Energetics and dynamics in MbCN: CN--vibrational relaxation from molecular dynamics simulations

The dynamics of the cyanide anion bound to sperm-whale myoglobin is investigated using atomistic simulations. With density-functional theory, a 2D potential energy surface for the cyanide-heme complex is calculated. Two deep minima with a stabilization energy of approximately 50 kcal/mol corresponding to two different binding orientations (Fe-CN and Fe-NC) of the ligand are found. The Fe-CN conformation is favored over Fe-NC by several kcal/mol. Mixed quantum mechanics/molecular mechanics calculations show that the binding orientation affects the bond strength of the ligand, with a significantly different bond length and a 25 cm-1 shift in the fundamental CN-frequency. For the molecular dynamics (MD) simulations, a 3-center fluctuating charge model for the Fe-CN unit is developed that captures polarization and ligand-metal charge transfer. Stability arguments based on the energetics around the active site and the CN- frequency shifts suggest that the Fe-CN conformation with epsilon-protonation of His epsilon 64 are most likely, which is in agreement with experiment. Both equilibrium and nonequilibrium MD simulations are carried out to investigate the relaxation time scale and possible relaxation pathways in bound MbCN. The nonequilibrium MD simulations with a vibrationally excited ligand reveal that vibrational relaxation takes place on a time scale of hundreds of picoseconds within the active site. This finding supports the hypothesis that the experimentally observed relaxation rate (3.6 ps) reflects the repopulation of the electronic ground state.     

Spreading dynamics of chain-like monolayers: a molecular dynamics study

Using large-scale molecular dynamics simulations, we have shown previously that the spreading dynamics of sessile drops on solid surfaces can be described in detail using the molecular-kinetic theory of dynamic wetting. Here we present our first steps in extending this approach to investigate the spreading dynamics of Langmuir-Blodgett monolayers. We make use of a monolayer model originally developed by Karaborni and Toxvaerd, but somewhat simplified to facilitate large-scale simulations. Our preliminary results are in good agreement with recent experimental observations and also support a molecular-kinetic interpretation in which the driving force for spreading is the lateral pressure in the monolayer. Away from equilibrium, initial spreading rates are constant and logarithmically dependent on pressure. However, near equilibrium, spreading is pseudo-diffusive and follows the square root of time. In both regimes the controlling factor is the equilibrium frequency of molecular displacements within the monolayer.     

Structure and Energetics of model amphiphilic molecules at the water liquid-vapor interface. A molecular dynamics study

A molecular dynamics study of adsorption of p-n-pentylphenol at infinite dilution at the water liquid-vapor interface is reported. The calculated free energy of adsorption is -8.8 +/- 0.7 kcal/mol, in good agreement with the experimental value of -7.3 kcal/mol. The transition between the interfacial region and the bulk solution is sharp and well-defined by energetic, conformational, and orientational criteria. At the water surface, the phenol head group is mostly immersed in aqueous solvent. The most frequent orientation of the hydrocarbon tail is parallel to the interface, due to dispersion interactions with the water surface. This arrangement of the phenol ring and the alkyl chain requires that the chain exhibits a kink. As the polar head group is being moved into the solvent, the chain length increases and the tail becomes increasingly aligned toward the surface normal, such that the nonpolar part of the molecule exposed to water is minimized. The same effect was achieved when phenol was replaced by a more polar head group, phenolate. This result underscores the difference between hydrophobic hydration at the surface and in the bulk solvent, when nonpolar molecular fragments adopt compact conformations.     

H-Bond in methanol: a molecular dynamics study

A set of molecular dynamics (MD) simulations of methanol-d₄ at three temperatures in the liquid range (200, 250 and 300K) have been carried out. The equations of motion of 256 molecules interacting through a potential model due to Haughney et al. [J. Phys. Chem., 91 (1987) 4934] were solved using the velocity version of the Verlet algorithm. This rather large number of molecules was required for studying the behaviour of the system at momentum transfers as low as 0.25 Å⁻¹. It was found that the system experiences long period fluctuations, and therefore very long MD runs (of the order of 100 ps) are necessary in order to obtain accurate statistical averages. Computed static properties are in good agreement with those reported by Haughney et al. and the neutron weighted g(r) and the static structure factor compare favourably with available neutron diffraction data. The study of time-dependent properties through centre-of-mass autocorrelation functions (VACF, F_s(Q,t) and F(Q,t)) and their memory functions reveals features unknown in simple liquids and very similar to those found in liquid water. A close agreement between centre-of-mass single-particle autocorrelation functions and the translational part of QENS data is also observed. The dynamic structure factor for the centres of mass show distinctive side peaks in the same region of the (Q,ω) plane where recently collective excitations have been studied using coherent neutron scattering thus establishing the presence of propagating short wavelength modes. fa]Presented at the International Symposium on Hydrogen Bond Physics held at Il Ciocco, Barga, Italy, 11–14 September 1990.     

