The calculation of vibrational energy levels of polyatomic molecules including anharmonic effect using contact transformation perturbation method

Using contact transformation perturbation method based on the Taylor expansion of the potential energy function in terms of dimensionless normal coordinates up to sixth‐order, the vibrational energy levels in terms of force constants are derived. The contact transformation theory has been applied to simplify the calculation of perturbation effects. To calculate the second‐order vibrational energy correction, the third and fourth‐order terms of potential function have been placed in the first‐order perturbation Hamiltonian and the second‐order Hamiltonian contains hexatic ones. We present expressions which give relations between the fourth‐ and sixth‐order terms in dimensionless normal coordinates of the potential and the anharmonicity coefficients. For illustration, a set of vibrational energies levels of SO₂, and H₂O molecules including anharmonic effects has been calculated. © 2013 Wiley Periodicals, Inc.     

Ultrafast dynamics in noble metal clusters: The role of internal vibrational redistribution

We present a theoretical study of the ultrafast dynamics in noble metal clusters interacting with molecular oxygen which is of fundamental importance for the understanding and design of cluster-based heterogenous nanocatalysts. We demonstrate that intrinsic dynamical properties can significantly promote the reactivity of small noble metal clusters towards O₂. This concept is illustrated by performing collision simulations between and clusters and O₂ in the framework of the ab initio molecular dynamics (MD) using density functional theory (DFT). We show that different nature and efficiency of the internal vibrational energy redistribution (IVR) during the collisions with O₂ are responsible for considerably different sticking probabilities of O₂ to silver and gold clusters, respectively. In the case of , resonant IVR between the cluster and the O₂ subunit activates the O–O bond and promotes the subsequent oxidation reaction. In contrast, in the case of fast dissipative IVR on the time scale of 1 ps leads to a higher sticking probability for O₂ but the O–O bond is very rapidly deactivated and cannot participate in further oxidation processes. These findings allow us to introduce the nature of IVR as a criterion for promoting the reactivity of noble metal clusters. Such different behaviour of silver and gold clusters colliding with O₂ originates from difference in relativistic effects which are considerably more pronounced in the case of gold clusters causing more directional rigid bonding in contrast to silver clusters with more s-metallic floppy character. Moreover, we demonstrate that breaking of O–O bond can be induced in by a selective excitation of the O–O bond with an ultrashort pulse in the infrared spectral range. This opens the perspective to control the action of nanocatalysts by employing shaped laser pulses and thus bridges the fields of femtochemistry and cluster nanocatalysis.     

Nonadiabatic relaxation dynamics of water anion cluster and its isotope effects by ring‐polymer molecular dynamics simulation

We have applied a recently developed hybrid quantum ring‐polymer molecular dynamics method to the nonadiabatic p → s relaxation dynamics in water anion clusters to understand the isotope effects observed in previous experiments. The average relaxation times for (H₂O)₅₀^? and (D₂O)₅₀^? were calculated at 120 and 207 fs, respectively, and are comparable to the experimental results. Therefore, we conclude that nuclear quantum effects play an essential role in understanding the observed isotope effects for water anion cluster nonadiabatic dynamics. The nonadiabatic relaxation mechanisms are also discussed in detail. © 2014 Wiley Periodicals, Inc.     

Electrode polarization effects on interfacial kinetics of ionic liquid at graphite surface: An extended lagrangian-based constant potential molecular dynamics simulation study

Computational models including electrode polarization can be essential to study electrode/electrolyte interfacial phenomena more realistically. We present here a constant-potential classical molecular dynamics simulation method based on the extended Lagrangian formulation where the fluctuating electrode atomic charges are treated as independent dynamical variables. The method is applied to a graphite/ionic liquid system for the validation and the interfacial kinetics study. While the correct adiabatic dynamics is achieved with a sufficiently small fictitious mass of charge, static properties have been shown to be almost insensitive to the fictitious mass. As for the kinetics study, electrical double layer (EDL) relaxation and ion desorption from the electrode surface are considered. We found that the polarization slows EDL relaxation greatly whereas it has little impact on the ion desorption kinetics. The findings suggest that the polarization is essential to estimate the kinetics in nonequilibrium processes, not in equilibrium. © 2019 Wiley Periodicals, Inc.     

Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: all-atom molecular dynamics in implicit solvent

The influences of temperature, friction, and random forces on the folding of protein A have been analyzed. A series of all-atom molecular dynamics folding simulations with the Amber ff99 potential and Generalized Born solvation, starting from the fully extended chain, were carried out for temperatures from 300 to 500 K, using (a) the Berendsen thermostat (with no explicit friction or random forces) and (b) Langevin dynamics (with friction and stochastic forces explicitly present in the system). The simulation temperature influences the relative time scale of the major events on the folding pathways of protein A. At lower temperatures, helix 2 folds significantly later than helices 1 and 3. However, with increasing temperature, the folding time of helix 2 approaches the folding times of helices 1 and 3. At lower temperatures, the complete formation of secondary and tertiary structure is significantly separated in time whereas, at higher temperatures, they occur simultaneously. These results suggest that some earlier experimental and theoretical observations of folding events, e.g., the order of helix formation, could depend on the temperature used in those studies. Therefore, the differences in temperature used could be one of the reasons for the discrepancies among published experimental and computational studies of the folding of protein A. Friction and random forces do not change the folding pathway that was observed in the simulations with the Berendsen thermostat, but their explicit presence in the system extends the folding time of protein A.     

Libra: An open‐Source “methodology discovery” library for quantum and classical dynamics simulations

The “methodology discovery” library for quantum and classical dynamics simulations is presented. One of the major foci of the code is on nonadiabatic molecular dynamics simulations with model and atomistic Hamiltonians treated on the same footing. The essential aspects of the methodology, design philosophy, and implementation are discussed. The code capabilities are demonstrated on a number of model and atomistic test cases. It is demonstrated how the library can be used to study methodologies for quantum and classical dynamics, as well as a tool for performing detailed atomistic studies of nonadiabatic processes in molecular systems. The source code and additional information are available on the Web at http://www.acsu.buffalo.edu/~alexeyak/libra/index.html . © 2016 Wiley Periodicals, Inc.     

A new extension of classical molecular dynamics: An electron transfer algorithm

The molecular dynamics is one of the most widely used methods for the simulation of the properties corresponding to ionic motion. Unfortunately, classical molecular dynamics cannot be applied for electron transfer simulation. Suggested modification of the molecular dynamics allows performing the electron transfer from one particle to another during simulation runtime. All additional data structure and the corresponding algorithms are presented in this article. The method can be applied to the systems with pair Van der Waals and Coulomb interactions. Moreover, it may be extended for many‐bodied interatomic interactions. In addition, an algorithm of transference numbers calculation has been designed. This extension is not an independent method but it can be useful for simulating the systems with high concentration of electron donors and acceptors. © 2017 Wiley Periodicals, Inc.     

Performance evaluation of the zero‐multipole summation method in modern molecular dynamics software

The zero‐multiple summation method (ZMM) is a cutoff‐based method for calculating electrostatic interactions in molecular dynamics simulations, utilizing an electrostatic neutralization principle as a physical basis. Since the accuracies of the ZMM have been revealed to be sufficient in previous studies, it is highly desirable to clarify its practical performance. In this paper, the performance of the ZMM is compared with that of the smooth particle mesh Ewald method (SPME), where the both methods are implemented in molecular dynamics software package GROMACS. Extensive performance comparisons against a highly optimized, parameter‐tuned SPME implementation are performed for various‐sized water systems and two protein–water systems. We analyze in detail the dependence of the performance on the potential parameters and the number of CPU cores. Even though the ZMM uses a larger cutoff distance than the SPME does, the performance of the ZMM is comparable to or better than that of the SPME. This is because the ZMM does not require a time‐consuming electrostatic convolution and because the ZMM gains short neighbor‐list distances due to the smooth damping feature of the pairwise potential function near the cutoff length. We found, in particular, that the ZMM with quadrupole or octupole cancellation and no damping factor is an excellent candidate for the fast calculation of electrostatic interactions. © 2018 Wiley Periodicals, Inc.     

