Vibrational frequencies in Car-Parrinello molecular dynamics

Car-Parrinello molecular dynamics (CPMD) are widely used to investigate the dynamical properties of molecular systems. An important issue in such applications is the dependence of dynamical quantities such as molecular vibrational frequencies upon the fictitious orbital mass μ. Although it is known that the correct Born-Oppenheimer dynamics are recovered at zero μ, it is not clear how these dynamical quantities are to be rigorously extracted from CPMD calculations. Our work addresses this issue for vibrational frequencies. We show that when the system is sufficiently close to the ground state the calculated ionic vibrational frequencies are ω(M) = ω(0M)[1 -C(μ/M)] for small μ/M, where ω(0M) is the Born-Oppenheimer ionic frequency, M the ionic mass, and C a constant that depends upon the ion-orbital coupling force constants. Our analysis also provides a quantitative understanding of the orbital oscillation amplitudes, leading to a relationship between the adiabaticity of a system and the ion-orbital coupling constants. In particular, we show that there is a significant systematic dependence of calculated vibrational frequencies upon how close the CPMD trajectory is to the Born-Oppenheimer surface. We verify our analytical results with numerical simulations for N(2), Sn(2), and H/Si(100)-(2×1).     

Hydration of Y3+ ion: a Car-Parrinello molecular dynamics study

The solvation shell structure of Y3+ and the dynamics of the hydrated ion in an aqueous solution of 0.8 M YCl3 are studied in two conditions with and without an excess proton by using first principles molecular dynamics method. We find that the first solvation shell around Y3+ contains eight water molecules forming a square antiprism as expected from x-ray absorption near edge structure in both the conditions we examined. A detailed analysis relying upon localized orbitals reveals that the complexation of water molecules with yttrium cation leads to a substantial amount of charge redistribution particularly on the oxygen atoms, giving rise to the chemical shifts of approximately -20 ppm in 17O nuclear magnetic resonance relative to the computed nuclear shieldings of the bulk water.     

Car-Parrinello molecular dynamics study of anharmonic systems: a Mannich base in solution

A Car-Parrinello molecular dynamics study was performed for 4,5-dimethyl-2-(N,N-dimethylaminomethyl)phenol, a Mannich base, to investigate the vibrational properties in solution of its intramolecular hydrogen bond. The dynamic behavior of this hydrogen-bonded system was investigated using an explicit solvent model. Addition of a nonpolar solvent permitted inclusion of delicate environmental effects on the strongly anharmonic system which was studied from first principles. Molecular dynamics and a posteriori quantization of the O-H motion were applied to reproduce the vibrational features of the O-H stretching mode. Consistent application of Car-Parrinello dynamics based on the density functional theory with subsequent solution of the vibrational Schr?dinger equation for the O-H stretching motion offers an effective method for strongly anharmonic systems, and this is supported by the comparison of the results with experimental spectra. As a further element of the intramolecular hydrogen bond study, the effects of deuteration were taken into account and a successful application of the O-H stretching mode quantization technique to the liquid phase is demonstrated. This provides a valuable computational methodology for investigations incorporating nuclear quantum effects in the liquid phase and enzyme active centers and can be used to investigate numerous systems that are not readily susceptible to experimental analysis.     

On-the-fly localization of electronic orbitals in Car-Parrinello molecular dynamics

The ab initio molecular-dynamics formalism of Car and Parrinello is extended to preserve the locality of the orbitals. The supplementary term in the Lagrangian does not affect the nuclear dynamics, but ensures "on the fly" localization of the electronic orbitals within a periodic supercell in the Gamma-point approximation. The relationship between the resulting equations of motion and the formation of a gauge-invariant Lagrangian combined with a gauge-fixing procedure is briefly discussed. The equations of motion can be used to generate a very stable and easy to implement numerical integration algorithm. It is demonstrated that this algorithm can be used to compute the trajectory of the maximally localized orbitals, known as Wannier orbitals, in ab initio molecular dynamics with only a modest increase in the overall computer time. In the present paper, the new method is implemented within the generalized gradient approximation to Kohn-Sham density-functional theory employing plane wave basis sets and atomic pseudopotentials. In the course of the presentation, we briefly discuss how the present approach can be combined with localized basis sets to design fast linear scaling ab initio molecular-dynamics methods.     

