Car-Parrinello Molecular Dynamics Method Research Articles

Are Isolated Nucleic Acid Bases Really Planar? A Car−Parrinello Molecular Dynamics Study

Car-Parrinello molecular dynamics simulations of the flexibility of isolated DNA bases have been carried out. The comparison of lowest ring out-of-plane vibrations calculated by using MP2/cc-pvdz and BLYP/PW methods reveals that the DFT method with the plane wave basis set reasonably reproduces out-of-plane deformability of the pyrimidine ring in nucleic acid bases and could be used for reliable modeling of conformational flexibility of nucleobases. The conformational phase space of pyrimidine rings in thymine, cytosine, guanine, and adenine has been investigated by using the ab initio Car-Parrinello molecular dynamics method. It is demonstrated that all nucleic acid bases are highly flexible molecules and possess a nonplanar effective conformation of the pyrimidine ring despite the fact that the planar geometry corresponds to a minimum on the potential energy surface. The population of the planar geometry of the pyrimidine ring does not exceed 30%. Among the nonplanar conformations of the pyrimidine rings, the boat-like and half-chair conformations are the most populated.

Analysis of Nuclear Quantum Effects on Hydrogen Bonding

The impact of nuclear quantum effects on hydrogen bonding is investigated for a series of hydrogen fluoride (HF)n clusters and a partially solvated fluoride anion, F-(H2O). The nuclear quantum effects are included using the path integral formalism in conjunction with the Car-Parrinello molecular dynamics (PICPMD) method and using the second-order vibrational perturbation theory (VPT2) approach. For the HF clusters, a directional change in the impact of nuclear quantum effects on the hydrogen-bonding strength is observed as the clusters evolve toward the condensed phase. Specifically, the inclusion of nuclear quantum effects increases the F-F distances for the (HF)n=2-4 clusters and decreases the F-F distances for the (HF)n>4 clusters. This directional change occurs because the enhanced electrostatic interactions between the HF monomers become more dominant than the zero point energy effects of librational modes as the size of the HF clusters increases. For the F-(H2O) system, the inclusion of nuclear quantum effects decreases the F-O distance and strengthens the hydrogen bonding interaction between the fluoride anion and the water molecule because of enhanced electrostatic interactions. The vibrationally averaged 19F shielding constant for F-(H2O) is significantly lower than the value for the equilibrium geometry, indicating that the electronic density on the fluorine decreases as a result of the quantum delocalization of the shared hydrogen. Deuteration of this system leads to an increase in the vibrationally averaged F-O distance and nuclear magnetic shielding constant because of the smaller degree of quantum delocalization for deuterium.

Dipole Moment, Hydrogen Bonding and IR Spectrum of Confined Water

Drastic changes can take place in the structure, dynamics, and thermodynamics of a fluid when it is confined to spaces of molecular dimensions, as compared to its bulk counterpart. Water confinement in the nanometer-scale channels and pores of inorganic open framework materials, such as zeolites, are of great scientific interest. Zeolites are crystalline aluminosilicates, with various controlled pore sizes and connectivities. [1] From a practical point of view, water plays a key role in many applications, includingion-exchang e and separation. From a more general point of view the interaction of water with solid surfaces is of key importance for many chemical and physical processes. However, our present understandingof interfacial or confined water at the molecular level is still very limited. Most of the experimental techniques are difficult to carry out in nanometer environments. Theoretical investigation is, thus, a great help for a better understanding of confined water properties. Classical simulations have recently been performed aimed at understandingthe structure, dynamics, and thermodynamics of water confined in carbon micropores or nanotubes [2, 3] and zeolites. [4–8] However, the quantum nature of bondingin water can only be captured by ab initio calculations. Elaborate treatments of the electronic density are usually limited to small clusters (or a few adsorbed molecules) and restricted to equilibrium structures. The Car–Parrinello molecular dynamics method (CPMD) [9] offers an alternative route to capture the electronic properties of molecules, as well as dynamical effects. Such DFT-based ab initio molecular dynamics calculations have been already applied to bulk water, [10] interfacial water on Si surfaces, [11] and zeolitic materials. [12, 13] Most of the CPMD stud

