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PubMed2005

A multiscale coarse-graining method for biomolecular systems.

A new approach is presented for obtaining coarse-grained (CG) force fields from fully atomistic molecular dynamics (MD) trajectories. The method is demonstrated by applying it to derive a CG model for the dimyristoylphosphatidylcholine (DMPC) lipid bilayer. The coarse-graining of the interparticle force field is accomplished by an application of a force-matching procedure to the force data obtained from an explicit atomistic MD simulation of the biomolecular system of interest. Hence, the method is termed a "multiscale" CG (MS-CG) approach in which explicit atomistic-level forces are propagated upward in scale to the coarse-grained level. The CG sites in the lipid bilayer application were associated with the centers-of-mass of atomic groups because of the simplicity in the evaluation of the forces acting on them from the atomistic data. The resulting CG lipid bilayer model is shown to accurately reproduce the structural properties of the phospholipid bilayer.

Chemistry, Physical↗
PubMed2005

Structure and decompression melting of a novel, high-pressure nanoconfined 2-D ice.

Molecular dynamics (MD) simulations of water confined in nanospaces between layers of talc (system composition Mg(3)Si(4)O(10)(OH)(2) + 2H(2)O) at 300 K and pressures of approximately 0.45 GPa show the presence of a novel 2-D ice structure, and the simulation results at lower pressures provide insight into the mechanisms of its decompression melting. Talc is hydrophobic at ambient pressure and temperature, but weak hydrogen bonding between the talc surface and the water molecules plays an important role in stabilizing the hydrated structure at high pressure. The simulation results suggest that experimentally accessible elevated pressures may cause formation of a wide range of previously unknown water structures in nanoconfinement. In the talc 2-D ice, each water molecule is coordinated by six O(b) atoms of one basal siloxane sheet and three water molecules. The water molecules are arranged in a buckled hexagonal array in the a-b crystallographic plane with two sublayers along [001]. Each H(2)O molecule has four H-bonds, accepting one from the talc OH group and one from another water molecule and donating one to an O(b) and one to another water molecule. In plan view, the molecules are arranged in six-member rings reflecting the substrate talc structure. Decompression melting occurs by migration of water molecules to interstitial sites in the centers of six-member rings and eventual formation of separate empty and water-filled regions.

Journal Article↗
PubMed2005

O triclusters revisited: classical MD and quantum cluster results for glasses of composition (Al(2)O(3))2(SiO(2)).

The (17)O NMR spectrum of CaAl(2)Si(2)O(8) glass shows two types of O sites that are not present in the crystalline material. One of these, with (17)O NMR parameters C(Q) = 2.3 MHz and delta = +20 ppm, has been assigned to a "tricluster" O, a local geometry in which the O is coordinated to three tetrahedrally coordinated atoms, either Al or Si. For crystalline CaAl(4)O(7), a tricluster site (with three Al linkages to O, i.e., OAl(3)) has been characterized experimentally, with a C(Q) of 2.5 MHz and a delta of about +40 ppm. Thus, a C(Q) value of 2.5 MHz or less seems to be a characteristic of such sites, although they may show a range of delta values. However, several different quantum chemical cluster calculations employing energy-optimized geometries for various tricluster species have given C(Q) values considerably larger than that seen experimentally in the CaAl(2)Si(2)O(8) glass (with minimum C(Q) values of 3.0 MHz even for all Al species). We have recently shown that for edge-sharing geometries, in which the tricluster O atoms participate in "two-membered rings" of composition Al(2)O(2), the calculated C(Q) values are considerably lower, in the range identified in the glass. However, such two-membered ring geometries had been observed only in crystalline inorganic alumoxanes. Ab initio MD calculations on related compositions, such as the calcium aluminosilicate, CAS, (CaO)(0.21)(Al(2)O(3))(0.12)(SiO(2))(0.67), show a small percentage of O triclusters, but none in two-membered rings of the Al(2)O(2) type, and the calculated C(Q) values for the triclusters that do exist are higher than seen in the original experiments on CaAl(2)Si(2)O(8) glass and not significantly different from those for two-coordinate O in Si-O-Al sites. However, a classical MD simulation of the structure of glassy aluminum silicate AS2, (Al(2)O(3))2(SiO(2)), gave a predominance of O triclusters within two-membered rings, with structures much like those seen in the alumoxanes. We have now calculated (17)O nuclear quadrupole coupling constants and NMR shielding values for clusters extracted from these simulations, using standard quantum chemical methods. The calculated C(Q) values for these O triclusters are now in the range observed experimentally in the CaAl(2)Si(2)O(8) glass (around 2.3-2.6 MHz) when the tricluster O is surrounded by three Al, two of which are part of an Al(2)O(2) ring. This supports the experimentalists' contention that such tricluster O species do exist and have been seen by (17)O NMR.