Solvation structure of hydroxyl radical by Car-Parrinello molecular dynamics

Car-Parrinello molecular dynamics simulations of a hydroxyl radical in liquid water have been performed. Structural and dynamical properties of the solvated structure have been studied in details. The partial atom-atom radial distribution functions for the hydrated hydroxyl do not show drastic differences with the radial distribution functions for liquid water. The OH is found to be a more active hydrogen bond donor and acceptor than the water molecule, but the accepted hydrogen bonds are much weaker than for the hydroxide OH- ion. The first solvation shell of the OH is less structured than the water's one and contains a considerable fraction of water molecules that are not hydrogen bonded to the hydroxyl. Part of them are found to come closer to the solvated radical than the hydrogen bonded molecules do. The lifetime of the hydrogen bonds accepted by the hydroxyl is found to be shorter than the hydrogen bond lifetime in water. A hydrogen transfer between a water molecule and the OH radical has been observed, though it is a much rarer event than a proton transfer between water and an OH- ion. The velocity autocorrelation power spectrum of the hydroxyl hydrogen shows the properties both of the OH radical in clusters and of the OH- ion in liquid.     

Formation and decay of tetrazane derivatives--a Car-Parrinello molecular dynamics study

The complications during flight 510 of the Ariane Project were ascribed to problems in the upper stage engine that employs the bipropellant monomethylhydrazine (MMH) and nitrogen tetroxide (NTO). This has led to the question what conditions or reactions possibly cause an uncontrolled behaviour in the combustion process of MMH/NTO. We use first-principles molecular dynamics to investigate the reactions of the hypergolic mixture in different chemical situations. It was possible to observe the ultrafast redox reaction between the reactants on the timescale of an unconstrained simulation. We show that electrostatic attraction is crucial for the understanding of this reaction. Besides a cold reaction preceding the ignition, a reaction path leading to the highly reactive compound dimethyltetrazane could be identified.     

Anharmonic infrared and Raman spectra in Car-Parrinello molecular dynamics simulations

The infrared and Raman spectra of naphthalene crystal with inclusion of anharmonic effects have been calculated by adopting the generalized variational density functional perturbation theory in the framework of Car-Parrinello molecular dynamics simulations. The computational approach has been generalized for cells of arbitrary shape. The intermolecular interactions have been analyzed with and without the van der Waals corrections, showing the importance of such interactions in the naphthalene crystal to reproduce the structural, dynamical, and spectroscopic properties.     

Targeted Car-Parrinello molecular dynamics: elucidating double proton transfer in formic acid dimer

The targeted molecular dynamics method, making possible the study of rare events, has been assessed in the framework of Car-Parrinello ab initio molecular dynamics. As a test case, we have studied the staggered-eclipsed rotation of ethane. The technique has subsequently been applied to investigate the nature of double proton transfer in formic acid dimer. The latter is found to follow a concerted transfer mechanism involving an essentially planar transition state. A "funnel-like region" of the potential energy surface is identified, where floppy intermolecular modes stiffen upon approaching the transition state.     

Car-Parrinello molecular dynamics simulation of Fe 3+ (aq)

The optimized geometry and energetic properties of Fe(D2O)n 3+ clusters, with n = 4 and 6, have been studied with density-functional theory calculations and the BLYP functional, and the hydration of a single Fe 3+ ion in a periodic box with 32 water molecules at room temperature has been studied with Car-Parrinello molecular dynamics and the same functional. We have compared the results from the CPMD simulation with classical MD simulations, using a flexible SPC-based water model and the same number of water molecules, to evaluate the relative strengths and weaknesses of the two MD methods. The classical MD simulations and the CPMD simulations both give Fe-water distances in good agreement with experiment, but for the intramolecular vibrations, the classical MD yields considerably better absolute frequencies and ion-induced frequency shifts. On the other hand, the CPMD method performs considerably better than the classical MD in describing the intramolecular geometry of the water molecule in the first hydration shell and the average first shell...second shell hydrogen-bond distance. Differences between the two methods are also found with respect to the second-shell water orientations. The effect of the small box size (32 vs 512 water molecules) was evaluated by comparing results from classical simulations using different box sizes; non-negligible effects are found for the ion-water distance and the tilt angles of the water molecules in the second hydration shell and for the O-D stretching vibrational frequencies of the water molecules in the first hydration shell.     