Phase diagrams of alkali halides using two interaction models: a molecular dynamics and free energy study

Phase diagrams for potassium and sodium chlorides are determined by molecular dynamics and free energy calculations. Two rigid-ion interaction models, namely, the Born-Mayer-Huggins (BMH) and Michielsen-Woerlee-Graaf (MWG) effective pair potentials, have been used. The critical and triple point properties are discussed and compared with available experimental and simulation data. The MWG model reproduces the experimental liquid-gas equilibria better than the BMH model, being the accordance very good in the lowest temperature region of the coexistent liquids, particularly for NaCl. However, both models underestimate the critical temperatures of KCl and NaCl. Relatively to the solid-gas equilibria, the models do not reproduce well the experimental data. As for the solid-liquid coexistences either the BMH or the MWG models appear unrealistic.     

Microstructure of neat alcohols: a molecular dynamics study

Neat methanol and tert-butanol are studied by molecular dynamics with the focus on the microstructure of these two alcohols. The site-site radial distribution functions, the corresponding structure factors, and an effective local one-body density function are shown to be the appropriate statistical quantities that point in a complementary manner towards the same microstructure for any given liquid. Methanol is found to be a weakly associated liquid forming various chainlike patterns (open and closed) while tert-butanol is almost entirely associated and forms micellelike primary pattern. The presence of stable local microheterogeneity within homogeneous disordered phase appears as a striking feature of these liquids. The absence of any such apparent clustering in water--a stronger hydrogen bonding liquid--through the same two statistical quantities is analyzed.     

Thermophoresis in liquids: a molecular dynamics simulation study

Thermophoresis in liquids is studied by molecular dynamics simulation (MD). A theory is developed that divides the problem in the way consistent with the characteristic scales. MD is then conducted to obtain the solution of each problem, which is to be all combined for macroscopic predictions. It is shown that when the temperature gradient is applied to the nonconducting liquid bath that contains neutral particles, there occurs a pressure gradient tangential to the particle surface at the particle-liquid interface. This may induce the flow in the interfacial region and eventually the particle to move. This applies to the material system that interacts through van der Waals forces and may be a general source of the thermophoresis phenomenon in liquids. The particle velocity is linearly proportional to the temperature gradient. And, in a large part of the given temperature range, the particle motion is in the direction toward the cold end and decreases with respect to the temperature. It is also shown that the particle velocity decreases or even reverses its sign in the lowest limit of the temperature range or with a particle of relatively weak molecular interactions with the liquid. The characteristics of the phenomenon are analyzed in molecular details.     

Force-induced insulin dimer dissociation: a molecular dynamics study

Understanding the forces and dynamics of insulin dissociation is critical for devising formulations for the treatment of insulin-dependent diabetes. In earlier work, we applied AFM-based force spectroscopy to covalently tethered and oriented insulin monomers to assess the effect of molecular orientation on insulin-insulin binding forces. We report here on steered molecular dynamics simulations of the insulin dissociation force spectroscopy experiment. Consistent with our experiments, our simulation results suggest that insulin dimer dissociation occurs near the limit of extensibility of the B-chain. We have also found that the forced dissociation of the insulin dimer is a rate-dependent process, involving significant conformational changes to the monomer(s). The insulin dimer dissociation pathway also depends on the relative strength of the inter-monomer interactions across the antiparallel beta-sheet interface and the intra-monomer interactions of residues A1 and A30 with the insulin B-chain. Our simulation results strongly support the design of bioactive insulin analogues that involves altering hydrogen bonding and hydrophobic interactions across the beta-sheet dimer interface.     

