Density-functional study of liquid methanol

Tsuchida, Eiji; Kanada, Yasusi; Tsukada, Masaru

doi:10.1016/s0009-2614(99)00851-9

Cited by 84 publications

(78 citation statements)

References 28 publications

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“…This geometry is reasonably close to those obtained by ab initio quantum chemical calculations. 33 In theoretical cluster model calculations one approach is to perform geometry optimization for each cluster size. In this manner a self-consistent description of all geometrical parameters is obtained at the chosen level of theory.…”

Section: Dft Analysismentioning

confidence: 99%

X-ray Absorption Spectroscopy of Liquid Methanol Microjets: Bulk Electronic Structure and Hydrogen Bonding Network

et al. 2005

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We have measured the X-ray absorption (XA) spectrum of liquid (298 K) methanol at the oxygen and carbon K edges. The 4a 1 orbital at the O K edge exhibits a pronounced sensitivity to the formation of intermolecular hydrogen bonds, with significant differences observed between the vapor and bulk spectra, whereas the C K edge reveals only subtle corresponding spectral changes. Comparison with DFT computed spectra of model methanol clusters indicates that the bulk liquid comprises long chains (n > 6) and rings of hydrogen-bonded monomers.

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Section: Dft Analysismentioning

confidence: 99%

X-ray Absorption Spectroscopy of Liquid Methanol Microjets: Bulk Electronic Structure and Hydrogen Bonding Network

et al. 2005

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“…DFT has been applied to a number of molecular liquids under ambient conditions in which hydrogen bonding plays an important role: water, 35) hydrogen fluoride, 36,37) ammonia, [38][39][40] methanol, [41][42][43][44] and formamide. 45) Review articles are also available for these applications.…”

Section: Introductionmentioning

confidence: 99%

Ab InitioMolecular-Dynamics Simulation of Concentrated Phosphoric Acid

Tsuchida

2006

J. Phys. Soc. Jpn.

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We have investigated the properties of 100% phosphoric acid (H 3 PO 4 ) in the liquid state by the combination of gradient-corrected density-functional theory and norm-conserving pseudopotentials. Various structural properties as well as the vibrational density of states have been calculated through molecular-dynamics simulations under the Born-Oppenheimer approximation. Proton transfer is found to occur frequently between adjacent PO 4 groups along the OH···O hydrogen bonds, which makes the single and double bonds indistinguishable.

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“…molecular liquids [1][2][3] and biomolecules in aqueous solution, 4) are emerging in the past few years. Since these calculations are computationally very demanding, clever use of CPU time is crucial.…”

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confidence: 99%

Large Timesteps in First-Principles Molecular Dynamics Simulations

Tsuchida¹,

Terakura²

2001

J. Phys. Soc. Jpn.

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A number of first-principles molecular dynamics simulations of biologically important systems, e.g. molecular liquids [1][2][3] and biomolecules in aqueous solution, 4) are emerging in the past few years. Since these calculations are computationally very demanding, clever use of CPU time is crucial. One way to accelerate the simulations is to use the largest possible timestep, which is mainly limited by the highest vibrational frequency of the system. In the systems mentioned above, the highest frequencies arise from stretching motion of the covalent bonds, which are only weakly coupled to other modes in most cases. Therefore, by freezing these fast modes, we can use much larger timesteps without changing the long-time behavior of the system. 5, 6) Bond-angle constraints, on the other hand, will not be considered in this article, since they can significantly alter the properties of the system, with little gain in efficiency. 5, 6)Although the constrained molecular dynamics (CMD) is a well-established technique for classical simulations, 5, 6) its applications within the first-principles calculations are limited to the estimation of free-energy differences associated with chemical reactions.7-9) In these simulations, constraints were imposed only on the reaction coordinates, and the time evolution of the system was followed by the fictitious dynamics.10) In contrast, CMD has rarely been used for the Born-Oppenheimer dynamics (BOD), in which the electronic ground state is reached at every ionic step. In general, the number of iterations for electronic minimization increases for larger timesteps in BOD, since the quality of the extrapolated wavefunctions deteriorates.11) Therefore, it is not obvious if CMD provides any improvement of the performance. In this article, we investigate the efficiency of CMD within BOD as well as the effects of using deuterium atoms in place of hydrogen atoms.We have implemented CMD within our first-principles molecular dynamics code, FEMTECK,[12][13][14] along the lines of RATTLE algorithm.15) Note that the computational efforts to calculate the constraint forces are negligible compared with those for the (unconstrained) ionic forces in the first-principles calculations. Therefore, we solve the nonlinear equations for the bond lengths (eqs. (A1) and (A3) gives constraint forces converged to machine precision in three to four iterations. Linear equations for the velocities (eqs. (A2) and (A4) of ref. 15) are also solved directly by matrix inversion.The performance of CMD has been examined by constant-NVE molecular dynamics simulations of a cytosine molecule in the amino-oxo form (Fig. 1) in a cubic supercell of (16 a.u.) 3 . The local density approximation 17) of the density functional theory 18) was used with an average cutoff energy of 39.5 Ry. The equations of motion for the ions were integrated with the velocity-Verlet algorithm.19) The wavefunctions were extrapolated from previous ionic steps 11) during the simulations. Bond lengths were fixed at their equilibrium values when con...

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Density-functional study of liquid methanol

Cited by 84 publications

References 28 publications

X-ray Absorption Spectroscopy of Liquid Methanol Microjets: Bulk Electronic Structure and Hydrogen Bonding Network

X-ray Absorption Spectroscopy of Liquid Methanol Microjets: Bulk Electronic Structure and Hydrogen Bonding Network

Ab InitioMolecular-Dynamics Simulation of Concentrated Phosphoric Acid

Large Timesteps in First-Principles Molecular Dynamics Simulations

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