Biomedical subjects

Paul Geerlings

Publications and source records attributed to Paul Geerlings.

At least 19 recordsLinked to original sources

PubMed2007

On the quality of the hardness kernel and the Fukui function to evaluate the global hardness.

An approximated hardness kernel, which includes the second derivative with respect to the density of the kinetic energy, the electron-electron coulomb repulsion, and the exchange density functionals, has been tested for the calculation of the global hardness. The results obtained for a series of 40 cations and neutral systems and 16 anions represent in most cases an improvement of the results obtained using the HOMO-LUMO gap approach and indicate the viability of this approach to evaluate global hardness. In addition, the relevance of the Fukui function approximation and the role of the three components of the hardness kernel in the evaluation of the global hardness have been analyzed.

Anions↗

PubMed2006

Analogies and differences between two ways to evaluate the global hardness.

The weight of the energetic components (electronic kinetic, electron-nucleus and electron-electron Coulombic, and correlation energies) of the ionization potential, electron affinity, chemical potential, and global hardness is evaluated and contrasted with the energetic components of the hardness kernel and the experimental values of these properties for 40 systems. The contrast of the hardness terms obtained from finite difference and hardness kernel gives some insight on the possible implications to differentiate the electronic energy with respect to the number electrons or the electron density.

Journal Article↗

PubMed2006

Understanding the concept of basicity in zeolites. A DFT study of the methylation of Al-O-Si bridging oxygen atoms.

DFT calculations on a 4-ring cluster and on ONIOM models of faujasite were carried out to assess the concept of basicity in zeolites, exchanged with alkali cations. The considered reaction is the methylation of the Si-O-Al bridging oxygen by methanol and methyl iodide. The reaction involves both the dissociation of the H3C-OH or H3C-I bonds and the formation of the C-O-zeolite bond. The former involves the hardness of the alkaline cation. The latter reflects the charge density of the basic oxygen, well described by the "hard" descriptor: the molecular electrostatic potential. The harder is the alkali metal, the easier is the H3C-OH or H3C-I bond dissociation, and the lower is the basicity of the bridging oxygen, and thus the more difficult is the C-O-zeolite bond formation. The fact that these two processes compete has been established by comparing the energy profiles for the methylation with methyl iodide and methanol. For methanol the role of the alkaline metal on the bond dissociation prevails because of the larger hardness of the OH group as compared to that of the iodine atom. For methyl iodide the oxygen basicity prevails over the interaction of I with metal. This study clearly shows that in both experimental and theoretical studies the role of the Lewis acidity or hardness of the alkali metal ion and the role of the basicity of the framework oxygen have to be separated from each other for a good interpretation of zeolite basicity. Also, the hardness of the probe molecule is particularly important when considering the interaction with the alkali metal ion.

Journal Article↗

PubMed2006

Woodward-Hoffmann rules in density functional theory: initial hardness response.

The Woodward-Hoffmann rules for pericyclic reactions, a fundamental set of reactivity rules in organic chemistry, are formulated in the language of conceptual density functional theory (DFT). DFT provides an elegant framework to introduce chemical concepts and principles in a quantitative manner, partly because it is formulated without explicit reference to a wave function, on whose symmetry properties the Woodward-Hoffmann [J. Am. Chem. Soc. 87, 395 (1965)] rules are based. We have studied the initial chemical hardness response using a model reaction profile for two prototypical pericyclic reactions, the Diels-Alder cycloaddition of 1,3-butadiene to ethylene and the addition of ethylene to ethylene, both in the singlet ground state and in the first triplet excited state. For the reaction that is thermally allowed but photochemically forbidden, the initial hardness response is positive along the singlet reaction profile. (By contrast, for the triplet reaction profile, a negative hardness response is observed.) For the photochemically allowed, thermally forbidden reaction, the behavior of the chemical hardness along the initial stages of the singlet and triplet reaction profiles is reversed. This constitutes a first step in showing that chemical concepts from DFT can be invoked to explain results that would otherwise require invoking the phase of the wave function.

Journal Article↗

PubMed2006

Molecular quantum similarity of enantiomers: substituted allenes.

Molecular quantum similarity is evaluated for enantiomers in the case of molecules possessing a chiral axis, as an extension of previous studies on molecules with a single asymmetric carbon atom. As a case study, the enantiomers of substituted allenes are examined. Next to studying global similarity, using the already existing similarity indices defined by Carbó and Hodgkin-Richards, we evaluate local similarity using our earlier proposed local similarity index based on the Hirshfeld partitioning, to quantify the consequences of Mezey's holographic electron density theorem in chiral systems. Furthermore, the relation between the optical activity and the dissimilarity is studied.