Polymer-nanoparticle interfacial behavior revisited: a molecular dynamics study

By tuning the polymer-filler interaction, filler size and filler loading, we use a coarse-grained model-based molecular dynamics simulation to study the polymer-filler interfacial structural (the orientations at the bond, segment and chain length scales, chain size and conformation), dynamic and stress-strain properties. Simulated results indicate that the interfacial region is composed of partial segments of different polymer chains, which is consistent with the experimental results presented by Chen et al. (Macromolecules, 2010, 43, 1076). Moreover, it is found that the interfacial region is within one single chain size (R(g)) range, irrespective of the polymer-filler interaction and the filler size, beyond which the bulk behavior appears. In the interfacial region, the orientation and dynamic behaviors are induced by the interfacial enthalpy, while the size and conformation of polymer chains near the filler are controlled by the configurational entropy. In the case of strong polymer-filler interaction (equivalent to the hydrogen bond), the innerest adsorbed polymer segments still undergo adsorption-desorption process, the transport of chain mass center in the interfacial region exhibits away from the glassy behavior, and no plastic-like yielding point appears in the stress-strain curve, which indicates that although the mobility of interfacial polymer chains is restricted, there exist no "polymer glassy layers" surrounding the filler. In addition, it is evidenced that the filler particle prefers selectively adsorbing the long polymer chains for attractive polymer-filler interaction, validating the experimental explanation of the change of the bound rubber (BR). In short, this work provides important information for further experimental and simulation studies of polymer-nanoparticle interfacial behavior.     

Characterizing hydrophobicity at the nanoscale: a molecular dynamics simulation study

We use molecular dynamics (MD) simulations of water near nanoscopic surfaces to characterize hydrophobic solute-water interfaces. By using nanoscopic paraffin like plates as model solutes, MD simulations in isothermal-isobaric ensemble have been employed to identify characteristic features of such an interface. Enhanced water correlation, density fluctuations, and position dependent compressibility apart from surface specific hydrogen bond distribution and molecular orientations have been identified as characteristic features of such interfaces. Tetrahedral order parameter that quantifies the degree of tetrahedrality in the water structure and an orientational order parameter, which quantifies the orientational preferences of the second solvation shell water around a central water molecule, have also been calculated as a function of distance from the plate surface. In the vicinity of the surface these two order parameters too show considerable sensitivity to the surface hydrophobicity. The potential of mean force (PMF) between water and the surface as a function of the distance from the surface has also been analyzed in terms of direct interaction and induced contribution, which shows unusual effect of plate hydrophobicity on the solvent induced PMF. In order to investigate hydrophobic nature of these plates, we have also investigated interplate dewetting when two such plates are immersed in water.     

Liquid-vapor interface of methanol-water mixtures: a molecular dynamics study

Molecular dynamics simulations were carried out to investigate the structural and thermodynamic properties and variations in the dipole moments of the liquid-vapor interfaces of methanol-water mixtures. Various methanol-water compositions were simulated at room temperature. We found that methanol tends to concentrate at the interface, and the computed surface tension shows a composition dependence that is consistent with experimental measurements. The methanol molecule shows preferred orientation near the interface with the methyl group pointing into the vapor phase. The methanol in the mixture is found to have larger dipole moments than that of pure liquid methanol. The strong local field induced by the surrounding water molecules is partly the reason for this difference. The dependence of hydrogen-bonding patterns between methanol and water on the interface and the composition of the mixture is also discussed in the paper.     

Ligand-to-metal charge-transfer dynamics in a blue copper protein plastocyanin: a molecular dynamics study

