Dipole Moment of A-agents series via Molecular Dynamics Simulations (original) (raw)
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Flexible Models of Novichok Agents (A230, A232, A234) for Molecular Dynamics Simulations
Journal of Engineering Science and Technology Review, 2023
Treatment and antidote research for chemical warfare agents (CWAs) is an issue that has concerned the whole western civilization for many years. Specifically, relating to the fourth generation of CWAs, including the Soviet-manufactured Novichok agents, possible deployment has or may be an issue in the near future due to the global terrorism threat. Flexible models for Novichok agents (A230, A232 & A234) have been created for the first time, using a new step-by-step approach, for molecular dynamics simulations. The new models were tested against experiments for available thermodynamic properties. An array of thermodynamic and structural properties is presented but not compared with other simulations and experimental studies due to the lack of them in the literature. Presenting calculated properties for these controlled substances might be vital in the effort for new ways to treat the threat from them.
Physchem
The flexible models of Novichok agents (A230, A232, and A234) from previous molecular dynamics simulations (MDSs) have been employed to create a parameter set for the Antoine equation of each of the three liquids. Furthermore, for the needs of this paper, new models of Novichok agents were created and studied via MDS due to the fact that the exact molecular structure of these compounds has been a matter of discussion in the last few years; however, recently, the literature favors a particular set of structures. Therefore, to cover our study holistically, both of the proposed molecular formulas were employed in the simulations and discussion. A range of ambient conditions was selected, and the data from the molecular dynamics simulations were employed to give the best possible fit in the selected vapor pressure range. When looking at the results for the two structures of A230, A232, and A234, we can see that, despite their differences, the A and B coefficients have the same magnitude...
Introduction to Molecular Dynamics Simulation
In this chapter a summary is given of the key ingredients necessary to carry out a molecular dynamics simulation, with particular emphasis on macromolecular systems. We discuss the form of the intermolecular potential for molecules composed of atoms, and of non-spherical sub-units, giving examples of how to compute the forces and torques. We also describe some of the MD algorithms in current use. Finally, we briefly refer to the factors that influence the size of systems, and length of runs, that are needed to calculate statistical properties.
Introduction fo the molecular dynamic simulation
In this chapter a summary is given of the key ingredients necessary to carry out a molecular dynamics simulation, with particular emphasis on macromolecular systems. We discuss the form of the intermolecular potential for molecules composed of atoms, and of non-spherical sub-units, giving examples of how to compute the forces and torques. We also describe some of the MD algorithms in current use. Finally, we briefly refer to the factors that influence the size of systems, and length of runs, that are needed to calculate statistical properties.
Royal Society Open Science, 2019
Novichoks are the suspected nerve agents in the March 2018 Skripal poisoning. In this context, the novichok agent A234 (chemical structure proposed by Mirzayanov) was studied using computational methods to shed light on its molecular, electronic, spectroscopic, thermodynamic and toxicity parameters as well as on potential thermal and hydrolysis degradation pathways. The poisoning action and antidote of A234 were also investigated. Some of these parameters were compared to three common G- and V-series nerve agents, namely GB, VR and VX. The research findings should be useful towards the detection, development of antidotes and destruction of A234.
Molecular dynamics simulations: from structure function relationships to drug discovery
In Silico Pharmacology, 2014
Molecular dynamics (MD) simulation is an emerging in silico technique with potential applications in diverse areas of pharmacology. Over the past three decades MD has evolved as an area of importance for understanding the atomic basis of complex phenomena such as molecular recognition, protein folding, and the transport of ions and small molecules across membranes. The application of MD simulations in isolation and in conjunction with experimental approaches have provided an increased understanding of protein structure-function relationships and demonstrated promise in drug discovery.
Journal of Computational Chemistry, 2003
We present an approximation, which allows reduction of computational resources needed to explicitly incorporate electrostatic polarization into molecular simulations utilizing empirical force fields. The proposed method is employed to compute three-body energies of molecular complexes with dipolar electrostatic probes, gas-phase dimerization energies, and pure liquid properties for five systems that are important in biophysical and organic simulations-water, methanol, methylamine, methanethiol, and acetamide. In all the cases, the three-body energies agreed with high level ab initio data within 0.07 kcal/mol, dimerization energies-within 0.43 kcal/mol (except for the special case of the CH 3 SH), and computed heats of vaporization and densities differed from the experimental results by less than 2%. Moreover, because the presented method allows a significant reduction in computational cost, we were able to carry out the liquid-state calculations with Monte Carlo technique. Comparison with the full-scale point dipole method showed that the computational time was reduced by 3.5 to more than 20 times, depending on the system in hand and on the desired level of the full-scale model accuracy, while the difference in energetic results between the full-scale and the presented approximate model was not great in the most cases. Comparison with the nonpolarizable OPLS-AA force field for all the substances involved and with the polarizable POL3 and q90 models for water and methanol, respectively, demonstrates that the presented technique allows reduction of computational cost with no sacrifice of accuracy. We hope that the proposed method will be of benefit to research employing molecular modeling technique in the biophysical and physical organic chemistry areas.
Application of Molecular Dynamics Simulation to Small Systems
2012
The study of chemical behavior includes answering questions as ’which isomer is the most stable?’, ’which relative orientation is the most favorable for such-and-such interaction?’, ’which conformer is the global minimum?’, ’what are the lowest energy configurations and their relative energies?’. The answer to these questions–and many others–depends on the ability to find and study a variety of configurations of the system of interest. Recently, (Atilgan, 2007) briefly reviewed the use of molecular dynamics simulation for conformational search in the process of drug design, concluding that its use could reduce the errors in estimating binding affinities and finding more viable conformations. In addition, (Corbeil, 2009) considered the need to include ring flexibility in the conformational searches used in flexible docking. Most of the flexible docking algorithms skip searching for conformations in rings, even though a protein may stabilize a conformation other than the most stable one.