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Mark E Tuckerman

Publications and source records attributed to Mark E Tuckerman.

At least 19 recordsLinked to original sources
PubMed2006

Molecular grand-canonical ensemble density functional theory and exploration of chemical space.

We present a rigorous description of chemical space within a molecular grand-canonical ensemble multi-component density functional theory framework. A total energy density functional for chemical compounds in contact with an electron and a proton bath is introduced using Lagrange multipliers which correspond to the energetic response to changes of the elementary particle densities. From a generalized Gibbs-Duhem equation analog, reactivity indices such as the nuclear hardness and a molecular Fukui function, which couples the grand-canonical electronic and nuclear degrees of freedom, are obtained. Maxwell relations between composition particles, ionic displacements, and the external potential are discussed. Numerical results for the molecular Fukui function are presented as well as finite temperature estimates for the oxidation of ammonia.

Journal Article↗
PubMed2006

Structure of liquid water at ambient temperature from ab initio molecular dynamics performed in the complete basis set limit.

Structural properties of liquid water at ambient temperature were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (CPAIMD) simulations combined with the Kohn-Sham (KS) density functional theory and the BLYP exchange-correlation functional for the electronic structure. Unlike other recent work on the same subject, where plane-wave (PW) or hybrid Gaussian/plane-wave basis sets were employed, in the present paper, a discrete variable representation (DVR) basis set is used to expand the KS orbitals, so that with the real-space grid adapted in the present work, the properties of liquid water could be obtained very near the complete basis set limit. Structural properties of liquid water were extracted from a 30 ps CPAIMD-BLYP/DVR trajectory at 300 K. The radial distribution functions (RDFs), spatial distribution functions, and hydrogen bond geometry obtained from the CPAIMD-BLYP/DVR simulation are generally in good agreement with the most up to date experimental measurements. Compared to recent ab initio MD simulations based on PW basis sets, less significant overstructuring was found in the RDFs and the distributions of hydrogen bond angles, suggesting that previous plane-wave and Gaussian basis set calculations have exaggerated the tendency toward overstructuring.

Journal Article↗
PubMed2006

Efficient and precise solvation free energies via alchemical adiabatic molecular dynamics.

A new molecular dynamics method for calculating free energies associated with transformations of the thermodynamic state or chemical composition of a system (also known as alchemical transformations) is presented. The new method extends the adiabatic dynamics approach recently introduced by Rosso et al. [J. Chem. Phys. 116, 4389 (2002)] and is based on the use of an additional degree of freedom, lambda, that is used as a switching parameter between the potential energy functions that characterize the two states. In the new method, the coupling parameter lambda is introduced as a fictitious dynamical variable in the Hamiltonian, and a system of switching functions is employed that leads to a barrier in the lambda free energy profile between the relevant thermodynamic end points. The presence of such a barrier, therefore, enhances sampling in the end point (lambda = 0 and lambda = 1) regions which are most important for computing relevant free energy differences. In order to ensure efficient barrier crossing, a high temperature T(lambda) is assigned to lambda and a fictitious mass m(lambda) is introduced as a means of creating an adiabatic separation between lambda and the rest of the system. Under these conditions, it is shown that the lambda free energy profile can be directly computed from the adiabatic probability distribution function of lambda without any postprocessing or unbiasing of the output data. The new method is illustrated on two model problems and in the calculation of the solvation free energy of amino acid side-chain analogs in TIP3P water. Comparisons to previous work using thermodynamic integration and free energy perturbation show that the new lambda adiabatic free energy dynamics method results in very precise free energy calculations using significantly shorter trajectories.

Journal Article↗
PubMed2006

Molecular dynamics simulations of aqueous solutions of ethanolamines.

We report on molecular dynamics simulations performed at constant temperature and pressure to study ethanolamines as pure components and in aqueous solutions. A new geometric integration algorithm that preserves the correct phase space volume is employed to study molecules having up to three ethanol chains. The most stable geometry, rotational barriers, and atomic charges were obtained by ab initio calculations in the gas phase. The calculated dipole moments agree well with available experimental data. The most stable conformation, due to intramolecular hydrogen bonding interactions, has a ringlike structure in one of the ethanol chains, leading to high molecular stability. All molecular dynamics simulations were performed in the liquid phase. The interaction parameters are the same for the atoms in the ethanol chains, reducing the number of variables in the potential model. Intermolecular hydrogen bonding is also analyzed, and it is shown that water associates at low water mole fractions. The force field reproduced (within 1%) the experimental liquid densities at different temperatures of pure components and aqueous solutions at 313 K. The excess and partial molar volumes are analyzed as a function of ethanolamine concentration.