Equilibrium and nonequilibrium dynamics of a blue copper protein plastocyanin in an oxidized state are studied by molecular dynamics (MD) simulation. Potential energy functions of the lowest seven electronic states, including ligand-to-metal charge-transfer (LMCT) and copper d --> d excited states, were taken from our previous work (Ando, K. J. Phys. Chem. B 2004, 108, 3940), which employed ab initio molecular orbital and density functional calculations on the active-site model. The equilibrium MD simulations in the ground state indicate that ligand motions coupled to transition from the ground state to the LMCT state are mostly represented by stretching and bending vibrations of the Cu-S(Cys) distance, Ndelta(His)-Cu-Ndelta(His) angle, and S(Cys)-Cu-[Ndelta(His)]2 trigonal pyramid structure. The nonequilibrium dynamics on the LMCT potential exhibit rapid decays in which surface crossings to the d --> d and the first excited states occur in 70-80 fs. The crossing dynamics mostly correlate with cleavage of the Cu-S(Cys) bond and the associated response in the Ndelta(His)-Cu-Ndelta(His) moiety. The average dynamics of the vertical energy gap coordinates exhibit an overdamped decay with a recurrence oscillation in 500 fs, which shows clear coherence surviving after the ensemble averaging. This oscillation stems mostly from the recoiling motion of the Ndelta(His)-Cu-Ndelta(His) part. The dynamics of the energy gaps after this coherent oscillation are randomized such that the ensemble average yields flat profiles along time, although each single trajectory exhibits fluctuations with amplitudes large enough to reach surface crossings. These indicate that the relaxation from the LMCT state first occurs via ballistic and coherent potential crossings in 70-80 and 500 fs, followed by thermally activated random transitions.     

Water network dynamics at the critical moment of a peptide's beta-turn formation: a molecular dynamics study

All-atom molecular dynamics simulations for a single molecule of Leu-Enkephalin in aqueous solution have been used to study the role of the water network during the formation of beta-turns. We give a detailed account of the intramolecular hydrogen bonding, the water-peptide hydrogen bonding, and the orientation and residence times of water molecules focusing on the short critical periods of transition to the stable beta-turns. These studies suggest that, when intramolecular hydrogen bonding between the first and fourth residue of the beta-turn is not present, the disruption of the water network and the establishment of water bridges constitute decisive factors in the formation and stability of the beta-turn. Finally, we provide possible explanations and mechanisms for the formations of different kinds of beta-turns.     

High-temperature decomposition of the cellulose molecule: a stochastic molecular dynamics study

The kinetics and products of cellulose pyrolysis can be studied using large-scale molecular dynamics simulations at high temperatures, where the reaction rates are high enough to make the simulation times practical. We carried out molecular dynamics simulations employing the ReaxFF reactive force field to study the initial step of the thermal decomposition process. We gathered statistics of simulated reactive events at temperatures ranging from 1400 to 2200 K, considering cellulose molecules with different molecular weights and initial conformations. Our simulations suggest that, in gas-phase conditions at these high temperatures, the decomposition occurs primarily through random cleavage of the β(1 → 4)-glycosidic bonds, for which we obtained an activation energy of (171 ± 2) kJ mol^?1 and a frequency factor of \(\left( {1.07 \pm 0.12} \right) \times 10^{15}\) s^?1. We did not observe dependency of the kinetic parameters on the molecular weight or initial conformation. Some of the decomposition reactions involved the release of low-molecular-weight products. Excluding radicals, the most commonly observed species were glycolaldehyde, water, formaldehyde and formic acid. Many of our observations are supported by the existing experimental and theoretical knowledge. We did not, however, observe the formation of levoglucosan, which is the dominant product in conventional pyrolysis experiments at much lower temperatures. This is understandable, since the high temperatures can force the dominance of radical reactions over pericyclic reactions. Nevertheless, our results support further use of ReaxFF-based molecular dynamics simulations in the study of cellulose pyrolysis.     

The role of the torsional potential in relaxation dynamics: a molecular dynamics study of polyethylene

The role of the torsional potential in bulk polymer chain dynamics is investigated via molecular dynamics simulation using polyethylene as a model system. A number of three-fold barrier values, both greater and less than the standard one, were invoked. The one-fold potential that determines the gauche vs trans energy difference was also varied. For each of the selected torsional potentials, the MD volumetric glass transition temperature, T_g, was located. It was found that T_g is quite sensitive to the three-fold barrier magnitude, moving from below 100 K to nearly 400 K as the barrier goes from zero to twice the standard value. However T_g was found to be quite insensitive to the gauche trans energy difference. Details of the conformational dynamics were studied for the case of a zero torsional potential. This included the rate and location of conformational transitions, the decay of the torsional angle autocorrelation function (ACF) and the cooperativity of conformational transitions, all as a function of temperature. The temperature dependence of the conformational transition rate remains Arrhenius at all temperatures. The relaxation time characterizing the torsional angle ACF decay exhibits WLF temperature behavior. The conformational transitions are randomly distributed over the bonds at high temperature, but near T_g they become spatially heterogeneous and localized. The transitions show next-neighbor correlation as well as self-correlated forward-backward transitions. All of these features are similar to those found in previous simulations under the standard torsional potential.     

