Mechanisms molecular dynamics studies

As computer power and computational algorithms advance, work described here will certainly be improved upon. For example, combined quantum mechanical-molecular dynamics studies of molecular solvation and protein-ligand interactions are becoming more conunon and may soon become routine for thermochemical calculations, as well as binding site studies, of the sort described here. 

Fatmi MQ, Hofer TS, Rode BM (2010) The stability of Zn(NHa)4 in water a quantum mechanical/molecular mechanical molecular dynamics study. Phys Chem Chem Phys 12 9713-9718... 

In molecular mechanics and molecular dynamics studies of proteins, assig-ment of standard, non-dynamical ionization states of protein titratable groups is a common practice. This assumption seems to be well justified because proton exchange times between protein and solution usually far exceed the time range of the MD simulations. We investigated to what extent the assumed protonation state of a protein influences its molecular dynamics trajectory, and how often our titration algorithm predicted ionization states identical to those imposed on the groups, when applied to a set of structures derived from a molecular dynamics trajectory [34]. As a model we took the bovine... 

Once the model of a ligand-receptor complex is built, its stability should be evaluated. Simple molecular mechanics optimization of the putative ligand-receptor complex leads only to the identification of the closest local minimum. However, molecular mechanics optimization of molecules lacks two crucial properties of real molecular systems temperature and, consequently, motion. Molecular dynamics studies the time-dependent evolution of coordinates of complex multimolecular systems as a function of inter- and intramolecular interactions (see Chapter 3). Because simulations are usually performed at nonnal temperature (—300 K), relatively low energy barriers, on the order of kT (0.6 kcal), can... 

The most desirable property of polycarbonates is their high ductility on impact, relative to other engineering polymers in the unmodified state. There is no consensus on the mechanism of ductility researchers continue to explore this behavior through molecular dynamics studies of chain segment motion during the formation of crazes and propagation of the failure. 

The utility of spline functions to molecular dynamic studies has been tested by Sathyamurthy and Raff by carrying out quassiclassical trajectory and quantum mechanical calculations for various surfaces. However, the accuracy of spline interpolation deteriorated with an increase in dimension from 1 to 2 to 3. Various other numerical interpolation methods, such as Akima s interpolation in filling ab initio PES for reactive systems, have been used. 

B. Mortazavi, S. Ahzi,V. Toniazzo.Y. Remond, Nitrogen doping and vacancy effects on the mechanical properties of graphene A molecular dynamics study., Physics Letters A, vol. 376, pp. 1146-1153, 2012. 

B. Mortazavi, S. Ahzi, Molecular dynamics study on the thermal conductivity and mechanical properties of boron doped graphene., Solid State Communications, vol. 152, pp. 1503-1507, 2012. 

A review of the Journal of Physical Chemistry A, volume 110, issues 6 and 7, reveals that computational chemistry plays a major or supporting role in the majority of papers. Computational tools include use of large Gaussian basis sets and density functional theory, molecular mechanics, and molecular dynamics. There were quantum chemistry studies of complex reaction schemes to create detailed reaction potential energy surfaces/maps, molecular mechanics and molecular dynamics studies of larger chemical systems, and conformational analysis studies. Spectroscopic methods included photoelectron spectroscopy, microwave spectroscopy circular dichroism, IR, UV-vis, EPR, ENDOR, and ENDOR induced EPR. The kinetics papers focused on elucidation of complex mechanisms and potential energy reaction coordinate surfaces. 

A conformational study of novel polyhydroxylated azepanes has been reported in which the 1H NMR spectroscopy and molecular modeling (molecular mechanics, molecular dynamics, and Monte Carlo methods) afforded insights into aspects of the conformational analysis <2004EJ04119>. 

In this chapter we survey the molecular mechanics and dynamics studies of bioinorganic systems reported to date. We also address the problems involved in carrying out such studies and point to possible strategies for dealing with them. 

