Cyclohexane force field calculation

Fig. 17. Calculated conformations (top and side views, drawn to scale) of cyclohexane (force field of ref. (79) outer values bond lengths in A and angles in degrees, inner values torsion angles). The quantities below the symmetry symbols are calculated A V- and AH-values (kcal mole-1 T = 298 K reference chair conformation)...

In 1968 Bartell published an article on the use of molecular models in the curriculum. In this paper the qualitative valence shell electron pair repulsion (VSEPR) model and the relative role of bonded and nonbonded interaaion in directed valence is discussed. The author correctly predicted the increasing importance of model force fields for geometry prediction. An early discussion of the use of molecular mechanics in teaching can be found in a paper by Cox. 07 A cursory description of the methodology of force field calculations is presented, along with computational results on the relative energy of the rotamers of butane and the conformers of cyclohexane. 

Alder RW, Sessions RB (1985) Force Field Calculations on Molecular Belts built from Cyclohexane -1,4-diene Rings. J Chem Soc Perkin Trans II 1849... 

In a similar way the potential constant method as described here allows the simultaneous vibrational analysis of systems which differ in other strain factors. Furthermore, conformations and enthalpies (and other properties see Section 6.5. for examples) may be calculated with the same force field. For instance, vibrational, conformational, and energetic properties of cyclopentane, cyclohexane and cyclodecane can be analysed simultaneously with a single common force field, despite the fact that these cycloalkanes involve different distributions of angle and torsional strain, and of nonbonded interactions 8, 17). This is not possible by means of conventional vibrational spectroscopic calculations. 

We conclude the above methodical discussion by giving a few details of the calculation (with the help of our alkene/alkane force field (19)) of conformational transitions of cyclohexane (39). 

Exhaustive catalytic hydrogenation of triptycene affords an equilibrium mixture of perhydrotriptycene isomers. As expected, Boyd s force field (37) calculations, with a modified torsional constant, reproduced the observed composition fairly well (Table 6). All important conformations were taken into account for each isomer. The most stable conformations agree with the results of the X-ray analysis (131) and have the characteristic that the cyclohexane rings are invariably either boat or deformed chair. The most stable conformation of all is 20 (ttt). The predominant conformation of ccc, in which all cyclohexane rings are boat, has an enthalpy only 2.56 kcal/mol above that of 20. The difference is virtually all due to angle and torsional terms. 

Dynamic NMR gives information on the number and symmetries of conformations present in solution and on the energy barriers separating these conformations. This is particularly true for systems with barriers between about 25 and 90 kJ mol-1, a situation which often occurs in the medium ring. The interpretation of the NMR data can be carried out by the examination of molecular models, but this is a relatively crude and sometimes misleading method. Empirical force field (or molecular mechanics) calculations are much superior, even though the parametrization of heteroatoms may be open to question. Quantum mechanical calculations are not very suitable the semiempirical type, e.g. MINDO, do not reproduce conformational properties of even cyclohexane satisfactorily, and the ab initio... 

These conclusions were based on the severe curvature of the plots of chemical shift against reaction field calculated from both the simple Onsager and the more complex Diehl and Freeman equations. Fontaine et al. have found similar curvature in plots of for acetone versus the Onsager reaction field of cyclohexane-acetone mixtures. Some interesting results recently obtained show that if e is substituted for the dielectric function (e —l)/(e- - ) of equation (5), the curvature of these plots is effectively removed, especially for protons near the dipole location in the large molecules studies by Laszlo and Musher. No explanation for the dependence of on e has been offered. Deviations from linearity in plots of versus in some haloethylenes are explained by the occurrence of excess dispersion forces in the solvents producing the deviations. 

FIGURE 6.2 Amino acid side chain analog insertion profiles with explicit (red) and implicit (purple, black) membrane models. The explicit lipid profiles were calculated with the OPLS force field [87], implicit profiles were calculated with both CHARMM [92] and OPLS force fields [93]. Experimental water-cyclohexane transfer free energies [85] are indicated as red dots. 

MaccaUum, J.L., Heleman, D.P. Calculation of the water-cyclohexane transfer free energies of neutral amino add side-chain analogs using the OPLS aU-atom force field, J. Comp. Chem. 2003, 24(15), 1930-5. 

In this study, n-hexane, n-hexadecane and cyclohexane are assumed as lubricants. The 3-D models of lubricants are shown in Figure 2. The intramolecular and intermolecular interactions are calculated using the OPLS-AA, optimized potentials for liquid simulations -all atom, force field potential [10,11]. In this force field, the potential energy function consists of harmonic bondstretching and angle-bending terms, a Fourier series for torsional energetics, and Coulomb and Lennard-Jones terms for the nonbonded interactions, as defined in eqs. (l)to(4). 

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