Changes, conformational

Ligand Conformational Changes.— The hWWW -tetramethylethylenediamine complex [Mo(CO)4(tmeda)] undergoes a conformational change interconverting axial and equatorial ring substituents with activation parameters AG =38.8 4.6 kJ 

Investigations of racemization and ligand exchange reactions of manganese complexes [Mn(7j -C5H4R)L L L ] have continued and more evidence to support a dissociative mechanism with a chiral three-co-ordinate intermediate has been obtained. Reaction (1) is so slow that chiral four-co-ordinate alkyl intermediates formed by carbonyl 

Substitution and CO exchange in six-co-ordinate complexes cis-[MBr(CO)4L] (M = Mn or Re, L=PPh3, P(OR)2, or py] occur via a five-co-ordinate intermediate which is subject to rapid intramolecular rearrangement during its lifetime. The species [MX(CO)5] (M = Mn or Re, X=H or I) are stereochemically rigid on the n.m.r. time-scale over a range of temperatures, as are similar iron-group complexes 

In the heterobimetallic complexes [(CO)3Fe(y -C7H7)M(CO) l (M=Mn or Re, = 3 M=Rh, n=2) rapid ring whizzing of the C7H7 ligand and local carbonyl exchange at M(CO)a units occur but no intermetallic interchan of carbonyl groups is observed.  

General.—Intramolecular rearrangements of trigonal-bipyramidal complexes [M P(OR)3 s] (M=Fe, Ru, or Os) have been studied and some activation parameters are listed in Table 2. The trends are consistent with previous results from 

The ability to create molecular level actuators has been taken even further in the example of thiophene-based molecular muscles by Madden and Hunter. Conformational rearrangement of the polymer backbone in molecules such as calix[4]arene-bithiophene was created at the molecular level [118]. This work has recently been reviewed and prospects for future research in this area considered [119]. 

If the metal ion to which a ligand is co-ordinated is in a non-zero oxidation state, it will exert an electrostatic effect upon the bonding electrons of the ligand. This will result in the induction of a net permanent dipole in the ligand, with any associated chemical and physical effects. Even zero-oxidation state metal centres may induce a polarisation in the ligand through electronegativity or induced dipole-dipole effects. 

The introduction of 7i-bonding interactions between the metal and the ligand results in a metal-to-ligand or ligand-to-metal transfer of electron density. This occurs in accord with the electroneutrality principle, and in many cases, it opposes the polarisation effects of the metal ion. Furthermore, the effect will be expressed in orbitals possessing rather specific symmetry properties which may play important roles in the reactivity of the ligands. 

Before we consider the ways in which these effects may be expressed, it is worth mentioning that a number of other classification schemes have been developed to explain the reactivity of co-ordinated ligands. These schemes are most often based upon the observed reactivity of the co-ordinated ligand, and as such are rather more complex than the simple scheme presented above, which is derived from a consideration of the origins of the interaction. For further details of these, the reader is referred to the suggestions for further reading at the end of this chapter. 

What are the ways in which co-ordination to a metal ion may affect the conformation of a ligand, and what are the consequences of these changes The simplest effect is expressed in the ground state equilibrium geometry of the co-ordinated ligand. The bond 

The term conformation (Koenig, 1980) is used to describe the spatial arrangements of various atoms in a molecule that may occur because of rotations about single bonds. The planar cis and planar trans conformations of a n-butane molecule produced by rotations about the bond joining carbons 2 and 3 are illustrated in Fig. 

For a polymer, the above type of steric interactions occur at a local level in short sequences of chain segments, the conformation about a given chain segment being, however, dependent upon the conformations about the segments on either side to which it is directly coimected. Such interdependent steric restrictions influence the local chain conformations all along the polymer chain and thus affect its shape and size. 

The short-range interactions, as shown above, are important in determining the relative probabilities of existence of different conformations in a polymer chain. Thus the ratio of the number of trans (nt) to gauche (jig) states is given by 

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Muller D J, Baumeister W and Engel A 1996 Conformational change of the hexagonally packed intermediate layer of Deinococcus radiodurans monitored by atomic force microscopy J. Bactehol. 178 3025... 

Van Tassel P R, Guemourl L, Ramsden J J, Tar]us G, VIot P and Talbot J 1998 A model for the Influence of conformational change on protein adsorption kinetics J. Colloid Interfaoe Sc/. 207 317-23... 