Computer Simulation↗
PubMed2006

Ab initio molecular dynamics with discrete variable representation basis sets: techniques and application to liquid water.

Finite temperature ab initio molecular dynamics (AIMD), in which forces are obtained from "on-the-fly" electronic structure calculations, is a widely used technique for studying structural and dynamical properties of chemically active systems. Recently, we introduced an AIMD scheme based on discrete variable representation (DVR) basis sets, which was shown to have improved convergence properties over the conventional plane wave (PW) basis set [Liu,Y.; et al. Phys. Rev. B 2003, 68, 125110]. In the present work, the numerical algorithms for the DVR based AIMD scheme (DVR/AIMD) are provided in detail, and the latest developments of the approach are presented. The accuracy and stability of the current implementation of the DVR/AIMD scheme are tested by performing a simulation of liquid water at ambient conditions. The structural information obtained from the present work is in good agreement with the result of recent AIMD simulations with a PW basis set (PW/AIMD). Advantages of using the DVR/AIMD scheme over the PW/AIMD method are discussed. In particular, it is shown that a DVR/AIMD simulation of liquid water in the complete basis set limit is possible with a relatively small number of grid points.

Journal Article↗
PubMed2006

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.

Journal Article↗
PubMed2006

Unexpected deacetylation mechanism suggested by a density functional theory QM/MM study of histone-deacetylase-like protein.

To characterize the catalytic mechanism for zinc-dependent histone deacetylases (HDAC), we have carried out density functional theory QM/MM studies on the deacetylation reaction catalyzed by a histone-deacetylase-like protein (HDLP). The calculation results do not support the previous mechanistic hypothesis, but suggest a lower protonation state for the active site as well as a 4-fold zinc coordination during the reaction process. To characterize such mechanistic difference is not only significant for our fundamental understanding of its inner workings but also crucial for the design of HDAC inhibitors.

Acetylation↗
PubMed2006

Ab initio molecular dynamics simulation of the structure and proton transport dynamics of methanol-water solutions.

Ab initio molecular dynamics simulations are employed to study the structural and proton transport properties of methanol-water mixtures. Structural characteristics analyzed at two different methanol mole fractions (X(M) = 0.25 and X(M) = 0.5) reveal enhanced structuring of water as the methanol mole fraction increases in agreement with recent neutron diffraction experiments. The simulations reveal the existence of separate hydrogen-bonded water and methanol networks, also in agreement with the neutron diffraction data. The addition of a single proton to the X(M) = 0.5 mixture leads to an anomalous structural or Grotthuss-type diffusion mechanism of the charge defect in which water-to-water, methanol-to-water, and water-to-methanol proton transfer reactions play the dominant role with methanol-to-methanol transfers being much less significant. Unlike in bulk water, where coordination number fluctuations drive the proton transport process, suppression of the coordination number of waters in the first solvation shell of the defect diminish the importance of coordination number fluctuations as a driving force in the structural diffusion process. The charge defect is found to reside preferentially at the interface between water and methanol networks. The length of the ab initio molecular dynamics run (approximately 120 ps), allowed the diffusion constant of the charge defect to be computed, yielding a value of D = 4.2 x 10(-5) cm2/s when deuterium masses are assigned to all protons in the system. The relation of this value to excess proton diffusion in bulk water is discussed. Finally, a kinetic theory is introduced to identify the relevant time scales in the proton transfer/transport process.

Journal Article↗
PubMed2006

Structure and dynamics of OH-(aq).

Topological defects in aqueous solution in the form of H(+)(aq) and OH(-)(aq) ions undergo anomalously fast transport via the structural Grotthuss diffusion mechanism. However, while the microscopic details of this process are well understood for H(+)(aq), the corresponding picture for OH(-)(aq) remains unresolved. Mechanistic scenarios proposed previously are critically reviewed with the help of the presolvation concept, which provides a unifying framework for understanding charge migration mechanisms in hydrogen-bonded networks. It is argued that OH(-)(aq) features a nonclassical, in the Lewis sense, hypercoordinated solvation structure. The resulting mechanism deviates substantially from the traditional "mirror image" picture. Within the presolvation concept, it can also be suggested why alternative scenarios are inconsistent with experimental data.

