Investigating the Bioactive Conformation of Angiotensin II Using Markov State Modeling Revisited with Web-Scale Clustering.

Molecular dynamics simulation is a powerful technique for studying the structure and dynamics of biomolecules in atomic-level detail by sampling their various conformations in real time. Because of the long timescales that need to be sampled to study biomolecular processes and the big and complex nature of the corresponding data, relevant analyses of important biophysical phenomena are challenging. Clustering and Markov state models (MSMs) are efficient computational techniques that can be used to extract dominant conformational states and to connect those with kinetic information. In this work, we perform Molecular Dynamics simulations to investigate the free energy landscape of Angiotensin II (AngII) in order to unravel its bioactive conformations using different clustering techniques and Markov state modeling. AngII is an octapeptide hormone, which binds to the AT1 transmembrane receptor, and plays a vital role in the regulation of blood pressure, conservation of total blood volume, and salt homeostasis. To mimic the water-membrane interface as AngII approaches the AT1 receptor and to compare our findings with available experimental results, the simulations were performed in water as well as in water-ethanol mixtures. Our results show that in the water-ethanol environment, AngII adopts more compact U-shaped (folded) conformations than in water, which resembles its structure when bound to the AT1 receptor. For clustering of the conformations, we validate the efficiency of an inverted-quantized k-means algorithm, as a fast approximate clustering technique for web-scale data (millions of points into thousands or millions of clusters) compared to k-means, on data from trajectories of molecular dynamics simulations with reasonable trade-offs between time and accuracy. Finally, we extract MSMs using various clustering techniques for the generation of microstates and macrostates and for the selection of the macrostate representatives.

Fingerprints of the Crossing of the Frenkel and Melting Line on the Properties of High-Pressure Supercritical Water.

Using molecular dynamics simulations in combination with the two-phase thermodynamic model, we reveal novel characteristic fingerprints of the crossing of the Frenkel and melting line on the properties of high-pressure water at a near-critical temperature (1.03Tc). The crossing of the Frenkel line at about 1.17 GPa is characterized by a crossover in the rotational and translational entropy ratio Srot/Strans, indicating a change in the coupling between translational and rotational motions which is also reflected in the shape of the rotational density of states. The observed isosbestic points in the translational and rotational density of states are also blue-shifted at density and pressure conditions higher than the ones corresponding to the Frenkel line. The first-order phase transition from a rigid liquid to a face-centered cubic plastic crystal phase at about 8.5 GPa is reflected in the discontinuous changes in the translational and rotational entropy, particularly in the significant increase of the ratio Srot/Strans. A noticeable discontinuous increase of the dielectric constant has also been revealed when crossing this melting line, which is attributed to the different arrangement of the water molecules in the plastic crystal phase. The reorientational dynamics in the plastic crystal phase is faster in comparison with the "rigid" liquid-like phase, but it remains unchanged upon a further pressure increase in the range of 8.5-11 GPa.

On the Different Faces of the Supercritical Phase of Water at a Near-Critical Temperature: Pressure-Induced Structural Transitions Ranging from a Gaslike Fluid to a Plastic Crystal Polymorph.

The present study reports a systematic analysis of a wide variety of structural, thermodynamic, and dynamic properties of supercritical water along the near-critical isotherm of T = 1.03Tc and up to extreme pressures, using molecular dynamics and Monte Carlo simulations. The methodology employed provides solid evidence about the existence of a structural transition from a liquidlike fluid to a compressed, tightly packed liquid, in the density and pressure region around 3.4ρc and 1.17 GPa, introducing an alternative approach to locate the crossing of the Frenkel line. Around 8.5 GPa another transition to a face-centered-cubic plastic crystal polymorph with density 5.178ρc is also observed, further confirmed by Gibbs free energy calculations using the two-phase thermodynamic model. The isobaric heat capacity maximum, closely related to the crossing of the Widom line, has also been observed around 0.8ρc, where the local density augmentation is also maximized. Another structural transition has been observed at 0.2ρc, related to the transformation of the fluid to a dilute gas at lower densities. These findings indicate that a near-critical isotherm can be divided into different domains where supercritical water exhibits distinct behavior, ranging from a gaslike one to a plastic crystal one.

Local structure of dilute aqueous DMSO solutions, as seen from molecular dynamics simulations.