Car-Parrinello molecular dynamics study of the rearrangement of the valeramide radical cation

Car-Parrinello molecular dynamics (CPMD) studies of neutral (1) and ionized (1 (+.)) valeramide are performed with the aim of providing a rationalization for the unusual temperature effect on the dissociation pattern of 1(+.) observed in mass spectrometric experiments. According to CPMD simulations of neutral valeramide 1 performed at approximately 500 K, the conformation with the fully relaxed carbon backbone predominates (96 %). Conformational changes involving folding of the carbon backbone into conformers that would allow intramolecular H transfers are predicted not to take place spontaneously at this temperature because of the barrier heights associated with these transitions (3.5 and 6.9 kcal mol(-1)), which cannot be overcome by thermal motion alone. For 1(+.), CPMD simulations performed at approximately 300 K reveal a substantial stability of a conformation in which the carbon backbone is fully relaxed; no reaction is observed even after 7 ps. However, when conformers with already folded carbon-backbones are used as initial geometries in the CPMD simulations, the gamma-hydrogen migration (McLafferty rearrangement resulting in C(3)H(6)) is already completed within 2 ps. For this important process, the free activation energy associated with both a required conformational change and the subsequent H transfer equals 4.5 kcal mol(-1), while for the formally related delta-H shift (which eventually gives rise to the elimination of C(2)H(4)/C(2)H(5.)) it amounts to 7.0 kcal mol(-1). Since the barriers associated with conformational changes are energetically more demanding than those of the corresponding hydrogen transfers, 1(+.) is essentially trapped by conformational barriers and long-lived at approximately 300 K. At elevated temperatures (500 K), the preferred reaction (within 7.3 ps) in the CPMD simulation corresponds to the McLafferty rearrangement. The estimated free activation energy associated with this process amounts to 2.5 kcal mol(-1), while the free activation energy for the delta-H transfer equals 4.4 kcal mol(-1). This relatively small free activation energy for the McLafferty rearrangement might cause dissociation of a substantial fraction of 1(+.) prior to the time-delayed mass selection, which would reduce the C3/C2 ratio in the experiments conducted with metastable ions that have a lifetime in the order of some micros at a source temperature of 500 K.     

Probing irradiation induced DNA damage mechanisms using excited state Car-Parrinello molecular dynamics

Photoinduced proton transfer in the Watson-Crick guanine (G)-cytosine (C) base pair has been studied using Car-Parrinello molecular dynamics (CP-MD). A flexible mechanical constraint acting on all three hydrogen bonds in an unbiased fashion has been devised to explore the free energy profile along the proton transfer coordinate. The lowest barrier has been found for proton transfer from G to C along the central hydrogen bond. The resulting charge transfer excited state lies energetically close to the electronic ground state suggesting the possibility of efficient radiationless decay. It is found that dynamic, finite temperature fluctuations significantly reduce the energy gap between the ground and excited states for this charge transfer product, promoting the internal conversion process. A detailed analysis of the internal degrees of freedom reveals that the energy gap is considerably reduced by out-of-plane molecular vibrations, in particular. Consequently, it appears that considering only the minimum energy path provides an upper-bound estimate of the associated energy gap compared to the full-dimension dynamical reaction coordinate. Furthermore, the first CP-MD simulations of the G-C base pair in liquid water are presented, and the effects of solvation on its electronic structure are analyzed.     