Journal Article↗
PubMed2005

Efficient evaluation of nonlocal pseudopotentials via Euler exponential spline interpolation.

An Euler exponential spline (EES) based formalism is employed to derive new expressions for the electron-atom nonlocal pseudopotential interaction (NL) in electronic structure calculations performed using a plane wave basis set that can be computed more rapidly than standard techniques. Two methods, one that is evaluated by switching between real and reciprocal space via fast Fourier transforms, and another that is evaluated completely in real space, are described. The reciprocal-space or g-space-based technique, NLEES-G, scales as NMlogM approximately N2logN, where N is the number of electronic orbitals and M is the number of plane waves. The real-space based technique, NLEES-R, scales as N2. The latter can potentially be used within a maximally spatially localized orbital method to yield linear scaling, while the former could be employed within a maximally delocalized orbital method to yield NlogN scaling. This behavior is to be contrasted with standard techniques, which scale as N3. The two new approaches are validated using several examples, including solid silicon and liquid water, and demonstrated to be improvements on other, reduced-order nonlocal techniques. Indeed, the new methods have a low overhead and become more efficient than the standard technique for systems with roughly 20 or more atoms. Both NLEES methods are shown to work stably and efficiently within the Car-Parrinello ab initio molecular dynamics framework, owing to the existence of p-2 continuous derivatives of a pth-order spline.

Journal Article↗
PubMed2005

A polarizable multistate empirical valence bond model for proton transport in aqueous solution.

A multistate empirical valence bond model for proton transport in water, which explicitly includes solvent polarization, is presented. Polarization is included for each valence-bond state via induced point dipoles, and the model is parametrized to be used with an effective path integral derived potential surface, so as to include quantum effects of the transferring proton. The new model is shown to reproduce ab initio geometries and energetics for small protonated clusters. It is also shown that the new model gives a diffusion constant for the excess proton in water, which is in good agreement with experiment, and that the qualitative features of ab initio path integral simulations [D. Marx, M. E. Tuckerman, J. Hutter, and M. Parrinello, Nature (London) 397, 601 (1999)] are well reproduced.

Journal Article↗
PubMed2005

Decomposing total IR spectra of aqueous systems into solute and solvent contributions: a computational approach using maximally localized Wannier orbitals.

The theoretical principles underpinning the calculation of infrared spectra for condensed-phase systems in the context of ab initio molecular dynamics have been recently developed in literature. At present, most ab initio molecular dynamics calculations are restricted to relatively small systems and short simulation times. In this paper we devise a method that allows well-converged results for infrared spectra from ab initio molecular dynamics simulations using small systems and short trajectories characteristic of simulations typically performed in practice. We demonstrate the utility of our approach by computing the imaginary part of the dielectric constant epsilon"(omega) for H2O and D2O in solid and liquid phases and show that it compares well with experimental data. We further demonstrate that maximally localized Wannier orbitals can be used to separate the individual contributions of different molecular species to the linear spectrum of complex systems. The new spectral decomposition method is shown to be useful in present-day ab initio molecular dynamics calculations to compute the magnitude of the "continuous absorption" generated by excess protons in aqueous solutions with good accuracy even when other species present in the solutions absorb strongly in the same frequency window.

Journal Article↗
PubMed2005

Ab initio molecular dynamics: concepts, recent developments, and future trends.

The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated by using forces computed "on the fly" from electronic structure calculations, has had a profound influence in modern theoretical research. Ab initio molecular dynamics allows chemical processes in condensed phases to be studied in an accurate and unbiased manner, leading to new paradigms in the elucidation of microscopic mechanisms, rationalization of experimental data, and testable predictions of new phenomena. The purpose of this work is to give a brief introduction to the technique and to review several important recent developments in the field. Several illustrative examples showing the power of the technique have been chosen. Perspectives on future directions in the field also will be given.

Biophysics↗
PubMed2005

First-principles calculation of the 17O NMR parameters of a calcium aluminosilicate glass.