The information about the structure of dimethyl sulfoxide (DMSO)-water mixtures at relatively low DMSO mole fractions is an important step in order to understand their cryoprotective properties as well as the solvation process of proteins and amino acids. Classical MD simulations, using the potential model combination that best reproduces the free energy of mixing of these compounds, are used to analyze the local structure of DMSO-water mixtures at DMSO mole fractions below 0.2. Significant changes in the local structure of DMSO are observed around the DMSO mole fraction of 0.1. The array of evidence, based on the cluster and the metric and topological parameters of the Voronoi polyhedra distributions, indicates that these changes are associated with the simultaneous increase of the number of DMSO-water and decrease of water-water hydrogen bonds with increasing DMSO concentration. The inversion between the dominance of these two types of H-bonds occurs around XDMSO = 0.1, above which the DMSO-DMSO interactions also start playing an important role. In other words, below the DMSO mole fraction of 0.1, DMSO molecules are mainly solvated by water molecules, while above it, their solvation shell consists of a mixture of water and DMSO. The trigonal, tetrahedral, and trigonal bipyramidal distributions of water shift to lower corresponding order parameter values indicating the loosening of these orientations. Adding DMSO does not affect the hydrogen bonding between a reference water molecule and its first neighbor hydrogen bonded water molecules, while it increases the bent hydrogen bond geometry involving the second ones. The close-packed local structure of the third, fourth, and fifth water neighbors also is reinforced. In accordance with previous theoretical and experimental data, the hydrogen bonding between water and the first, the second, and the third DMSO neighbors is stronger than that with its corresponding water neighbors. At a given DMSO mole fraction, the behavior of the intensity of the high orientational order parameter values indicates that water molecules are more ordered in the vicinity of the hydrophilic group while their structure is close-packed near the hydrophobic group of DMSO.

Structure and dynamics of liquid CS2: Going from ambient to elevated pressure conditions.

Molecular dynamics simulation studies were performed to investigate the structural and dynamic properties of liquid carbon disulfide (CS2) from ambient to elevated pressure conditions. The results obtained have revealed structural changes at high pressures, which are related to the more dense packing of the molecules inside the first solvation shell. The calculated neutron and X-ray structure factors have been compared with available experimental diffraction data, also revealing the pressure effects on the short-range structure of the liquid. The pressure effects on the translational, reorientational, and residence dynamics are very strong, revealing a significant slowing down when going from ambient pressure to 1.2 GPa. The translational dynamics of the linear CS2 molecules have been found to be more anisotropic at elevated pressures, where cage effects and librational motions are reflected on the shape of the calculated time correlation functions and their corresponding spectral densities.

Solvation structure and dynamics of cis- and trans-1,2 dichloroethene isomers in supercritical carbon dioxide. A molecular dynamics simulation study.

Molecular dynamics simulation techniques have been employed to investigate the solvation structure and dynamics in dilute mixtures of cis- and trans-1,2-dichloroethene in supercritical carbon dioxide. The calculations were performed for state points along a near-critical isotherm (1.02 T(c)) over a wide range of densities, using new developed optimized potential models for both isomers. The similarities and differences in the solvation structures around each isomer have been presented and discussed. The local density augmentation and enhancement factors of CO(2) around the isomers have been found significantly larger than the corresponding values for pure supercritical CO(2). The dynamic local density reorganization has been investigated and related to previously proposed relaxation mechanisms. The density dependence of the calculated self-diffusion coefficients has revealed the existence of a plateau in the region of 0.7-1.1 ρ(c), where the local density augmentation exhibits the maximum value. The reorientational dynamics of the C═C bond vector have been also studied, exhibiting significant differences between the two isomers in the case of the second-order Legendre time correlation functions.

Hydrogen bond, electron donor-acceptor dimer, and residence dynamics in supercritical CO(2)-ethanol mixtures and the effect of hydrogen bonding on single reorientational and translational dynamics: A molecular dynamics simulation study.

