Biomedical subjects

M Rafat

Publications and source records attributed to M Rafat.

6 recordsLinked to original sources

PubMed2007

Atom-atom partitioning of total (super)molecular energy: the hidden terms of classical force fields.

Classical force fields describe the interaction between atoms that are bonded or nonbonded via simple potential energy expressions. Their parameters are often determined by fitting to ab initio energies and electrostatic potentials. A direct quantum chemical guide to constructing a force field would be the atom-atom partitioning of the energy of molecules and van der Waals complexes relevant to the force field. The authors used the theory of quantum chemical topology to partition the energy of five systems [H2, CO, H2O, (H2O)2, and (HF)2] in terms of kinetic, Coulomb, and exchange intra-atomic and interatomic contributions. The authors monitored the variation of these contributions with changing bond length or angle. Current force fields focus only on interatomic interaction energies and assume that these purely potential energy terms are the only ones that govern structure and dynamics in atomistic simulations. Here the authors highlight the importance of self-energy terms (kinetic and intra-atomic Coulomb and exchange).

Journal Article↗

PubMed2006

A convergent multipole expansion for 1,3 and 1,4 Coulomb interactions.

Traditionally force fields express 1,3 and 1,4 interactions as bonded terms via potentials that involve valence and torsion angles, respectively. These interactions are not modeled by point charge terms, which are confined to electrostatic interactions between more distant atoms (1,n where n>4). Here we show that both 1,3 and 1,4 interactions can be described on the same footing as 1,n (n>4) interactions by a convergent multipole expansion of the Coulomb energy of the participating atom pairs. The atomic multipole moments are generated by the theory of quantum chemical topology. The procedure to make the multipole expansion convergent is based on a "shift procedure" described in earlier work [L. Joubert and P. L. A. Popelier, Molec. Phys. 100, 3357 (2002)].

Journal Article↗

PubMed2005

The electrostatic potential generated by topological atoms. II. Inverse multipole moments.

Quantum chemical topology defines finite atoms, whose bounded electron density generates a well-defined electrostatic potential. A multipole expansion based on spherical tensors provides a potential that is formally convergent outside the divergence sphere. Part I of this series [P. L. A. Popelier and M. Rafat, Chem. Phys. Lett.376, 148 (2003)] showed that a continuous multipole expansion expands the convergence region, thereby allowing the electrostatic potential to be evaluated at short range. Here, we propose a different method, based on "inverse" multipole moments, enabling an expansion that converges everywhere. These moments are defined by inverse (i.e., negative) powers of the magnitude of the position vector describing the electron density inside the atom. We illustrate this technique on nitrogen in N(2), oxygen in H(2)O, and oxygen in the phenolic group of the amino acid tyrosine. The proposed method constitutes a considerable advance over the method presented in Part I.

Journal Article↗

PubMed2005

Rendering of quantum topological atoms and bonds.

In this article, we describe and apply an algorithm that visualizes atoms and bonds in molecules and van der Waals complexes, based on the topology of the electron density. The theory of quantum chemical topology defines both atoms and bonds via a single consistent procedure, and enables the association of an atomic shape with an atomic property (charge, dipole moment, volume, ...). Special attention is paid to the bridging of gaps arising in interatomic surfaces, in the presence of ring critical points or high ellipticity. This algorithm, in conjunction with the graphical user interface of the computer program MORPHY enables robust and efficient rendering of complicated interatomic surfaces, as found in larger systems.

Adamantane↗

PubMed2004

The quantum topological electrostatic potential as a probe for functional group transferability.

The electrostatic potential can be used as an appropriate and convenient indicator of how transferable an atom or functional group is between two molecules. Quantum-chemical topology (QCT) is used to define the electron density of a molecular fragment and the electrostatic potential it generates. The potential generated on a grid by the terminal aldehyde group of the biomolecule retinal is compared with the corresponding aldehyde group in smaller molecules derived from retinal. The terminal amino group in the free amino acid lysine was treated in a similar fashion. Each molecule is geometry-optimized by an ab initio calculation at B3LYP/6-311G+(2d,p)//HF/6-31G(d) level. The amino group in lysine is very little influenced by any part of the molecule further than two C atoms away. However, the aldehyde group in retinal is influenced by molecular fragments six C atoms away. This dramatic disparity is ascribed to the difference in saturation in the carbon chains; retinal contains a conjugated hydrocarbon chain but lysine an aliphatic one.

Aldehydes↗

PubMed2004

[Identification of elevated carbohydrate-deficient transferrin (CDT) serum level as transferrin (Tf)-D-variant by means of isoelectric focusing].

Many studies have shown carbohydrate-deficient transferrin (CDT) to be a sensitive and specific marker of chronic alcohol abuse. We present the case of a 23-year-old, healthy professional soccer player who caused a car accident due to alcohol consumption. Several CDT test results were elevated above the laboratory reference range and were considered to be caused by alcohol intake at a level commensurate with misuse and thus license reapplication was refused. In addition, assuming chronic alcohol abuse, the young man suffered from increasing social isolation. He was finally referred to our out-patient clinic for further evaluation on the assumption of a liver disease. Since chronic alcohol consumption was denied, and there was no evidence of liver disease, a qualitative characterization of the transferrin isoforms was performed. Isoelectric focusing of serum transferrin revealed a pattern atypical for chronic alcohol intake but detected a genetically determined transferrin (Tf)-D-variant. The changed amino acid sequence caused an overlapping of transferrin isoforms with different degrees of sialylation, thus revealing false-positive serum CDT values. Determination of this Tf-D-variant heterozygosity resulted in his social rehabilitation and license reinstatement. Thus, where the evidence for alcohol dependency is either uncertain or uncorroborated, qualitative isoelectric focusing of transferrin is a useful method for analyzing unexplained CDT elevations, thus increasing the value of CDT as a marker for chronic alcoholic abuse.

Adult↗