtain from experiments.

A molecular dynamics investigation of the structure of PbO---PbF2 glasses*1

The structure of PbO---PbF2 glasses has been studied using molecular dynamics (MD). The existence of [OPb4] structural units is observed over the entire glass-forming range, in conformity with a model proposed earlier based on various structural investigations of this system. Various other features of the structural model are also supported by the MD calculations.