Intramolecular interaction energy

Isolated Linear Molecule Figure 6 shows the error in total energy for an isolated linear molecule H-(-C=C-)5-H. It is obvious that for the same level of accuracy, the time step in the SISM can be ten times or more larger as in the LFV. Furthermore, the LFV method is stable for only very short time steps, up to 5 fs, while the SISM is stable even for a time step up to 200 fs. However, such large time steps no longer represent physical reality and arc a particular property identified with linear molecules without bending or torsional intramolecular interactions. 

Suppose we are using an empirical energy function such as the following to describe the inter- and intramolecular interactions in our ethanol/ethane thiol system ... 

Once the model of a ligand-receptor complex is built, its stability should be evaluated. Simple molecular mechanics optimization of the putative ligand-receptor complex leads only to the identification of the closest local minimum. However, molecular mechanics optimization of molecules lacks two crucial properties of real molecular systems temperature and, consequently, motion. Molecular dynamics studies the time-dependent evolution of coordinates of complex multimolecular systems as a function of inter- and intramolecular interactions (see Chapter 3). Because simulations are usually performed at nonnal temperature (—300 K), relatively low energy barriers, on the order of kT (0.6 kcal), can... 

The rapid rise in computer power over the last ten years has opened up new possibilities for modelling complex chemical systems. One of the most important areas of chemical modelling has involved the use of classical force fields which represent molecules by atomistic potentials. Typically, a molecule is represented by a series of simple potential functions situated on each atom that can describe the non-bonded interaction energy between separate atomic sites. A further set of atom-based potentials can then be used to describe the intramolecular interactions within the molecule. Together, the potential functions comprise a force field for the molecule of interest. 

Molecules with polar atoms or charged groups can form intramolecular interactions such as internal H-bonds or cation-rr interactions. As a consequence energy minimization in vacuo often results in electrostatically collapsed conformations due to the dominance of these intramolecular interactions. Several compounds in... 

Gresh N, Claverie P, Pullman A (1984) Theoretical studies of molecular conformation. Derivation of an additive procedure for the computation of intramolecular interaction energies. Comparison with ab initio SCF computations. Theor Chim 66(l) l-20... 

The capability of 2-hydroxybenzophenone derivatives to dissipate light energy has been ascribed to rapid deactivation of the excited singlet state by intramolecular interaction between the carbonyl and hydroxyl groups, possibly involving reversible H-transfer. These proposals are outlined in Scheme I, where P and PP represent the polymer and photoproduct, respectively. 

An alternative approach to calculating the free energy of solvation is to carry out simulations corresponding to the two vertical arrows in the thermodynamic cycle in Fig. 2.6. The transformation to nothing should not be taken literally -this means that the perturbed Hamiltonian contains not only terms responsible for solute-solvent interactions - viz. for the right vertical arrow - but also all the terms that involve intramolecular interactions in the solute. If they vanish, the solvent is reduced to a collection of noninteracting atoms. In this sense, it disappears or is annihilated from both the solution and the gas phase. For this reason, the corresponding computational scheme is called double annihilation. Calculations of... 

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