Russell J. Boyd

Electron affinities and ionization potentials of nucleotide bases

Abstract Density-functional theory (B3LYP functional) is used to investigate the ionization potentials and electron affinities of the DNA and RNA nucleotide bases. For the first time, anions lying lower in energy than the neutral species have been calculated for both thymine and uracil (i.e., positive adiabatic electron affinities). Additionally, the calculations show that anion formation leads to significant geometrical changes to the nucleobases. This is a very important finding as previous calculations have indicated that the anions are very similar in geometry to the neutral species and reported negative valence adiabatic electron affinities.

The shell structure of atoms and the Laplacian of the charge density

It is shown that the form of the Laplacian of the charge density provides a more complete resolution of the shell structure of atoms than the radial density function. The complete shell structure is resolved for s‐block and most p‐block atoms, but only the inner shells are resolved in the d‐block elements. The shell structures revealed by the Laplacian of the charge density and the radial density function parallel one another where direct comparison is possible.

A theoretical study of 5-halouracils: electron affinities, ionization potentials and dissociation of the related anions

Abstract The gas phase and solution electron affinities and ionization potentials of uracil, thymine and a series of 5-halouracils ( 5XU, X=F, Cl, Br ) are investigated with B3LYP. Halogen substitution has a smaller effect on the IP than the EA of U . The EAs are calculated to increase according to T U 5FU 5ClU 5BrU . The calculated barriers for the dissociation of the resulting 5XU anions to X − plus uracil-centered radicals decrease along the series 5FU − > 5ClU − > 5BrU − . The calculated trends are consistent with suggestions that 5XUs enhance the sensitivity of deoxyribonucleic acid, DNA (ribonucleic acid, RNA) to ionizing radiation and that 5BrU leads to the greatest enhancement.

A Density Functional Study of Methanol Clusters.

The potential energy surfaces of methanol clusters, (CH3OH)n, n = 2-12, have been studied using density functional theory at the B3LYP/6-31G(d) and higher levels of theory. Cyclic clusters in which n methanol molecules are joined in a ring structure formed by n hydrogen bonds are shown to be more stable than structures of the same number of methanol molecules where one or more methanol molecules are outside the ring and are hydrogen-bonded to oxygens of methanols in rings of n - 1, n - 2, and so forth. So-called chain structures are generally even less stable. Furthermore, the hydrogen-bonding energy per methanol molecule of the n-ring clusters is shown to converge to an asymptotic value of about 27 kJ/mol at B3LYP/6-311+G(d,p)//B3LYP/6-31G(d) after five to six methanols are included in the cluster. As expected, there are many minima on the potential energy surfaces of the methanol clusters, the number increasing rapidly with n. A cyclic cluster of five to six methanol molecules appears to be sufficient to mimic liquid behavior as far as vibrational frequencies are concerned.

A bond-length-bond-order relationship for intermolecular interactions based on the topological properties of molecular charge distributions.

Abstract Ab initio SCF MO calculations for the hydrogen-bonded complexes between nitriles and hydrogen fluoride suggest a strong linear relationship between the charge density at the hydrogen-bond critical point and the hydrogen-bond energy. Further investigation of the topological properties of the charge density indicates that the generalization of the bond-length-bond-order relationship of CC bonds due to Bader et al. may be extended to intermolecular hydrogen bonding. Calculations at the 6–31G ** level, including complete geometry optimization, are reported for the complexes, where R  H, Li, F, Cl, HO, LiO, NC, HCC, CH 3 and CH 3 O.

Hydrogen bonding between nitriles and hydrogen halides and the topological properties of molecular charge distributions

Abstract The topological properties of the charge density of the hydrogen-bonded complexes between nitrites and hydrogen chloride correlate linearly with theoretical estimates of the hydrogen-bond energy. At the 6-31G** level, the hydrogenbond energies range from a low of 10 kJ mol m NCCN—HC1 to a high of 38 kJ mol in LiCN—HCl. A linear relationship between the charge density at the hydrogen-bond critical point and the NH internuclear distance of the RCN—HC1 complexes indicates that the generalization of the bond-length-bond-order relationship of CC bonds due to Bader, Tang, Tal and Biegler-Konig can be extended to intermolecular hydrogen bonding.