The conformational flexibility of nucleic acid bases paired in gas phase: a Car-Parrinello molecular dynamics study

The flexibilities of pyrimidine and imidazole rings in the paired nucleobases are investigated using Car-Parrinello molecular dynamics simulation in gas phase. The pairing influence on the stiffness of rings is analyzed based on the molecular structure of the nucleobases and constraints caused by pairing. We prove that the flexibilities of pyrimidine rings in isolated state have subtle correlation with the degree of aromaticity of the rings. The pairings in nucleic base pairs cause the rings to be more rigid for G, T, and U but more flexible for A and the same for C.     

Distorted five-fold coordination of Cu2+(aq) from a Car-Parrinello molecular dynamics simulation

The solvation shell structure and dynamics of a single Cu2+ ion in a periodic box with 32 water molecules under ambient conditions has been investigated using Car-Parrinello molecular dynamics simulations in a time-window of 18 ps. Five-fold coordination with four equidistant equatorial water molecules at 2.00 A and one axial water molecule at 2.45 A from the Cu2+ ion is found. A "hole" without water molecules is found on the opposite side of the axial water. The ion-water bonding character for the equatorial water molecules is different from that of the axial water molecules, as shown by a localized orbital analysis of the electronic structure. Moreover, the calculated OD stretching vibrational band for the equatorial water molecules lies ca. 175 cm-1 below the axial-water band, in good agreement with experimental data. The equatorial-water band lies below, and the axial-water band above, the pure liquid D2O band, also in agreement with experimental data.     

Hyperfine coupling tensors of the benzosemiquinone radical anion from Car-Parrinello molecular dynamics.

Based on Car-Parrinello ab initio molecular dynamics simulations of the benzosemiquinone radical anion in both aqueous solution and the gas phase, density functional calculations provide the currently most refined EPR hyperfine coupling (HFC) tensors of semiquinone nuclei and solvent protons. For snapshots taken at regular intervals from the molecular dynamics trajectories, cluster models with different criteria for inclusion of water molecules and an additional continuum solvent model are used to analyse the HFCs. These models provide a detailed picture of the effects of dynamics and of different intermolecular interactions on the spin-density distribution and HFC tensors. Comparison with static calculations allows an assessment of the importance of dynamical effects, and of error compensation in static DFT calculations. Solvent proton HFCs depend characteristically on the position relative to the semiquinone radical anion. A point-dipolar model works well for in-plane hydrogen-bonded protons but deviates from the quantum chemical values for out-of-plane hydrogen bonding.     

Revisiting the structure of (LiCH3)n aggregates using Car-Parrinello molecular dynamics

The theoretical study of (LiMe)(n) aggregates using Car-Parrinello molecular dynamics was undertaken. With respect to a quantum chemical static treatment, this approach furnishes supplementary information about the structural parameters. Equilibrium structures are indeed stable to ca. 300 K, provided the methyl groups in the aggregates are considered to rotate essentially freely. The Li-C distance depends on the coordination number of Li and not so much on the degree of aggregation. Finally, above 650 K, the cubic LiCH(3) tetramer (which is energetically favored) undergoes an entropy-driven rearrangement to a planar structure.     

Mechanism of copper(II) inhibiting Alzheimer's amyloid beta-peptide from aggregation: a molecular dynamics investigation

The aggregation of an amyloid beta peptide (Abeta) into fibrils is a key pathological event in Alzheimer's disease (AD). Under certain conditions, Cu2+ markedly inhibits Abeta from aggregation and is considered as a potential factor in the normal brain preventing Abeta from aggregation. The possible mechanism of the inhibitory effect of Cu2+ was investigated for the first time by molecular dynamics (MD) simulations. On the basis of the radial distribution function analysis of the MD data, a novel strategy, the Q function, was proposed to explore the binding sites of Cu2+ by evaluating the coordination priority of atoms in Abeta, and the [6-5-5] tri-ring 4N binding mode of the Cu2+-Abeta complexes was found. The mechanism of the conformational transition of Abeta from the beta conformation to distorted beta conformations, which destabilizes the aggregation of Abeta into fibrils, was also revealed. All the results provide helpful clues for an improved understanding of the role of Cu2+ in the pathogenesis of AD and contribute to the development of an anti-amyloid therapeutic strategy.