Van Aalten, D.M.F., Findlay, J.B.C., Amadei, A., Berendsen,H.J.C. Essential dynamics of the cellular retinol-binding protein. Evidence for ligand-induced conformational changes. Protein Engin. 8 (1995) 1129-1136. 

Hayward, S., Berendsen, H.J.C. Systematic analysis of domain motions in proteins from conformational change New results on citrate synthase and T4 lysozyme. Proteins 30 (1998) 144-154. 

Schlitter et al., 1993] Schlitter, J., Engels, M., Kruger, P., Jacoby, E., and Wollmer, A. Targeted molecular dynamics simulation of conformational change - application to the t <- r transition in insulin. Molecular Simulation. 10 (1993) 291-308... 

The classical microscopic description of molecular processes leads to a mathematical model in terms of Hamiltonian differential equations. In principle, the discretization of such systems permits a simulation of the dynamics. However, as will be worked out below in Section 2, both forward and backward numerical analysis restrict such simulations to only short time spans and to comparatively small discretization steps. Fortunately, most questions of chemical relevance just require the computation of averages of physical observables, of stable conformations or of conformational changes. The computation of averages is usually performed on a statistical physics basis. In the subsequent Section 3 we advocate a new computational approach on the basis of the mathematical theory of dynamical systems we directly solve a... 

These results allows us to connect the observed hysteresis to the conformational changes in the NA molecule and consider it not as a macroscopic phenomenon like capillary hysteresis, but as natural property of the NA-water system. Our experimental and numerical results are in agreement with the data of other authors [13], [12], [14]. 

The Cyc conformer represents the structure adopted by the linear peptide prior to disulfide bond formation, while the two /3-turns are representative stable structures of linear DPDPE. The free energy differences of 4.0 kcal/mol between pc and Cyc, and 6.3 kcal/mol between pE and Cyc, reflect the cost of pre-organizing the linear peptide into a conformation conducive for disulfide bond formation. Such a conformational change is a pre-requisite for the chemical reaction of S-S bond formation to proceed. 

The first chapter, on Conformational Dynamics, includes discussion of several rather recent computational approaches to treat the dominant slow modes of molecular dynamical systems. In the first paper, SCHULTEN and his group review the new field of steered molecular dynamics (SMD), in which large external forces are applied in order to be able to study unbinding of ligands and conformation changes on time scales accessible to MD... 

Molecules should never be treated as static systems which are not able to undergo conformational changes. 

Reduce the possibility of undesired conformational changes during a molecular dynamics simulation. 

Limiting Conformational Changes during High Temperature Simulations... 

High temperature searches of conformational space (see Quenched Dynamics" on page 78), can produce unwanted conformational changes, such as cis-tmnx peptide flips, ring inversions, and other changes that you cannot reverse easily by geometry optimization. You can use restraints to prevent these changes. 

Conformational Changes from IVlolecular Dynamics Simulations... 

The regioselectivity benefits from the increased polarisation of the alkene moiety, reflected in the increased difference in the orbital coefficients on carbon 1 and 2. The increase in endo-exo selectivity is a result of an increased secondary orbital interaction that can be attributed to the increased orbital coefficient on the carbonyl carbon ". Also increased dipolar interactions, as a result of an increased polarisation, will contribute. Interestingly, Yamamoto has demonstrated that by usirg a very bulky catalyst the endo-pathway can be blocked and an excess of exo product can be obtained The increased di as tereo facial selectivity has been attributed to a more compact transition state for the catalysed reaction as a result of more efficient primary and secondary orbital interactions as well as conformational changes in the complexed dienophile" . Calculations show that, with the polarisation of the dienophile, the extent of asynchronicity in the activated complex increases . Some authors even report a zwitteriorric character of the activated complex of the Lewis-acid catalysed reaction " . Currently, Lewis-acid catalysis of Diels-Alder reactions is everyday practice in synthetic organic chemistry. 

Many stereoselective reactions have been most thoroughly studied with steroid examples because the rigidity of the steroid nucleus prevents conformational changes and because enormous experience with analytical procedures has been gathered with this particular class of natural products (J. Fried, 1972). The name steroids (stereos (gr.) = solid, rigid) has indeed been selected very well, if one considers stereochemical problems. We shall now briefly point to some other interesting, more steroid-specific reactions. 

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