Biomedical subjects

Paul G Mezey

Publications and source records attributed to Paul G Mezey.

9 recordsLinked to original sources

PubMed2005

The degree of rotation independence of conjugation of S-N bonds.

The electron delocalization in pi-electron systems is frequently described qualitatively by the concept of conjugation between formal double bonds separated by a formal single bond. In carbon compounds the optimum conjugation usually requires a rather strict, geometrical condition: the exact or near coplanarity of the participating carbon atoms. However, the geometrical conditions are much less strict for third-row atoms if the bonding involves valence-shell d orbitals. In some sulfur compounds, such as N-sulfonylsulfilimines, the conjugation is almost unaffected within large ranges of bond-rotation angles, which amounts to rotation-independent conjugation. On the basis of the indications of earlier, limited studies using only minimal basis set and no geometry optimization, in the more extensive present study Density Functional Theory B3LYP calculations using 6-31G basis set provide more reliable evidence for such flexible conjugation in some sulfur compounds and give an explanation for the experimentally observed interconversion of chiral conformers of N-sulfonylsulfilimines.

Journal Article↗

PubMed2005

Evaluation of the field-adapted ADMA approach: absolute and relative energies of crambin and derivatives.

A large number of conformations and chemically modified variants of the protein crambin were used to extensively test the field-adapted adjustable density matrix assembler (FA-ADMA) method developed for ab initio quality quantum chemistry computations of proteins and other macromolecules, introduced in an earlier publication. In this method, the fuzzy density matrix fragmentation scheme of the original adjustable density matrix assembler (ADMA) method has been made more efficient by combining it with an approach of using point charges to approximate the effects of additional, distant parts of a given macromolecule in the quantum chemical calculation of each fragment. In this way, smaller parent molecules can be used for fragment generation, while achieving accuracy that can be obtained only with large parent molecules in the original ADMA method. Whereas in both methods the error relative to the Hartree-Fock result can be reduced below any threshold by choosing large enough parent molecules, this can be done more efficiently with the new method. In order to obtain reliable test results for the accuracy obtainable by the new method when compared to conventional Hartree-Fock calculations, we performed a large number of energy calculations for the protein crambin using various conformations available in the Protein Data Bank, various protonation states, and side chain mutations. Additionally, in order to test the performance of the method for protein-solvent interaction studies, the energy changes due to the formation of complexes with ethanol and single and multiple water molecules were investigated.

Chemical Phenomena↗

PubMed2005

Predicted high-energy molecules: helical all-nitrogen and helical nitrogen-rich ring clusters.

Helical all-nitrogen and nitrogen-rich ring clusters, new types of potential high-energy molecules, were investigated in the computational study reported here. Stable helical all-nitrogen clusters N26 and N46 and nitrogen-rich helical structure N26H16 formed by fused six-membered rings were found and characterized as proper energy minima by having real frequencies for all eigenvectors of the Hessian matrix. Furthermore, the stability of [6] N-ring helix was studied by calculating the barrier of dissociation reaction. The potential of these type molecules as high-energy density materials was studied. For a better intuitive understanding of the unusual bonding patterns, the molecular isodensity contour (MIDCO) surfaces for [6] N-ring helix and [6] N-helicene were compared at some characteristic density threshold values of 0.20, 0.32, and 0.35 au. As indicated at these threshold values of the isodensity surfaces, the bonds of all-nitrogen clusters appear stronger than those of nitrogen-rich clusters. Apparently, the nitrogen-rich clusters are of higher energy than the all-nitrogen structures, especially if one takes into account the energy balance of bonds involving hydrogen.

Journal Article↗

PubMed2005

A theoretical study of nitrogen-rich phosphorus nitrides P(Nn)m.

Ab initio calculations predict that structures P(Nn)m (n = 3, 4; m = 1-4; with linear N3, tetrahedral N4, and square N4) correspond to local energy minima characterized by having real frequencies for all eigenvectors of the Hessian matrix. The central P atom often prefers having an odd number of bonds, although we also found some stable structures where P is evenly bonded. The special role of the phosphorus atom in the geometrical arrangements of the P(Nn)m systems was investigated. The low barriers of P(N4)m in the gas-phase decomposition reactions mean that these nitrogen-rich systems require external stabilization if they are to be used as high-energy density materials or starting materials for further syntheses.

Journal Article↗

PubMed2003

Ab initio quality properties for macromolecules using the ADMA approach.

