Biomedical subjects

Chérif F Matta

Publications and source records attributed to Chérif F Matta.

12 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

Experimental and theoretical electron density study of estrone.

The electron density and the electrostatic potential (ESP) distributions of estrone have been determined using X-ray diffraction analysis and compared with theoretical calculations in the solid and gas phases. X-ray diffraction measurements are performed with a Rigaku Rapid rotating anode diffractometer at 20 K. The electron density in the estrone crystal has been described with the multipole model, which allowed extensive topological analysis and calculation of the ESP. From DFT calculations in the solid state a theoretical X-ray diffraction data set has been produced and treated in the same way as the experimental data. Two sets of single molecule DFT calculations were performed: (a) An electron density distribution was obtained via a single-point calculation with a large basis set at the experimental geometry and subsequently analyzed according to the quantum theory of atoms in molecules (AIM) to obtain the bond and most atomic properties, and (b) another electron density distribution was obtained with a smaller basis set, but at a geometry optimized using the same basis set for the analysis of atomic energies. An interesting locally stabilizing hydrogen-hydrogen bond path linking H(1) and H(11B) is found which represents the first characterization of such bonding in a steroid molecule. AIM delocalization indices were shown to be well correlated to the experimental electron density at the bond critical points through an exponential relationship. The aromaticity of ring A, chemical bonding, the O(1)...O(2) distance necessary for estrogenic activity, and the electrostatic potential features are also discussed.

Computer Simulation↗

PubMed2006

An experimentalist's reply to "What is an atom in a molecule?".

Parr, Ayers and Nalewajski have opined in this Journal that the concept of an atom in a molecule "is an object knowable by the mind or intellect, not by the senses." This view is countered by the two hundred years of experimental chemistry underlying the realization that the properties of some total system are the sum of its atomic contributions. This paper concludes that an experimentalist has no doubt but that he or she is measuring the properties of atoms when performing an experiment.

Journal Article↗

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

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↗

PubMed2004

Effect of absolute laser phase on reaction paths in laser-induced chemical reactions.

Potential surfaces, dipole moments, and polarizabilities are calculated by ab initio methods [unrestricted MP2(full)/6-311++G(2d,2p)] along the reaction paths of the F+CH4 and Cl+CH4 reaction systems. It is found that in general dipole moments and polarizabilities exhibit peaks near the transition state. In the case of X=F these peaks are on the products side and in the case of X=Cl they are on the reactants side indicating an early transition state in the case of fluorine and a late transition state in the case of chlorine. An analysis of the geometric changes along the reaction paths reveals a one-to-one correspondence between the peaks in the electric properties and peaks in the rate of change of certain internal geometric coordinates along the reaction path. Interaction with short infrared intense laser fields pulses leads to the possibility of interferences between the dipole and polarizability laser-molecule interactions as a function of laser phase. The larger dipole moment in the Cl+CH4 reaction can lead to the creation of deep wells (instead of energy barriers) and new strongly bound states in the transition state region. This suggests possible coherent control of the reaction path as a function of the absolute phase of the incident field, by significant modification of the potential surfaces along the reaction path and, in particular, in the transition state region.

Journal Article↗

PubMed2004

Chemistry on a peg-board: the effect of adatom-adatom separation on the reactivity of dihalobenzenes at Si(111)7 x 7 surfaces.

