Simulation, and Computational Chemistry

Further, molecular simulation and computational chemistry have evolved, and are evolving, into important tools for developing better characterization techniques where it is not possible to measure all data. Even so, it is precisely the molecular complexity of petroleum fluids that seems to be an inhibiting factor in the use of these methods for developing better characterization methods. However, identification of important functional groups in petroleum fluids applying molecular simulation and/or computational chemistry for use with group contribution methods to predict thermo-physical properties may be an area for further research. 

He, Y., Gray, J.R., Alkire, R.C. and Braatz, R.D. (2004) In Proceedings of the Topical Conference on Coupling Theory, Molecular Simulations and Computational Chemistry to the Physical World, AIChE Annual... 

Given the complexity and diversity of the problems involved a wide range of computational methods is needed. We will limit our discussion to the case of molecular dynamics simulations and quantum chemistry methods. Specific examples will be used to illustrate the benefit of various approaches for particular problems. 

Fundamental advances in theory and computation will radically change the way we do science. Simulation science will become even more multidisciplinary. Simulation and computation will fully come of age as the third branch of science, fulfilling the promise of the past 20 years. Simulation will be key to coupling multiple temporal and spatial scales while maintaining accuracy. New models will emerge that will completely replace the techniques that have been used so far. For example, new, fast methods will replace 50 years of traditional quantum chemistry approaches and we will have new solvation models. 

The combination of analytical pyrolysis, molecular modeling, and computational chemistry has also been stressed in investigating the structure of HS. It was reported that computational chemistry which allows to draw, construct and optimize in 3D space biomacromolecules, e.g., aquatic and terrestrial humic substances, with precise bond distances, bond angles, torsion angles, nonbonded distances, hydrogen bonds, charges, and chirality is a powerful tool, and molecular visualization and simulation can also be used to further understand the structure and dynamics of humic and dissolved organic matter. 

Markus Meuwly is professor of physical and computational chemistry at the Department of Chemistry of the University of Basel and adjunct research professor at Brown University, USA. He is interested in developing computational/theoretical methods for quantitative atomistic simulations, specifically multipolar force fields and reactive processes in complex systems. 

Before moving to the dipoles for specific ions, we should clarify the definition of p. Unlike for neutrals, p for an ion depends on the origin. Some molecular simulation and quantum chemistry codes compute p or p with respect to the ion center-of-charge. In IMS, the drag force due to molecular collisions acts on the ion center-of-mass and p should be referenced to that by expressing the distribution of charges over atoms (q,) as a dipole (plus likely higher multipoles) superposed on in... 

Boyd, D.B. Snoddy, J.D. Lin, H.-S. Molecular simulation of DD-peptidase, a model P-lactam-binding protein synergy between X-ray crystallography and computational chemistry. J. Compu. Chem. 1991,12, 635-644. 

The capacity of theoretical and computational chemistry continues to expand, and nowhere is the new growth more evident than in combined molecular dynamics simulation and quantum chemistry . The products, variously referred to as quantum, or mixed quantum-classical, molecular dynamics or as ab initio molecular dynamics, have already been widely used to... 

Capkovd P, Pospisil M, Vavra P, Zeman S (2003) Characterization of explosive materials using molecular dynamics simulations. In PolitzerP, Murray) (eds) Theoretical and computational chemistry, vol 13, Energetic Materials, Part 1, Decomposition, crystal and molecular properties. Elsevier, Amsterdam, p 49... 

Much of the distmst of computer simulation arises from reservations about the applicability of these approaches to chemical systems, and the validity of the results obtained by them. Nevertheless, as computer power increases and models become more complex and realistic some of these reservations are addressed and computational chemistry is increasingly accepted. 

Dinadayalane, T. C., Leszczynski, J. (2007a). Toward nanomaterials Structural, energetic and reactivity aspects of single-walled carbon nanotubes. In P. B. Balbuena J. M. Seminario (Eds.), Nanomaterials Design and simulation (Theoretical and computational chemistry, Vol. 18, pp. 167-199). Amsterdam Elsevier. 

Computer simulation has become a key scientific tool in the study of chemical and biochemical systems. Molecular modeling techniques are routinely being used in the study of a wide variety of chemical systems, such as proteins and DNA, and their interaction with potential pharmaceutical agents. The use of molecular simulations has become possible as a result of advances in theoretical and computational chemistry and the rapid development of cost-effective computing resources. Among the most popular tools in computer simulation studies of complex chemical systems are the thermodynamic cycle free energy methodologies. 

Ren J. (1985), A Thesis on the Development of a Mathematical Model of the Batch Dyeing Process and its Apphcation to the Simulation and Computer Control of A Dyeing Machine PhD Thesis, Dept, of Colour Chemistry, Leeds University. 

Pratt L R and Hummer G (eds) 1999 Simulation and theory of electrostatic interactions in solution computational chemistry, biophysics and aqueous solutions AlP Conf. Proc. (Sante Fe, NM, 1999) vol 492 (New York American Institute of Physics)... 

T.P. Lybrand, Computer simulations of biomolecular systems using molecular dynamics and free energy perturbation methods, in Reviews in Computational Chemistry, Vol. 1, K.B. Lipkowitz, D.B. Boyd (Eds.), VCH, New York, 1990, pp. 295-320. 

There is a lot of confusion over the meaning of the terms theoretical chemistry, computational chemistry and molecular modelling. Indeed, many practitioners use all three labels to describe aspects of their research, as the occasion demands "Theoretical chemistry is often considered synonymous with quantum mechanics, whereas computational chemistry encompasses not only quantum mechanics but also molecular mechaiucs, minimisation, simulations, conformational analysis and other computer-based methods for understanding and predicting the behaviour of molecular systems. Molecular modellers use all of these methods and so we shall not concern ourselves with semantics but rather shall consider any theoretical or computational tecluiique that provides insight into the behaviour of molecular systems to be an example of molecular modelling. If a distinction has to be... 

Kurst G R, R A Stephens and R W Phippen 1990. Computer Simulation Studies of Anisotropic iystems XIX. Mesophases Formed by the Gay-Berne Model Mesogen. Liquid Crystals 8 451-464. e F J, F Has and M Orozco 1990. Comparative Study of the Molecular Electrostatic Potential Ibtained from Different Wavefunctions - Reliability of the Semi-Empirical MNDO Wavefunction. oumal of Computational Chemistry 11 416-430. 

Dauber-Osguthorpe P and D J Osguthorpe 1993. Partitioning the Motion in Molecular Dynamii Simulations into Characteristic Modes of Motion. Journal of Computational Chemistry 14 1259-127... 

Guarnieri F and W C Still 1994. A Rapidly Convergent Simulation Method Mixed Monte Carlt Stochastic Dynamics. Journal of Computational Chemistry 15 1302-1310. 

---