DFT-based Molecular Dynamics Simulations Research Articles

Density functional theory based molecular dynamics simulation study on the bulk modulus of multi-shell fullerenes

We investigate the bulk modulus of single- and double-shell fullerenes as a function of diameter and shell distance at various temperatures using the DFT-based molecular dynamics simulation method. We found that total energies depend on the diameter and shell distance. The obtained results indicate that, with increasing diameter of single-shell fullerenes, the bulk modulus increases up to C180 fullerene and then decreases for larger diameter fullerenes. The bulk modulus of double-shell fullerenes is higher than both its internal and external constructing fullerenes and decreases as the shell distance increases. The bulk moduli of the considered systems are very weakly affected by the temperature.

Ab Initio Calculations of the Interaction between CO2 and the Acetate Ion

A series of ab initio calculations designed to investigate the interaction of CO(2) with acetate are presented. The lowest energy structure, AC-CO(2)-η(2), is predicted by CCSD(T)/aVTZ to be bound by -10.6 kcal/mol. Six of the bound complexes have binding energies on the order of -8 kcal/mol, but analysis shows that the η(1)-CT complex is fundamentally different from the others. The η(1)-CT complex is characterized by geometric distortion, large polarization and induction effects and charge transfer whereas the other five complexes have little geometric distortion and negligible charge transfer. The amount of charge that is transferred from the anion to the CO(2) in the η(1)-CT complex is estimated to be about half an electron by NPA, DMA, CHELPG, and Mulliken analyses, whereas the EDA-ALMO-CTA (B3LYP) approach predicts a charge transfer of 75 me(-). However, the transfer of this small amount of charge leads to an energy lowering of -56 kcal/mol, without which the complex would not be bound. The RI-MP2 geometries closely approximate those resulting from the CCSD optimizations, and the optimized second-order opposite spin (O2) method performs well for all the complexes except for the η(1)-CT complex. DFT methods do not reproduce all the ab initio geometries, binding energies and/or energy ordering of these complexes although the range-separated hybrid meta-GGA (M11) and nonlocal (VV10 and vdwDF10) functionals are shown to yield results significantly better than other functionals considered for this system. The fact that there is such variation among DFT methods has implications for DFT-based ab initio molecular dynamics simulations and for the parametrization of classical force fields based on DFT calculations.

Peptide salt bridge stability: From gas phase via microhydration to bulk water simulations

The salt bridge formation and stability in the terminated lysine-glutamate dipeptide is investigated in water clusters of increasing size up to the limit of bulk water. Proton transfer dynamics between the acidic and basic side chains is described by DFT-based Born-Oppenheimer molecular dynamics simulations. While the desolvated peptide prefers to be in its neutral state, already the addition of a single water molecule can trigger proton transfer from the glutamate side chain to the lysine side chain, leading to a zwitterionic salt bridge state. Upon adding more water molecules we find that stabilization of the zwitterionic state critically depends on the number of hydrogen bonds between side chain termini, the water molecules, and the peptidic backbone. Employing classical molecular dynamics simulations for larger clusters, we observed that the salt bridge is weakened upon additional hydration. Consequently, long-lived solvent shared ion pairs are observed for about 30 water molecules while solvent separated ion pairs are found when at least 40 or more water molecules hydrate the dipeptide. These results have implications for the formation and stability of salt bridges at partially dehydrated surfaces of aqueous proteins.

CORROSION INHIBITION OF CuNi10Fe ALLOY WITH PHENOLIC ACIDS

The purpose of this study was to investigate the efficiency of two phenolic acids, namely p-hydroxybenzoic acid (HBA) and protocatechuic acid (PCA), as corrosion inhibitors for CuNi10Fe alloy in a 0.5 mol dm−3 NaCl solution. In these investigations, open circuit potential measurements, potentiodynamic polarization measurements, and the linear polarization method have been used. It was found that both phenolic acids had similar corrosion inhibition effects on the CuNi10Fe alloy dissolution. The inhibition efficiency (IE) increased with increase in inhibitor concentration. The polarization shows that both compounds functioned as cathodic corrosion inhibitors by adsorption on the surface of CuNi10Fe alloy according to the Freundlich adsorption isotherm. The numerical values of free energies of adsorption indicate physical adsorption of the compounds on the electrode surface. DFT-based quantum chemical computations and molecular dynamics (MD) simulations revealed identical electronic and adsorption structures for both HBA and PCA, which could account for the similarities in the experimentally observed inhibiting effects.