Journal Article↗
PubMed2005

ReaxFF(MgH) reactive force field for magnesium hydride systems.

We have developed a reactive force field (ReaxFF(MgH)) for magnesium and magnesium hydride systems. The parameters for this force field were derived from fitting to quantum chemical (QM) data on magnesium clusters and on the equations of states for condensed phases of magnesium metal and magnesium hydride crystal. The force field reproduces the QM-derived cell parameters, density, and the equations of state for various pure Mg and MgH(2) crystal phases as well as and bond dissociation, angle bending, charge distribution, and reaction energy data for small magnesium hydride clusters. To demonstrate one application of ReaxFF(MgH), we have carried out MD simulations on the hydrogen absorption/desorption process in magnesium hydrides, focusing particularly on the size effect of MgH(2) nanoparticles on H(2) desorption kinetics. Our results show a clear relationship between grain size and heat of formation of MgH(2); as the particle size decreases, the heat of formation increases. Between 0.6 and 2.0 nm, the heat of formation ranges from -16 to -19 kcal/Mg and diverges toward that of the bulk value (-20.00 kcal/Mg) as the particle diameter increases beyond 2 nm. Therefore, it is not surprising to find that Mg nanoparticles formed by ball milling (20-100 nm) do not exhibit any significant change in thermochemical properties.

Journal Article↗
PubMed2005

Computational model of hole transport in DNA.

A computational model based on the molecular dynamics (MD) simulation for the hole transport in DNA has been developed and applied to study hole current in DNA strands consisting of different numbers of GC pairs. The approach is based on the hopping mechanism which is thermally activated. The calculations show that the hole hopping intensifies with the temperature and the transport rate increases in agreement with the experimental evidence. It is also determined that the degree of structural ordering in the DNA strand enhances the hole conductivity and reasons are provided why this may occur.

Base Pairing↗
PubMed2005

Molecular dynamics study of hydrated faujasite-type zeolites.

Molecular dynamics (MD) simulations of hydrated zeolite NaX (Si/Al = 1.0) and NaY (Si/Al = 2.0) were done at a temperature of 300 K. The calculation results show that the adsorption of water occurs via a three-step mechanism in zeolite NaX: (1) adsorption around Na, (2) formation of a monolayer on the walls, and (3) pore filling in the supercage during which adsorbed water molecules are localized around the 12-membered rings. Zeolite NaY adsorbs in a similar manner. However, at intermediate hydration states, cluster formation occurs around Na instead of monolayer formation. The calculated energy distribution functions suggest that in zeolite NaX, the water vapor adsorption can be expressed by using the Langmuir model with two adsorption sites, but in zeolite NaY, it is not Langmuir-type adsorption.

Journal Article↗
PubMed2005

Using MD snapshots in ab initio and DFT calculations: OH vibrations in the first hydration shell around Li+(aq).

The average OH stretching vibrational frequency for the water molecules in the first hydration shell around a Li(+) ion in a dilute aqueous solution was calculated by a hybrid molecular dynamics + quantum-mechanical ("MD + QM") approach. Using geometry configurations from a series of snapshots from an MD simulation, the anharmonic, uncoupled OH stretching frequencies were calculated for 100 first-shell OH oscillators at the B3LYP and HF/6-31G(d,p) levels of theory, explicitly including the first shell and the relevant second shell water molecules into charge-embedded supermolecular QM calculations. Infrared intensity-weighting of the density-of-states (DOS) distributions by means of the squared dipole moment derivatives (which vary by a factor of 20 over the OH stretching frequency band at the B3LYP level), changes the downshift from approximately -205 to -275 cm(-1) at the B3LYP level. Explicit inclusion of relevant third-shell water molecules in the supermolecular cluster leads to a further downshift by approximately -30 cm(-1). Our final estimated average downshift is approximately -305 cm(-1). The experimental value lies somewhere in the range between -290 and -420 cm(-1). Also, the absolute nu(OH) frequency is well reproduced in our calculations. "In-liquid" instantaneous correlation curves between nu(OH) and various typical H-bond strength parameters such as R(O...O), R(H...O), the intramolecular OH bond length, and the IR intensity are presented. Some of these correlations are robust and persist also for the rather distorted instantaneous geometries in the liquid; others are less so.