Molecular mechanics and dynamics studies of metal-nucleotide and metal-DNA interactions to date have been limited almost exclusively to modeling the interactions involving platinum-based anticancer drugs. As with metal-amino-acid complexes, there have been surprisingly few molecular mechanics studies of simple metal-nucleotide complexes that provide a means of deriving reliable force field parameters. A study of bis(purine)diamine-platinum(II) complexes successfully reproduced the structures of such complexes and demonstrated how steric factors influenced the barriers to rotation about the Pt(II)-N(purine) coordinate bonds and interconversion of the head-to-head (HTH) to head-to-tail (HTT) isomers (Fig. 12.4)[2011. In the process, force field parameters for the Pt(II)/nucleotide interactions were developed. A promising new approach involving the use of ab-initio calculations to calculate force constants has been applied to the interaction between Pt(II) and adenine[202]. 

Dang, L. X. (1995) Mechanism and Thermodynamics of Ion Selectivity in Aqueous- Solutions of 18-Crown-6 Ether - a Molecular-Dynamics Study, J. Am. Chem. Soc. 117, 6954-60. 

Grootenhuis, P. D. J., Kollman, P. A. (1989), Molecular Mechanics and Dynamics Studies of Crown Ether-Cation Interactions Free Energy Calculations on the Cation Selectivity of Dibenzo-18-Crown-6 and Dibenzo-30-Crown-10, J. Am. Chem. Soc. Ill, 2152-2158. 

One of the main assets of the time-dependent theory is the possibility of treating some degrees of freedom quantum mechanically and others classically. Such composite methods necessarily lead to time-dependent Hamiltonians which obviously exclude time-independent approaches. We briefly outline three approximations that are frequently used in molecular dynamics studies. To be consistent with the previous sections we consider the collinear triatomic molecule ABC with Jacobi coordinates R and r. 

B. Mennucci J.M. Martinez, How to model solvation of peptides Insights from a quantum mechanical and molecular dynamics study of N-methylacetamide. 2. 15N and 170 nuclear shielding in water and in acetone. J. Phys. Chem. B, 109, 9818, 9830 (2005)... 

Y. Wu et al., On the Mechanisms of OH- Radical Induced DNA-Base Damage A Comparative Quantum Chemical and Car-Parrinello Molecular Dynamics Study. J. Phys. Chem. A 108, 2922-2929 (2004)... 

Sewell and co workers [145-148] have performed molecular dynamics simulations using the HMX model developed by Smith and Bharadwaj [142] to predict thermophysical and mechanical properties of HMX for use in mesoscale simulations of HMX-containing plastic-bonded explosives. Since much of the information needed for the mesoscale models cannot readily be obtained through experimental measurement, Menikoff and Sewell [145] demonstrate how information on HMX generated through molecular dynamics simulation supplement the available experimental information to provide the necessary data for the mesoscale models. The information generated from molecular dynamics simulations of HMX using the Smith and Bharadwaj model [142] includes shear viscosity, self-diffusion [146] and thermal conductivity [147] of liquid HMX. Sewell et al. have also assessed the validity of the HMX flexible model proposed by Smith and Bharadwaj in molecular dynamics studies of HMX crystalline polymorphs. 

A subsequent molecular dynamics study using the REBO potential was used to demonstrate how information on reaction mechanisms gleaned from MD simulations can be used to design an explosive with specific performance properties [169]. Because the first step of the initiation reactions requires that a critical degree of compression must be attained in order for the material to atomize, there is an implication that a REBO crystal can be tailored in such a way that this critical degree of compression cannot be reached. Rice et al. [169] used molecular dynamics and REBO crystals that included heavy inert... 

Frecer, V., Ho, B., Ding, J.L. Molecular dynamics study on lipid A from Escherichia coli insights into its mechanism of biological action. Biochim Biophys Acta 1466 (2000a) 87-104. 

These three critical points, namely the neglect of non-Coulombic contributions for solute atoms, a fluctuating charge distribution of the QM particles and electrostatic embedding of MM partial charges, lead to the formulation of the quantum mechanical charge field (QMCF) ansatz [54] which has been applied in molecular dynamics studies of various hydrated systems, recently. 

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