The hydrogen bonding and dynamics in a supercritical mixture of carbon dioxide with ethanol as a cosolvent (X(ethanol) approximately 0.1) were investigated using molecular dynamics simulation techniques. The results obtained reveal that the hydrogen bonds formed between ethanol molecules are significantly more in comparison with those between ethanol-CO(2) molecules and also exhibit much larger lifetimes. Furthermore, the residence dynamics in the solvation shells of ethanol and CO(2) have been calculated, revealing much larger residence times for ethanol molecules in the ethanol solvation shell. These results support strongly the ethanol aggregation effects and the slow local environment reorganization inside the ethanol solvation shell, reported in a previous publication of the authors [Skarmoutsos et al., J. Chem. Phys. 126, 224503 (2007)]. The formation of electron donor-acceptor dimers between the ethanol and CO(2) molecules has been also investigated and the calculated lifetimes of these complexes have been found to be similar to those corresponding to ethanol-CO(2) hydrogen bonds, exhibiting a slightly higher intermittent lifetime. However, the average number of these dimers is larger than the number of ethanol-CO(2) hydrogen bonds in the system. Finally, the effect of the hydrogen bonds formed between the individual ethanol molecules on their reorientational and translational dynamics has been carefully explored showing that the characteristic hydrogen bonding microstructure obtained exhibits sufficiently strong influence upon the behavior of them.

Conformational and solvation studies via computer simulation of the novel large scale diastereoselectively synthesized phosphinic MMP inhibitor RXP03 diluted in selected solvents.

Structure-activity relationship studies, regarding the influence of side chains of phosphinic pseudotripeptidic inhibitors on matrix metalloproteinases (MMPs), provided potent and selective inhibitors for this family of structurally and functionally related proteases. Among them, phosphinic pseudopeptide CbzPhepsi[P(O)(OH)CH(2)] phenylpropyl TrpNH(2), known as RXP03, has been extensively used for in vivo and in vitro studies so far. The large quantities of RXP03 required for in vivo studies, as well as the necessity for diastereoisomeric purity, motivated us to further explore and develop an efficient synthetic methodology, which allows separation of the four diastereoisomers of RXP03 based on the astonishing observed differences in solubility of the four isomers in various solvents. This fact prompted us to examine theoretically the conformational differences of these four isomers via computer simulations in the solvents used experimentally. Given the fact that the four examined diastereoisomeric forms of the phosphinic peptides exhibit different behavior in terms of potency and selectivity profiles toward zinc-metalloproteases, this theoretical study provides valuable information on the conformation of phosphinic inhibitors and therefore improves the design and synthesis of active structures. The differences in solubility of RXP03 diastereoisomers in the used solvents were examined in terms of intra- and intermolecular structure. It is found that the different solubility of the RRS and RSS diastereoisomers in EtOH is a result of the different number of hydrogen bonds formed by each isomer with EtOH molecules. In the case of SRS and SSS in Et(2)O, their different solubility might be attributed to the different intramolecular hydrogen bonds formed on these diastereoisomers.

The effect of intermolecular interactions on local density inhomogeneities and related dynamics in pure supercritical fluids. A comparative molecular dynamics simulation study.

The effect of intermolecular interactions of different strength on the local density inhomogeneities in pure supercritical fluids (scfs), with different intramolecular structure, was investigated by employing molecular dynamics (MD) simulation techniques. The simulations were performed at state points along an isotherm close to the critical temperature of each system (T(r) = T/T(c) = 1.03). The molecular fluids under study have been chosen on the basis of the electrostatic character of their intermolecular interactions as follows: monatomic, dipolar and hydrogen bonding (HB), quadrupolar, and octupolar. In the case of dipolar scfs, their HB nature when present was systematically explored and related to the behavior of the created local density inhomogeneities at all densities. The results obtained reveal strong influence of the dipolar and HB interactions of the investigated systems upon the local density augmentation. We found that this effect is fairly larger in the case of the dipolar and HB fluids (H2O, CH3OH, and NH3) compared to those for the non-dipolar ones (Xe, CH4, CO2, and N2). In the case of sc CO2, the dependence of the local density augmentation on the bulk density is in agreement with available experimental data as also reported previously. The estimated average number of hydrogen bonds per molecule (nHB) in these HB fluids shows an analogue nonlinear trend compared to the behavior of the average coordination numbers Nco(rho) of a particle with bulk density. The local density dynamics of the first and second solvation shell of each fluid were further analyzed and related to our previously proposed [Skarmoutsos, I.; Samios, J. J. Chem. Phys. 2007, 126, 044503] different time-scale relaxation mechanisms. Finally, the effect of the different strength of the molecular interactions corresponding to these fluids upon the local density dynamics has also been revealed in the behavior of the predicted appropriate time correlation functions and their corresponding correlation times.

