Molecular mechanics electrostatic interactions

As a further mechanism, electrostatic interactions of anionic lipids with cationic compounds may also induce domain formation. Due to the biochemical complexity of biological membranes, the molecular mechanisms responsible for phase separation are not easily distinguished experimentally. 

Electrostatic terms other than the simple charge interactions above are commonly included in molecular mechanics calculations. particularly dipole-dipole interactions. More recently, second-order electrostatic interactions like those describing polarizability have been added to some force fields. 

Molecular mechanics methods may work well or poorly for compounds containing alkali metals. The crucial factor is often how the force field computes charges for electrostatic interactions. 

Before running a molecular dynamics simulation with solvent and a molecular mechanics method, choose the appropriate dielectric constant. You specify the type and value of the dielectric constant in the Force Field Options dialog box. The dielectric constant defines the screening effect of solvent molecules on nonbonded (electrostatic) interactions. 

Absorption, metaboHsm, and biological activities of organic compounds are influenced by molecular interactions with asymmetric biomolecules. These interactions, which involve hydrophobic, electrostatic, inductive, dipole—dipole, hydrogen bonding, van der Waals forces, steric hindrance, and inclusion complex formation give rise to enantioselective differentiation (1,2). Within a series of similar stmctures, substantial differences in biological effects, molecular mechanism of action, distribution, or metaboHc events may be observed. Eor example, (R)-carvone [6485-40-1] (1) has the odor of spearrnint whereas (5)-carvone [2244-16-8] (2) has the odor of caraway (3,4). 

Theoretical studies aimed at rationalizing the interaction between the chiral modifier and the pyruvate have been undertaken using quantum chemistry techniques, at both ab initio and semi-empirical levels, and molecular mechanics. The studies were based on the experimental observation that the quinuclidine nitrogen is the main interaction center between cinchonidine and the reactant pyruvate. This center can either act as a nucleophile or after protonation (protic solvent) as an electrophile. In a first step, NH3 and NH4 have been used as models of this reaction center, and the optimal structures and complexation energies of the pyruvate with NH3 and NHa, respectively, were calculated [40]. The pyruvate—NHa complex was found to be much more stable (by 25 kcal/mol) due to favorable electrostatic interaction, indicating that in acidic solvents the protonated cinchonidine will interact with the pyruvate. 

Hartree-Fock, DFT or CCSD levels. Because they can reproduce such quantities, APMM procedures should account for an accurate description of the interactions including polarization cooperative effects and charge transfer. They should also enable the reproduction of local electrostatic properties such as dipole moments an also facilitate hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) embeddings. 

As the SIBFA approach relies on the use of distributed multipoles and on approximation derived form localized MOs, it is possible to generalize the philosophy to a direct use of electron density. That way, the Gaussian electrostatic model (GEM) [2, 14-16] relies on ab initio-derived fragment electron densities to compute the components of the total interaction energy. It offers the possibility of a continuous electrostatic model going from distributed multipoles to densities and allows a direct inclusion of short-range quantum effects such as overlap and penetration effects in the molecular mechanics energies. 

Gresh N, Piquemal J-P, Krauss M (2005) Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contribution of the intermolecular interaction energy. Comparisons with parallel ab initio computations. J Comput Chem 26 1113... 

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