Relative pKa Values from First-Principles Molecular Dynamics: The Case of Histidine Deprotonation

Accurate calculation of pK(a) values and free energies for acid/base reactions in the condensed phase has been a long-standing goal of theoretical chemistry. We present a novel application of the Car-Parrinello molecular dynamics method to the problem of relative pK(a) determination. As a particular example, we focus on the second stage in the dissociation of histidine, a process that holds special importance for biology. Using constrained molecular dynamics, we have analyzed the structural, electronic, and dynamical transformations taking place along a preselected, intuitive reaction coordinate. By integrating the potentials of mean force for the deprotonation of histidine and for a reference reaction, autodissociation of water, we obtain a pK(a) value of 6.8, which appears to be in good agreement with the experimental estimate of 6.1. Detailed analysis was undertaken to determine the value of the constraint, which transformed the N*-H* from a covalent to a hydrogen bond. This helped to identify a number of properties that could be successfully used in monitoring the dissociation process. Additional analysis in terms of electron localization functions provided valuable insight into the nature of the deprotonation reaction.

Hydrolysis of Al3+ from constrained molecular dynamics

We investigated the hydrolysis reactions of Al(3+) in AlCl(3) aqueous solution using the constrained molecular dynamics based on the Car-Parrinello molecular-dynamics method. By employing the proton-aluminum coordination number as a reaction coordinate in the constrained molecular dynamics the deprotonation as well as dehydration processes are successfully realized. From our free-energy difference of DeltaG(0) approximately 8.0 kcal mol(-1) the hydrolysis constant pK(a1) is roughly estimated as 5.8, comparable to the literature value of 5.07. We show that the free-energy difference for the hydrolysis of Al(3+) in acidic conditions is at least 4 kcal mol(-1) higher than that in neutral condition, indicating that the hydrolysis reaction is inhibited by the presence of excess protons located around the hydrated ion, in agreement with the change of the predominant species by pH.

Toward a DFT-based molecular dynamics description of Co(ii) binding in sulfur-rich peptides

In this paper, we investigated the reliability of a Car-Parrinello molecular dynamics (CPMD) approach to characterize the binding of Co(II) metal cation to peptide molecules containing cysteine. To this end, we compared pseudo-potentials and DFT plane wave expansion, which are used as key ingredients in the CPMD method, with standard all-electron Gaussian basis set DFT calculations. The simulations presented here are the first attempts to characterize interactions and dynamics of Co(II) metal with the building blocks of phytochelatin peptide molecules. Benchmark calculations are performed on [Co(Cys-H)]+ and [Co(Glutathione-H)]+ complexes, since they are the main fragments of the Co(II)-Cys and Co(II)-glutathione systems found in gas phase electrospray ionisation mass spectrometry (ESI-MS) experiments done in our laboratory. We also present benchmark calculations on the [Co(H2O)6)]2+ cluster with direct comparisons to highly correlated ab initio calculations and experiments. In particular, we investigated the dissociation path of one water molecule from the first hydration shell of Co(II) with CPMD. Overall, our molecular dynamics simulations shed some light on the nature of the Co(II) interaction and reactivity in Co(II)-phytochelatin building block systems related to the biological and environmental activity of the metal, either in the gas or liquid phase.

Electron Donor−Acceptor Interactions in Ethanol−CO2 Mixtures: An Ab Initio Molecular Dynamics Study of Supercritical Carbon Dioxide

