ReaxFF(MgH) reactive force field for magnesium hydride systems

We have developed a reactive force field (ReaxFF(MgH)) for magnesium and magnesium hydride systems. The parameters for this force field were derived from fitting to quantum chemical (QM) data on magnesium clusters and on the equations of states for condensed phases of magnesium metal and magnesium hydride crystal. The force field reproduces the QM-derived cell parameters, density, and the equations of state for various pure Mg and MgH(2) crystal phases as well as and bond dissociation, angle bending, charge distribution, and reaction energy data for small magnesium hydride clusters. To demonstrate one application of ReaxFF(MgH), we have carried out MD simulations on the hydrogen absorption/desorption process in magnesium hydrides, focusing particularly on the size effect of MgH(2) nanoparticles on H(2) desorption kinetics. Our results show a clear relationship between grain size and heat of formation of MgH(2); as the particle size decreases, the heat of formation increases. Between 0.6 and 2.0 nm, the heat of formation ranges from -16 to -19 kcal/Mg and diverges toward that of the bulk value (-20.00 kcal/Mg) as the particle diameter increases beyond 2 nm. Therefore, it is not surprising to find that Mg nanoparticles formed by ball milling (20-100 nm) do not exhibit any significant change in thermochemical properties.     

Development of a new parameter optimization scheme for a reactive force field based on a machine learning approach

Reactive molecular dynamics (MD) simulation is performed using a reactive force field (ReaxFF). To this end, we developed a new method to optimize the ReaxFF parameters based on a machine learning approach. This approach combines the k-nearest neighbor and random forest regressor algorithm to efficiently locate several possible ReaxFF parameter sets. As a pilot test of the developed approach, the optimized ReaxFF parameter set was applied to perform chemical vapor deposition (CVD) of an α-Al₂O₃ crystal. The crystal structure of α-Al₂O₃ was reasonably reproduced even at a relatively high temperature (2000 K). The reactive MD simulation suggests that the (110) surface grows faster than the (0001) surface, indicating that the developed parameter optimization technique could be used for understanding the chemical reaction in the CVD process. © 2019 Wiley Periodicals, Inc.     

The CHARMM–TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics,free energies,and excited state properties

The quantum mechanical (QM)/molecular mechanical (MM) interface between Chemistry at HARvard Molecular Mechanics (CHARMM) and TURBOMOLE is described. CHARMM provides an extensive set of simulation algorithms, like molecular dynamics (MD) and free energy perturbation, and support for mature nonpolarizable and Drude polarizable force fields. TURBOMOLE provides fast QM calculations using density functional theory or wave function methods and excited state properties. CHARMM–TURBOMOLE is well‐suited for extended QM/MM MD simulations using first principles methods with large (triple‐ζ) basis sets. We demonstrate these capabilities with a QM/MM simulation of Mg²⁺(aq), where the MM outer sphere water molecules are represented using the SWM4‐NDP Drude polarizable force field and the ion and inner coordination sphere are represented using QM PBE, PBE0, and MP2 methods. The relative solvation free energies of Mg²⁺ and Zn²⁺ were calculated using thermodynamic integration. We also demonstrate the features for excited state properties. We calculate the time‐averaged solution absorption spectrum of indole, the emission spectrum of the indole excited state, and the electronic circular dichroism spectrum of an oxacepham. © 2014 Wiley Periodicals, Inc.     

Towards the Accurate Thermodynamic Characterization of Enzyme Reaction Mechanisms

We employed QM/MM molecular dynamics (MD) simulations to characterize the rate-limiting step of the glycosylation reaction of pancreatic α-amylase with combined DFT/molecular dynamics methods (PBE/def2-SVP : AMBER). Upon careful choice of four starting active site conformations based on thorough reactivity criteria, Gibbs energy profiles were calculated with umbrella sampling simulations within a statistical convergence of 1–2 kcal ⋅ mol⁻¹. Nevertheless, Gibbs activation barriers and reaction energies still varied from 11.0 to 16.8 kcal ⋅ mol⁻¹ and −6.3 to +3.8 kcal ⋅ mol⁻¹ depending on the starting conformations, showing that despite significant state-of-the-art QM/MM MD sampling (0.5 ns/profile) the result still depends on the starting structure. The results supported the one step dissociative mechanism of Asp197 glycosylation preceded by an acid-base reaction by the Glu233, which are qualitatively similar to those from multi-PES QM/MM studies, and thus support the use of the latter to determine enzyme reaction mechanisms.     

