Low-frequency vibrational spectrum of water in the hydration layer of a protein: a molecular dynamics simulation study

An atomistic molecular dynamics simulation has been carried out to understand the low-frequency intermolecular vibrational spectrum of water present in the hydration layer of the protein villin headpiece subdomain or HP-36. An attempt is made to explore how the heterogeneous rigidity of the hydration layers of different segments (three alpha helices) of the protein, strength of the protein-water hydrogen bonds, and their differential relaxation behavior influence the distribution of the intermolecular vibrational density of states of water in the hydration layers. The calculations revealed that compared to bulk water these bands are nonuniformly blue-shifted for water near the helices, the extent of shifts being more pronounced for water molecules hydrogen bonded to the protein residues. It is further noticed that the larger blue shift observed for the water molecules hydrogen bonded to helix 2 residues correlates excellently with the slowest structural relaxation of these hydrogen bonds. These results can be verified by suitable experimental measurements.     

Energy relaxation of intermolecular motions in supercooled water and ice: a molecular dynamics study

We investigate the energy relaxation of intermolecular motions in liquid water at temperatures ranging from 220 K to 300 K and in ice at 220 K using molecular dynamics simulations. We employ the recently developed frequency resolved transient kinetic energy analysis, which provides detailed information on energy relaxation in condensed phases like two-color pump-probe spectroscopy. It is shown that the energy cascading in liquid water is characterized by four processes. The temperature dependences of the earlier three processes, the rotational-rotational, rotational-translational, and translational-translational energy transfers, are explained in terms of the density of states of the intermolecular motions. The last process is the slow energy transfer arising from the transitions between potential energy basins caused by the excitation of the low frequency translational motion. This process is absent in ice because the hydrogen bond network rearrangement, which accompanies the interbasin transitions in liquid water, cannot take place in the solid phase. We find that the last process in supercooled water is well approximated by a stretched exponential function. The stretching parameter, β, decreases from 1 to 0.72 with decreasing temperature. This result indicates that the dynamics of liquid water becomes heterogeneous at lower temperatures.     

Adsorption of water molecules inside a Au nanotube: a molecular dynamics study

A molecular dynamics simulation of water molecules through a Au nanotube with a diameter of 20 A at bulk densities 0.8, 1, and 1.2 gcm(3) has been carried out. The water molecules inside a nanoscale tube, unlike those inside a bulk tube, have a confined effect. The interaction energy of the Au nanotube wall has a direct influence on the distribution of water molecules inside the Au tube in that the adsorption of the water molecules creates shell-like formations of water. Moreover, the high number of adsorbed molecules has already achieved saturation at the wall of the Au nanotube at three bulk densities. This work compares the distribution percentage profiles of hydrogen bonds for different regions inside the tube. The structural characteristics of water molecules inside the tube have also been studied. The results reveal that the numbers of hydrogen bonds per water molecule influence the orientational order parameter q. In addition, the phenomenon of a group of molecules bonded inside the tube can be observed as the number of hydrogen bonds increase.     

Electron hydration dynamics in water clusters: A direct ab initio molecular dynamics approach

Electron attachment dynamics of excess electron in water cluster (H2O)n (n = 2 and 3) have been investigated by means of full-dimensional direct ab initio molecular dynamics (MD) method at the MP26-311++G(d,p) level. It was found that the hydrogen bond breaking due to the excess electron is an important process in the first stage of electron capture in water trimer. Time scale of electron localization and hydrogen bond breaking were determined by the direct ab initio MD simulation. The initial process of hydration in water cluster is clearly visualized in the present study. In n = 3, an excess electron is first trapped around the cyclic water trimer with a triangular form, where the excess electron is equivalently distributed on the three water molecules at time zero. After 50 fs, the excess electron is concentrated into two water molecules, while the potential energy of the system decreases by -1.5 kcal/mol from the vertical point. After 100 fs, the excess electron is localized in one of the water molecules and the potential energy decreases by -5.3 kcal/mol, but the triangular form still remained. After that, one of the hydrogen bonds in the triangular form is gradually broken by the excess electron, while the structure becomes linear at 100-300 fs after electron capture. The time scale of hydrogen bond breaking due to the excess electron is calculated to be about 300 fs. Finally, a dipole bound state is formed by the linear form of three water molecules. In the case of n = 2, the dipole bound anion is formed directly. The mechanism of electron hydration dynamics was discussed on the basis of theoretical results.     