A simple model of the thermal dihalogenation of a silicon surface by an adsorbate, Br-R-Br, is described for the first time. The model consists of a pair of silyl radicals (SiH(3)), treated by density functional theory, placed a distance d apart. Two adsorbates were considered, one with R = benzene and one with R = biphenyl. The Br...Br internuclear separation (r(Br, Br)) in 1,4-dibromobenzene is 6.6 A, whereas that in 4,4'-dibromobiphenyl is 10.9 A. In the former case the model yields a (most-favourable) 'critical' separation d* approximately 10.2 A, corresponding to the lowest-energy barrier, and in the latter case d* approximately 13.8 A. The dangling-bond separations, d, were restricted to values present at an Si(111)7 x 7 surface. The critical values, d*, exceeded the corresponding value of r(Br, Br) in the intact adsorbate in each case by ca. 3.5 A, corresponding to ca. 93% of the van der Waals molecular size. This is approximately the observed increase in separation of a pair of halogen atoms in reactions at a Si surface, as compared with the separation in the parent molecule. If the dangling bonds at the surface are too close to one another (d < d*), the adsorbate molecules' charge cloud extends too far for a favourable interaction, whereas if the dangling bonds are too far apart (d < d*) the adsorbate's charge cloud cannot reach them. When the second reagent is a peg-board, the factors governing chemical reactivity are more exposed to view.

Journal Article↗

PubMed2003

Atoms-in-molecules study of the genetically encoded amino acids. III. Bond and atomic properties and their correlations with experiment including mutation-induced changes in protein stability and genetic coding.

This article presents a study of the molecular charge distributions of the genetically encoded amino acids (AA), one that builds on the previous determination of their equilibrium geometries and the demonstrated transferability of their common geometrical parameters. The properties of the charge distributions are characterized and given quantitative expression in terms of the bond and atomic properties determined within the quantum theory of atoms-in-molecules (QTAIM) that defines atoms and bonds in terms of the observable charge density. The properties so defined are demonstrated to be remarkably transferable, a reflection of the underlying transferability of the charge distributions of the main chain and other groups common to the AA. The use of the atomic properties in obtaining an understanding of the biological functions of the AA, whether free or bound in a polypeptide, is demonstrated by the excellent statistical correlations they yield with experimental physicochemical properties. A property of the AA side chains of particular importance is the charge separation index (CSI), a quantity previously defined as the sum of the magnitudes of the atomic charges and which measures the degree of separation of positive and negative charges in the side chain of interest. The CSI values provide a correlation with the measured free energies of transfer of capped side chain analogues, from the vapor phase to aqueous solution, yielding a linear regression equation with r2 = 0.94. The atomic volume is defined by the van der Waals isodensity surface and it, together with the CSI, which accounts for the electrostriction of the solvent, yield a linear regression (r2 = 0.98) with the measured partial molar volumes of the AAs. The changes in free energies of transfer from octanol to water upon interchanging 153 pairs of AAs and from cyclohexane to water upon interchanging 190 pairs of AAs, were modeled using only three calculated parameters (representing electrostatic and volume contributions) yielding linear regressions with r2 values of 0.78 and 0.89, respectively. These results are a prelude to the single-site mutation-induced changes in the stabilities of two typical proteins: ubiquitin and staphylococcal nuclease. Strong quadratic correlations (r2 approximately 0.9) were obtained between DeltaCSI upon mutation and each of the two terms DeltaDeltaH and TDeltaDeltaS taken from recent and accurate differential scanning calorimetry experiments on ubiquitin. When the two terms are summed to yield DeltaDeltaG, the quadratic terms nearly cancel, and the result is a simple linear fit between DeltaDeltaG and DeltaCSI with r2 = 0.88. As another example, the change in the stability of staphylococcal nuclease upon mutation has been fitted linearly (r2 = 0.83) to the sum of a DeltaCSI term and a term representing the change in the van der Waals volume of the side chains upon mutation. The suggested correlation of the polarity of the side chain with the second letter of the AA triplet genetic codon is given concrete expression in a classification of the side chains in terms of their CSI values and their group dipole moments. For example, all amino acids with a pyrimidine base as their second letter in mRNA possess side-chain CSI < or = 2.8 (with the exception of Cys), whereas all those with CSI > 2.8 possess an purine base. The article concludes with two proposals for measuring and predicting molecular complementarity: van der Waals complementarity expressed in terms of the van der Waals isodensity surface and Lewis complementarity expressed in terms of the local charge concentrations and depletions defined by the topology of the Laplacian of the electron density. A display of the experimentally accessible Laplacian distribution for a folded protein would offer a clear picture of the operation of the "stereochemical code" proposed as the determinant in the folding process.