Journal Article↗
PubMed2005

The N6-methyl group of adenine further increases the BI stability of DNA compared to C5-methyl groups.

Methylated DNA bases are natural modifications which play an important role in protein-DNA interactions. Recent experimental and theoretical results have shown an influence of the base modification on the conformational behavior of the DNA backbone. MD simulations of four different B-DNA dodecamers (d(GC)(6), d(AT)(6), d(G(5mCG)(5)C), and d(A(T6mA)(5)T)) have been performed with the aim to examine the influence of methyl groups on the B-DNA backbone behavior. An additional control simulation of d(AU)(6) has also been performed to examine the further influence of the C5-methyl group in thymine. Methyl groups in the major groove (as in C5-methylcytosine, thymine, or N6-methyladenine) decrease the BII substate population of RpY steps. Due to methylation a clearer distinction of the BI substate stability between YpR and RpY (CpG/GpC or TpA/ApT) steps arises. A positive correlation between the BII substate population and base stacking distances is seen only for poly(GC). A methyl group added into the major groove increases mean water residence times around the purine N7 atom, which may stabilize the BI substate by improving the hydration network between the DNA backbone and the major groove. The N6-methyl group also forms a water molecule bridge between the N6 and O4 atoms, and thus further stabilizes the BI substate.

Adenine↗
PubMed2005

How to model solvation of peptides? Insights from a quantum-mechanical and molecular dynamics study of N-methylacetamide. 1. Geometries, infrared, and ultraviolet spectra in water.

This paper represents the first part of a study of solvation in peptides using quantum-mechanical and classical approaches. In this study, the peptide is modeled as its simplest analogue, namely, N-methyl-acetamide, and the effects of the solvent (here water, and in the second part of the study, water and acetone) are introduced at three different levels, e.g., through a continuum description, using solute-solvent clusters, and using the same clusters embedded in an external continuum. In turn, the solute-solvent clusters have been obtained in two alternative ways, either by using QM optimization procedures or extracting a proper set of structures from MD simulations. In this part of the study, geometries, IR, and UV spectra are calculated in terms of the different solvation models, and the results are analyzed and compared to get insights about different aspects of solvation involving dynamic and static effects on one hand and bulk or specific interactions on the other hand.

Acetamides↗
PubMed2005

Determination of structure and energetics for gibbs surface adsorption layers of binary liquid mixture 1. Acetone + water.

The orientation, structure, and energetics of the vapor/acetone-water interface are studied with sum frequency generation vibrational spectroscopy (SFG-VS). We used the polarization null angle (PNA) method in SFG-VS to accurately determine the interfacial acetone molecule orientation, and we found that the acetone molecule has its C=O group pointing into bulk phase, one CH3 group pointing up from the bulk, and the other CH3 group pointing into the bulk phase. This well-ordered interface layer induces an antiparallel structure in the second layer through dimer formation from either dipolar or hydrogen bond interactions. With a double-layer adsorption model (DAM) and Langmuir isotherm, the adsorption free energies for the first and second layer are determined as deltaG degrees (ads,1) = - 1.9 +/- 0.2 kcal /mol and deltaG degrees (ads,2) = - 0.9 +/- 0.2 kcal /mol, respectively. Since deltaG degrees (ads,1) is much larger than the thermal energy kT = 0.59 kcal /mol, and deltaG degrees (ads,2) is close to kT, the second layer has to be less ordered. Without either strong dipolar or hydrogen bonding interactions between the second and the third layer, the third layer should be randomly thermalized as in the bulk liquid. Therefore, the thickness of the interface is not more than two layers thick. These results are consistent with previous MD simulations for the vapor/pure acetone interface, and undoubtedly provide direct microscopic structural evidences and new insight for the understanding of liquid and liquid mixture interfaces. The experimental techniques and quantitative analysis methodology used for detailed measurement of the liquid mixture interfaces in this report can also be applied to liquid interfaces, as well as other molecular interfaces in general.

Journal Article↗
PubMed2005

Computational studies of DNA photolyase.

The electron transfer catalyzed (ETC) repair of the DNA photolesion cyclobutane pyrimidine dimer (CPD) is mediated by the enzyme DNA photolyase. Due to its importance as part of the cancer prevention mechanism in many organisms, but also due to its unique mechanism, this DNA photoreactivation is a topic of intense study. The progress in the application of computational methods to three aspects of the ETC repair of CPD is reviewed: (i) electronic structure calculations of the cycloreversion of the CPD radical cation and radical anion, (ii) MD simulations of the DNA photolyase and its complex to photodamaged DNA, and (iii) the structure and dynamics of photodamaged DNA. The contributions of this work to the overall understanding of the reaction and its relationship to the available experimental work are highlighted.