MILCH SHAKE: An efficient method for constraint dynamics applied to alkanes

We describe a method to impose constraints in a molecular dynamics simulation. A technique developed to solve the special case of a linear topology (MILC SHAKE) is hybridized with the SHAKE algorithm. The methodology, which we term MILC‐hybridized SHAKE (or MILCH SHAKE), applies to more complex topologies. Here we consider the important case of all atom models of alkanes. Exploiting the mass difference between carbon and hydrogen we show that for higher alkanes MILCH SHAKE can be an order of magnitude faster than SHAKE. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Polarization effects on intermolecular vibrational energy transfer analyzed by 2DIR spectroscopy

In the present work, we analyze the influence of the polarization effects taking place during the course of a 2DIR spectroscopy experiment performed on a molecular system undergoing an intermolecular vibrational energy transfer process. When both donor and acceptor molecules participating in the vibrational energy transfer are embedded in a host solvent, they face rotational diffusion that strongly distorts the resulting 2DIR spectra. It could be expected that the difference between rotational diffusion constants will be of particular interest. For this purpose, the polarization effects are discussed according to the different orderings of the laser-molecule interactions. Next, we study the distortions of the spectra as a function of the rotational diffusion constants of the individual molecules. The knowledge of these polarization effects is relevant to the interpretation of the spectra. Finally, the conclusions reached in this work for a vibrational energy transfer are valid for any other type of third-order optical process performed on the same molecular system.     

Automated exploration of stable isomers of H(+)(H(2)O)(n) (n = 5-7) via ab initio calculations: An application of the anharmonic downward distortion following algorithm

Isomers of protonated water clusters H(+)(H(2)O)(n) (n = 5-7) have been explored on ab initio potential energy surfaces by means of the anharmonic downward distortion following algorithm. Totally, 9, 24, and 131 isomers for n = 5, 6, and 7, respectively, were located by the automatic exploration, and all of known important isomers previously reported by conventional geometry optimization approaches have been included in the present results. Moreover, structure transitions depending on n and temperature, which were observed by experimental studies, could be reproduced via thermodynamic simulation on the basis of the superposition approach and the present isomer sets.     

Temperature effects on spreading of water nano‐droplet on poly(methyl methacrylate): A molecular dynamics simulation study

In this article, the effect of temperature on the spreading behavior of a water nano‐droplet on poly(methyl methacrylate) substrate is investigated. The contact angle analysis illustrates that the spreading process occurs in a stage‐like manner and the increase in temperature causes a regime change from partial to total wetting. The interaction energy distributions show that there exist sites on the surface which could trap water molecules and provide a better path for other molecules to overcome the asperities. Estimations of the coefficients of self‐diffusivity suggest that temperature has a major effect in the reorientation stage, which results in the formation of the interfacial layer. In the second stage of spreading, temperature affects the process by providing sufficient energy for water molecules to overcome the interactions with the substrate. Therefore, this stage is controlled by the movement of water molecules on the surface and is highly influenced by their interaction with the surface asperities, strong interaction sites, and the carbonyl groups. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 1532–1541     

Effect of bond exchange rate on dynamics and mechanics of vitrimers

Thermoset polymers are classified amongst the most challenging materials to recycle due to the permanent crosslinks that increase their strength and stiffness compared to their thermoplastic counterparts. Vitrimers provide a promising route to achieve the recyclability of thermosets by implementing dynamic covalent bonds within the network. In this study, a hybrid molecular dynamics (MD)-Monte Carlo (MC) technique is used to simulate these adaptive networks constructed by a coarse-grained model. The model proposed in this work describes the dynamic nature of the covalent bonds while maintaining a constant crosslink density. As this framework also shows flexibility in accommodating various exchange reaction activation energy via adjusting the energy difference in MC step, the dynamic and mechanical properties of the vitrimer system are intensely affected by the number of successful bond exchanges happening at every step. In both rubbery and glassy regimes, lowering the energy barrier of the bond exchange reaction results in enhanced motion for the vitrimer segments. This enhanced mobility, in turn, directly affects the stress–strain relationship of these networks, where a higher number of exchanges results in larger deformation before fracture even at low temperatures. Furthermore, the stress distribution in vitrimers shows more homogenous distribution before failure than in the thermoset network.     

Many-body effects on structure and dynamics of aqueous ionic solutions

We performed several molecular dynamic studies of metal cations in aqueous solution. The alkali metal ion Li(+) and the first-row transition metal ion Mn(2+) have been chosen as model systems. Two different three-body corrections are proposed to mimic the crucial many-body effects of electrolyte solutions. The correction function, which includes attractive features of the three-body potential, performs considerably better than the purely repulsive interaction function. Structural and dynamic results show that this simple enhancement is able to satisfactorily reproduce experimental and higher-level results for the first hydration shell.     

