Set Of Atomic Charges Research Articles

Toward a realistic force field for the treatment of ionic sugars

Heparin and other glycosaminoglycans involved in biological processes exist in solution as polyions: their specific activities are likely to depend on the geometrical arrangement of the charged (sulfate, carboxylate, amino) groups. Force-field methods, widely used in investigating molecular interactions, rely on proper interatomic potentials. However, in the case of these groups, little work has been done previously. Here we present a new parameter subset (to supplement an MM2-based force field) for N-and O-sulfate groups in sugars. Ab initio computations (RHF and MP2/6-31+ G ∗∗) on model compounds, in particular Mesulfate and N-Me-sulfate, yielded a set of atomic charges and the value of the energy barrier to bond rotations. Experimental crystal structures of ionic monosaccharides (five O-sulfated and one N-sulfated) were taken as standard for fitting a number of parameters and as starting points for energy minimizations in which counterions and water molecules were also considered within the crystallographic environment. Models computed using the current parameter set fit the six experimental structures with an overall root-mean-square deviation of 0.21 Å with respect to the heavy-atom positions.

An ab initio study of crystal field effects, part 3: Solid- and gas-phase geometry of formamide, modeling the changes in a peptide group due to hydrogen bonds

A model of the solid state of formamide is constructed by optimizing a central molecule in an electrostatic field of the proper symmetry. Attention is paid to the way the electrostatic charges are obtained. Point charges obtained from a Mulliken population analysis yield a final set of atomic charges in the central molecule that agree reasonably well with those obtained experimentally after ak-refinement of formamide. Point charges from a so-called stockholder partitioning agree slightly less. Furthermore, the simple crystal field adaptation of standard ab initio methods reproduces within experimental limits the differences in C=O and C-N lengths, observed between the gas-phase and the solid state geometry. Again, a Mulliken field agrees slightly better than a stockholder field, but the difference in performance is statistically insignificant. In a survey of 221 high-quality single-crystal x-ray determinations of compounds containing the peptide group N-C=O, we found evidence supporting quantitatively the conclusion that the increase of C=O and the decrease of C-N bond length in the gas-to-solid transition is dominated by the effects of hydrogen bonding. It was shown that the C=O bond lengthens by about 0.011 a per H-bond it accepts, while the N-C bond diminishes by about 0.015 a per H-bond it donates.

Atomic charges for DNA constituents derived from single-crystal X-ray diffraction data

We have derived a complete set of atomic charges for DNA from very high resolution, low temperature, single-crystal X-ray diffraction data, collected for a variety of nucleosides and nucleotides: cytidine; deoxycytidine 5′-monophosphate; deoxythymidine; guanosine 5′-monophosphate; deoxyadenosine; adenosine. This set of charges represents the first experimentally based parameterization of an important term in the energy function used in most modeling of DNA. The resulting charges are in good agreement with chemical intuition and experimental observations. They also agree qualitatively with the theoretically derived values now commonly used, but numerous and significant quantitative differences are observed. Possible reasons for the quantitative disagreement are discussed. An averaged set of charges (derived from the experimental results), which can be used in DNA modeling calculations, is presented.

An optimized potential function for the calculation of nucleic acid interaction energies I. Base stacking

An optimized potential function for base-stacking interactions is constructed. Stacking energies between the complementary pairs of a dimer are calculated as a function of the rotational angle and separation distance. Using several different sets of atomic charges, the electrostatic component in the monopole-monopole approximation (MMA) is compared to the more refined segmented multipole-multipole representation (SMMA); the general features of the stacking minima are found to be correctly reproduced with IEHT or CNDO atomic charges. The electrostatic component is observed to control the location of stacking minima.The MMA, in general, is not a reliable approximation of the SMMA in regions away from minima; however, the MMA is reliable in predicting the location and nature of stacking minima.The attractive part of the Lennard-Jones 6-12 potential is compared to and parameterized against the expressions for the second-order interaction terms composed of multipole-bond polarizability for the polarization energy and transition-dipole bond polariz abilities for approximation of the dispersion energy. The repulsive part of the Lennard-Jones potential is compared to a Kitaygorodski-type repulsive function; changing the exponent from its usual value of 12 to 11.7 gives significantly better agreement with the more refined repulsive function.Stacking minima calculated with the optimized potential method are compared with various perturbation-type treatments. The optimized potential method yields results that compare as well with melting data as do any of the more recent and expensive perturbation methods.

Molecular Structure Information From X‐Ray Photoelectron Spectroscopy

AbstractA discussion is given of the types of molecular structure information available from X‐ray photoelectron spectroscopy. A complete set of atomic charges in a molecule can be deduced from core‐level binding energy shifts. Atomic‐orbital composition of molecular orbitals is derived from relative intensities. Correlation peaks yield information about electron correlation. Relaxation energies are related to basicity for certain functional groups.