Biomedical subjects

Russell J Boyd

Publications and source records attributed to Russell J Boyd.

14 recordsLinked to original sources

PubMed2006

Atomic contributions to bond dissociation energies in aliphatic hydrocarbons.

This paper explores the atomic contributions to the electronic vibrationless bond dissociation enthalpy (BDE) at 0 K of the central C-C bond in straight-chain alkanes (C(n)H(2n+2)) and trans-alkenes (C(n)H(2n)) with an even number of carbon atoms, where n=2, 4, 6, 8. This is achieved using the partitioning of the total molecular energy according to the quantum theory of atoms in molecules by comparing the atomic energies in the intact molecule and its dissociation products. The study is conducted at the MP2(full)6-311++G(d,p) level of theory. It is found that the bulk of the electronic energy necessary to sever a single C-C bond is not supplied by these two carbon atoms (the alpha-carbons) but instead by the atoms directly bonded to them. Thus, the burden of the electronic part of the BDE is primarily carried by the two hydrogens attached to each of the alpha-carbons and by the beta-carbons. The effect drops off rapidly with distance along the hydrocarbon chain. The situation is more complex in the case of the double bond in alkenes, since here the burden is shared between the alpha-carbons as well as the atoms directly bonded to them, namely, again the alpha-hydrogens and the beta-carbons. These observations may lead to a better understanding of the bond dissociation process and should be taken into account when locally dense basis sets are introduced to improve the accuracy of BDE calculations.

Journal Article↗

PubMed2006

Modeling competitive reaction mechanisms of peroxynitrite oxidation of guanine.

5-Guanidino-4-nitroimidazole is a stable product from the peroxynitrite induced one-electron oxidation of guanine. Reaction mechanisms to form the 5-guanidino-4-nitroimidazole as well as 8-nitroguanine, through the combination of the guanine radical cation and nitrogen dioxide radical and through the combination of the deprotonated neutral guanine radical and nitrogen dioxide radical, have been investigated by the use of the B3LYP method of density functional theory. Our calculations suggest that the guanine radical cation mechanism is preferred over the neutral guanine radical mechanism and that a water molecule is involved in the reaction as a catalyst or as a reactant.

Cations↗

PubMed2006

Theoretical study of the thermolysis of beta-hydroxyl aldehydes.

A mechanism involving a six-membered cyclic transition state where the hydrogen of the hydroxyl group interacts with the oxygen of the carbonyl group has been proposed previously to describe the thermolysis of many beta-hydroxyl compounds. In this paper, the proposed mechanism is studied for a series of beta-hydroxyl aldehydes. Rate constants and activation energies are reported as well as a study of the influence of tunneling on the reaction rates. The electron density at the ring critical points, population analyses by the theory of atoms in molecules (AIM) and the natural bond orbital (NBO) method, as well as atomic energy analyses are used to gain insight into this interesting mechanism and into the effects of substituents.

Journal Article↗

PubMed2006

Modeling the reduction of hydrogen peroxide by glutathione peroxidase mimics.

Theoretical calculations have been performed on three model reactions representing the reduction of hydrogen peroxide by ebselen, ebselen selenol, and ebselen diselenide. The reaction surfaces have been investigated at the B3PW91/6-311G(2df,p) level, and single-point energies were calculated using the 6-311++G(3df,3pd) basis set. Solvent effects were included implicitly with the conductor-like polarizable continuum model and in one case with explicit inclusion of three water molecules. Mechanistic information is gained from investigating the critical points using the quantum theory of atoms in molecules. The barriers for the reduction of hydrogen peroxide with the ebselen, ebselen selenol, and ebselen diselenide models are 56.7, 53.4, and 35.3 kcal/mol, respectively, suggesting that ebselen diselenide may be the most active antioxidant in the ebselen GPx redox pathway. Results are also compared to that of the sulfur analogues of the model compounds.

Anilides↗

PubMed2006

Evaluation of effective core potentials and basis sets for the prediction of the geometries of alkyltin halides.

A systematic comparison of the optimized geometries of five organotin compounds, Cl(n)Sn(CH(3))(4-n), n = 0-4, with the available gas-phase electron diffraction results is reported. All optimizations were carried out with the B3LYP density functional method. Comparison of 10 basis sets and three effective core potentials leads to the conclusion that the combination of the SDB-aug-cc-pVTZ basis set and the LANL2 effective core potential for tin, together with the 6-31G(d,p) basis set for the other atoms, is recommended for the prediction of the geometries of organotin compounds.

Chlorides↗

PubMed2006

Extended weak bonding interactions in DNA: pi-stacking (base-base), base-backbone, and backbone-backbone interactions.