Alkadienes↗

PubMed2006

A group electronegativity equalization scheme including external potential effects.

By calculating the electron affinity and ionization energy of different functional groups, CCSD electronegativity values are obtained, which implicitly account for the effect of the molecular environment. This latter is approximated using a chemically justified point charge model. On the basis of Sanderson's electronegativity equalization principle, this approach is shown to lead to reliable "group in molecule" electronegativities. Using a slight adjustment of the modeled environment and first-order principles, an electronegativity equalization scheme is obtained, which implicitly accounts for the major part of the external potential effect. This scheme can be applied in a predictive manner to estimate the charge transfer between two functional groups, without having to rely on cumbersome calibrations. A very satisfactory correlation is obtained between these charge transfers and those obtained from an ab initio calculation of the entire molecule.

Journal Article↗

PubMed2006

Hartree-Fock energy partitioning in terms of Hirshfeld atoms.

A Hirshfeld decomposition scheme of the Hartree-Fock total molecular energy into atomic energies is presented. The calculations are performed by direct numerical integration and the results are compared for a set of 28 molecules containing different kinds of atoms. The calculated atomic energies show a strong dependency on changes of atomic electron population and hybridization. Linear correlations are found between the energy and the population for H, these being related to the electronegativity of this atom and to the external potential created by the remaining atoms. The proposed energy partitioning scheme appears to be useful for studies such as proton acidity, the anomeric effect and group transferability, and allows atomic virial ratios to be obtained. Finally, the atomic potential energies are found to mimic trends based on exact expressions as well as trends displayed by molecular quantities, thus lending credibility to the partitioning scheme used.

Journal Article↗

PubMed2006

Interplay between ion binding and catalysis in the thioredoxin-coupled arsenate reductase family.

In the thioredoxin (Trx)-coupled arsenate reductase family, arsenate reductase from Staphylococcus aureus plasmid pI258 (Sa_ArsC) and from Bacillus subtilis (Bs_ArsC) are structurally related detoxification enzymes. Catalysis of the reduction of arsenate to arsenite involves a P-loop (Cys10Thr11Gly12Asn13Ser14Cys15Arg16) structural motif and a disulphide cascade between three conserved cysteine residues (Cys10, Cys82 and Cys89). For its activity, Sa_ArsC benefits from the binding of tetrahedral oxyanions in the P-loop active site and from the binding of potassium in a specific cation-binding site. In contrast, the steady-state kinetic parameters of Bs_ArsC are not affected by sulphate or potassium. The commonly occurring mutation of a histidine (H62), located about 6 A from the potassium-binding site in Sa_ArsC, to a glutamine uncouples the kinetic dependency on potassium. In addition, the binding affinity for potassium is affected by the presence of a lysine (K33) or an aspartic acid (D33) in combination with two negative charges (D30 and E31) on the surface of Trx-coupled arsenate reductases. In the P-loop of the Trx-coupled arsenate reductase family, the peptide bond between Gly12 and Asn13 can adopt two distinct conformations. The unique geometry of the P-loop with Asn13 in beta conformation, which is not observed in structurally related LMW PTPases, is stabilized by tetrahedral oxyanions and decreases the pK(a) value of Cys10 and Cys82. Tetrahedral oxyanions stabilize the P-loop in its catalytically most active form, which might explain the observed increase in k(cat) value for Sa_ArsC. Therefore, a subtle interplay of potassium and sulphate dictates the kinetics of Trx-coupled arsenate reductases.

Amino Acid Sequence↗

PubMed2006

Interpretation of hydrogen bonding in the weak and strong regions using conceptual DFT descriptors.

Hydrogen bonding is among the most fundamental interactions in biology and chemistry, providing an extra stabilization of 1-40 kcal/mol to the molecular systems involved. This wide range of stabilization energy underlines the need for a general and comprehensive theory that will explain the formation of hydrogen bonds. While a simple electrostatic model is adequate to describe the bonding patterns in the weak and moderate hydrogen bond regimes, strong hydrogen bonds, on the other hand, require a more complete theory due to the appearance of covalent interactions. In this study, conceptual DFT tools such as local hardness, eta(r) and local softness, s(r), have been used in order to get an alternative view on solving this hydrogen-bonding puzzle as described by Gilli et al. [J. Mol. Struct. 2000, 552, 1]. A series of both homonuclear and heteronuclear resonance-assisted hydrogen bonds of the types O-H...N, N-H...O, N-H...N, and O-H...O with strength varying from weak to very strong have been studied. First of all, DeltaPA and DeltapK(a) values were calculated and correlated to the hydrogen bond energy. Then the electrostatic effects were examined as hard-hard interactions accessible through molecular electrostatic potential, natural population analysis (NPA) charge, and local hardness calculations. Finally, secondary soft-soft interaction effects were entered into the picture described by the local softness values, providing insight into the covalent character of the strong hydrogen bonds.

