Molecular mechanics analysis

Conversely, processes which convert carbons to sfp- carbons are more favorable for five-membered than for six-membered rings. This can be illustrated by the data for acetolysis of cyclopentyl versus cyclohexyl tosylate. The former proceeds with an enthalpy of activation about 3kcal/mol less than the latter." A molecular mechanics analysis found that the difference was largely accounted for by the relief of torsional strain in the cyclopentyl case." Notice that there is an angle-strain effect which is operating in the opposite direction, since there will be some resistance to the expansion of the bond angle at the reaction center to 120° in the cyclopentyl ring. 

C. E. Sansom, J. Wu, and 1. T. Weber, Molecular mechanics analysis of inhibitor binding... 

For the case of catalytic model sites based on metallocenes 23, a detailed molecular mechanics analysis has also been conducted for the case of primary or secondary propene insertions on secondary polypropylene chains... 

The preinsertion intermediates of our molecular mechanics analysis (when different from the coordination intermediates) would correspond to situations closer to the transition state for the insertion reactions. For an easier comparison, the labels (a-e) used for coordination and preinsertion intermediates in Figures 1.7a and b are also reported close to the schematic energy plots of Figures 1.11a and b, respectively. 

A second example relates to the complex bis(l,5-diazacyclooctane)nickel(II) (Fig. 6.6). A crystal structure analysis of this complex revealed apparently planar NCCCN moieties with unusual bond lengths and angles 231. A molecular mechanics analysis of the same complex showed that these moieties are puckered and concluded that the crystal structure result was a consequence of conformational disorder, the refined geometry corresponding to an average of two puckered conformations (see Fig. 6.6)T24]. 

As often is the case (see Chapter 2, Sections 2.2.6 and 2.7), the molecular mechanics analysis above does not include any electrostatic interaction energies. To include these, the charge distribution and the charge compensation by ion-pairing to counter ions (perchlorate) have to be known. Model calculations indicate that an effective charge of around +1.6 per copper site, a value that is expected from thermodynamic considerations, leads to electrostatic repulsion energies of ca. 17 kJ mol-1 and 10 kJ mol-1, respectively, for the folded and stretched conformers. In agreement with the experiment (EPR spectra), this qualitative analysis indicates a preference for the folded structure of A, and for the stretched structure of B1 201. 

Cryptands such as [222] (Fig. 14.2) have been subjected to molecular mechanics analysis using two different approaches. In the first of these, the conformational preferences of [222] alone and in the presence of the alkali metal cations were investigated... 

Experimental or theoretical delineation of the number of conformers of a system and of the population of each conformer. Also used to describe a molecular mechanics analysis of the conformers (see molecular mechanics). 

A detailed molecular mechanics analysis of model catalytic sites has rationalised these observed behaviours for homogeneous propylene isospecific polymerisation catalysts based on bridged rac.-metallocene [357], It is interesting that, in contrast to the discussed case of enantioselectivity of the models for the primary insertion of propylene, the enantioselectivity of the models for the secondary insertion of propylene is due to direct interactions of the... 

In one of the last transformations in a multistep synthesis of 1,2-dihydro-8-ep/-vernolepin (43), nucleophilic intramolecular substitution at an iodomethyl group was promoted by heating an ester precursor with an equivalent of NaOAc in DMF (Equation (18)) <95TL3ii>. Molecular mechanics analysis of the precursor produced a minimum energy conformer that showed the hydroxyl substituent too distant from the iodomethyl group to have interfered with this high yield transformation. 

Dinur, U., Bond contraction atul spectral blue-shift in hydrogen-bonded dimers. An atom-based molecular mechanics analysis, Chem. Phys. Lett. 192, 399 06 (1992). 

Studies of the mechanism of stereoselective synthesis of quadridentate open-chain ligands by copper(II)-directed condensation of amino acids have included molecular mechanics analysis of possible intermediates. From racemic aniline, the only condensation product detected for [Cu(2,5,8-trimethyl-5-nitro-3,7-diazanonanedioate)] was the (2R, 85) isomer. A model was proposed to explain this selectivity. With a racemic amino acid, one side is blocked, as shown in Figure 11. Molecular mechanics calculations were performed with... 

Lin and Marks have considered olefin insertion into the actinide-hydrogen bonds of Cp2An(H)(OR) complexes [Cp = ti -(CH3)5C5 An = Th, U R = achiral or chiral group].Calculations included molecular mechanics analysis of the interaction of Cp U(H) [l(S)-entfo]-bornoxide with norbor-nene. The DREIDING and MMP2 force fields were used to calculate the relative energetics of olefin approach trajectories toward the U center. Three reaction pathways were considered. The authors note that whereas this method is approximate, the energetically favored pathway corresponds to the stereo-chemically favored course of the reaction. 

Here we present the results of P3 studies of the VDEs of the most stable conformation of a dinucleotide—2, 2 -deoxyribodithymidine-3, 5 -monophosphate anion (dDTMP- or dTT-). The choice of this particular dinucleotide was dictated by (1) the availability of electrospray photodetachment photoelectron spectroscopy data, (2) the relatively small size of dTT-, and (3) the lack of tautomeric transitions in the parent nucleobase, thymine. The structure depicted in Figure 1 seems to be a global minimum. It was found among numerous conformations of dTT- by means of, first, molecular mechanics analysis and, second, reoptimization of the structures with the B3LYP/ 6-311 + + G model. The structure shown in Figure 1 is characterized by two H bonds between one of the phosphate oxygens and the two... 

Use of diisopinocampheyl boron chloride in place of the triflate affords E(0)-enolates, but the isopinocampheyl ligands were ineffective for anti aldol reactions [48]. Encouraged by the molecular mechanics analysis of the ZfOj-enolate additions, Gennari and Paterson used computational methods to design a new boron ligand for use with E(G)-enolates [97]. The design was cued by Still s comment [98] that cis-2-... 

Simple molecular models of budotitane suggested that the trans isomers are sterically preferred, and that the stabilization of the cis configurations is due to p -dn bonding [323, 324]. However, the molecular mechanics analysis shows that the assumption that the trans isomers are less strained than the cis configurations is in error. 

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