Computer Simulation↗
PubMed2005

Optimization and application of lithium parameters for the reactive force field, ReaxFF.

To make a practical molecular dynamics (MD) simulation of the large-scale reactive chemical systems of Li-H and Li-C, we have optimized parameters of the reactive force field (ReaxFF) for these systems. The parameters for this force field were obtained from fitting to the results of density functional theory (DFT) calculations on the structures and energy barriers for a number of Li-H and Li-C molecules, including Li(2), LiH, Li(2)H(2), H(3)C-Li, H(3)C-H(2)C-Li, H(2)C=C-LiH, HCCLi, H(6)C(5)-Li, and Li(2)C(2), and to the equations of state and lattice parameters for condensed phases of Li. The accuracy of the developed ReaxFF was also tested by comparison to the dissociation energies of lithium-benzene sandwich compounds and the collision behavior of lithium atoms with a C(60) buckyball.

Journal Article↗
PubMed2005

On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions.

Reliable studies of enzymatic reactions by combined quantum mechanics/molecular mechanics (QM/MM) approaches, with an ab initio description of the quantum region, presents a major challenge to computational chemists. The main problem is the need for a very large computer time for the evaluation of the QM energy, which in turn makes it extremely challenging to perform proper configurational sampling. A seemingly reasonable alternative is to perform energy minimization studies of the type used in gas-phase ab initio studies. However, it is hard to see why such an approach should give reliable results in protein active sites. To examine the problems with energy minimization QM/MM approaches, we chose the hypothetical reaction of a metaphosphate ion with water in the Ras.GAP complex. This hypothetical reaction served as a simple benchmark reaction. The possible problems with the QM/MM minimization were explored by generating several protein configurations from long MD simulations and using energy minimization and scanning of the reaction coordinates to evaluate the corresponding potential energy surfaces of the reaction for each of these different protein configurations. Comparing these potential energy surfaces, we found major variations of the corresponding minima. Furthermore, the reaction energies and activation energies also varied significantly even for similar protein configurations. The specific coordination of a magnesium ion, present in the active center of the protein complex, turned out to influence the energetics of the reaction in a major way, where a direct coordination to the reactant leads to an increase of the activation energy by 17 kcal/mol. Apparently, using energy minimization to generate potential surfaces for an enzymatic reaction, while starting from a single protein structure, could lead to major errors in calculations of activation free energies and binding free energies. Thus we believe that extensive samplings of the configurational space of the protein are essential for meaningful determination of the energetics of enzymatic reactions. The possible relevance of our conclusion with regard to a recent study of the RasGAP reaction is discussed.

Computational Biology↗
PubMed2005

Electrostatic DFT map for the complete vibrational amide band of NMA.

An anharmonic vibrational Hamiltonian for the amide I, II, III, and A modes of N-methyl acetamide (NMA), recast in terms of the 19 components of an external electric field and its first and second derivative tensors (electrostatic DFT map), is calculated at the DFT(BPW91/6-31G(d,p)) level. Strong correlations are found between NMA geometry and the amide frequency fluctuations calculated using this Hamiltonian together with the fluctuating solvent electric field obtained from the MD simulations in TIP3 water. The amide I and A frequencies are strongly positively correlated with the C=O and N-H bond lengths. The C=O and C-N amide bond lengths are negatively correlated, suggesting the solvent-induced fluctuations of the contribution of zwitterionic resonance form. Sampling the global electric field in the entire region of the transition charge densities (TCDs) is required for accurate infrared line shape simulations. Collective electrostatic solvent coordinates which represent the fluctuations of the 10 lowest amide fundamental and overtone states are reported. Normal-mode analysis of an NMA-3H(2)O cluster shows that the 660 cm(-1) to 1100 cm(-1) oscillation found in the frequency autocorrelation functions of the amide modes may be ascribed to the two bending vibrations of intermolecular hydrogen bonds with the amide oxygen of NMA.

Amides↗
PubMed2005

Nonadiabatic molecular dynamics study of electron transfer from alizarin to the hydrated Ti4+ ion.