We report on several weak interactions in nucleic acids, which, collectively, can make a nonnegligible contribution to the structure and stability of these molecules. Fragments of DNA were obtained from previously determined accurate experimental geometries and their electron density distributions calculated using density functional theory (DFT). The electron densities were analyzed topologically according to the quantum theory of atoms in molecules (AIM). A web of closed-shell bonding interactions is shown to connect neighboring base pairs in base-pair duplexes and in dinuleotide steps. This bonding underlies the well-known pi-stacking interaction between adjacent nucleic acid bases and is characterized topologically for the first time. Two less widely appreciated modes of weak closed-shell interactions in nucleic acids are also described: (i) interactions between atoms in the bases and atoms belonging to the backbone (base-backbone) and (ii) interactions among atoms within the backbone itself (backbone-backbone). These interactions include hydrogen bonding, dihydrogen bonding, hydrogen-hydrogen bonding, and several other weak closed-shell X-Y interactions (X, Y = O, N, C). While each individual interaction is very weak and typically accompanied by perhaps 0.5-3 kcal/mol, the sum total of these interactions is postulated to play a role in stabilizing the structure of nucleic acids. The Watson-and-Crick hydrogen bonding is also characterized in detail at the experimental geometries as a prelude to the discussion of the modes of interactions listed in the title.

Base Pairing↗

PubMed2005

An evaluation of various computational methods for the treatment of organoselenium compounds.

A reliable computational method for the prediction of organoselenium geometries and bond dissociation energies (BDEs) has been determined on the basis of the performance of density functional theory (DFT: B3LYP and B3PW91) and ab initio molecular orbital procedures (Hartree-Fock (HF)) in conjunction with various Pople basis sets including (but not limited to) the 6-31G(d), 6-31G(d,p), 6-311G(d), 6-311G(d,p), 6-311G(2df,p), and 6-311G(3df,3pd) sets. Predicted geometries and BDEs are compared with available experimental data and quadratic configuration interaction including single and double substitutions (QCISD) results. The B3PW91/6-311G(2df,p) level of theory is recommended for the prediction of the geometries and energetics of organoselenium compounds.

Computer Simulation↗

PubMed2005

Characterization of a closed-shell fluorine-fluorine bonding interaction in aromatic compounds on the basis of the electron density.

A bond path linking two saturated fluorine atoms is found to be ubiquitous in crowded difluorinated aromatic compounds. The bond path is shown to persist for a range of internuclear distances (2.3-2.8 A) and a range of relative orientations of the two C-F internuclear axes. The F. . .F bonding is shown to exhibit all the hallmarks of a closed-shell weak interaction. The presence of such a bond path can impart as much as 14 kcal/mol of local stabilization to the molecule in which it exists, a stabilization that can be offset or even overwhelmed by destabilization of other regions in the molecule. Several other weak closed-shell interactions were also found and characterized including F. . .C, F. . .O, and C. . .C interactions, hydrogen bonding, dihydrogen bonding, and hydrogen-hydrogen bonding. This study represents another example of the usefulness and richness of the bond path concept and of the theory of atoms in molecules in general.

Journal Article↗

PubMed2003

Modeling the reaction mechanisms of the amide hydrolysis in an N-(o-carboxybenzoyl)-L-amino acid.

Reaction mechanisms of the amide hydrolysis from the protonated, neutral, and deprotonated forms of N-(o-carboxybenzoyl)-l-amino acid have been investigated by use of the B3LYP density functional method. Our calculations reveal that in the amide hydrolysis the reaction barrier is significantly lower in solution than that in the gas phase, in contrast with the mechanism for imide formation in which the solvent has little influence on the reaction barrier. In the model reactions, the water molecules function both as a catalyst and as a reactant. The reaction mechanism starting from the neutral form of N-(o-carboxybenzoyl)-l-amino acid, which corresponds to pH 0-3, is concluded to be the most favored, and a concerted mechanism is more favorable than a stepwise mechanism. This conclusion is in agreement with experimental observations that the optimal pH range for amide hydrolysis of N-(o-carboxybenzoyl)-l-leucine is pH 0-3 where N-(o-carboxybenzoyl)-l-leucine is predominantly in its neutral form. We suggest that besides the acid-catalyzed mechanism the addition-elimination mechanism is likely to be an alternative choice for cleaving an amide bond. For the reaction mechanism initiated by protonation at the amidic oxygen (hydrogen ion concentration H(0) < -1), the reaction of the model compound with two water molecules lowers the transition barrier significantly compared with that involving a single water molecule.

Amides↗

PubMed2003

Modeling the reaction mechanisms of the imide formation in an N-(o-carboxybenzoyl)-L-amino acid.

Reaction mechanisms of the imide formation in an N-(o-carboxybenzoyl)-l-amino acid have been studied using density functional theory. Our results suggest that the reaction route initiated by protonation at the oxygen of the carboxyl group of the amino acid is favored, while those initiated by deprotonation at the oxygen of the carboxyl group of phthalic acid and at the amidic nitrogen are minor pathways. During the dehydration process, water functions as a catalyst. These conclusions are in good agreement with the experimental facts that at highly acidic conditions (hydrogen ion concentration H(0) < -1), imide formation is the most favorable pathway, whereas in the pH range 0-5, cyclization to the imide is not the dominant reaction. Our calculations also show that the carboxyl group of the amino acid is involved in the catalytic reaction in both the favored and minor pathways and that solvent effects have little influence on the reaction barriers.