N–H + vibrational anharmonicities directly revealed from DFT-based molecular dynamics simulations on the Ala 7H + protonated peptide

Abstract The present investigation reports DFT-based Born–Oppenheimer molecular dynamics simulations of the gas phase Ala 7H + protonated peptide, in order to unravel the structure and dynamics of the peptide and its Infrared vibrational signatures. At 350 K, the most statistically relevant conformations adopted by the globular folded Ala 7H + peptide have the NH 3 + N-terminus involved in two NH + → O C charge-solvated hydrogen bonds. The dynamics performed here nicely provide a clear understanding of the IR-MPD features experimentally recorded, with an excellent matching of the dynamically simulated IR spectrum with the experiment in terms of band-positions and band-shapes. In particular, the diverse vibrational anharmonicities displayed by the N–H + stretches depending on the number of simultaneous hydrogen bonds that the NH 3 + can form at the N-terminus of the Ala 7H + peptide chain, are remarkably reproduced by the present dynamics at finite temperature. This gives rise to a proper understanding of the different IR active bands, especially the supplementary band between 3100 and 3300 cm −1 present for the Ala 7H + peptide and absent for the smaller peptide chain lengths. Vibrational anharmonicities are naturally taken into account in the dynamical treatment of the movements, and this has once more been illustrated in the present work. Our results on the N–H + stretching motions in relation with the number of hydrogen bonds formed by the NH 3 + group, can be used as general guidelines in order to precisely interpret IR-MPD spectra of molecules containing NH 3 + groups, taking into account vibrational anharmonicities.

Acidity constants from DFT-based molecular dynamics simulations

In this contribution we review our recently developed method for the calculation of acidityconstants from density functional theory based molecular dynamics simulations.The method is based on a half reaction scheme in which protons are formallytransferred from solution to the gas phase. The corresponding deprotonation freeenergies are computed from the vertical energy gaps for insertion or removalof protons. Combined to full proton transfer reactions, the deprotonationenergies can be used to estimate relative acidity constants and also the BrønstedpKa when the deprotonation free energy of a hydronium ion is used as a reference. We verified themethod by investigating a series of organic and inorganic acids and bases spanning a wide range ofpKa values (20 units). The thermochemical corrections for the biasing potentials assisting anddirecting the insertion are discussed in some detail.

Impact of Mercury(II) on proteinase K catalytic center: investigations via classical and Born-Oppenheimer molecular dynamics

Mercury(II) has a strong affinity for the thiol groups in proteins often resulting in the disruption of their biological functions. In this study we present classical and first-principles, DFT-based molecular dynamics (MD) simulations of a complex of Hg(II) and proteinase K, a well-known serine protease with a very broad and diverse enzymatic activity. It contains a catalytic triad formed by Asp39, His69, and Ser224, which is responsible for its biological activity. It was found previously by X-ray diffraction experiments that the presence of Hg(II) inhibits the enzymatic action of proteinase K by affecting the stereochemistry of the triad. Our simulations predict that (i) the overall structure as well as the protein backbone dynamics are only slightly affected by the mercury cation, (ii) depending on the occupied mercury site, the hydrogen bonds of the catalytic triad are either severely disrupted (both bonds for mercury at site 1, and the His69-Ser224 contact for mercury at site 2) or slightly strengthened (the Asp39-His69 bond when mercury is at site 2), (iii) the network of hydrogen bonds of the catalytic triad is not static but undergoes constant fluctuations, which are significantly modified by the presence of the Hg(II) cation, influencing in turn the triad's ability to carry out the enzymatic function--these facts explain the experimental findings on the inhibition of proteinase K by Hg(II).

