Initial Decomposition Mechanism of 3-Nitro-1,2,4-triazol-5-one (NTO) under Shock Loading: ReaxFF Parameterization and Molecular Dynamic Study

We report a reactive molecular dynamic (ReaxFF-MD) study using the newly parameterized ReaxFF-lg reactive force field to explore the initial decomposition mechanism of 3-Nitro-1,2,4-triazol-5-one (NTO) under shock loading (shock velocity >6 km/s). The new ReaxFF-lg parameters were trained from massive quantum mechanics data and experimental values, especially including the bond dissociation curves, valence angle bending curves, dihedral angle torsion curves, and unimolecular decomposition paths of 3-Nitro-1,2,4-triazol-5-one (NTO), 1,3,5-Trinitro-1,3,5-triazine (RDX), and 1,1-Diamino-2,2-dinitroethylene (FOX-7). The simulation results were obtained by analyzing the ReaxFF dynamic trajectories, which predicted the most frequent chain reactions that occurred before NTO decomposition was the unimolecular NTO merged into clusters ((C₂H₂O₃N₄)_n). Then, the NTO dissociated from (C₂H₂O₃N₄)_n and started to decompose. In addition, the paths of NO₂ elimination and skeleton heterocycle cleavage were considered as the dominant initial decomposition mechanisms of NTO. A small amount of NTO dissociation was triggered by the intermolecular hydrogen transfer, instead of the intramolecular one. For α-NTO, the calculated equation of state was in excellent agreement with the experimental data. Moreover, the discontinuity slope of the shock-particle velocity equation was presented at a shock velocity of 4 km/s. However, the slope of the shock-particle velocity equation for β-NTO showed no discontinuity in the shock wave velocity range of 3–11 km/s. These studies showed that MD by using a suitable ReaxFF-lg parameter set, could provided detailed atomistic information to explain the shock-induced complex reaction mechanisms of energetic materials. With the ReaxFF-MD coupling MSST method and a cheap computational cost, one could also obtain the deformation behaviors and equation of states for energetic materials under conditions of extreme pressure.     

Thorpe尺度估算库尔勒、茂名、拉萨大气光学湍流廓线

在新疆库尔勒、广东茂名海边、西藏拉萨三个地区释放的探空气球, 实现了温度、气压、风速等常规气象参数以及大气折射率结构常数的廓线测量。基于Tatarski湍流参数化方案以及以上地区探空数据, 利用Thorpe尺度估算了新疆库尔勒、广东茂名海边、西藏拉萨三个地区的高空大气光学湍流廓线, 并将这三个地区实测的廓线与其对应的估算结果做了对比, 结果表明: 估算值与实测值在量级和变化趋势上表现出较好的一致性, 相关性分别为69%, 60%, 68%;Thorpe尺度相较于其他估算湍流廓线的参数化方法输入参数少、更简便。     

Exploring the parameter space of the coarse‐grained UNRES force field by random search: Selecting a transferable medium‐resolution force field

We explored the energy‐parameter space of our coarse‐grained UNRES force field for large‐scale ab initio simulations of protein folding, to obtain good initial approximations for hierarchical optimization of the force field with new virtual‐bond‐angle bending and side‐chain‐rotamer potentials which we recently introduced to replace the statistical potentials. 100 sets of energy‐term weights were generated randomly, and good sets were selected by carrying out replica‐exchange molecular dynamics simulations of two peptides with a minimal α‐helical and a minimal β‐hairpin fold, respectively: the tryptophan cage (PDB code: 1L2Y) and tryptophan zipper (PDB code: 1LE1). Eight sets of parameters produced native‐like structures of these two peptides. These eight sets were tested on two larger proteins: the engrailed homeodomain (PDB code: 1ENH) and FBP WW domain (PDB code: 1E0L); two sets were found to produce native‐like conformations of these proteins. These two sets were tested further on a larger set of nine proteins with α or α + β structure and found to locate native‐like structures of most of them. These results demonstrate that, in addition to finding reasonable initial starting points for optimization, an extensive search of parameter space is a powerful method to produce a transferable force field. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Empirical formulation and parameterization of cation-π interactions for protein modeling