Conformational dynamics of the nicotinic acetylcholine receptor channel: a 35-ns molecular dynamics simulation study

The nicotinic acetylcholine receptor (AChR) is the paradigm of ligand-gated ion channels, integral membrane proteins that mediate fast intercellular communication in response to neurotransmitters. A 35-ns molecular dynamics simulation has been performed to explore the conformational dynamics of the entire membrane-spanning region, including the ion channel pore of the AChR. In the simulation, the 20 transmembrane (TM) segments that comprise the whole TM domain of the receptor were inserted into a large dipalmitoylphosphatidylcholine (DPPC) bilayer. The dynamic behavior of individual TM segments and their corresponding AChR subunit helix bundles was examined in order to assess the contribution of each to the conformational transitions of the whole channel. Asymmetrical and asynchronous motions of the M1-M3 TM segments of each subunit were revealed. In addition, the outermost ring of five M4 TM helices was found to convey the effects exerted by the lipid molecules to the central channel domain. Remarkably, a closed-to-open conformational shift was found to occur in one of the channel ring positions in the time scale of the present simulations, the possible physiological significance of which is discussed.     

Cooperativity in drug-DNA recognition: a molecular dynamics study.

NMR studies have shown that the minor groove-binding ligand Hoechst 33258 binds to the two T4/A4 tracts within the duplex d(CTTTTCGAAAAG)2 in a highly cooperative manner, such that in titration experiments no intermediate 1:1 complex can be detected. The NMR-derived structures of the free DNA and the 2:1 complex have been obtained, but can shed little light on what the origins of this cooperativity may be. Here we present the results of a series of molecular dynamics simulations on the free DNA, the 1:1 complex, and the 2:1 complex, which have been designed to enable us to calculate thermodynamic parameters associated with the molecular recognition events. The results of the molecular dynamics studies confirm that structural factors alone cannot explain the cooperativity observed, indeed when enthalpic and hydration factors are looked at in isolation, the recognition process is predicted to be slightly anticooperative. However, when changes in configurational entropy are taken into account as well, the overall free energy differences are such that the calculated cooperativity is in good agreement with that observed experimentally. The results indicate the power of molecular dynamics methods to provide reasonable explanations for phenomena that are difficult to explain on the basis of static models alone, and provide a nice example of the concept of "allostery without conformational change".     

Silsesquioxane dendrimers as catalysts: a bite-sized molecular dynamics study

A method of calculating the bite (P-M-P) angle for dendritic ligands is reported. Diphenylphosphine terminated dendritic ligands were modified with either a single rhodium or a rhodium complex [HRh(CO)(2)] and molecular dynamics techniques used to run simulations to determine the dynamic bite angle (beta(d)) as a time averaged property. The effects of changing the composition of the dendritic branches is investigated and comparison with experimental hydroformylation data reveals that the dendrimer with the highest linear: branched ratio also has a dynamic bite angle closest to the theoretical ideal value of 120 degrees .     

Long-chain alkyl sulfonate micelle fission: a molecular dynamics study

In this study, we investigate micelle fission of long-chain alkyl sulfonate molecules using atomistic scale simulation. GROMACS software code with the united atom force field was applied. 0.5-μs parallel molecular dynamics simulation study was conducted for a surfactant/water system consisting of 192 sodium pentadecyl sulfonate and 40,553 water molecules. The large preassembled micelle was ruptured at Krafft above T?=?323-K temperature, and we track two ellipsoid-like micelles over the course of the production run. To estimate the micelle shape, we determined the principal moments of inertia and the eccentricity, which proved that the micelles have a pronounced prolate spheroid shape, which agrees well with our previous experimental data. The mechanism of micelle fission was explored in detail. The aggregation number, ionization degree, and other parameters obtained from simulation were consistent with existing experimental finding. The determined parameters in addition to simple visual inspection of trajectories revealed monomer-micelle exchange—with the estimated relaxation time τ ₁?=?10^??9s. We assume that the exchange process is conditioned by the unequal size of micelles leading to adjustment of aggregation number.