Conformational sensitivity of polyether macrocycles to electrostatic potential: Partial atomic charges,molecular mechanics,and conformational prediction

Molecular recognition (whether by enzymes, the immune system, or chelating ligands) depends critically on molecular conformation. Molecular mechanics predicts energetically favorable molecular conformations by locating low energy conformations using an empirical fit of molecular potential energy as a function of internal coordinates. Molecular mechanics analysis of 18-crown-6 demonstrates that the nonbonded term (primarily the electrostatic part) is the largest contributor to the conformational energy. Nevertheless, common methods of treating the electrostatic interaction for 18-crown-6 yield inconsistent values for conformational energies partly because partial charges assigned to each atom can change with conformation due to through-space inductive effects which are not considered in most molecular mechanics programs. Similar findings from several other groups are reviewed to support our conclusions. We argue for care and caution in predicting conformational preferences of molecules with two or more highly polar atoms. We also discuss the desirability of using an empirical method of partial charge determination such as the charge equilibration algorithm of Rappé and Goddard (or a suitable generalization which includes polarization) as a method of including these effects in molecular mechanics and molecular dynamics calculations.     

X-ray crystal structure analyses and atomic charges of color former and developer. I. Color developers

The crystal and molecular structures of 2,2-bis(4-hydroxyphenyl)propane (Bisphenol A, BPA) (1), benzyl 4-hydroxybenzoate (2), 1,7-bis(4-hydroxyphenylthio)-3,5-dioxaheptane (3) and 4-hydroxyphenyl 4-isopropoxyphenyl sulfone (4) have been determined by X-ray crystal structure analysis. Theoretical calculations of the steric hindrance and semiempirical quantum chemical calculations to determine the color characteristics have been carried out. It is clear that the energy barriers for the variation of the orientation of phenol group in 1 to 4 are due to steric hindrance caused by the other moiety and the peak profiles are due to repulsive interactions of the other moiety. Net atomic charges on the hydrogen of the OH group are larger than those on the other atoms in the molecules. This high electron charge of the para orientation will cause the different thermosensitivity and stabilization.     

X-ray crystal structure analyses and atomic charges of color former and developer. I. Color developers

The crystal and molecular structures of 2,2-bis(4-hydroxyphenyl)propane (Bisphenol A, BPA) (1), benzyl 4-hydroxybenzoate (2), 1,7-bis(4-hydroxyphenylthio)-3,5-dioxaheptane (3) and 4-hydroxyphenyl 4-isopropoxyphenyl sulfone (4) have been determined by X-ray crystal structure analysis. Theoretical calculations of the steric hindrance and semiempirical quantum chemical calculations to determine the color characteristics have been carried out. It is clear that the energy barriers for the variation of the orientation of phenol group in 1 to 4 are due to steric hindrance caused by the other moiety and the peak profiles are due to repulsive interactions of the other moiety. Net atomic charges on the hydrogen of the OH group are larger than those on the other atoms in the molecules. This high electron charge of the para orientation will cause the different thermosensitivity and stabilization.     

Theoretical approach to the evaluation of spin-only magnetic form factors for many-electron atomic systems

General expressions for evaluating spin-only magnetic form factors for many-electron atomic systems are derived using Racah algebra techniques. The formulas are derived in the |αLSM_LM_S〉 representation. The general formalism allows the evaluation of spin-only magnetic form factors beyond the Hartree-Fock approximation.     

A new definition of atomic charges in molecules

A new definition of atomic charges in molecules is presented which conserves charge and dipole moment. It contains the Mulliken and Löwdin definitions as special cases of zero and first order truncations of commutator expansions. The definition allows for a systematic improvement of charges paralleling the improvement of the basis set in the LCAO approximation. We have tested the definition in thirteen selected diatomics and polyatomics in optimal minimal Slater basis set SCF calculations by means of 4G-level Gaussian expansions. The results suggest that the proposed definition is better than either Mulliken's or Löwdin's definition.Presented in part at the E. U. Condon Symposium, Sanibel Island, Florida, 21–27 January 1973.     

