Noncovalent interactions, potential energy

These are potential energy descriptors accounting for the total noncovalent interaction potential energy, which determines the binding affinity of a molecule to the considered receptor. They are generally calculated as the pairwise sum of the interaction energies between each probe atom and each target atom as [Wade, 1993]... 

In a solution of a solute in a solvent there can exist noncovalent intermolecular interactions of solvent-solvent, solvent-solute, and solute—solute pairs. The noncovalent attractive forces are of three types, namely, electrostatic, induction, and dispersion forces. We speak of forces, but physical theories make use of intermolecular energies. Let V(r) be the potential energy of interaction of two particles and F(r) be the force of interaction, where r is the interparticle distance of separation. Then these quantities are related by... 

Methyl rotors pose relatively simple, fundamental questions about the nature of noncovalent interactions within molecules. The discovery in the late 1930s1 of the 1025 cm-1 potential energy barrier to internal rotation in ethane was surprising, since no covalent chemical bonds are formed or broken as methyl rotates. By now it is clear that the methyl torsional potential depends sensitively on the local chemical environment. The barrier is 690 cm-1 in propene,2 comparable to ethane,... 

The quantities defined by Eqs. (2)—(7) plus Vs max, Vs min, and the positive and negative areas, A and, enable detailed characterization of the electrostatic potential on a molecular surface. Over the past ten years, we have shown that subsets of these quantities can be used to represent analytically a variety of liquid-, solid-, and solution-phase properties that depend on noncovalent interactions [14-17, 84] these include boiling points and critical constants, heats of vaporization, sublimation and fusion, solubilities and solvation energies, partition coefficients, diffusion constants, viscosities, surface tensions, and liquid and crystal densities. 

The two possible coconformational isomers of such catenanes can be interchanged by appropriate stimuli. In a diagram of potential energy against rotation angle of the asymmetric macrocycle, the two coconformations correspond to energy minima, provided by the intercomponent noncovalent bonding interactions. The... 

Noncovalent interactions between the two separate molecules define, in the gas phase analogue of this reactive system, the preferential channels of approach (in the simpler cases there is just one channel leading to the reaction) with shape and strength determined only by these interactions. As a general rule, these channels carry the reactants to a stationary point on the potential energy surface called the initial reaction complex. 

Van der Waals interactions are noncovalent and nonelectrostatic forces that result from three separate phenomena permanent dipole-dipole (orientation) interactions, dipole-induced dipole (induction) interactions, and induced dipole-induced dipole (dispersion) interactions [46]. The dispersive interactions are universal, occurring between individual atoms and predominant in clay-water systems [23]. The dispersive van der Waals interactions between individual molecules were extended to macroscopic bodies by Hamaker [46]. Hamaker s work showed that the dispersive (or London) van der Waals forces were significant over larger separation distances for macroscopic bodies than they were for singled molecules. Through a pairwise summation of interacting molecules it can be shown that the potential energy of interaction between flat plates is [7, 23]... 

Some sample potential energy curves for covalent and noncovalent interactions between two atoms are given in Fig. 4.1. The left side shows an interaction curve for the two oxygen atoms in the 0, molecule. This has a large dissociation energy (about 117 kcal/ mol in this case), so that at room temperature where RT approximates 0.6 kcal/mol R is the universal gas constant and T is the absolute temperature), the fraction of "broken" bonds at equilibrium is very small. By con-... 

The size and complexity of extended biomacromolecules makes the understanding of the various energy contributions which contribute to their stabilization difficult, since only calculations using simple empirical potential calculations are tractable. Fortunately, the most importance biomacromolecules, DNA and proteins, consist of characteristic building blocks-the nucleic acid bases and amino acids-interacting through noncovalent interactions. The system can therefore be fragmented into smaller components, each of which can be described by means of ab initio quantum chemical methods. 

In the original CoMFA method only two fields of noncovalent ligand-receptor interactions were calculated the steric field that is a Lennard-Jones 6-12 potential function and the electrostatic field that is a Goulomb potential energy function. Usually, the two fields are kept separate to facilitate the interpretation of the final results. As steric and electrostatic... 

Another very important type of noncovalent interaction is that between solutes and solvents. We have developed GIPF relationships in which the free energies of solvation in seven different solvents, with various polarities, are expressed in terms of quantities characterizing the solute s molecular surface electrostatic potentials [153,154]. However, there have been many more elaborate treatments that explicitly evaluate the energy of the interaction between the solute and the solvent the latter may be described, e.g., as a dielectric continuum, as a fixed lattice, or in terms of individual molecules. Detailed accounts can be found in several reviews [23,155-158]. 

Van der Waals interactions, or noncovalent-bonded interactions, play an essential role of intermolecular interaction potentials in condensed matter physics, materials chemistry, and structural biology. These interactions are crucial for understanding and predicting the thermodynamic properties of liquids and solids [1], the energy transfers among molecular complexes [2], and the conformational tertiary structures of nanostructures. Intermolecular bonds do not originate from sharing of electrons... 

Flick, J. C., Kosenkov, D., Hohenstein, E. G Sherrill, C. D., and Slipchenko, L. V. (2012]. Accurate prediction of noncovalent interaction energies with the effective fragment potential method Comparison of energy components to symmetry-adapted perturbation theory for the S22 test set,/. Chem. Theory Comput 8, pp. 2835-2843, doi 10.1021/ct200673a. 

Takatani, T, and Sherrill, C. D. (2007). Performance of spin-component-scaled M0ller-Plesset theory (SCS-MP2) for potential energy curves of noncovalent interactions, Phys. Chem. Chem. Phys. 9, pp. 6106-6114, doi 10.1039/b709669k... 

The belief that electrostatic (Coulomb) interactions exhibit little directionality (i.e., that their energy hardly depends on the bond angle) is widespread. This is because the concept of net atomic charges (atom-centered monopoles) has become ingrained in chemists thinking, so that Coulomb interactions with a polar atom are believed to be necessarily isotropic and directionahty of Coulomb interactions only to be the result of secondary interactions with more distant atoms. Neither of these assumptions is correct and the reasons have been known for decades. Nonetheless, directionality in noncovalent interactions is still often attributed to covalent contributions or donor-acceptor interactions because the Coulomb interaction is believed not to be able to give rise to significant directionality. The purpose of this chapter is to discuss Coulomb interactions with special emphasis on directionality and anisotropy of the molecular electrostatic potential (MEP) [1] around atoms. 

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