Structure, dynamics and vibrational spectrum of supercritical CO2/H2O mixtures from ab initio molecular dynamics as a function of water cluster formation

In this study, we investigate the effect of water-cluster formation in the supercritical (SC) systems CO(2)/(H(2)O)(n) as a function of water content using DFT-based molecular dynamics simulations. The dependence of the intermolecular and intramolecular structure and dynamic properties upon water concentration in the supercritical CO(2)/H(2)O phase at a density of 0.74 g cm(-3) and temperature of 318.15 K is investigated in detail and compared to previous studies of the pure sc-CO(2) system, single D(2)O in sc-CO(2), and Monte-Carlo simulations of a single water molecule in sc-CO(2) phase. Analysis of radial and orientational distribution functions of the intermolecular interactions shows that the presence of water molecules does not disturb the previously established distorted T-shaped orientation of CO(2) molecules, though there is evidence of perturbation of the second shell structure which enhances the preference for the slipped parallel orientation in this region. There is also evidence of short-lived hydrogen bonds between CO(2) and water molecules. For higher water concentrations, water clustering is observed, consistent with the low solubility of water in CO(2) under these conditions of temperature and pressure. Finally, the water-water and water-CO(2) interactions are discussed and analyzed in terms of the water self-association and thermodynamic quantities derived from the molecular dynamics simulations.

Infrared spectroscopy of the alanine dipeptide analog in liquid water with DFT-MD. Direct evidence for PII/β conformations

Following our previous work [J. Phys. Chem. B. Lett., 2009, 113, 10059], DFT-based molecular dynamics (DFTMD) simulations of 2-Ala peptide (i.e. Ac-Ala-NHMe dialanine peptide analog with methyl group caps at the extremities) immersed in liquid water at room temperature are reported. Our goal here is the theoretical calculation of the infrared spectrum of aqueous 2-Ala, in order to provide a definitive understanding of the average conformation adopted by this peptide in the liquid phase, taking into account solute and solvent at the same theoretical level of representation. We find that the experimental Amide I-II band predominantly results from a mixture of partially unfolded P(II) and unfolded beta conformational equilibrium of aqueous 2-Ala at room temperature.

Theoretical spectroscopy of floppy peptides at room temperature. A DFTMD perspective: gas and aqueous phase

Theoretical spectroscopy is mandatory for a precise understanding and assignment of experimental spectra recorded at finite temperature. We review here room temperature DFT-based molecular dynamics simulations for the purpose of interpreting finite temperature infrared spectra of peptides of increasing size and complexity, in terms of temperature-dependent conformational dynamics and flexibility, and vibrational anharmonicities (potential energy surface anharmonicities, vibrational mode couplings and dipole anharmonicities). We take examples from our research projects in order to illustrate the main key-points and strengths of dynamical spectra modeling in that context. The calculations are presented in relation to room temperature gas phase IR-MPD experiments and room temperature liquid phase IR absorption experiments. These illustrations of floppy polypeptides have been chosen in order to convey the following ideas: temperature-dependent spectra modeling is pivotal for a precise understanding of gas phase spectra recorded at room temperature, including conformational dynamics and vibrational anharmonicities; harmonic spectroscopy (as commonly performed in the literature) can be misleading and even erroneous for a proper interpretation of spectra recorded at finite temperature; taking into account vibrational anharmonicities is pivotal for a proper interplay between theory and experiments; amide I-III bands are not necessarily the most relevant fingerprints for unraveling the local structures of peptides and more complex systems; liquid phase simulations have unraveled relationships between the zwitterionic properties of the peptide bonds and infrared signatures. The review presents a state-of-the-art account of the domain and offers perspectives and new developments for future still more challenging applications.

Hydrated Structure of Ag(I) Ion from Symmetry-Dependent, K- and L-Edge XAFS Multiple Scattering and Molecular Dynamics Simulations

Details of the first-shell water structure about Ag(+) are reported from a corefinement of the K- and L(2)-edge multiple scattering signal in the X-ray absorption fine structure (XAFS) spectra. Detailed fits of the Ag K-edge data that include the contributions from multiple scattering processes in the hydrated ion structure cannot distinguish between models containing tetrahedral symmetry versus those containing collinear O-Ag-O bonds. However, we show that the multiple scattering oscillations at the L(2)-edges have distinctly different phase and amplitude functions than at the K-edge. These phase and amplitude functions depend not only on the symmetry of the multiple scattering paths but also on the nature of the final state electronic wave function probed by the dipole-allowed transition. Hence the multiple scattering portions of K- and L(2)-edge spectra provide independent measurements of the local symmetry--not a redundant measurement as is commonly believed. On the basis of the enhanced information content obtained by the simultaneous assessment of both the K- and L(2)-edges, we report that the hydrated Ag(+) structure contains five or six water molecules in the first shell with a significant number of nearly collinear and 90 degrees O-Ag-O bond angles. Finally, the K- and L(2)-edge spectra are used to benchmark the hydration structure that is generated from both DFT-based and classical molecular dynamics simulations. Simulated first-shell structures are compared to the experimental structures.