Role of water molecules in the KcsA protein channel by molecular dynamics calculations

Molecular dynamics simulations supported by electrostatic calculations have been conducted on the KcsA channel to determine the role of water molecules in the pore. Starting from the X-ray structure of the KcsA channel in its closed state at 2.0 angstroms resolution, the opening of the pore towards a conformation built on the basis of EPR results is studied. We show that water molecules act as a structural element for the K+ ions inside the filter and the hydrophobic cavity of the channel. In the filter, water tends to enhance the depth of the wells occupied by the K+ ions, while in the cavity there is a strong correlation between the water molecules and the cavity ion. As a consequence, the protein remains very stable in the presence of three K+ ions in the selectivity filter and one in the cavity. The analysis of the dynamics of water molecules in the cavity reveals preferred orientations of the dipoles along the pore axis, and a correlated behavior between this dipole orientation and the displacement of the K+ ion during the gating process.     

How protein surfaces induce anomalous dynamics of hydration water

Water around biomolecules slows down with respect to pure water, and both rotation and translation exhibit anomalous time dependence in the hydration shell. The origin of such behavior remains elusive. We use molecular dynamics simulations of water dynamics around several designed protein models to establish the connection between the appearance of the anomalous dynamics and water-protein interactions. For the first time we quantify the separate effect of protein topological and energetic disorder on the hydration water dynamics. When a static protein structure is simulated, we show that both types of disorder contribute to slow down water diffusion, and that allowing for protein motion, increasing the spatial dimensionality of the interface, reduces the anomalous character of hydration water. The rotation of water is, instead, altered by the energetic disorder only; indeed, when electrostatic interactions between the protein and water are switched off, water reorients even faster than in the bulk. The dynamics of water is also related to the collective structure--à voir the hydrogen bond (H-bond) network--formed by the solvent enclosing the protein surface. We show that, as expected for a full hydrated protein, when the protein surface offers pinning sites (charged or polar sites), the superficial water-water H-bond network percolates throughout the whole surface, hindering the water diffusion, whereas it does not when the protein surface lacks electrostatic interactions with water and the water diffusion is enhanced.     

An ab initio molecular dynamics study on hydrogen bonds between water molecules

The quantitative estimation of the total interaction energy of a molecular system containing hydrogen bonds (H bonds) depends largely on how to identify H bonding. The conventional geometric criteria of H bonding are simple and convenient in application, but a certain amount of non-H bonding cases are also identified as H bonding. In order to investigate the wrong identification, we carry out a systematic calculation on the interaction energy of two water molecules at various orientation angles and distances using ab initio molecular dynamics method with the dispersion correction for the Becke-Lee-Yang-Parr (BLYP) functionals. It is shown that, at many orientation angles and distances, the interaction energies of the two water molecules exceed the energy criterion of the H bond, but they are still identified as H-bonded by the conventional "distance-angle" criteria. It is found that in these non-H bonding cases the wrong identification is mainly caused by short-range interaction between the two neighbouring water molecules. We thus propose that, in addition to the conventional distance and angle criteria of H bonding, the distance d(H···H) between the two neighbouring hydrogen atoms of the two water molecules should also be taken as a criterion, and the distance r(O···H) between the hydrogen atom of the H-bond donor molecule and the oxygen atom of the acceptor molecule should be restricted by a lower limit. When d(H···H) and r(O···H) are small (e.g., d(H···H) < 2.0 ? and r(O···H) < 1.62 ?), the repulsion between the two neighbouring atoms increases the total energy of the two water molecules dramatically and apparently weakens the binding of the water dimer. A statistical analysis and comparison of the numbers of the H bonds identified by using different criteria have been conducted on a Car-Parrinello ab initio molecular dynamics simulation with dispersion correction for a system of 64 water molecules at near-ambient temperature. They show that the majority of the H-bonds counted by using the conventional criteria combined with the d(H···H) criterion and the restriction of r(O···H) match what is identified by the binding energy criteria (e.g., E ≤ -10 kJ/mol), while some of them still have a binding energy that exceeds the energy criterion, indicating that the complicated quantum effects in H bonding can only be described by the three geometric parameters to a certain extent.     

Ab initio molecular dynamics study of formate ion hydration

We perform ab initio molecular dynamics simulations of the aqueous formate ion. The mean number of water molecules in the first solvation shell, or the hydration number, of each formate oxygen is found to be consistent with recent experiments. Our ab initio pair correlation functions, however, differ significantly from many classical force field results and hybrid quantum mechanics/molecular mechanics predictions. They yield roughly one less hydrogen bond between each formate oxygen and water than force field or hybrid methods predict. Both the BLYP and PW91 exchange correlation functionals give qualitatively similar results. The time dependence of the hydration numbers are examined, and Wannier function techniques are used to analyze electronic configurations along the molecular dynamics trajectory.     

