Interactions intramolecular

The effect was easiest to study first in intramolecular cases because this allows NMR to be used to best effect. Complex 5 proved to be a useful test bed so as to get some idea of the energetics of the interaction. 

Our NMR method for estimating the H -H bond energy involves looking at the C-NH2 rotation barrier by variable temperature NMR in species such as 5. In the transition state for 5 5, shown in Equation 2, the H- H bond is broken 

We suggested fast relaxation as a criterion for the presence of close H-H distances in dihydrogen complexes, and Morris et and our own group have detected a substantial excess relaxation for H -H bonding. Making the usual assumptions, the excess in cases such as 5 and 6 can be interpreted in terms of an H- H distance of about 1.8 A in all the cases studied, a value consistent with the structural data in related systems. 

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V (the potential) is identified with the enthalpy, i.e. the number n of base pairings (contacts), and T corresponds to the entropy. At each stage in the folding process, as many as possible new favourable intramolecular interactions are fonned, while minimizing the loss of confonnational freedom (the principle of sequential minimization of entropy loss, SMEL). The entropy loss associated with loop closure is (and the rate of loop closure exp... 

Page, M. L., Jencks, W. P. Entropic contributions to rate accelerations in enzymic and intramolecular interactions and the chelate effect. Proc. Natl. Acad. Sci. USA 68 (1971) 1678-1683... 

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 However, such large time steps no longer represent physical reality and arc a particular property identified with linear molecules without bending or torsional intramolecular interactions. 

Z-matriccs arc commonly used as input to quantum mechanical ab initio and serai-empirical) calculations as they properly describe the spatial arrangement of the atoms of a molecule. Note that there is no explicit information on the connectivity present in the Z-matrix, as there is, c.g., in a connection table, but quantum mechanics derives the bonding and non-bonding intramolecular interactions from the molecular electronic wavefunction, starting from atomic wavefiinctions and a crude 3D structure. In contrast to that, most of the molecular mechanics packages require the initial molecular geometry as 3D Cartesian coordinates plus the connection table, as they have to assign appropriate force constants and potentials to each atom and each bond in order to relax and optimi-/e the molecular structure. Furthermore, Cartesian coordinates are preferable to internal coordinates if the spatial situations of ensembles of different molecules have to be compared. Of course, both representations are interconvertible. 

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 ... 

The systematic study of piezochromism is a relatively new field. It is clear that, even within the restricted definition used here, many more systems win be found which exhibit piezochromic behavior. It is quite possible to find a variety of potential appUcations of this phenomenon. Many of them center around the estimation of the pressure or stress in some kind of restricted or localized geometry, eg, under a localized impact or shock in a crystal or polymer film, in such a film under tension or compression, or at the interface between bearings. More generally it conveys some basic information about inter- and intramolecular interactions that is useful in understanding processes at atmospheric pressure as well as under compression. 

Proper condensed phase simulations require that the non-bond interactions between different portions of the system under study be properly balanced. In biomolecular simulations this balance must occur between the solvent-solvent (e.g., water-water), solvent-solute (e.g., water-protein), and solute-solute (e.g., protein intramolecular) interactions [18,21]. Having such a balance is essential for proper partitioning of molecules or parts of molecules in different environments. For example, if the solvent-solute interaction of a glutamine side chain were overestimated, there would be a tendency for the side chain to move into and interact with the solvent. The first step in obtaining this balance is the treatment of the solvent-solvent interactions. The majority of biomolecular simulations are performed using the TIP3P [81] and SPC/E [82] water models. 

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... 

Weak intramolecular interactions between sulfur or selenium and nitrogen are a recurrent phenomenon in large biomolecules. They may occur in the same residue or between neighbours of a peptide chain. The formation of four- or five-membered rings of the types 15.1 and 15.2, respectively, is most common. A feature that is unique to proteins is the participation of sulfur atoms in bifurcated N S N contacts. 

The involvement of a chalcogen atom in an intramolecular interaction may influence the reactivity of the chalcogen centre as a result of steric or electronic effects. This feature may lead to unique reaction patterns. Eor example, the sulfur(II) centre involved in an intramolecular contact... 

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. 

The combination of positive and negative charges within the same molecule causes a more complicated situation, which obviously has not been well-defined to date. A quite large number of pyrrolizidine alkaloids are related to Otonecine (8) (Scheme 3). Spectroscopic investigations show that these alkaloids exist in the nonionized form in CDCI3, and in the zwitterionic form in D2O (00JNP857, 71TL3421). The dipolar structure is the result of an intramolecular interaction between a nucleophilic and an electrophilic center. 

The alternate schemes that have been developed for achieving removal of the side chain similarly depend on intramolecular Interaction of some derivative of the amine with the amide oxygen to afford some easily hydrolyzed intermediate at an oxidation stage analogous to... 

The biological function of biopolymers such as polypeptides, proteins, nucleic acids etc. depends strongly on their ordered structure which is determined by the pattern of inter- and intramolecular interactions given by the primary structure. 

The structure of the chain, i.e., whether it is a helix or a random coil, might influence not only the rate but also the stereospecificity of the growing polymer. For example, it is plausible to expect that in normal vinyl polymerization helix formation might favor specific placement, say isotactic, while either placement would be approximately equally probable in a growing random coil. Formation of a helix requires interaction between polymer segments, and this intramolecular interaction is enhanced by bad solvents particularly those which precipitate the polymer. 

Another way in which the function of adaptor proteins is regulated is through modulation of intramolecular interactions. Often one domain will bind to another domain in the same adaptor molecular, preventing... 

Small Ubiquitin-like modifier (SUMO) is a conserved protein that is ubiquitously expressed in eukaryotes and is essential for viability. It serves as a reversible posttranslational modifier by forming an isopeptide bond with lysine residues in many target proteins, in a catalytic process termed SUMOylation. SUMOylation of proteins results in altered inter- or intramolecular interactions of the modified target (Fig. 1). 

The current understanding on activation of Tec kinases fits into a two-step model. In the first step an intramolecular interaction between the SH3 domain and aproline-rich region in the TH domain is disrupted by binding ofthe PH domain to phosphoinositides, G protein subunits, or the FERM domain of Fak. These interactions lead to conformational changes of Tec and translocation to the cytoplasmic membrane where, in a second step, Src kinases phosphorylate a conserved tyrosine residue in the catalytic domain thereby increasing Tec kinase activity. Autophosphorylation of a tyrosine residue in the SH3 domain further prevents the inhibitory intramolecular interaction resulting in a robust Tec kinase activation. 

For this kind of cooperative processes, it is characteristic that the formation of the nucleus is thermodynamically more difficult than for further propagation steps (positive cooperativity). This implies that the elementary transition step of an individual chain segment (tripeptide unit) is influenced by the state of adjacent segments through intramolecular interactions. 

However, in more recent years it has become usual to employ ar or crR-type constants, either together in the dual substituent-parameter equation or individually in special linear regression equations which hold for particular infrared magnitudes. In this connection a long series of papers by Katritzky, Topsom and their colleagues on Infrared intensities as a quantitative measure of intramolecular interactions is of particular importance. We will sample this series of papers, insofar as they help to elucidate the electronic effects of sulfinyl and sulfonyl groups. 

Table 6. Total Lattice Sums for Trans and Gauche Conformations in PET and Contributions from Intramolecular Interactions...

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