Molecular Dynamics and Room Temperature Vibrational Properties of Deprotonated Phosphorylated Serine

The local structure of phosphorylated residues in peptides and proteins may have a decisive role on their functional properties. Recent IRMPD experiments have started to provide spectroscopic signatures of such structural details; however, a proper modeling of these signatures beyond the harmonic approximation, taking into account temperature and entropic effects, is still lacking. In order to bridge this gap, DFT-based Car-Parrinello molecular dynamics simulations have been carried out for the first time on a phosphorylated amino acid, gaseous deprotonated phosphoserine. It is found that all vibrational signatures are successfully reproduced, and new deconvolution techniques enable the assignment of the vibrational spectrum directly from the dynamics results and the comparison of vibrational modes at several temperatures. The lowest energy structure is found to involve a strong hydrogen bond between the deprotonated phosphate and the acid with relatively small free energy barriers to proton transfer; however, we find that proton shuttling between the two sites does not occur frequently. Anharmonicities turn out to be important to reproduce the frequencies and shapes of several experimental bands. Comparison of room temperature and 13 K, effectively harmonic dynamics, allows insight to be obtained into vibrational anharmonicities. In particular, a significant blue-shift and broadening of the C═O stretching frequency from 13 to 300 K can be ascribed to intrinsic anharmonicity rather than to anharmonic coupling to other modes. On the other hand, significant couplings are found for the stretching motions of the hydrogen bonded P-O bond and of the free P-OH bond, mainly with modes within the phosphate group.

Unravelling the Conformational Dynamics of the Aqueous Alanine Dipeptide with First-Principle Molecular Dynamics

First principle DFT-based molecular dynamics simulations are performed in order to bring new insights into the conformational dynamics of the alanine dipeptide analogue Ac-Ala-NHMe (with methyl group caps at the extremities) immersed in liquid water at ambient temperature. Two simulations have been run for a total of 100 ps, which allows for a relevant statistical sampling of the phase space, at the ab initio level. PII-beta equilibrium and (PII-beta)-alphaR conformational interconversions are obtained, without a free-energy barrier for the Phi angle and with a rather low barrier of 2-3 kcal/mol for the Psi angle, easily overcome from solute-solvent energy transfers. We furthermore give first insights into the rather strong zwitterionic character of the peptide bonds of the dipeptide when immersed in the liquid. The structural and zwitterionic properties extracted from first-principle dynamics in the liquid phase will be useful as benchmarks for force field developments.

Vibrational Spectra of Small Protonated Peptides from Finite Temperature MD Simulations and IRMPD Spectroscopy.

Finite temperature Born-Oppenheimer DFT-based molecular dynamics simulations are presented for the vibrational spectroscopy of the prototype gas-phase Ala2H(+) and Ala3H(+) protonated peptides. The dynamics and the vibrational signatures are used to interpret IR-MPD spectra recorded in the NH/OH stretch region. Molecular dynamics simulations are one way to go beyond the harmonic approximations commonly applied for the calculations of infrared spectra, naturally including all anharmonicities, i.e. mode couplings, vibrational and dipole anharmonicities. The dynamics of the peptides allows understanding of the evolution of the shape and width of the N-H bands when increasing the size of the peptide, as demonstrated here with the two small prototypes Ala2H(+) and Ala3H(+). Hence, the conformational dynamics of Ala2(+) at room temperature participates to the broadening of the IR active bands. The complex N-H broadband of Ala3H(+) is shown to result from the dynamics of the N-H groups in the different peptide families, with a special role from breaking/reforming of hydrogen bonds involving the N-H groups. Taking this dynamics into account is thus mandatory for the understanding of this band in the 300-400 K experimental spectrum.