Acrylates↗

PubMed2006

Study of molecular quantum similarity of enantiomers of amino acids.

Molecular quantum similarity is evaluated for enantiomers in the case of molecules showing conformational flexibility, using our earlier proposed Boltzmann weighted similarity index. The conformers of the enantiomers of the amino acids alanine, asparagine, cysteine, leucine, serine, and valine were examined. Next to studying global indices, the evaluation of local similarity is carried out using our earlier proposed local similarity index based on the Hirshfeld partitioning, to further illustrate Mezey's holographic electron density theorem in chiral systems and to quantify dissimilarity of enantiomers.

Amino Acids↗

PubMed2006

Origin of the pKa perturbation of N-terminal cysteine in alpha- and 3(10)-helices: a computational DFT study.

It is well documented that helices in proteins can decrease the pKa of residues located at the N-terminus, but the real nature of this perturbation remains unclear. In the present work, the origin of the effect of 3(10)- and alpha-polyalanine helices on the pKa of an N-terminal cysteine residue is examined in gas phase as well as in aqueous solution by means of density functional theory. In a systematic study of the helix dipole, the proton affinity (PA), and the pKa of the N-terminal cysteine, in relation to both the helix length and the strength of the hydrogen bonds between the helix backbone amides and the Sgamma of the N-terminal cysteine, a direct relation between the terminal hydrogen bonds and the pKa perturbation is revealed.

Cysteine↗

PubMed2006

The activation of electrophile, nucleophile and leaving group during the reaction catalysed by pI258 arsenate reductase.

The reduction of arsenate to arsenite by pI258 arsenate reductase (ArsC) combines a nucleophilic displacement reaction with a unique intramolecular disulfide cascade. Within this reaction mechanism, the oxidative equivalents are translocated from the active site to the surface of ArsC. The first reaction step in the reduction of arsenate by pI258 ArsC consists of a nucleophilic displacement reaction carried out by Cys10 on dianionic arsenate. The second step involves the nucleophilic attack of Cys82 on the Cys10-arseno intermediate formed during the first reaction step. The onset of the second step is studied here by using quantum chemical calculations in a density functional theory context. The optimised geometry of the Cys10-arseno adduct in the ArsC catalytic site (sequence motif: Cys10-Thr11-Gly12-Asn13-Ser14-Cys15-Arg16-Ser17) forms the starting point for all subsequent calculations. Thermodynamic data and a hard and soft acids and bases (HSAB) reactivity analysis show a preferential nucleophilic attack on a monoanionic Cys10-arseno adduct, which is stabilised by Ser17. The P-loop active site of pI258 ArsC activates first a hydroxy group and subsequently arsenite as the leaving group, as is clear from an increase in the calculated nucleofugality of these groups upon going from the gas phase to the solvent phase to the enzymatic environment. Furthermore, the enzymatic environment stabilises the thiolate form of the nucleophile Cys82 by 3.3 pH units through the presence of the eight-residue alpha helix flanked by Cys82 and Cys89 (redox helix) and through a hydrogen bond with Thr11. The importance of Thr11 in the pKa regulation of Cys82 was confirmed by the observed decrease in the kcat value of the Thr11Ala mutant as compared to that of wild-type ArsC. During the final reaction step, Cys89 is activated as a nucleophile by structural alterations of the redox helix that functions as a pKa control switch for Cys89; this final step is necessary to expose a Cys82-Cys89 disulfide.

Arsenates↗

PubMed2005

The importance of the external potential on group electronegativity.

The electronegativity of groups placed in a molecular environment is obtained using CCSD calculations of the electron affinity and ionization energy. A point charge model is used as an approximation of the molecular environment. The electronegativity values obtained in the presence of a point charge model are compared to the isolated group property to estimate the importance of the external potential on the group's electronegativity. The validity of the "group in molecule" electronegativities is verified by comparing EEM (electronegativity equalization method) charge transfer values to the explicitly calculated natural population analysis (NPA) ones, as well as by comparing the variation in electronegativity between the isolated functional group and the functional group in the presence of a modeled environment with the variation based on a perturbation expansion of the chemical potential.

