Alcohols, ethers, carbohydrates, and related compounds. I. The MM4 force field for simple compounds

Abstract

Simple alcohols and ethers have been studied with the MM4 force field. The structures of 13 molecules have been well fit using the MM4 force field. Moments of inertia have been fit with rms percentage errors as indicated: 18 moments for ethers, 0.28%; 21 moments for alcohols, 0.22%. Rotational barriers and conformational equilibria have also been examined, and the experimental and ab initio results are reproduced substantially better with MM4 than they were with MM3. Much of the improvement comes from the use of additional interaction terms in the force constant matrix, of which the torsion-bend and torsion-torsion are particularly important. Induced dipoles are included in the calculation, and dipole moments are reasonably well fit. It has been possible for the first time to fit conformational energetic data for both open chain and cyclic alcohols (e.g., propanol and cyclohexanol) with the same parameter set. For vibrational spectra, over a total of 82 frequencies, the rms error is 27 cm(-1), as opposed to 38 cm(-1) with MM3. Both the alpha and beta bond shortening resulting from the presence of the electronegative oxygen atom in the molecule are well reproduced. The electronegativity of the oxygen is sufficient that one must also include not only the alpha and beta electronegativity effects on bond lengths, but also on angle distortions, if structures are to be well reproduced. The heats of formation of 32 alcohols and ethers were fit overall to within experimental error (weighted standard deviation error 0.26 kcal/mol).

Polarizable Empirical Force Field for the Primary and Secondary Alcohol Series Based on the Classical Drude Model

“…Hydroxyl groups located on tertiary carbon atoms are not common in biological macromolecules and, therefore, were not considered in this study. For the alcohol series the aliphatic carbon and hydrogen parameters previously determined in our laboratory 27 were applied directly with the exception of the electrostatic parameters on CH (1)(2)(3) fragments directly adjacent to the oxygen and of the LJ parameters for the methyl group in methanol. The remaining parameters were optimized as part of the present work.…”

“…Isothermal compressibilities were calculated from (3) according to Klauda et al,62 where V is the volume, 〈δV 2 〉 is the volume fluctuation, and k B is Boltzmann's constant. The slope of the mean squared displacement versus time was used to determine the self-diffusivity for the periodic boundary condition, D PBC .…”

Empirical force fields for biological macromolecules: Overview and issues

“…Recently, a MM4 force field for carbohydrates was reported. [283][284][285][286] This force field treats simple alcohols and ethers as well as a number of hexoses, although no tests on disaccharides have been preformed and, because the model was developed for the gas phase, its applicability for condensed phase simulations is unclear. Another example of a carbohydrate force field that is based on gas phase energies is that developed for the commercial CHARMm package 232 based on a variety of QM data.…”

“…Several force fields have addressed this problem directly. These include MMFF, 24,194 CVFF, 21,314 the commercial CHARMm force field, 232 CFF, 315 COMPASS, 316 the MM2/MM3/MM4 series, 16,283,317 UFF, 27 Dreiding, 26 the Tripos force field (Tripos, Inc.), among others. Typically, these force fields have been designed primarily to reproduce internal geometries, vibrations, and conformational energies, often sacrificing the quality of the nonbond interactions, 318 which are of obvious importance for accurately treating ligand-protein interactions.…”

Molecular Self‐Assembly of Jointed Molecules on a Metallic Substrate: From Single Molecule to Monolayer

“…[19] Contrary to the case of adsorbed rubrene molecules, whereby the intramolecular steric hindrance induces a twisted conformation of central tetracene backbone, [5] the VL board stays almost flat above the surface (Figure 1). With the MM4A C H T U N G T R E N N U N G (2003) force-field, [21] the physisorption energy is found to be around 145 kcal mol…”