Bonding and nonbonding interactions

There are three types of interaction that result in atoms bonding together into more elaborate structures. Ionic bonds arise from the electrostatic attraction between cations and anions and give rise to typically hard, brittle arrays known as ionic solids . Covalent bonds are due to the sharing of electrons and are responsible for the existence of discrete molecules, such as HjO and elaborate proteins. Metallic bonds arise when atoms are able to pool one or more of their electrons into a common sea and give rise to metals with their characteristic lustre and electrical conductivity. 

Lewis structures of all but the simplest molecules do not show the shape of the molecule. A collection of rules known as valence-shell electron repulsion theory (VSEPR theory), in which regions of electron density (attached atoms and lone pairs) are supposed to adopt positions that minimize their repulsions, is often a helpful guide to the local shape at an atom, such as the tetrahedral arrangement of single bonds around a carbon atom. This theory should also be familiar from introductory chemistry courses. 

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They also treated 71 electron diffraction measurements involving both bonds and nonbonded interactions in the distance range 1.217 5.618 A and established... 

The initial series of simulations was performed for 0 < p < 1. Because the purpose of these simulations was to test the common assumption that the nonbonded interactions did not contribute to the deviatoric stress, the sum in Eq. (6) was separated as in Eq. (9) to show the bonded and nonbonded interactions explicitly. The first sum is over all atom pairs that interact through u/, the second is over all pairs that interact through unh. 

At the atomic level, the design of all materials begins with an understanding of the basic interatomic interactions. These bonding and nonbonding interactions set the framework for the material and define its physical and thermodynamic properties. 

Force Fields. The basic assumption underlying molecular mechanics is that classical physical concepts can be used to represent the forces between atoms. In other words, one can approximate the potential energy surface by the summation of a set of equations representing pairwise and multibody interactions. These equations represent forces between atoms related to bonded and nonbonded interactions. Pairwise interactions are often represented by a harmonic potential - 6q) ]... 

For a more detailed understanding of complex fluid molecules, a valence force field [54] representing many-body interactions is commonly used. In this approach, the potential energy of a system is expressed as a sum of valence (or bonded) and nonbonded interactions... 

Eq. (13) makes the distinction between bonded (interactions between atoms that are connected by no more than three bonds) and nonbonded (interactions between atoms that are not connected to each other at all) interactions. The nonbonded energy accounts for repulsion, van der Waals attraction, and electrostatic interactions, van der Waals attraction occurs at short range and rapidly dies off as the interacting atoms move apart by a few angstroms. Repulsion occurs when the distance between interacting atoms becomes even slightly less than the sum of their contact radii. 

The criteria for selecting a force field include the accuracy, transfer-ability and computational speed. A typical interaction potential U may consist of a number of bonded and nonbonded interaction terms ... 

A typical PEE used in biomolecular simulations consists of bonded and nonbonded interaction terms ... 

The SCFT is an approach in which the bonded and nonbonded interactions in a polymeric system are converted into a fidd theory, and the partition function of the overall system is reduced to the partition function of a single chain under the influence of one or more auxiliary potential Adds. The chain statistics are then described as those of a random walk under an average potential field. In prindple, any partide-based model can be converted to a field theory. The suitability of field and partide methods largdy depends on the system and the properties of interest. The SCFT is often applied in polymer modding and over the last decade it has become the standard computational tool. It is, therefore, worthwhile to spend some time on this approach here. 

Fukunaga H, Takimoto J, Doi M A coarse-graining procedure for flexible polymer chains with bonded and nonbonded interactions, / Chem Phys 116 8183—8190, 2002. 

In molecular systems, the potential energy function V(r) includes bonded interactions between atoms connected by chemical bonds, and nonbonded interactions between atoms of different molecules, or between atoms of the same molecule which are not chemically bonded, for example between the atoms of nonadjacent monomers of the same polymer chain. 

DPD does not restrict the form of the conservative force. Hence, it is easy to include various bonded and nonbonded interactions as conservative force for complex molecules. For the case of the chain-type molecule (e.g., polymer), a simple harmonic potential is used ... 

The reaction of previously reported compound [(Cp Nb)2(B2Hg)2] with elemental sulfur in decane afforded a trimetallic sulfido cluster [(Cp Nb)3SgB(SH)] [217]. In the solid-state structure, it reveals that three Nb atoms form an equilateral triangle, with edges spanned by the corners of a BS tetrahedron. The occupation of the two electrons of the three niobium core leads to the formation of equal M-M bonds of the formal bond order 2/3. This fact reflects through the Nb-Nb distances of 3.157(3) A, which are between bonding and nonbonding interactions. 

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