Functionally relevant protein motions: extracting basin-specific collective coordinates from molecular dynamics trajectories

Functionally relevant motion of proteins has been associated with a number of atoms moving in a concerted fashion along so-called "collective coordinates." We present an approach to extract collective coordinates from conformations obtained from molecular dynamics simulations. The power of this technique for differentiating local structural fluctuations between classes of conformers obtained by clustering is illustrated by analyzing nanosecond-long trajectories for the response regulator protein Spo0F of Bacillus subtilis, generated both in vacuo and using an implicit-solvent representation. Conformational clustering is performed using automated histogram filtering of the inter-C(alpha) distances. Orthogonal (varimax) rotation of the vectors obtained by principal component analysis of these interresidue distances for the members of individual clusters is key to the interpretation of collective coordinates dominating each conformational class. The rotated loadings plots isolate significant variation in interresidue distances, and these are associated with entire mobile secondary structure elements. From this we infer concerted motions of these structural elements. For the Spo0F simulations employing an implicit-solvent representation, collective coordinates obtained in this fashion are consistent with the location of the protein's known active sites and experimentally determined mobile regions.     

Ion condensation behavior and dynamics of water molecules surrounding the sodium poly(methacrylic acid) chain in water: a molecular dynamics study

All-atom molecular dynamics simulations are used to study the condensation behavior of monovalent (Na(+)) and multivalent (Ca(2+)) salt counterions associated with the co-ions (Cl(-)) surrounding the charged poly(methacrylic acid) (PMAA) chain in water. The study is extended to the influences on chain conformation, local arrangement, and dynamics of water in the highly diluted aqueous solutions. We find that even when the salt ions are monovalent, they attract more than one charged monomer and act as a bridging agent within the chain, as the multivalent salt ions. In principle, the salt ions bridge between not only the "non-adjacent" but also the "adjacent" charged monomers, leading to a more coil-like and a locally stretched conformation, respectively. With an increase in the salt concentration, the amount of coiled-type condensed ions increase and reach a maximum when the chain conformation becomes the most collapsed; whereas, the stretched-type shows an opposite trend. Our results show that the attractive interactions through the condensed salt ions between the non-adjacent monomers are responsible for the conformational collapse. When the salt concentration increases high enough, a significant increase for the stretched-type condensed ions makes an expansion effect on the chain. These stretched-type salt ions, followed by the adsorption of the co-ions and water molecules, tend to form a multilayer organization outside surrounding the PMAA chain. Thus, the expansion degree of the chain conformation is greatly limited. When only the monovalent Na(+) ions are present in the solutions, water molecules are primarily adsorbed into either the condensed Na(+) ions or the COO(-) groups. These adsorbed water molecules form hydrogen bonds with each other and enhance the local bridging behavior associated with the Na(+) condensation on the resultant chain conformation. With an increase in the amount of multivalent Ca(2+) salt ions, more water molecules are bonded directly with the condensed Ca(2+) ions. In this case, only the condensed Ca(2+) ions provide a strong bridging effect within the polymer chain. We observe a significant shift towards a higher frequency of the oxygen vibration spectrum and only a slight shift towards a higher frequency of the hydrogen spectrum for the water molecules associated with the ion condensation.     

Investigating hydration dependence of dynamics of confined water: monolayer, hydration water and Maxwell-Wagner processes

The dynamics of water confined in silica matrices MCM-41 C10 and C18, with pore diameter of 21 and 36 A, respectively, is examined by broadband dielectric spectroscopy (10(-2)-10(9) Hz) and differential scanning calorimetry for a wide temperature interval (110-340 K). The dynamics from capillary condensed hydration water and surface monolayer of water are separated in the analysis. Contrary to previous reports, the rotational dynamics are shown to be virtually independent on the hydration level and pore size. Moreover, a third process, also reported for other systems, and exhibiting a saddlelike temperature dependence is investigated. We argue that this process is due to a Maxwell-Wagner process and not to strongly bound surface water as previously suggested in the literature. The dynamics of this process is strongly dependent on the amount of hydration water in the pores. The anomalous temperature dependence can then easily be explained by a loss of hydration water at high temperatures in contradiction to previous explanations.     

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.     

An implemented potential of non-rigid water molecules for molecular dynamics simulations

The central force model for a water molecule is corrected by adding a three-body term. The present potential fits both an accurate ab initio potential energy surface and the fundamental vibrational frequencies of gas-phase water. The three-body terms allow us to reproduce the gas-phase IR spectrum by molecular dynamics simulations. Some problems connected with MD simulations of IR spectra are discussed.     

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.     