Amino Acids↗

PubMed2003

Comparison of two needle types for intraosseus access in an animal model.

OBJECTIVES: This study was designed to investigate the success rate, time for insertion and perceived difficulty in gaining intraosseus access in a porcine-derived animal model. The model was selected to have bone characteristics similar to human adult bone. Prehospital care personnel used two varieties of commercially available intraosseus needles, Cook Paediatric Intraosseus Insertion Needles and Cook Osteo-site needles. METHODS: Sixteen ambulance paramedic trainees were trained to use both of two intraosseus needle types. They were timed from start of insertion attempt to successful insertion and asked to score perceived difficulty of intraosseus needle insertion using a modified Likert scale. RESULTS: Sixteen of 16 (100%) of the insertions with the Cook Osteo-site needle were successful. Eleven of 16 (69%) insertions with the Cook Paediatric Intraosseus Insertion needle were successful. There was a statistically significant difference between the two groups (P = 0.033). The Cook Osteo-site needle was perceived to be significantly easier to use than the Cook Paediatric Intraosseus Insertion needle (P = 0.0085) and there was a non-significant trend to shorter insertion times for the Cook Osteo-site needle. CONCLUSIONS: Use of intraosseus needles to gain access in an animal model is possible. The use of the Cook Osteo-site needle is associated with excellent success rates for insertion and appears easier to use than the Cook Paediatric Intraosseus Insertion needle. Further work to evaluate the use of the intraosseus access device in the prehospital care situation is required.

Animals↗

PubMed2002

Molecular structures and excited states of CpM(CO)(2) (Cp = eta(5)-C(5)H(5); M = Rh, Ir) and [Cl(2)Rh(CO)(2)](-). Theoretical evidence for a competitive charge transfer mechanism.

Molecular structures and excited states of CpM(CO)(2) (Cp = eta(5)-C(5)H(5); M = Rh, Ir) and [Cl(2)Rh(CO)(2)](-) complexes have been investigated using the B3LYP and the symmetry-adapted cluster (SAC)/SAC-configuration interaction (SAC-CI) theoretical methods. All the dicarbonyl complexes have singlet ground electronic states with large singlet-triplet separations. Thermal dissociations of CO from the parent dicarbonyls are energetically unfavorable. CO thermal dissociation is an activation process for [Cl(2)Rh(CO)(2)](-) while it is a repulsive potential for CpM(CO)(2). The natures of the main excited states of CpM(CO)(2) and [Cl(2)Rh(CO)(2)](-) are found to be quite different. For [Cl(2)Rh(CO)(2)](-), all the strong transitions are identified to be metal to ligand CO charge transfer (MLCT) excitations. A significant feature of the excited states of CpM(CO)(2) is that both MLCT excitation and a ligand Cp to metal and CO charge transfer excitation are strongly mixed in the higher energy states with the latter having the largest oscillator strength. A competitive charge transfer excited state has therefore been identified theoretically for CpRh(CO)(2) and CpIr(CO)(2). The wavelength dependence of the quantum efficiencies for the photoreactions of CpM(CO)(2) reported by Lees et al. can be explained by the existence of two different types of excited states. The origin of the low quantum efficiencies for the C-H/S-H bond activations of CpM(CO)(2) can be attributed to the smaller proportion of the MLCT excitation in the higher energy states.

Journal Article↗

PubMed2002

Theoretical studies of the cross-linking mechanisms between cytosine and tyrosine.

DNA-protein cross-linking is one of the many DNA lesions mediated by hydroxyl radicals, the most damaging among the reactive oxygen species in biological systems. Density functional theory methods are employed to investigate the complex reaction mechanisms of the formation of cytosine-tyrosine cross-links as observed in gamma-irradiated aqueous solutions of cytosine and tyrosine, as well as in gamma-irradiated nucleohistone. The majority of the radical addition mechanisms considered are found to have significant barriers and therefore to be thermodynamically unfavorable for the formation of the initial cross-linked product. Our calculated reaction potential energy surfaces suggest that a feasible complete mechanism consists of radical combination forming the initial cross-linked product, a hydrogen shuffle within the initial cross-linked product, and an acid-catalyzed dehydration reaction. Water and hydrogen-bonding interactions are suggested to play a key role in catalyzing the hydrogen-transfer step of the reaction.

Cytosine↗

PubMedDate not supplied

Fluorine-fluorine spin-spin coupling constants in aromatic compounds: correlations with the delocalization index and with the internuclear separation.

This paper describes a new empirical approach for the evaluation of fluorine-fluorine spin-spin coupling constants (J(FF)) in aromatic compounds. The correlations between J(FF) and the delocalization index calculated within the framework of the theory of atoms in molecules (AIM) and with the fluorine-fluorine internuclear separation are investigated. Both the internuclear separation and the delocalization index are found to be highly correlated with J(FF). A regression model in which the experimental J(FF) coupling constant is fitted exponentially to the internuclear separation and linearly to the delocalization index yields a squared correlation coefficient as high as 0.96 for a data set consisting of 33 coupling constants spread over a range of 85 Hz.

Fluorine↗