Variation of atomic charges on proton transfer in strong hydrogen bonds: the case of anionic and neutral imidazole-acetate complexes

The variation of atomic charges upon proton transfer in hydrogen bonding complexes of 4-methylimidazole, in both neutral and protonated cationic forms, and acetate anion, is investigated. These complexes model the histidine (neutral and protonated)-aspartate pair present in active sites of proteases where strong N--H...O hydrogen bonds are formed. Three procedures (Merz-Kollman scheme, Natural Population Analysis, and Atoms in Molecules Method) are used to compute atomic charges and explore their variation upon H-transfer in the gas phase and in the presence of two continuum media with dielectric constants 5 (protein interiors) and 78.39 (water). The effect of electron correlation was also studied by comparing Hartree-Fock and MP2 results for both complexes in the gas phase. Greater net charge interchanged upon H-transfer is observed in the anionic complex with respect to the neutral complex. Raising the polarity of the medium increases the amount of net charge transfer in both complexes, although the neutral system exhibits a larger sensitivity to the presence of solvent. Charge transfer associated to N--H...O and N...H--O bonds reveal the ionic contribution to the interaction depending on the number of charged subunits but the presence of solvent affects little this quantity. The lack of electron correlation overestimates all the charges as well as their variations and so uncorrelated calculations should be avoided.     

Comparison of atomic charges derived via different procedures

Atomic charges were obtained from ab initio molecular orbital calculations using a variety of procedures to compare them and assess their utility. Two procedures based on the molecular orbitals were examined, the Mulliken population analysis and the Weinhold–Reed Natural Population Analysis. Two procedures using the charge density distribution were included; the Hirshfeld procedure and Bader's Atoms in Molecules method. Charges also were derived by fitting the electrostatic potential (CHELPG) and making use of the atomic polar tensors (GAPT). The procedures were first examined for basis set independence, and then applied to a group of hydrocarbons. The dipole moments for these molecules were computed from the various atomic charges and compared to the total SCF dipole moments. This was followed by an examination of a series of substituted methanes, simple hydrides, and a group of typical organic compounds such as carbonyl derivatives, nitriles, and nitro compounds. In some cases, the ability of the charges to reproduce electrostatic potentials was examined. © John Wiley & Sons, Inc.     

Theoretical conformational analysis of rutin

Abstract  

The structural properties of rutin were determined by using a computational multistep progression. In the first step a stochastic strategy based on a molecular mechanics calculation was adopted to obtain a preliminary screening of the low-energy rutin conformations. The most stable structures obtained by the random conformational search were used as a starting point for an Austin Model 1 (AM1) semiempirical optimization. After this treatment, 16 structures characterized by a more stable frontal in respect to back disposition of the glycosidic chain of rutin were identified. To validate the results found from the stochastic search a molecular dynamics simulation was carried out. The results evidenced the presence of a global minimum highly stabilized by a hydrogen bond between the hydroxyl in the 3′ position of the B ring and the endocyclic oxygen of the rhamnose unit followed by approximately 8 kJ mol⁻¹ less stable local minima with similar energy values. Finally, the reliability of the molecular model was confirmed by comparing the calculated electronic absorption spectrum with that measured on a methanolic rutin solution.     

Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges

A method is presented for the rapid calculation of atomic charges in σ-bonded and nonconjugated π-systems. Atoms are characterized by their orbital electronegativities. In the calculation only the connectivities of the atoms are considered. Thus only the topology of a molecule is of importance. Through an iterative procedure partial equalization of orbital electronegativity is obtained. Excellent correlations of the atomic charges with core electron binding energies and with acidity constants are observed. This establishes their value in predicting experimental data.     

Quantitative determination of neutral lipids on chromarods

Five lots of ten chromarods were spotted with 2, 4, 6, or 8 μg of cholesterol ester, cholestero, triglyceride, methyl ester and free fatty acid and then analyzed using an Iatroscan. Rod-to-rod and lot-to-lot differences in the detector response were evident n the data. The standard deviation for the rod within lot response appeared to increase linearly as the amount of lipid applied was increased. The logarithms of the detector response data were analysed statistically to determine the relative magnitude of the rod-to-rod and lot-to-lot variances. When methyl ester was used as an internal standard or as a covariate, the variation from rod to rod and lot to lot was much smaller than in the original analysis.