Changing Weak Halogen Bonds into Strong Ones through Cooperativity with Beryllium Bonds

The mutual interaction between beryllium bonds and halogen bonds within H2Be···FCl···Base complexes, where Base includes a wide set of N- and O-containing Lewis bases, has been studied at the M06-2X/6-31+G(d,p) level of theory. The reliability of this theoretical model was assessed by comparison with ab initio CCSD/aug-cc-pVTZ reference calculations. Cooperative effects were investigated within the framework of the atoms in molecules theory (AIM) by analyzing the topology of the electron density and the changes in the atomic energy components. The decomposition of the total stabilization energy into atomic components is found to be a very reliable tool to describe halogen bond interactions. Both the topological analysis of the electron density and the changes in the atomic energy components of the binding energy show the existence of strong cooperative effects between beryllium and halogen bonds, which are in some cases very intense. In general, there is a correlation between the intrinsic basicity of the Lewis base participating in the halogen bond and the resulting cooperativity in the sense that the stronger the base, the larger the cooperative effects.

QTAIM Study of an α-Helix Hydrogen Bond Network

The structures of 19 alpha-helical alanine-based peptides, 13 amino acids in length, have been fully optimized using density functional theory and analyzed by means of the quantum theory of atoms in molecules. Two types of N-H...O bonds and one type of C-H...O bond have been identified. The value of the electron density at hydrogen bond critical points corresponding to N-H...O interactions is higher than that of C-H...O interactions. The effect of amino acid substitution at the central position of the peptide on the hydrogen bond network of the alpha-helix has been assessed. The strength of the hydrogen bond network, measured as the summation of the electron density over the hydrogen bond critical points, may be used to explain experimental relative helix propensities of amino acids in cases where solvation and entropic effects cannot.

A hybrid quantum mechanical force field molecular dynamics simulation of liquid methanol: Vibrational frequency shifts as a probe of the quantum mechanical/molecular mechanical coupling

A hybrid quantum mechanical molecular dynamics method is used to study liquid methanol at room temperature and normal density. Frequencies of the twelve vibrational modes are calculated from the simulation data at the ab initio Hartree–Fock/3‐21G(d,p) level. Good overall agreement is found between the experimental and calculated frequencies. Three different, successive levels of quantum mechanical/molecular mechanical (QM/MM) coupling schemes are investigated using gas‐to‐liquid vibrational frequency shifts as a probe. The results suggest, somewhat surprisingly, that the method with the weakest QM/MM coupling gives the best overall agreement between the experimental and simulated results for vibrational frequency shifts. The most elaborate coupling scheme overestimates the shifts towards the red direction due to overestimation of the attractive interactions between quantum mechanical and molecular mechanical molecules, while it is found to be most successful in describing the O–H stretch. The effects of t...

Effects of Ionizing Radiation on Crystalline Cytosine Monohydrate.

Possible radical reaction products observed when subjecting monohydrate crystals of the DNA base cytosineto ionizing radiation are characterized and analyzed by means of density functional theory. Comparison ismade with data from a recently published detailed ESR and ENDOR study by Sagstuen et al. (Sagstuen, E.;Hole, E. O.; Nelson, W. H.; Close, D. M. J. Phys. Chem. 1992, 96, 8269), as well as earlier studies onmethylcytosine and cytidine monophosphates. For cytosine monohydrate it is found, when comparing computedand measured radical hyperfine coupling constants, that products other than those initially assumed are possiblybeing formed. Instead of the original model that irradiation leads to the net reaction of dehydrogenation atthe N1 position of one cytosine molecule and hydrogenation at the N3 position of a second cytosine, wepresent an alternative mechanism where water is involved in the process. This alternative mechanism leadsto the formation of N3 hydrogenation and C5 hydroxylation net products, as the main reactions. Not only dothe hyperfine couplings provide a better match for the latter but they are also energetically favored over thefirst mechanism.