Structure and Energy

Pople J A 1973 Theoretical models for chemistry Energy, Structure, and Reactivity ed D W Smith and W B McRae (New York Wiley) p 51-67... 

Wu S., Interfacial energy, structure and adhesion between polymers. Polymer Blends, Vol. 1 (Paul D.R. and Newman S., eds.). Academic Press, New York, 1978. 

Wang, J., Wang, G. and Zhao, J. (2002) Density-functional study of Au (2-20) clusters Lowest-energy structures and electronic properties. Physical Review B -Condensed Matter, 66,035418-1-035418-6. 

It is important to propose molecular and theoretical models to describe the forces, energy, structure and dynamics of water near mineral surfaces. Our understanding of experimental results concerning hydration forces, the hydrophobic effect, swelling, reaction kinetics and adsorption mechanisms in aqueous colloidal systems is rapidly advancing as a result of recent Monte Carlo (MC) and molecular dynamics (MO) models for water properties near model surfaces. This paper reviews the basic MC and MD simulation techniques, compares and contrasts the merits and limitations of various models for water-water interactions and surface-water interactions, and proposes an interaction potential model which would be useful in simulating water near hydrophilic surfaces. In addition, results from selected MC and MD simulations of water near hydrophobic surfaces are discussed in relation to experimental results, to theories of the double layer, and to structural forces in interfacial systems. 

Theoretical calculations of minimum energy structures and thermodynamic terms using SCF theory with thermodynamic and solvation corrections have been made of the cyclization of l-amino-8-(acetylamino)naphthalene (136) to give 2-methylperimidine... 

Pople, J.A. In Energy, Structure and Reactivity Proceedings of the 1972 Boulder Summer Research Conference on Theoretical Chemistry Smith, D.W., McRae, W.B., Eds. Wiley New York, 1973 pages 51-61. 

A. J. Coleman, A-representabihty circunvented, in Energy, Structure and Reactivity—Boulder Conference (D.W Smith and W. McRae, eds.), John Wiley Sons, Hoboken, NJ, 1973. 

K. Ruedenberg, R.C. Raffenetti and R. Bardo, 1973, in Energy, Structure and Reactivity, Proceedings of the 1972 Boulder Conference on Theoretical Chemistry, Wiley, New York... 

Table I. Intra-Residue Energies of Phenylalanine in Vasopressin Minimum Energy Structures and in minimum energy conformations of Ac-Phe-NMe.

Theoretical calculations of minimum-energy structures and thermodynamic terms using self-consistent field theory with thermodynamic and solvation corrections concluded that the cyclization of l-hydroxy-8-(acetylamino)naphtha-lene 1 to give 2-methylnaphth[l,8-r7,< ][l,3]oxazine 2 with the liberation of water was much less favorable (AG = —2.0kj moP, A/7 = 4-31.0kj mol , and TAS = 4-33.1 kjmoP at 298.2 K) in the gas phase than the corresponding ring closure of l-amino-8-(acetylamino)naphthalene, which was in qualitative agreement with experimental observations for the reactions in solution <1998J(P2)635>. 

There are actually very few. Modern optimization techniques practically guarantee location of a minimum energy structure, and only where the initial geometry provided is too symmetric will this not be the outcome. With a few notable exceptions (Hartree-Fock models applied to molecules with transition metals), Hartree-Fock, density functional and MP2 models provide a remarkably good account of equilibrium structure. Semi-empirical quantum chemical models and molecular mechanics models, generally fare well where they have been explicitly parameterized. Only outside the bounds of their parameterization is extra caution warranted. Be on the alert for surprises. While the majority of molecules assume the structures expected of them, some will not. Treat "unexpected" results with skepticism, but be willing to alter preconceived beliefs. 

M. Cossi, N. Rega, G. Scalmani and V. Barone, Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model, J. Comput. Chem., 24 (2003) 669. 

Primas, H. Separability in many-electron systems. In Modem quantum chemistry. Istanbul lectures. Sinanoglu, O. (ed.). New York Academic Press 1965 s°) Paldus, J., Ctzek, J. Relation of coupled-pair theory, Cl and some other many-body approaches. In Energy, Structure, and Reactivity. Proceedings of the 1972 Boulder Summer Research Conference on Theoretical Chemistry. Smith, D. W., McRae, W. B. (eds.). New York Wiley 1973, pp. 198-212... 

J. Sadlej et al., Ab initio study of energy, structure and dynamics of the water-carbon dioxide complex. J. Chem. Phys. 109, 3919 (1998)... 

If the first bond can for whatever reason only be of the nonhelical (disordered) kind, then a helical polymer has to be nucleated if this nonhelical bond represents an excited state, so g > 0. The size of the critical nucleus depends in that case on how favorable the helical bond is relative to the nonhelical bond, in other words, on how strongly negative h is, and on the frustration free energy / > 0 because there is at least one monomer involved in two types of bonding. Within the model, the assemblies of size 2 < N <2-(j + g)/(g + h) with h < — g < 0 are high-energy structures and are therefore statistically suppressed. 

Energy Structure and Reactivity , ed. D. W. Smith and W. B. McRae, John Wiley, New York,... 

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