Aqueous peptides as experimental models for hydration water dynamics near protein surfaces

We report quasi-elastic neutron scattering experiments to contrast the water dynamics as a function of temperature for hydrophilic and amphiphilic peptides under the same level of confinement, as models for understanding hydration dynamics near chemically heterogeneous protein surfaces. We find that the hydrophilic peptide shows only a single non-Arrhenius translational process with no evidence of spatial heterogeneity unlike the amphiphilic peptide solution that exhibits two translational relaxations with an Arrhenius and non-Arrhenius dependence on temperature. Together these results provide experimental proof that heterogeneous dynamical signatures near protein surfaces arise in part from chemical heterogeneity (energy disorder) as opposed to mere topological roughness of the protein surface.     

Structure and dynamics of short chain molecules in disordered porous materials: a molecular dynamics simulation study

The static and dynamic properties of short polymer chains in disordered materials are studied using discontinuous molecular dynamics simulations. The polymers are modeled as chains of hard spheres and the matrix is a collection of fixed hard spheres. The simulations show that the chain size is a nonmonotonic function of the matrix concentration for all polymer concentrations. The dependence of polymer diffusion D on the degree of polymerization N becomes stronger as the matrix concentration is increased. At high matrix concentrations we observe a decoupling between translational and rotational diffusion, i.e., the rotational relaxation time becomes very large but the translational diffusion is not affected significantly. We attribute this to the trapping of a small number of polymers. Under these conditions the polymer chains diffuse via a hopping mechanism.     

Atomic motions in the alphabeta-merging region of 1,4-polybutadiene: a molecular dynamics simulation study

We present fully atomistic molecular dynamics simulations on 1,4-polybutadiene in a wide temperature range from 200 to 280 K, i.e., in the region where the alpha- and beta-relaxations merge and above. A big computational effort has been performed-especially for the lowest temperatures investigated-to extend the simulation runs to very long times (up to 1 mus for 200 K). The simulated sample has been carefully validated by using previous neutron scattering data on the real sample with similar microstructure. Inspecting the trajectories of the different hydrogens in real space, we have observed a heterogeneous dynamical behavior (each kind of hydrogen moves in a different way) with signatures of combined hopping and diffusive motions in the whole range investigated. The application of a previously proposed model [Colmenero et al., Europhys. Lett. 71, 262 (2005)] is successful and a characterization of the local motions and diffusion is possible. The comparison of our results to those reported in the literature provides a consistent scenario for polybutadiene dynamics and puts into a context the different experimental observations. We also discuss the impact of the hopping processes on the observation and interpretation of experimentally accessible magnitudes and the origin of the deviations from Gaussian behavior in this system.     

Structure and ultrafast dynamics of liquid water: a quantum mechanics/molecular mechanics molecular dynamics simulations study

A quantum mechanics/molecular mechanics molecular dynamics simulation was performed for liquid water to investigate structural and dynamical properties of this peculiar liquid. The most important region containing a central reference molecule and all nearest surrounding molecules (first coordination shell) was treated by Hartree-Fock (HF), post-Hartree-Fock [second-order Moller-Plesset perturbation theory (MP2)], and hybrid density functional B3LYP [Becke's three parameter functional (B3) with the correlation functional of Lee, Yang, and Parr (LYP)] methods. In addition, another HF-level simulation (2HF) included the full second coordination shell. Site to site interactions between oxygen-oxygen, oxygen-hydrogen, and hydrogen-hydrogen atoms of all ab initio methods were compared to experimental data. The absence of a second peak and the appearance of a shoulder instead in the gO-O graph obtained from the 2HF simulation is notable, as this feature has been observed so far only for pressurized or heated water. Dynamical data show that the 2HF procedure compensates some of the deficiency of the HF one-shell simulation, reducing the difference between correlated (MP2) and HF results. B3LYP apparently leads to too rigid structures and thus to an artificial slow down of the dynamics.     

Backbone motions of free and pheromone-bound major urinary protein I studied by molecular dynamics simulation

Molecular motions of free and pheromone-bound mouse major urinary protein I, previously investigated by NMR relaxation, were simulated in 30 ns molecular dynamics (MD) runs. The backbone flexibility was described in terms of order parameters and correlation times, commonly used in the NMR relaxation analysis. Special attention was paid to the effect of conformational changes on the nanosecond time scale. Time-dependent order parameters were determined in order to separate motions occurring on different time scales. As an alternative approach, slow conformational changes were identified from the backbone torsion angle variances, and "conformationally filtered" order parameters were calculated for well-defined conformation states. A comparison of the data obtained for the free and pheromone-bound protein showed that some residues are more rigid in the bound form, but a larger portion of the protein becomes more flexible upon the pheromone binding. This finding is in general agreement with the NMR results. The higher flexibility observed on the fast (fs-ps) time scale was typically observed for the residues exhibiting higher conformational freedom on the ns time scale. An inspection of the hydrogen bond network provided a structural explanation for the flexibility differences between the free and pheromone-bound proteins in the simulations.