Cation-π interaction is comparable and as important as other main molecular interaction types, such as hydrogen bond, electrostatic interaction, van der Waals interaction, and hydrophobic interaction. Cation-π interactions frequently occur in protein structures, because six (Phe, Tyr, Trp, Arg, Lys, and His) of 20 natural amino acids and all metallic cations could be involved in cation-π interaction. Cation-π interactions arise from complex physicochemical nature and possess unique interaction behaviors, which cannot be modeled and evaluated by existing empirical equations and force field parameters that are widely used in the molecular dynamics. In this study, the authors present an empirical approach for cation-π interaction energy calculations in protein interactions. The accurate cation-π interaction energies of aromatic amino acids (Phe, Tyr, and Try) with protonated amino acids (Arg and Lys) and metallic cations (Li(+), Na(+), K(+), and Ca(2+)) are calculated using B3LYP/6-311+G(d,p) method as the benchmark for the empirical formulization and parameterization. Then, the empirical equations are built and the parameters are optimized based on the benchmark calculations. The cation-π interactions are distance and orientation dependent. Correspondingly, the empirical equations of cation-π interactions are functions of two variables, the distance r and the orientation angle θ. Two types of empirical equations of cation-π interactions are proposed. One is a modified distance and orientation dependent Lennard-Jones equation. The second is a polynomial function of two variables r and θ. The amino acid-based empirical equations and parameters provide simple and useful tools for evaluations of cation-π interaction energies in protein interactions.     

Efficient newton–raphson/singular value decomposition-based optimization scheme with dynamically updated critical condition number for rapid convergence of weighted histogram analysis method equations

Selection of the successful optimization strategy is an essential part of solving numerous practical problems yet often is a nontrivial task, especially when a function to be optimized is multidimensional and involves statistical data. Here we propose a robust optimization scheme, referred to as NR/SVD-Cdyn, which is based on a combination of the Newton–Raphson (NR) method along with singular value decomposition (SVD), and demonstrate its performance by numerically solving a system of the weighted histogram analysis method equations. Our results show significant improvement over the direct iteration and conventional NR optimization methods. The proposed scheme is universal and could be used for solving various optimization problems in the field of computational chemistry such as parameter fitting for the methods of molecular mechanics and semiempirical quantum-mechanical methods. © 2019 Wiley Periodicals, Inc.     

Simultaneous identification of unknown time delays and model parameters in uncertain dynamical systems with linear or nonlinear parameterization by autosynchronization

In this paper, we propose a general method to simultaneously identify both unknown time delays and unknown model parameters in delayed dynamical systems based on the autosynchronization technique. The design procedure is presented in detail by constructing a specific Lyapunov function and linearizing the model function with nonlinear parameterization. The obtained result can be directly extended to the identification problem of linearly parameterized dynamical systems. Two Wpical numerical examples confirming the effectiveness of the identification method are given.     

A note on likelihood asymptotics in normal linear regression

Higher-order likelihood methods often give very accurate results. A way to evaluate accuracy is the comparison of the solutions with the exact ones of the classical theory, when these exist. To this end, we consider inference for a scalar regression parameter in the normal regression setting. In particular, we compare confidence intervals computed from the likelihood and its higher-order modifications with the ones based on the Studentt distribution. It is shown that higher-order likelihood methods give accurate approximations to exact results.     

One-to-one piecewise linear mappings over triangulations

We call a piecewise linear mapping from a planar triangulation to the plane a convex combination mapping if the image of every interior vertex is a convex combination of the images of its neighbouring vertices. Such mappings satisfy a discrete maximum principle and we show that they are one-to-one if they map the boundary of the triangulation homeomorphically to a convex polygon. This result can be viewed as a discrete version of the Radó-Kneser-Choquet theorem for harmonic mappings, but is also closely related to Tutte's theorem on barycentric mappings of planar graphs.

     

Consistent valence force-field parameterization of bond lengths and angles with quantum chemical ab initio methods applied to some heterocyclic dopamine D3-receptor agonists

To secure a broad utilization of molecular mechanics in medicinal chemistry appropriate parameters (e.g., reference values and force constants) are required to describe correctly all possible atomic interactions. For this purpose parameters for bond lengths and bond angles were derived for some heterocyclic dopamine D₃-receptor agonists. Some new atom types were introduced and consistent valence force-field (CVFF) was supplied with several bond-stretching and angle-bending force constants as well as reference values. Representative fragments containing these missing parameters were minimized at the HF/6-31G* level of theory using Gaussian-92. After frequency calculation, corresponding force constants were extracted from the Hessian matrix. The values were then appropriately converted and scaled. Also, reference values were taken from quantum mechanically minimized structures, applying the same basis set. The transferability of the calculated force constants to CVFF was investigated using fragments with already known parameters. The quality of the extended force field was checked in comparison with “automatic parameters” and ab initio-minimized structures. Finally, the evaluated procedure was applied successfully to related structures. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 935–946, 1998