Atomistic-scale simulations of the initial chemical events in the thermal initiation of triacetonetriperoxide

To study the initial chemical events related to the detonation of triacetonetriperoxide (TATP), we have performed a series of molecular dynamics (MD) simulations. In these simulations we used the ReaxFF reactive force field, which we have extended to reproduce the quantum mechanics (QM)-derived relative energies of the reactants, products, intermediates, and transition states related to the TATP unimolecular decomposition. We find excellent agreement between the QM-predicted reaction products and those observed from 100 independent ReaxFF unimolecular MD cookoff simulations. Furthermore, the primary reaction products and average initiation temperature observed in these 100 independent unimolecular cookoff simulations match closely with those observed from a TATP condensed-phase cookoff simulation, indicating that unimolecular decomposition dominates the thermal initiation of the TATP condensed phase. Our simulations demonstrate that thermal initiation of condensed-phase TATP is entropy-driven (rather than enthalpy-driven), since the initial reaction (which mainly leads to the formation of acetone, O(2), and several unstable C(3)H(6)O(2) isomers) is almost energy-neutral. The O(2) generated in the initiation steps is subsequently utilized in exothermic secondary reactions, leading finally to formation of water and a wide range of small hydrocarbons, acids, aldehydes, ketones, ethers, and alcohols.     

Quantum mechanics/molecular mechanics strategies for docking pose refinement: distinguishing between binders and decoys in cytochrome C peroxidase

We investigate the effect of systematically applying molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) to docked poses in an attempt to improve the correspondence between theoretical prediction and experimental observation. The proposed scheme involves running a short time scale MD simulation on a docked ligand pose (and any known structurally important crystal structure waters in the active site), followed by QM/MM minimization. Both of these steps are relatively fast for moderately sized ligands; longer time scale MD involving the protein is not found to improve the results. The final binding energy is given in terms of the QM/MM total energy, a van der Waals correction, and a term to account for desolvation effects. This methodology is first tested with a trypsin inhibitor, for which we establish the importance of running MD before reoptimizing with QM/MM. The method is then applied to cytochrome c peroxidase using a set of binders and decoys. In this example, the proposed methodology affords much better discrimination between binders and decoys than the traditional docking approach used. For both systems presented, application of this protocol results in a significantly better energetic ranking and a smaller root mean squared deviation from known crystallographic ligand poses. This work highlights the importance of including polarization effects through QM/MM and of sampling with MD to refine a set of initial docked poses.     

Development of the ReaxFF reactive force field for describing transition metal catalyzed reactions, with application to the initial stages of the catalytic formation of carbon nanotubes

With the aim of developing a computationally inexpensive method for modeling the high-temperature reaction dynamics of transition metal catalyzed reactions we have developed a ReaxFF reactive force field in which the parameters are fitted to a substantial quantum mechanics (QM) training set, containing full reaction pathways for relevant reactions. In this paper we apply this approach to reactions involving carbon materials plus Co, Ni, and Cu atoms. We find that ReaxFF reproduces the QM reaction data with good accuracy while also reproducing the binding characteristics of Co, Ni, and Cu atoms to hydrocarbon fragments. To demonstrate the applicability of ReaxFF we performed high-temperature (1500 K) molecular dynamics simulations on a nonbranched all-carbon feedstock in the presence and absence of Co, Ni, and Cu atoms. We find that the presence of Co and Ni leads to substantial amounts of branched carbon atoms, leading eventually to the formation of carbon-nanotube-like species. In contrast, we find that under the same simulation conditions Cu leads to very little branching and leads to products with no nanotube character. In the absence of metals no branching is observed at all. These results suggest that Ni and Co catalyze the production of nanotube-like species whereas Cu does not. This is in excellent agreement with experimental observations, demonstrating that ReaxFF can provide a useful and computational tractable tool for studying the dynamics of transition metal catalytic chemistry.     