Solvation of Co(III)-Cysteinato Complexes in Water: A DFT-based Molecular Dynamics Study

Structural, dynamical, and vibrational properties of complexes made of metal cobalt(III) coordinated to different amounts of cysteine molecules were investigated with DFT-based Car-Parrinello molecular dynamics (CPMD) simulations in liquid water solution. The systems are composed of Co(III):3Cys and Co(III):2Cys immersed in liquid water which are modeled by about 110 explicit water molecules, thus one of the biggest molecular systems studied with ab initio molecular simulations so far. In such a way, we were able to investigate structural and dynamical properties of a model of a typical metal binding site used by several proteins. Cobalt, mainly a toxicological agent, can replace the natural binding metal and thus modify the biochemical activity. The structure of the surrounding solvent around the metal-ligands complexes is reported in detail, as well as the metal-ligands coordination bonds, using radial distribution functions and electronic analyses with Mayer bond orders. Structures of the Cocysteine complexes are found in very good agreement with EXAFS experimental data, stressing the importance of considering the surrounding solvent in the modeling. A vibrational analysis is also conducted and compared to experiment, which strengthens the reliability of the solvent interactions with the Cocysteine complexes from our molecular dynamics simulations, as well as the dynamics of the systems. From this preliminary analysis, we could suggest a vibrational fingerprint able to distinguish Co(III):2Cys from Co(III):3Cys. Our simulations also show the importance of considering a quantum explicit solvent, as solute-to-solvent proton transfer events have been observed.

Resonant infrared multiphoton dissociation spectroscopy of gas-phase protonated peptides. Experiments and Car–Parrinello dynamics at 300 K

The gas-phase structures of protonated peptides are studied by means of resonant infrared multiphoton dissociation spectroscopy (R-IRMPD) performed with a free electron laser. The peptide structures and protonation sites are obtained through comparison between experimental IR spectra and their prediction from quantum chemistry calculations. Two different analyses are conducted. It is first supposed that only well-defined conformations, sufficiently populated according to a Boltzmann distribution, contribute to the observed spectra. On the contrary, DFT-based Car-Parrinello molecular dynamics simulations show that at 300 K protonated peptides no longer possess well-defined structures, but rather dynamically explore the set of conformations considered in the first conventional approach.

Structural properties of various sodium thiogermanate glasses through DFT-based molecular dynamics simulations

We present a study of the structural properties of $(x){\mathrm{Na}}_{2}\mathrm{S}\text{\ensuremath{-}}(1\ensuremath{-}x){\mathrm{GeS}}_{2}$ glasses through density-functional-theory-based molecular dynamics simulations, at different sodium concentrations $(0<x<0.5)$. We computed the radial pair correlation functions as well as the total and partial structure factors. We also analyzed the evolution of the corner- and edge-sharing intertetrahedral links with the sodium concentration and show that the sodium ions exclusively destroy the former. With the increase of the sodium concentration the ``standard'' first sharp diffraction peak disappears and a new prepeak appears in the structure factor which can be traced back in the $\mathrm{Na}\text{\ensuremath{-}}\mathrm{Na}$ partial structure factor. This self-organization of the sodium ions is coherent with Na-rich zones that we find at high modifier concentration.

Calculated vibrational and electronic properties of various sodium thiogermanate glasses

We study the vibrational and electronic properties of ( x)Na 2S–(1 − x)GeS 2 glasses through DFT-based molecular dynamics simulations, at different sodium concentrations (0 < x < 0.5). We compute the vibrational density of states for the different samples in order to determine the contribution of the Na + ions in the VDOS. With an in-depth analysis of the eigenvectors we determine the spatial and atomic localization of the different modes, and in particular in the zone corresponding to the Boson peak. We also calculate the electronic density of states as well as the partial EDOS, in order to determine the impact of the introduction of the sodium modifiers on the electronic properties of the GeS 2 matrix.

Hydration of methanol in water. A DFT-based molecular dynamics study

We studied the hydration of a single methanol molecule in aqueous solution by first-principle DFT-based molecular dynamics simulation. The calculations show that the local structural and short-time dynamical properties of the water molecules remain almost unchanged by the presence of the methanol, confirming the observation from recent experimental structural data for dilute solutions. We also see, in accordance with this experimental work, a distinct shell of water molecules that consists of about 15 molecules. We found no evidence for a strong tangential ordering of the water molecules in the first hydration shell.