Amino Acids↗

PubMed2003

Hydrogen-hydrogen bonding: a stabilizing interaction in molecules and crystals.

Bond paths linking two bonded hydrogen atoms that bear identical or similar charges are found between the ortho-hydrogen atoms in planar biphenyl, between the hydrogen atoms bonded to the C1-C4 carbon atoms in phenanthrene and other angular polybenzenoids, and between the methyl hydrogen atoms in the cyclobutadiene, tetrahedrane and indacene molecules corseted with tertiary-tetra-butyl groups. It is shown that each such H-H interaction, rather than denoting the presence of "nonbonded steric repulsions", makes a stabilizing contribution of up to 10 kcal mol(-1) to the energy of the molecule in which it occurs. The quantum theory of atoms in molecules-the physics of an open system-demonstrates that while the approach of two bonded hydrogen atoms to a separation less than the sum of their van der Waals radii does result in an increase in the repulsive contributions to their energies, these changes are dominated by an increase in the magnitude of the attractive interaction of the protons with the electron density distribution, and the net result is a stabilizing change in the energy. The surface virial that determines the contribution to the total energy decrease resulting from the formation of the H-H interatomic surface is shown to account for the resulting stability. It is pointed out that H-H interactions must be ubiquitous, their stabilization energies contributing to the sublimation energies of hydrocarbon molecular crystals, as well as solid hydrogen. H-H bonding is shown to be distinct from "dihydrogen bonding", a form of hydrogen bonding with a hydridic hydrogen in the role of the base atom.

Journal Article↗

PubMed2003

Application of the quantum theory of atoms in molecules to selected physico-chemical and biophysical problems: focus on correlation with experiment.

This article reviews how the quantum theory of atoms in molecules (QTAIM) can be used to predict experimental physico-chemical properties of molecules of biologic interest: the amino acids, the polycyclic aromatic hydrocarbons (PAH), and the opiates, for example, morphine and PEO. The predicted experimental properties are as diverse as the partial molar volumes, the free energies of hydration, the second code-letter in the genetic code, the resonance energies, and the proton spin-spin coupling constants. Recent examples of the utilization of QTAIM to construct excellent statistical models (with squared correlation coefficients (r(2)) > 0.9) correlating properties of the electron density and of the pair density to experiment are reviewed. Some new results on the solvent effects on electron delocalization are also presented.

Algorithms↗

PubMed2002

Atoms-in-molecules study of the genetically encoded amino acids. II. Computational study of molecular geometries.

The geometries of the 20 genetically encoded amino acids were optimized at the restricted Hartree-Fock level of theory using the 6-31+G* basis set. A detailed comparison showed the calculated geometries to be in excellent agreement with those determined by X-ray crystallography. The study demonstrated that the geometric parameters for the main-chain group and for the bonds and common functional groups of the side-chains exhibit a high degree of transferability among the members of this set of molecules. This geometric transferability is a necessary prerequisite for the corresponding transferability of their electron density distributions and hence of their bond and atomic properties. The transferability of the electron distributions will be demonstrated and exploited in the following paper of this series, which uses the topology of the electron density to define an atom within the quantum theory of atoms in molecules. Particular features of the geometries of the amino acids are discussed. It has been shown, for example, how the apparent anomaly of the Calpha-N bond length in a peptide being shorter than in the charged species Calpha-NH3+ is resolved when the charge separation is gauged by the differences in the charges of the Calpha and N atoms as opposed to the use of formal charges. A compilation of literature sources on experimental geometries covering each member of the 20 amino acids is presented. A set of rules for labeling the atoms and bonds, complementing the generally accepted IUPAC-IUB rules, is proposed to uniquely identify every atom and bond in the amino acids.

Amino Acids↗

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↗