An extensible interface for QM/MM molecular dynamics simulations with AMBER

We present an extensible interface between the AMBER molecular dynamics (MD) software package and electronic structure software packages for quantum mechanical (QM) and mixed QM and classical molecular mechanical (MM) MD simulations within both mechanical and electronic embedding schemes. With this interface, ab initio wave function theory and density functional theory methods, as available in the supported electronic structure software packages, become available for QM/MM MD simulations with AMBER. The interface has been written in a modular fashion that allows straight forward extensions to support additional QM software packages and can easily be ported to other MD software. Data exchange between the MD and QM software is implemented by means of files and system calls or the message passing interface standard. Based on extensive tests, default settings for the supported QM packages are provided such that energy is conserved for typical QM/MM MD simulations in the microcanonical ensemble. Results for the free energy of binding of calcium ions to aspartate in aqueous solution comparing semiempirical and density functional Hamiltonians are shown to demonstrate features of this interface. © 2013 Wiley Periodicals, Inc.     

ReaxFF reactive force field for molecular dynamics simulations of hydrocarbon oxidation

To investigate the initial chemical events associated with high-temperature gas-phase oxidation of hydrocarbons, we have expanded the ReaxFF reactive force field training set to include additional transition states and chemical reactivity of systems relevant to these reactions and optimized the force field parameters against a quantum mechanics (QM)-based training set. To validate the ReaxFF potential obtained after parameter optimization, we performed a range of NVT-MD simulations on various hydrocarbon/O2 systems. From simulations on methane/O2, o-xylene/O2, propene/O2, and benzene/O2 mixtures, we found that ReaxFF obtains the correct reactivity trend (propene > o-xylene > methane > benzene), following the trend in the C-H bond strength in these hydrocarbons. We also tracked in detail the reactions during a complete oxidation of isolated methane, propene, and o-xylene to a CO/CO2/H2O mixture and found that the pathways predicted by ReaxFF are in agreement with chemical intuition and our QM results. We observed that the predominant initiation reaction for oxidation of methane, propene, and o-xylene under fuel lean conditions involved hydrogen abstraction of the methyl hydrogen by molecular oxygen forming hydroperoxyl and hydrocarbon radical species. While under fuel rich conditions with a mixture of these hydrocarbons, we observed different chemistry compared with the oxidation of isolated hydrocarbons including a change in the type of initiation reactions, which involved both decomposition of the hydrocarbon or attack by other radicals in the system. Since ReaxFF is capable of simulating complicated reaction pathways without any preconditioning, we believe that atomistic modeling with ReaxFF provides a useful method for determining the initial events of oxidation of hydrocarbons under extreme conditions and can enhance existing combustion models.     

Structures and stability of medium-sized silicon clusters. III. Reexamination of motif transition in growth pattern from Si15 to Si20

It has been established from experiments that stable medium-sized ionic clusters Si15-Si20 are prolate in shape. Density-functional theories (DFTs) also predict that nearly all low-lying neutral clusters in this size range are prolate in shape. Moreover, most of them are built onto two generic structural motifs, either the tricapped-trigonal-prism (TTP) Si9 motif or the six/six Si6Si6 (sixfold-puckered hexagonal ring Si6 plus six-atom tetragonal bipyramid Si6) motif. However, it appears that the exact location of the TTP-to-six/six motif transition is dependent on the functional (e.g., PBE or BLYP) used in the DFT calculations. Here, we present total-energy calculations for two series of clusters (one series containing six/six motif and the other containing the TTP motif) in the size range of Si16-Si20. The calculations were based on all-electron DFT methods with a medium [6-311G (2d)] and a large (cc-pVTZ) basis sets, as well as coupled-cluster single and double substitutions (including triple excitations) [CCSD(T)] method with a modest (cc-pVDZ) basis set. In the DFT calculations, two popular hybrid density functionals, the B3LYP and PBE1PBE, were selected. It is found that the B3LYP total-energy calculations slightly favor the six/six motif, whereas the PBE1PBE calculations slightly favor the TTP motif. The CCSD(T) total-energy calculations, however, show that isomers based on the six/six motif are energetically slightly favorable in the size range of Si16-Si20. Hence, the TTP-to-six/six motif transition is more likely to occur at Si16.     