New effective method for quantitative analysis of diffusion jumps, applied in molecular dynamics simulations of small molecules dispersed in short chain systems.

Diffusion jumps of small molecules dispersed in chain molecules or other kinds of slow-moving matrices have already been observed in many previous simulations of such systems, and their treatment led to important qualitative conclusions. In the present work, a new, very simple yet effective method is described, allowing for both identification of individual penetrant jump events and their quantitative treatment in a statistical sense. The method is applied in equilibrium Molecular Dynamics simulations for systems of gaseous alkanes, methane through n-butane, including also a mixture of methane and n-butane, dispersed in n-decane or n-eicosane. Equilibration and attainment of a linear diffusion regime is confirmed by means of various criteria, and the jumps detection method is applied to all systems studied. The results obtained clearly show the existence of distinct jump events in all cases, although the average jump length is reduced with penetrant or liquid alkane molecular weight. The method allows one to determine the average jump length and the corresponding jumps frequency. On the basis of these results, it was possible to estimate a random walk type diffusion coefficient, D(s,jumps), of the penetrants, which was found to be substantially lower compared with the overall diffusion coefficient D(s,MSD) obtained by the mean square displacement method. This finding led us to assume that the overall penetrants' diffusion in the studied systems is a combination of longer jumps with a smoother and more gradual displacement, a result that confirms assumptions suggested in previous studies.

Investigation of the local composition enhancement and related dynamics in supercritical CO2-cosolvent mixtures via computer simulation: the case of ethanol in CO2.

The supercritical mixture ethanol-carbon dioxide (EtOH-CO2) with mole fraction of ethanol X(EtOH) congruent with 0.1 was investigated at 348 K, by employing the molecular dynamics simulation technique in the canonical ensemble. The local intermolecular structure of the fluid was studied in terms of the calculated appropriate pair radial distribution functions. The estimated average local coordination numbers and mole fractions around the species in the mixture reveal the existence of local composition enhancement of ethanol around the ethanol molecules. This finding indicates the nonideal mixing behavior of the mixture due to the existence of aggregation between the ethanol molecules. Furthermore, the local environment redistribution dynamics have been explored by analyzing the time correlation functions (TCFs) of the total local coordination number (solvent, cosolvent) around the cosolvent molecules in appropriate parts. The analysis of these total TCFs in the auto-(solvent-solvent, cosolvent-cosolvent) and cross-(solvent-cosolvent, cosolvent-solvent) TCFs has shown that the time dependent redistribution process of the first solvation shell of ethanol is mainly determined by the redistribution of the CO2 solvent molecules. These results might be explained on the basis of the CO2-CO2 and EtOH-CO2 intermolecular forces, which are sufficiently weaker in comparison to the EtOH-EtOH hydrogen bonding interactions, creating in this way a significantly faster redistribution of the CO2 molecules in comparison with EtOH. Finally, the self-diffusion coefficients and the single reorientational dynamics of both the cosolvent and solvent species in the mixture have been predicted and discussed in relationship with the local environment around the species, which in the case of the EtOH molecules seem to be strongly affected.

Effect of curvature and chirality for hydrogen storage in single-walled carbon nanotubes: a combined ab initio and Monte Carlo investigation.

Combined ab initio and grand canonical Monte Carlo simulations have been performed to investigate the dependence of hydrogen storage in single-walled carbon nanotubes (SWCNTs) on both tube curvature and chirality. The ab initio calculations at the density functional level of theory can provide useful information about the nature of hydrogen adsorption in SWCNT selected sites and the binding under different curvatures and chiralities of the tube walls. Further to this, the grand canonical Monte Carlo atomistic simulation technique can model large-scale nanotube systems with different curvature and chiralities and reproduce their storage capacity by calculating the weight percentage of the adsorbed material (gravimetric density) under thermodynamic conditions of interest. The author's results have shown that with both computational techniques, the nanotube's curvature plays an important role in the storage process while the chirality of the tube plays none.

Local density augmentation and dynamic properties of hydrogen-and non-hydrogen-bonded supercritical fluids: a molecular dynamics study.