Journal Article↗

PubMed2005

Hardness and softness reactivity kernels within the spin-polarized density-functional theory.

Generalized hardness and softness reactivity kernels are defined within a spin-polarized density-functional theory (SP-DFT) conceptual framework. These quantities constitute the basis for the global, local (i.e., r-position dependent), and nonlocal (i.e., r and r'-position dependents) indices devoted to the treatment of both charge-transfer and spin-polarization processes in such a reactivity framework. The exact relationships between these descriptors within a SP-DFT framework are derived and the implications for chemical reactivity in such context are outlined.

Journal Article↗

PubMed2005

Density-functional theory-based chemical reactivity indices in the Hartree-Fock method. I. Unrestricted Hartree-Fock method for a noninteger number of electrons.

Correct evaluation of the reactivity indices, such as chemical potential, hardness, and Fukui function demands for the extension of the formalism beyond the integer particle picture. An ensemble approach is used as an extension of the unrestricted Hartree-Fock (UHF) method for noninteger electron number systems. A prescription is given for the construction of an ensemble Fock operator for a system with partially filled spin-orbitals. The comparison between the ensemble HF method and the hyper-HF method in terms of density matrices and spin-orbitals is presented. The equivalence of the equiensemble case and the ensemble UHF case with unequal weight factors is shown.

Journal Article↗

PubMed2005

DFT-based chemical reactivity indices in the Hartree-Fock method. II. Fukui function, chemical potential, and hardness.

A derivation of the density-functional-theory- (DFT) based reactivity indices in the ensemble unrestricted Hartree-Fock (eUHF) method is presented. The comparison between the properties of the reactivity indices evaluated in one and two sets of spin-orbital approach of the eUHF and hyper-unrestricted Hartree-Fock (UHF) methods are shown. All approaches give similar Fukui function irrespective of methodology used, but significantly differ for the global indices, containing important chemical information, and so their interpretation in terms of DFT- based indices can be questionable. The calculation scheme for the indices using the first- and second-order coupled perturbed eHF equations is proposed. A method for the identification of the spinorbitals involved in the change of the total number of electrons is included. The illustrative examples (water and hydrogen cyanide) show that the ground-state (GS) properties of the (Z +/- 1)-electron systems can be predicted from the GS properties of the Z-electron systems with an accuracy comparable with the UHF calculations. The relaxation effect, important for the HCN system in which a change in the symmetry of the highest-occupied spin-orbital occurs, is effectively predicted.

Journal Article↗

PubMed2005

Spin-polarized conceptual density functional theory study of the regioselectivity in the [2+2] photocycloaddition of enones to substituted alkenes.

A study of the regioselectivity of the photochemical [2+2] cycloaddition of triplet enones with a series of ground-state electron-rich and electron-poor alkenes using density functional theory (DFT)-based reactivity descriptors is presented. Using the concepts of local softness combined with a local hard and soft acids and bases principle and a softness matching approach, the regioselectivity of this reaction can only be explained in the case of the interaction of the triplet enones with electron-rich alkenes. In the next part, the regioselectivity was assessed within the framework of conceptual spin-polarized conceptual DFT, considering response functions of the system's external potential v, number of electrons N, and spin number NS (with NS being the difference between the number of alpha and beta electrons in the spin-polarized system). Within this theory, the concepts of local spin philicity and donicity are introduced. Using the spin philicity concept, the regioselectivity can almost be completely interpreted as resulting from the interaction of the site on the alkene with the highest spin philicity (i.e., lowest destabilization upon increasing spin number) with the site showing the highest change of spin number on the enone expected to result in the largest stabilization of this species.

Journal Article↗

PubMed2005

Stiffness and Raman intensity: a conceptual and computational DFT study.

A DFT-based reactivity descriptor, the nuclear stiffness, is related to the Raman scattering intensity, which is experimentally accessible. The application of this new relationship obtained within certain approximations has been checked in two different sets of molecules. First, we study a favorable case, where the contribution of the anisotropy to the Raman intensity is zero (symmetric stretching mode in 15 tetrahedral molecules). Second, we consider a "worst" case scenario, where the anisotropy contribution can be expected to be important (stretching mode in 32 diatomic molecules). The numerical results clearly show a relationship between stiffness and Raman intensity reflecting the expected anisotropy influence.

Journal Article↗