Interaction intermolecular/intramolecular

Potential functions such as MM+ discussed in Chapter 1 are fine for intramolecular interactions. MD was developed long before such sophisticated force fields became available, and in any case the aims of MM and MD simulations tend to be quite different. MM studies tend to be concerned with the identification of equihbrium geometries of individual molecules whilst MD calculations tend to be concerned with the simulation of bulk properties. Inspection of Figure 2.2 suggests that the intramolecular details ought to be less important than the intermolecular ones, and early MD studies concentrated on the intermolecular potential rather than the intramolecular one. 

Here, is the magnetization of spin i at thermal equilibrium, p,j is the direct, dipole-dipole relaxation between spins i and j, a-y is the crossrelaxation between spins i and j, and pf is the direct relaxation of spin i due to other relaxation mechanisms, including intermolecular dipolar interactions and paramagnetic relaxation by dissolved oxygen. Under experimental conditions so chosen that dipolar interactions constitute the dominant relaxation-mechanism, and intermolecular interactions have been minimized by sufficient dilution and degassing of the sample, the quantity pf in Eq. 3b becomes much smaller than the direct, intramolecular, dipolar interactions, that is. 

This simple relation rests on literal validity of both the intermolecular and the intramolecular interaction theories hence its unqualified acceptance is open to question). 

It is located on a crystallographic mirror plane that lies perpendicular to the molecular plane. Each CTC is planar with gold-gold intramolecular interactions of 3.309(2) and 3.346(3) A. The intermolecular Au Au contacts are shorter than the intramolecular Au -Au contacts and fall in the range 3.105(2)-3.143(3)A. Both CTC complexes [ t-N, C -pyAu]3 and [ t-C(OMe)=N(C6Hn)Au]3 form dimers with a chair conformation of the gold atoms, but complex [ t-N, C -pyAu]3 is further assembled by the apical gold atoms of the chairs to form extended stepwise chains. 

The difference between the log P of a given compound in its neutral form (log P ) and its fully ionized form (log P ) has been termed dialog P ) and contains series-specific information, and expresses the influence of ionization on the intermolecular forces and intramolecular interactions of a solute [44, 51, 52]. 

The stability of a trivial assembly is simply determined by the thermodynamic properties of the discrete intermolecular binding interactions involved. Cooperative assembly processes involve an intramolecular cyclization, and this leads to an enhanced thermodynamic stability compared with the trivial analogs. The increase in stability is quantified by the parameter EM, the effective molarity of the intramolecular process, as first introduced in the study of intramolecular covalent cyclization reactions (6,7). EM is defined as the ratio of the binding constant of the intramolecular interaction to the binding constant of the corresponding intermolecular interaction (Scheme 2). The former can be determined by measuring the stability of the self-assembled structure, and the latter value is determined using simple monofunctional reference compounds. 

Intermolecular Interactions and Long-Range Intramolecular Interactions... 

The intermolecular interactions and long-range intramolecular interactions are incorporated via a pair-wise interaction potential. All pairs of beads from... 

In order to ensure accurate CG potentials, one needs to conduct MD simulations with a reliable atomistic potential model. The most desirable theoretical approach for the atomistic-scale simulations would be to use a level of quantum mechanics (QM) that can treat both intermolecular and intramolecular interactions with acceptable accuracy. Realistically, the minimal QM levels of theory that can adequately treat all different types of chemical forces are second order perturbation theory [32] (MP2)... 

As the temperature is decreased, the chains become increasingly rigid zc then approaches 1 if we assume that there is only one fully ordered crystalline structure and Zconf for the liquid becomes smaller than 1. This means that, at this level of approximation, the disordered state becomes less favorable than the crystalline ground state. A first-order disorder-order phase transition is expected to occur under these conditions. Flory interpreted this phase transition as the spontaneous crystallization of bulk semiflexible polymers [12], However, since the intermolecular anisotropic repulsion essential in the Onsager model is not considered in the calculation, only the short-range intramolecular interaction is responsible for this phase transition. 

Functions and partly also constants for nonbonded interactions within single molecules (intramolecular interactions) have been taken over in many cases from investigations of interactions between different molecules (intermolecular interactions) (7,3). The derivation of parameters for nonbonded interactions presents further difficulties, e.g. the problem of the anisotropy of such interactions (8, 23) and parameter correlations (Section 2.4.). There is no agreement on the question whether pairs of atoms separated by a chain of only three bonds should be counted as nonbonded interactions. Some authors include these pairs,... 

The SH3 domain consists of approximately 60 amino acid residues and is C-terminal to the unique domain. Its five P strands form a globular structure whose N- and C-termini are in proximity to each other. SH3 domains mediate both intermolecular and intramolecular interactions, targeting short amino acid sequences that consist of specific proline-rich motifs in a left-handed helix - polyproline... 

The favorable bismuth-sulfur bond translates into thermal and hydrolytic stability for the thiolates of bismuth, which are currently more numerous than the alkoxide derivatives (Table II). Various monomeric trithiolates have been identified, and most adopt predictable structural formulas, although the solid-state structures reveal interesting intermolecular and intramolecular interactions. 

The important result of the LIESST experiments in (bt, S) is that the pho-toinduced species are not only [HS-LS] but also [HS-HS] pairs. The appearance of [HS-LS] species should be interpreted in terms of a synergy between intramolecular and intermolecular cooperative interactions which energetically stabilise the mixed pairs. However, the time dependent measurements (Fig. 14) reveal that [HS-HS] pairs are unstable and revert with time to both [HS-LS] and [LS-LS] configurations [17]. This observation is important in the comparative analysis of the two-step transition in (bt, S) (see Sect. 6). 

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