The local density inhomogeneities in neat supercritical fluids were investigated via canonical molecular dynamics simulations. The selected systems under investigation were the polar and hydrogen-bonded fluid methanol as well as the quadrupolar non-hydrogen-bonded carbon dioxide one. Effective local densities, local density augmentation, and enhancement factors were calculated at state points along an isotherm close to the critical temperature of each system (T(r)=1.03). The results obtained reveal strong influence of the polarity and hydrogen bonding upon the intensity of the local density augmentation. It is found that this effect is sufficiently larger in the case of the polar and associated methanol in comparison to those predicted for carbon dioxide. For both fluids the local density augmentation values are maximized in the bulk density region near 0.7rho(c), a result that is in agreement with experiment. In addition, the local density dynamics of each fluid were investigated in terms of the appropriate time correlation functions. The behavior of these functions reveals that the bulk density dependence of the local density reorganization times is very sensitive to the specific intermolecular interactions and to the size of the local region. Also, the estimated local density reorganization time as a function of bulk density of each fluid was further analyzed and successfully related to two different time-scale relaxation mechanisms. Finally, the results obtained indicate a possible relationship between the single-molecule reorientational dynamics and the local density reorganization ones.

Local density inhomogeneities and dynamics in supercritical water: A molecular dynamics simulation approach.

Molecular dynamics atomistic simulations in the canonical ensemble (NVT-MD) have been used to investigate the "Local Density Inhomogeneities and their Dynamics" in pure supercritical water. The simulations were carried out along a near-critical isotherm (Tr = T/Tc = 1.03) and for a wide range of densities below and above the critical one (0.2 rho(c) - 2.0 rho(c)). The results obtained reveal the existence of significant local density augmentation effects, which are found to be sufficiently larger in comparison to those reported for nonassociated fluids. The time evolution of the local density distribution around each molecule was studied in terms of the appropriate time correlation functions C(Delta)rhol(t). It is found that the shape of these functions changes significantly by increasing the density of the fluid. Finally, the local density reorganization times for the first and second coordination shell derived from these correlations exhibit a decreasing behavior by increasing the density of the system, signifying the density effect upon the dynamics of the local environment around each molecule.

SiC nanotubes: A novel material for hydrogen storage.

A multiscale theoretical approach is used for the investigation of hydrogen storage in silicon-carbon nanotubes (SiCNTs). First, ab initio calculations at the density functional level of theory (DFT) showed an increase of 20% in the binding energy of H2 in SiCNTs compared with pure carbon nanotubes (CNTs). This is explained by the alternative charges that exist in the SiCNT walls. Second, classical Monte Carlo simulation of nanotube bundles showed an even larger increase of the storage capacity in SiCNTs, especially in low temperature and high-pressure conditions. Our results verify in both theoretical levels that SiCNTs seem to be more suitable materials for hydrogen storage than pure CNTs.

Pressure and temperature dependence of the hydrogen bonding in supercritical ethanol: a computer simulation study.

As a step toward deeper insight on the "hydrogen bonding" in supercritical ethanol (scEtOH), we carried out NVT molecular dynamics simulations of the fluid over a wide range of temperatures and pressures. The fluid was studied at SC conditions for which thermodynamic and spectroscopic (NMR, infrared, Raman, dielectric) data are available. The various site-site pair distribution functions (pdf's) were calculated, and their temperature and pressure dependence was obtained. It was found that over the thermodynamic conditions investigated here, scEtOH remains highly structured. Moreover, the characteristic behavior of the first peaks in H-H, O-O, and H-O pdf's reveals that hydrogen bonds still exist in scEtOH. The analysis focuses also on the reorientational dynamics of the bond unit vectors O-H, C-O, and of the permanent dipole moment of the molecules as well as the total dipole moment of the sample. The corresponding Legendre time correlation functions were discussed in connection to the "hydrogen bonding" in the fluid and in the context of experimental results. Specifically, the behavior of the O-H dynamics exhibits the well-known associative nature of the molecules in the system. A further analysis of the hydrogen bonds was carried out, and the degree of aggregation (average number of H-bonds per molecule) was obtained and compared with results from NMR chemical shift studies. Also the estimated monomer and free O-H groups in the fluid were compared with results from IR and Raman vibrational spectroscopy. The percentage analysis fi of the liquid and scEtOH molecules, with i = 0, 1, 2, 3, ... hydrogen bonds per molecule, has been obtained. The results show the existence of small, linear-chain oligomers formed mainly by two molecules, whereas the number of the three body oligomers, and specifically that of four body oligomers in the sample, is relatively small.