Ab initio real-time nonadiabatic (NA) molecular dynamics (MD) simulations are performed in order to investigate the photoinduced electron transfer (ET) from alizarin to the hydrated Ti4+ ion and compare it with the ET into bulk TiO2 that forms the basis of the Grätzel type solar cell. The experimental data and electronic structure calculations indicate that the photoexcitation spectra of alizarin attached to either bulk TiO2 or the Ti4+ ion in solution are very similar. In contrast, the NAMD simulations at ambient temperature predict marked differences between the ET dynamics that follow the photoexcitation in the two systems. The simulation of ET between alizarin and the TiO2 surface shows predominantly adiabatic transfer that occurs within 8 fs (Duncan et al. J. Am. Chem. Soc. 2005, 127, 7941), in agreement with the time-resolved experimental data. The simulation of alizarin attached to the hydrated Ti4+ ion reported presently predicts that the ET does occur, but on a slower 30 fs time scale, with a substantially reduced amplitude and by a predominantly NA mechanism. The differences are attributed to the disparity in the acceptor states of bulk TiO2 and the Ti4+ ion in solution. It is shown that the predicted alizarin-Ti4+ ET dynamics can be verified experimentally.

Journal Article↗
PubMed2005

Effect of the choice of the pressure coupling method on the spontaneous aggregation of DPPC molecules.

The self-assembly of DPPC molecules starting from a random, solution-like configuration in the presence of water molecules is described in the present MD simulation study. Simulations were performed with either anisotropic or isotropic pressure coupling. Use of anisotropic pressure coupling led to the formation of a bilayer/bilayerlike aggregate; the features of the bilayer are in agreement with those reported from earlier simulation and experimental studies. In contrast, simulating the same system with isotropic pressure coupling led to the formation of a cylindrical micelle/lamellar structure with a large water hole. The formation of micelles seems unrealistic since diacylphosphatidylcholines having hydrocarbon tails with nine or more carbon atoms have been shown to form only bilayers. Simulations were also performed with preformed bilayerlike configurations with either anisotropic or isotropic pressure coupling. The bilayer characteristics deduced from simulations using anisotropic pressure coupling are in better agreement with those reported from earlier experimental and simulation studies. Thus, the choice of the pressure coupling method has a significant effect on the spontaneous aggregation of DPPC molecules but makes relatively lesser effect if the bilayer has formed already.

Androstanes↗
PubMed2005

An explicit quantum chemical method for modeling large solvation shells applied to aminocoumarin C151.

The absorption spectra of aminocoumarin C151 in water and n-hexane solution are investigated by an explicit quantum chemical solvent model. We improved the efficiency of the frozen-density embedding scheme, as used in a former study on solvatochromism (J. Chem. Phys. 2005, 122, 094115) to describe very large solvent shells. The computer time used in this new implementation scales approximately linearly (with a low prefactor) with the number of solvent molecules. We test the ability of the frozen-density embedding to describe specific solvent effects due to hydrogen bonding for a small example system, as well as the convergence of the excitation energy with the number of solvent molecules considered in the solvation shell. Calculations with up to 500 water molecules (1500 atoms) in the solvent system are carried out. The absorption spectra are studied for C151 in aqueous or n-hexane solution for direct comparison with experimental data. To obtain snapshots of the dye molecule in solution, for which subsequent excitation energies are calculated, we use a classical molecular dynamics (MD) simulation with a force field adapted to first-principles calculations. In the calculation of solvatochromic shifts between solvents of different polarity, the vertical excitation energy obtained at the equilibrium structure of the isolated chromophore is sometimes taken as a guess for the excitation energy in a nonpolar solvent. Our results show that this is, in general, not an appropriate assumption. This is mainly due to the fact that the solute dynamics is neglected. The experimental shift between n-hexane and water as solvents is qualitatively reproduced, even by the simplest embedding approximation, and the results can be improved by a partial polarization of the frozen density. It is shown that the shift is mainly due to the electronic effect of the water molecules, and the structural effects are similar in n-hexane and water. By including water molecules, which might be directly involved in the excitation, in the embedded region, an agreement with experimental values within 0.05 eV is achieved.

Journal Article↗
PubMed2005

Modeling water exchange on an aluminum polyoxocation.

For the first time, water exchange on a polymeric complex has been modeled using a combination of gas-phase ab initio calculations and molecular dynamics (MD) simulations. The GaO4Al12(OH)24(H2O)12(7+)aq ion (GaAl12) was chosen because high-quality experimental data exist, including an activation enthalpy (+63 +/- 7 kJ/mol) and an activation volume (+3 +/- 1 cm3/mol). We took a two-step approach. First, the local solvent structure and the initial states for reaction were inferred from the molecular dynamics simulations. Second, we used this information to evaluate initial-state structures in the ab initio calculations. The energy differences between the initial and transition states from the ab initio calculations varied from +59 kJ/mol to +53 kJ/mol depending upon details, closely approximating the activation enthalpy.

Journal Article↗