A QM/MM study of the binding of RAPTA ligands to cathepsin B

We have carried out quantum mechanical (QM) and QM/MM (combined QM and molecular mechanics) calculations, as well as molecular dynamics (MD) simulations to study the binding of a series of six RAPTA (Ru(II)-arene-1,3,5-triaza-7-phosphatricyclo-[3.3.1.1] decane) complexes with different arene substituents to cathepsin B. The recently developed QM/MM-PBSA approach (QM/MM combined with Poisson–Boltzmann solvent-accessible surface area solvation) has been used to estimate binding affinities. The QM calculations reproduce the antitumour activities of the complexes with a correlation coefficient (r ²) of 0.35–0.86 after a conformational search. The QM/MM-PBSA method gave a better correlation (r ² = 0.59) when the protein was fixed to the crystal structure, but more reasonable ligand structures and absolute binding energies were obtained if the protein was allowed to relax, indicating that the ligands are strained when the protein is kept fixed. In addition, the best correlation (r ² = 0.80) was obtained when only the QM energies were used, which suggests that the MM and continuum solvation energies are not accurate enough to predict the binding of a charged metal complex to a charged protein. Taking into account the protein flexibility by means of MD simulations slightly improves the correlation (r ² = 0.91), but the absolute energies are still too large and the results are sensitive to the details in the calculations, illustrating that it is hard to obtain stable predictions when full flexible protein is included in the calculations.     

The MM2QM tool for combining docking,molecular dynamics,molecular mechanics,and quantum mechanics†

The use of the MM2QM tool in a combined docking + molecular dynamics (MD) + molecular mechanics (MM) + quantum mechanical (QM) binding affinity prediction study is presented, and the tool itself is discussed. The system of interest is Mycobacterium tuberculosis (MTB) pantothenate synthetase in complexes with three highly similar sulfonamide inhibitors, for which crystal structures are available. Starting from the structure of MTB pantothenate synthetase in the “open” conformation and following the combined docking + MD + MM + QM procedure, we were able to capture the closing of the enzyme binding pocket and to reproduce the position of the ligands with an average root mean square deviation of 1.6 Å. Protein–ligand interaction energies were reproduced with an average error lower than 10%. The discussion on the MD part and a protein flexibility importance is carried out. The presented approach may be useful especially for finding analog inhibitors or improving drug candidates. © 2012 Wiley Periodicals, Inc.     

ReaxFF reactive force field for the Y-doped BaZrO3 proton conductor with applications to diffusion rates for multigranular systems

Proton-conducting perovskites such as Y-doped BaZrO 3 (BYZ) are promising candidates as electrolytes for a proton ceramic fuel cell (PCFC) that might permit much lower temperatures (from 400 to 600 degrees C). However, these materials lead to relatively poor total conductivity ( approximately 10 (-4) S/cm) because of extremely high grain boundary resistance. In order to provide the basis for improving these materials, we developed the ReaxFF reactive force field to enable molecular dynamics (MD) simulations of proton diffusion in the bulk phase and across grain boundaries of BYZ. This allows us to elucidate the atomistic structural details underlying the origin of this poor grain boundary conductivity and how it is related to the orientation of the grains. The parameters in ReaxFF were based entirely on the results of quantum mechanics (QM) calculations for systems related to BYZ. We apply here the ReaxFF to describe the proton diffusion in crystalline BYZ and across grain boundaries in BYZ. The results are in excellent agreement with experiment, validating the use of ReaxFF for studying the transport properties of these membranes. Having atomistic structures for the grain boundaries from simulations that explain the overall effect of the grain boundaries on diffusion opens the door to in silico optimization of these materials. That is, we can now use theory and simulation to examine the effect of alloying on both the interfacial structures and on the overall diffusion. As an example, these calculations suggest that the reduced diffusion of protons across the grain boundary results from the increased average distances between oxygen atoms in the interface, which necessarily leads to larger barriers for proton hopping. Assuming that this is the critical issue in grain boundary diffusion, the performance of BYZ for multigranular systems might be improved using additives that would tend to precipitate to the grain boundary and which would tend to pull the oxygens atoms together. Possibilities might be to use a small amount of larger trivalent ions, such as La or Lu or of tetravalent ions such as Hf or Th. Since ReaxFF can also be used to describe the chemical processes on the anode and cathode and the migration of ions across the electrode-membrane interface, ReaxFF opens the door to the possibility of atomistic first principles predictions on models of a complete fuel cell.