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We report here the development of hybrid quantum mechanics/molecular mechanics (QM/MM) interface between the plane-wave density functional theory based CPMD code and the empirical force-field based GULP code for modeling periodic solids and surfaces. The hybrid QM/MM interface is based on the electrostatic coupling between QM and MM regions. The interface is designed for carrying out full relaxation of all the QM and MM atoms during geometry optimizations and molecular dynamics simulations, including the boundary atoms. Both Born-Oppenheimer and Car-Parrinello molecular dynamics schemes are enabled for the QM part during the QM/MM calculations. This interface has the advantage of parallelization of both the programs such that the QM and MM force evaluations can be carried out in parallel to model large systems. The interface program is first validated for total energy conservation and parallel scaling performance is benchmarked. Oxygen vacancy in α-cristobalite is then studied in detail and the results are compared with a fully QM calculation and experimental data. Subsequently, we use our implementation to investigate the structure of rhodium cluster (Rhn ; n = 2 to 6) formed from Rh(C2 H4 )2 complex adsorbed within a cavity of Y-zeolite in a reducible atmosphere of H2 gas. © 2016 Wiley Periodicals, Inc.

Car-Parrinello and path integrals molecular dynamics (CPMD and PIMD) simulations were carried out for the 10π-electron aromatic systems: 2-hydroxy-2,4,6-cycloheptatrien-1-one, commonly known as Tropolone (I) and 2-hydroxy-2,4,6-cycloheptatriene-1-thione, called Thiotropolone (II) in vacuo and in the solid state. The extremely fast proton transfer (FPT) and "prototropy" tautomerism in the keto-enol (thione-enethiol) systems have been analyzed on the basis of CPMD and PIMD methods level. Comparisons of two-dimensional (2D) free-energy landscapes of reaction coordinate δ-parameter and RO…O or RO…S distances shows that the OH… tautomer to be more favorable in the Thiotropolone. The hydrogen between the oxygen and the sulfur atoms adopts a starkly asymmetrical position in the double potential well. The values of the energy barriers for the FPT were calculated and suggested a strong hydrogen bond with low barrier for FPT mechanism. These studies and the 2D average index of π-delocalization 〈λ〉 landscape of time evolutions of RO1…O2 and RC7O2 or RC7S1 distances for the both crystals indicate that hydrogen bonds in the crystals of Tropolone (I) and Thiotropolone (II) have characteristic properties for the type of bonding model resonance-assisted hydrogen bonds and also low-barrier hydrogen bonds. In the crystal of the Thiotropolone (II), we found the hydrogen bond OH…S existing without the equilibrium of the two tautomers whereas in the crystal of the Tropolone (I) has been confirmed the hydrogen bond OH…O existing with the equilibrium of the two tautomers. It was also found the significant differences in frequency, speed, and the image of the FPT in the studied crystals. © 2018 Wiley Periodicals, Inc.

The interplay between electrostatic and van der Waals (vdW) interactions in porphyrin-C60 dyads is still under debate despite its importance in influencing the structural characteristics of such complexes considered for various applications in molecular photovoltaics. In this article, we sample the conformational space of a porphyrin-C60 dyad using Car–Parrinello molecular dynamics simulations with and without empirical vdW corrections. Long-range vdW interactions, which are poorly described by the commonly used density functional theory functionals, prove to be essential for a proper dynamics of the dyad moieties. Inclusion of vdW corrections brings porphyrin and C60 close together in an orientation that is in agreement with experimental observations. The structural differences arising from the vdW corrections are shown to be significant for several properties and potentially less important for others. Additionally, our Mulliken population analysis reveals that contrary to the common belief, porphyrin is not the primary electron donating moiety for C60. In the considered dyad, fullerene's affinity for electrons is primarily satisfied by charge transfer from the amide group of the linker. However, we show that in the absence of another suitable bound donor, C60 can withdraw electrons from porphyrin if it is sufficiently close. © 2015 Wiley Periodicals, Inc.

The presence of intramolecular hydrogen bonds influences the binding energy, tautomeric equilibrium, and spectroscopic properties of various classes of organic molecules. This article discusses the O-H...S bridge, one of the less commonly investigated types of intramolecular interactions. 3-mercapto-1,3-diphenylprop-2-en-1-one was considered as the model structure. This compound exhibits photochromic properties. Car-Parrinello molecular dynamics (CPMD) was applied to investigate the spectroscopic and molecular properties of this compound in the gas phase and in the solid state. The second part of the study is devoted to the effects of the quantization of nuclear motions, with special attention to the O-H...S moiety. Path integral molecular dynamics (PIMD) of the molecular crystal of 3-mercapto-1,3-diphenylprop-2-en-1-one was carried out for this purpose. The employment of this fully quantum mechanical technique enables one to study, in a time-averaged sense, the zero-point motion important for flat potential energy surfaces. Finally, the potentials of mean force (Pmfs) were calculated from the CPMD and PIMD data obtained for the solid-state calculations. The effect of including quantum nuclear motion was investigated. In the studied compound, quantum effects shortened the H-bridge and provided a better description of the free energy minimum. The computational results place this uncommon intramolecular H-bonding among the class of strong hydrogen bonds with large red shifts of O-H stretching modes, which correspond well with previously presented experimental data in the literature concerning this structure.

Many systems of great importance in material science, chemistry, solid-state physics, and biophysics require forces generated from an electronic structure calculation, as opposed to an empirically derived force law to describe their properties adequately. The use of such forces as input to Newton's equations of motion forms the basis of the ab initio molecular dynamics method, which is able to treat the dynamics of chemical bond-breaking and -forming events. However, a very large number of electronic structure calculations must be performed to compute an ab initio molecular dynamics trajectory, making the efficiency as well as the accuracy of the electronic structure representation critical issues. One efficient and accurate electronic structure method is the generalized gradient approximation to the Kohn-Sham density functional theory implemented using a plane-wave basis set and atomic pseudopotentials. The marriage of the gradient-corrected density functional approach with molecular dynamics, as pioneered by Car and Parrinello (R. Car and M. Parrinello, Phys Rev Lett 1985, 55, 2471), has been demonstrated to be capable of elucidating the atomic scale structure and dynamics underlying many complex systems at finite temperature. However, despite the relative efficiency of this approach, it has not been possible to obtain parallel scaling of the technique beyond several hundred processors on moderately sized systems using standard approaches. Consequently, the time scales that can be accessed and the degree of phase space sampling are severely limited. To take advantage of next generation computer platforms with thousands of processors such as IBM's BlueGene, a novel scalable parallelization strategy for Car-Parrinello molecular dynamics is developed using the concept of processor virtualization as embodied by the Charm++ parallel programming system. Charm++ allows the diverse elements of a Car-Parrinello molecular dynamics calculation to be interleaved with low latency such that unprecedented scaling is achieved. As a benchmark, a system of 32 water molecules, a common system size employed in the study of the aqueous solvation and chemistry of small molecules, is shown to scale on more than 1500 processors, which is impossible to achieve using standard approaches. This degree of parallel scaling is expected to open new opportunities for scientific inquiry.