We have computed the (17)O NMR parameters of an amorphous calcium aluminosilicate (CAS) from first-principles. The atomic coordinates of a CAS glass of composition (CaO)(0.21)(Al(2)O (3))(0.12)(SiO (2))(0.67) were obtained by quenching a liquid to room temperature by the means of ab initio molecular-dynamics simulations of the Car-Parrinello type. The structure of the glass is found to be overall in good agreement with diffraction experiments. Some excess nonbridging O (NBO) atoms are found and are compensated by tricluster O atoms, i.e., by 3-fold coordinated O atoms to 4-fold coordinated Al or Si atoms. The glass coordinates were used to compute the (17)O NMR parameters using GGA-DFT and a correction of the Ca 3d orbital energy. The chemical shifts and the electric field gradients were obtained with the gauge including projector augmented-wave (GIPAW) and the projector augmented-wave (PAW) methods, respectively. The simulated 2D-3QMAS NMR spectrum of the CAS glass is in very good agreement with the available experimental data, notably because it takes into account the disorder present in the glass. This agreement further validates our CAS glass model. We show that the oxygen triclusters are not visible in a 2D-3QMAS NMR (17)O spectrum since their NMR parameters overlap with those of the Al-O-Si, Si-O-Si, or Al-O-Al sites. Finally, correlations between the structural characteristics and the values of the NMR parameters are extracted from the calculation with the aim of helping the interpretation of NMR spectra of glasses of similar compositions.

Journal Article↗
PubMed2005

Mapping the backbone dihedral free-energy surfaces in small peptides in solution using adiabatic free-energy dynamics.

Ramachandran surfaces for the alanine di- and tripeptides in gas phase and solution are mapped out using the recently introduced adiabatic free-energy dynamics (AFED) approach introduced by Rosso et al. (J. Chem. Phys. 2002, 116, 4389) as applied to the CHARMM22 force field. It is shown that complete surfaces can be mapped out with an order of magnitude of greater efficiency with the AFED approach than they can using the popular umbrella sampling method. In the alanine dipeptide, it is found, in agreement with numerous other studies using the CHARMM22 force field, that the lowest free-energy structure is the extended beta conformation, (phi, psi) = (-81, 81), while in solution, the extended beta, (phi, psi) = (-81, 153) and right-handed alpha-helical, (phi, psi) = (-81, 63) conformations are nearly isoenergetic. In solution, a secondary minimum at (phi, psi) = (63, -81), corresponding to a C(7)ax conformation, occurs approximately 2.3 kcal/mol above the global free-energy minimum. The alanine tripeptide, a system that has received considerably less attention in the literature, is found to exhibit a similar structure to the alanine dipeptide with the extended beta conformation being the free-energy minimum in the gas phase and the beta and right-handed alpha-helical conformations being isoenergetic in solution. These studies indicate that the AFED method can be a powerful tool for studying multidimensional free-energy surfaces in complex systems.

Peptides↗
PubMed2005

Reaction mechanism of cis-1,3-butadiene addition to the Si(100)-2 x 1 surface.

A set of 40 finite temperature ab initio molecular dynamics trajectories is employed to investigate the distribution of addition products and underlying microscopic mechanism of the addition of 1,3-butadiene to the Si(100)-2 x 1 surface. The product yields are in good agreement with recent STM measurements and include a Diels-Alder [4 + 2] adduct with a surface dimer acting as the dienophile, a [4 + 2]-like adduct that bridges two dimers within a row, a [4 + 2]-like adduct that bridges two dimers in adjacent rows, and an interdimer [2 + 2]-like adduct. The trajectories indicate that a common mechanism underlies the distribution and is predominantly a nonconcerted stepwise mechanism that proceeds via an intermediate zwitterion composed of a carbocation bonded to a negatively charged surface dimer.

Journal Article↗
PubMed2004

Long range interactions on wires: a reciprocal space based formalism.

There are many atomic scale systems in materials, chemistry, and biology that can be effectively modeled as finite in two of the physical spatial dimensions and periodically replicated in the third including nanoscale metallic and semiconducting wires, carbon nanotubes, and DNA. However, it is difficult to design techniques to treat long range forces in these systems without truncation or recourse to slowly convergent supercells or computationally inefficient Poisson solvers. In this paper, a rigorous reciprocal space based formalism which permits long range forces on wires to be evaluated simply and easily via a small modification of existing methods for three dimensional periodicity is derived. The formalism is applied to determine long range interactions both between point particles using an Ewald-like approach and the continuous charge distributions that appear in electronic structure calculations. In this way, both empirical force field calculations and, for example, plane-wave based density functional theory computations on wires can be performed easily. The methodology is tested on model and realistic systems including a lithium doped carbon nanotube.

Journal Article↗