We describe new developments of an earlier linear scaling algorithm for ab initio quality macromolecular property calculations based on the adjustable density matrix assembler (ADMA) approach. In this approach, a large molecule is divided into fuzzy fragments, for which quantum chemical calculations can easily be done using moderate-size "parent molecules" that contain all the local interactions within a selected distance. If greater accuracy is required, a larger distance is chosen. With the present extension of this approximation, properties of the large molecules, like the electron density, the electrostatic potential, dipole moments, partial charges, and the Hartree-Fock energy are calculated. The accuracy of the method is demonstrated with test cases of medium size by comparing the ADMA results with direct quantum chemical calculations.

Journal Article↗

PubMedDate not supplied

Theoretical derivation of heuristic molecular lipophilicity potential: a quantum chemical description for molecular solvation.

We present the theoretical derivation of a heuristic molecular lipophilicity potential (HMLP), which gives a structure-based and quantum chemical description of an important aspect of molecular solvation. The quantum mechanical electrostatic potential (ESP) V(r) on a formal molecular surface is calculated, and then the molecular lipophilicity potential L(r) is constructed by comparing the local electron density with the ESP on the surrounding atoms using a screening function. The screening function is derived from statistical mechanical theory treating the polar solvent molecules as dipoles. HMLP is able to describe the main interactions of solute molecules with polar and nonpolar solvent molecules. HMLP is a unified lipophilicity and hydrophilicity potential: its positive values represent lipophilicity, and its negative values represent hydrophilicity. In this paper, several examples show that HMLP gives more reliable descriptions for the molecular solvation than some other methods, such as atomic partial charges and the empirical lipophilicity potential.

Hydrophobic and Hydrophilic Interactions↗

PubMedDate not supplied

Stability and properties of polyhelicenes and annelated fused-ring carbon helices: models toward helical graphites.

The geometrical structures and properties of conjugated polyhelicenes and annelated fused-ring carbon helices with analogous frameworks were theoretically studied at the HF/6-31G and B3LYP/6-31G levels. These studies focused on the stability of the fused-ring structures with special emphasis on the helical geometrical arrangements. To elucidate bonding patterns, the orbitals, electron density contours, and the electrostatic potential of these helical compounds were analyzed. The structure of fused polynaphthalenes arranged in a helical spiral can be regarded as part of a locally helical graphite lattice that is expected to give rise to special electronic properties along the helically layered conjugated single sheet that can be regarded as a single extended pi system but also involving local layer-to-layer pi-pi interactions that are typical in ordinary graphite. This dual feature might lead to novel materials.

Journal Article↗

PubMedDate not supplied

The electronic structures and properties of open-ended and capped carbon nanoneedles.

The existence of a family of very thin carbon needlelike nanostructures is predicted: the geometry and stability of several carbon nanoneedles (CNNs) formed by C4 and C6 units have been studied by quantum chemistry computational modeling methods. The structures of carbon nanoneedles are tighter than even the smallest single wall nanotubes (SWNTs) based on (4, 0) naphthacene. The electronic properties, energetic stability of geometrical structures with various terminal units are investigated. The relatively large band gaps, the strong bonding, and additional orbital interactions within the C4 rings and between the C4 layers make the H4(C4)(n)H4 type molecules nonmetallic. We have found indications that if the CNN (3, 0) structures are very long (in the limit of infinite-length), then they are likely to have semiconducting properties and could possibly be used as actual semiconductors. The studied families of CNNs can be considered as carbon nanostructures with unique structural and chemical properties and with possible potential for unusual electronic properties, with likely practical applications as nanomaterials and nanostructure devices.

Journal Article↗

PubMedDate not supplied

Stability and electronic properties of nitrogen nanoneedles and nanotubes.

The electronic structures and stability of nitrogen nanostructures, nanotubes, and fiberlike nanoneedles of various diameters, formed by units N2m (m = 2-6), were studied by quantum chemistry computational modeling methods. The geometrical structures with various cross-sections and terminal units, their energetic stability, and their rather peculiar electron density distributions were investigated. The tightest nitrogen nanoneedle (NNN) studied theoretically in this work is the structure (N4n with D2h symmetry, whereas the nitrogen nanotube (NNT) with the largest diameter discussed here is the structure (N12)n with D2 symmetry. These families of NNNs and NNTs can be considered as nanostructures not only for potential applications as devices in nanotechnology or as possible scaffold structures but also as ligands in synthetic chemistry and high-energy density materials (HEDMs). As a consequence of the lone-pair electrons present around the walls of these NNNs and NNTs, these nitrogen nanostructures and the nitrogen nano-bundles (NNB) formed by aligning and combining them using intermediate carbon atoms, can have highly variable electronic properties controlled by the changing charge environment. In particular, for extended systems based on the units studied here, the band gaps of each of these systems can be affected greatly by the local charge of the environment.

Journal Article↗