Harmonic vibrational frequencies: scale factors for pure, hybrid, hybrid meta, and double-hybrid functionals in conjunction with correlation consistent basis sets

Scale factors for (a) low (<1000 cm(-1)) and high harmonic vibrational frequencies, (b) thermal contributions to enthalpy and entropy, and (c) zero-point vibrational energies have been determined for five hybrid functionals (B3P86, B3PW91, PBE1PBE, BH&HLYP, MPW1K), five pure functionals (BLYP, BPW91, PBEPBE, HCTH93, and BP86), four hybrid meta functionals (M05, M05-2X, M06, and M06-2X) and one double-hybrid functional (B2GP-PLYP) in combination with the correlation consistent basis sets [cc-pVnZ and aug-cc-pVnZ, n = D(2),T(3),Q(4)]. Calculations for vibrational frequencies were carried out on 41 organic molecules and an additional set of 22 small molecules was used for the zero-point vibrational energy scale factors. Before scaling, approximately 25% of the calculated frequencies were within 3% of experimental frequencies. Upon application of the derived scale factors, nearly 90% of the calculated frequencies deviated less than 3% from the experimental frequencies for all of the functionals when the augmented correlation consistent basis sets were used.     

Ab initio molecular dynamics of protonated water clusters by integrated multicenter molecular-orbital method

To analyze large-scale cluster systems theoretically, we recently developed an "integrated multicenter molecular-orbital" (IMiC-MO) method. This method calculates the force of an entire system by dividing the system into small regions. We used the method to analyze the effect of cluster size and the process of hydrogen bond network (HBN) growth to form H(+)(H(2)O)(n) (n = 9, 17, and 33) clusters. Our simulations reveal that H(3)O(+) and water molecules in the first solvation shell function take an important role to grow the HBN. In addition, the number of hydrogen donors in each water molecule is strongly related to the shape of the HBN.     

Solvent effect on the synthesis of clarithromycin: A molecular dynamics study

Clarithromycin (6-O-methylerythromycin A) is a 14-membered macrolide antibiotic which is active in vitro against clinically important gram-positive and gram-negative bacteria. The selectivity of the methylation of the C-6 OH group is studied on erythromycin A derivatives. To understand the effect of the solvent on the methylation process, detailed molecular dynamics (MD) simulations are performed in pure DMSO, pure THF and DMSO:THF (1:1) mixture by using the anions at the C-6, C-11 and C-12 positions of 2',4"-[O-bis(TMS)]erythromycin A 9-[O-(dimethylthexylsilyl)oxime] under the assumption that the anions are stable on the sub-nanosecond time scale. The conformations of the anions are not affected by the presence of the solvent mixture. The radial distribution functions are computed for the distribution of different solvent molecules around the 'O-' of the anions. At distances shorter than 5 A, DMSO molecules are found to cluster around the C-11 anion, whereas the anion at the C-12 position is surrounded by the THF molecules. The anion at the C-6 position is not blocked by the solvent molecules. The results are consistent with the experimental finding that the methylation yield at the latter position is increased in the presence of a DMSO:THF (1:1) solvent mixture. Thus, the effect of the solvent in enhancing the yield during the synthesis is not by changing the conformational properties of the anions, but rather by creating a suitable environment for methylation at the C-6 position.     

Pt-Au合金团簇热力学性质分子动力学模拟研究

采用分子动力学方法和原子嵌入法模型势模拟了Pt原子和Au原子合金纳米团簇的熔化过程,研究了这些金属原子纳米团簇熔点与团簇组分的关系,发现不同组分纳米团簇的熔点不是单调变化的,同时均出现了负热容现象.通过对各种团簇溶化前后结构的比较研究,分析了导致这种现象的原因.     

An improved method for nonbonded list generation: rapid determination of near-neighbor pairs

Generation of the list of near-neighbor pairs of atoms not bonded to each other is a key feature of many programs for calculating the energy and energy derivatives for large molecules. Because this step can take a significant amount of CPU time, more efficient nonbonded list generation can speed up the energy calculations. In this article, a novel nonbonded list generation algorithm, BYCC, is introduced. It combines certain features of other algorithms and achieves more rapid nonbonded list generation; a factor of approximately 2.5 for a molecule of 5000 atoms with a cutoff in the 10 A range is obtained on Hewlett-Packard (HP) and Alpha processors, without greatly increasing memory requirements.