The nature of interactions between ethanol and carbon dioxide has been characterized using simulations via the Car-Parrinello molecular dynamics (CPMD) method. Optimized geometries and energetics of free-standing ethanol-CO2 clusters exhibit evidence for a relatively more stable electron donor-acceptor (EDA) complex between these two species rather than a hydrogen-bonded configuration. This fact has also been confirmed by the higher formation rate of the EDA complex in supercritical carbon dioxide-ethanol mixtures. The probability density distribution of CO2 molecules around ethanol in the supercritical state shows two high probability regions along the direction of the lone pairs on the oxygen atom of ethanol. The EDA interaction between ethanol and CO2 as well as that between CO2 molecules themselves leads to significant deviations from linearity in the geometry of the CO2 molecule. The vibrational spectra of carbon dioxide obtained from the atomic velocity correlation functions in the bulk system as well as from isolated complexes show splitting of the nu2 bending mode that arises largely from CO2-CO2 interactions, with ethanol contributing only marginally because of its low concentration in the present study. The stretching frequency of the hydroxyl group of ethanol is shifted to lower frequencies in the bulk mixture when compared to its gas-phase value, in agreement with experiments.

Ab initio molecular dynamics simulation of the H/InP(100)–water interface

A first principles simulation study of the H-terminated InP(100)–water interface is presented with an aim to understand the electronic structure of the interface. The simulation has been carried out using the ab initio Car–Parrinello molecular dynamics method within a pseudopotential formalism and the Becke–Lee–Yang–Parr generalized gradient approximation to the exchange-correlation potential. Dissociative adsorption of H2O molecules onto H/InP(100) surfaces, leading to formation of In–OH and In–H bonds on the (100) surface, occurs at the interface, in a manner similar to the experimentally demonstrated dissociative adsorption of H2O onto n-InP(110) surface. This process indicates a very strong coupling between the semiconductor and the water states. Also, simulation carried out for two H/InP(100) surfaces reveal that more H2O dissociations occur near the rougher atomically corrugated surface, in accordance with observations from experimental studies designed to determine the morphological influences on H2O dissociation near semiconductor surfaces. An analysis of the electronic structure of the interface further reveals the charge density profile of the H/InP(100) surface states to be strongly influenced by the water states, especially those arising from the first overlayer. Additionally, the net charge of the solvated H/InP(100) slab is found to be positive and the net atomic charges on the chemisorbed H atoms are found to be negative, indicating a charge transfer, particularly, from the surface-In atoms to the chemisorbed H atoms.

Ab initio simulation of ‘liquid’ water on a Pd surface

We report on the application of the Car–Parrinello molecular dynamics method (CPMD) to the interaction of water ensembles with Pd(100) model surfaces. Periodic Pd50O8 and Pd18O2 slabs covered with nine and 18 water molecules, respectively, were employed to analyze the balance of adsorbate–adsorbate and adsorbate–surface interactions as a function of water ensemble size, in the limiting cases of a clean surface and high surface coverage with atomic oxygen. Our simulations suggest that ‘liquid’ water molecules are distributed, for the most part, randomly on Pd(100) at 300 K, with a characteristic intermolecular distance distribution in distinct regions of the water/metal interface. The structure of low-mobility local water clusters which stay close to the surface resembles that of earlier proposals based on thin film experiments. In addition, our results corroborate the experimental finding that a high surface coverage with oxygen reduces the water–Pd interaction compared to that on the clean solid.

First-principles molecular dynamics study of surface vibrations and vibrational mode coupling on the H/Si(111)1×1 surface

The vibrational dynamics of hydrogen on the H/Si(111)1×1 surface are studied using the first principles Car–Parrinello molecular dynamics method. The calculated frequencies of the surface vibrations are found to be in good agreement with experimental results. The combination band spectra indicate there are anharmonic couplings between the Si–H stretching mode and other lower frequency silicon surface phonon modes.

Molecular dynamics without effective potentials via the Car-Parrinello approach

An introduction to the Car-Parrinello molecular-dynamics method is given, written from the viewpoint of a molecular physicist. This scheme makes it possible to simulate atomic and molecular motion in cluster or bulk systems on an energy surface that is determined ‘on the fly’, by finding an adiabatic electronic state appropriate to the instantaneous nuclear positions. The crucial stability of the method is discussed at length. The development of computationally tractable expressions is considered in detail, using (local) density-functional techniques to describe the electronic energy surface. An extended account of these techniques is given, suitable for those unfamiliar with them.