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Paul Geerlings

Publications and source records attributed to Paul Geerlings.

32 records · Page 2Linked to original sources
PubMed2005

Comprehensive study of density functional theory based properties for group 14 atoms and functional groups, -XY3 (X = C, Si, Ge, Sn, Pb, Element 114; Y = CH3, H, F, Cl, Br, I, At).

All electron nonrelativistic and relativistic density functional theory calculations at the BP86/QZ4P (Slater type) level are reported for a set of fundamentally useful DFT based reactivity descriptors for group 14 elements (C, Si, Ge, Sn, Pb, Element 114 (abbreviated as Uuq)) and functional groups, -XY3 (X = C, Si, Ge, Sn, Pb, Element 114 (Uuq); Y = CH3, H, F, Cl, Br, I, At); these include electronegativity (chi), chemical hardness (eta), global softness (S), and electrophilicity index (omega). This approach permits an evaluation of the discrepancies in electronegativity scales and associated properties at uniform levels affording a nonempirical analysis for the first time. The vital importance of the spin-orbit interaction, in addition to the scalar relativistic terms, is demonstrated in reproducing the experimental trends on going from top to bottom of the group. The order for isolated atoms is altered when passing to -XY3 groups for all of the properties studied. For example, the calculated atomic electronegativities show a uniform decrease from C to Pb increasing again to Uuq as verified in the experimental data for C-Pb but at variance with several other scales. The sequence for functional groups is different and in accordance with experimental NMR data where available. The experimental hardness sequence for the isolated atoms (C > Pb > Si > Ge > Sn) is opposed to the trends of decreasing hardness on going down the periodic table as is found, e.g., in the halogen group and confirmed by this study. The -XY3 functional groups however follow the C > Si > Ge > Sn > Pb sequence. The recently developed electrophilicity index (omega) has been shown to be highly correlated with the electron affinity rather than the electronegativity. Finally, regression analyses that discriminate between the properties are carried out to investigate the nature of additivity of atomic contributions in functional group properties.

Journal Article↗
PubMed2005

Influence of the pi-pi interaction on the hydrogen bonding capacity of stacked DNA/RNA bases.

The interplay between aromatic stacking and hydrogen bonding in nucleobases has been investigated via high-level quantum chemical calculations. The experimentally observed stacking arrangement between consecutive bases in DNA and RNA/DNA double helices is shown to enhance their hydrogen bonding ability as opposed to gas phase optimized complexes. This phenomenon results from more repulsive electrostatic interactions as is demonstrated in a model system of cytosine stacked offset-parallel with substituted benzenes. Therefore, the H-bonding capacity of the N3 and O2 atoms of cytosine increases linearly with the electrostatic repulsion between the stacked rings. The local hardness, a density functional theory-based reactivity descriptor, appears to be a key index associated with the molecular electrostatic potential (MEP) minima around H-bond accepting atoms, and is inversely proportional to the electrostatic interaction between stacked molecules. Finally, the MEP minima on surfaces around the bases in experimental structures of DNA and RNA-DNA double helices show that their hydrogen bonding capacity increases when taking more neighboring (intra-strand) stacking partners into account.

Base Pairing↗
PubMed2005

Theoretical study of the addition patterns of C60 fluorination: C60Fn (n = 1-60).

A systematic study is presented of addition patterns occurring upon fluorination of C60. We use the program SACHA, which increments the number of fluorine addends, tests all available addition sites within a given cutoff radius, and selects the most energetically stable structure for further addition on the basis of full AM1 optimizations for every isomer. The lowest energy structures are optimized at HF/3-21G level of theory. A number of distinct addition routes are predicted, based on octahedral, 'S', and 'T' addition patterns, leading both to experimentally observed C60F(n) isomers and to isomers not previously described in the literature. Furthermore the main addition routes were analyzed for C60F2n isomers, using ab initio global and local aromaticity calculations. For this, magnetizability and NICS calculations have been carried out at HF/3-21G level of theory. We show the possibility of using NICS to predict the next preferential addition site, matching the above-described addition routes.

Journal Article↗
PubMed2005

Hard-soft acid-base interactions of silylenes and germylenes.

A detailed investigation of the electrophilic and nucleophilic character of singlet silylenes and germylenes, divalent compounds of silicon and germanium, respectively, substituted by first- and second-row elements is presented. In a first part, the Lewis acid properties of these compounds were studied through their complexation reaction with the Lewis bases NH3, PH3, and AsH3. The results indicate that this complexation is most favorable with the hardest base NH3, classifying these compounds as hard Lewis acids. This is confirmed by the linear correlation between the interaction energies and the value of the electrostatic potential, used as an approximation to the local hardness, near the empty p orbital of these compounds, indicating a charge-controlled interaction in the complex. Also the electrophilicity index, proposed by Parr et al., computed both at the global and the local level, correlates linearly with the complexation energies of the compounds with NH3. The Lewis base character of these silylenes has been investigated, through their interaction with the acids BH3 and AlH3. Also in this case, the electrostatic potential can be used to probe the reactivity of the compounds. It will finally be demonstrated that an increasing stability of the silylenes and germylenes is accompanied by an increase in their nucleophilicity and a decrease of the electrophilicity.

Journal Article↗
PubMed2005

Gas-phase stability of tetrahedral multiply charged anions: a conceptual and computational DFT study.

Multiply charged anions (MCA's) are unstable relative to electron autoejection; however, the repulsive Coulomb barrier (RCB) provides electronic stability. In view of their interest in biological systems, the behavior of isolated AsO(4)(3-), PO(4)(3-), SO(4)(2-), and SeO(4)(2-) in the gas phase and in solution has been studied. To calculate the RCB values, the electrostatic and point charge model-two methods currently used in the literature-are applied, together with a recently introduced Conceptual Density Functional Theory (DFT) based approach. The relative stability of the above-mentioned MCA's is compared. The trends of the RCB are analyzed by including analogous compounds from the second and third row and by passing from dianionic to trianionic systems. Considering the effect of solvent, using the SCI-PCM solvent model, the evolution of the RCB when passing to higher dielectric constants is evaluated. The RCB is related to the properties of the system as polarizability/softness. Both a numerical and a conceptual correlation between the RCB and the global softness is found.

Anions↗
PubMed2005

Substrate-assisted leaving group activation in enzyme-catalyzed N-glycosidic bond cleavage.

In enzymatic depurination of nucleosides, the 5'-OH group of the ribose moiety of the substrate is often shown to contribute substantially to catalysis. The purine-specific nucleoside hydrolase from Trypanosoma vivax (TvNH) fixes the 5'-OH group in a gauche,trans orientation about the C4'-C5' bond, enabling the 5'-oxygen to accept an intramolecular hydrogen bond from the C8-atom of the purine leaving group. High level ab initio quantum chemical calculations indicate that this interaction promotes protonation of the purine at N7. Steady state kinetics comprising engineered substrates confirm that a considerable fraction of the catalytic 5'-OH effect can be attributed to leaving group activation.

Animals↗
PubMed2004

Leaving group activation by aromatic stacking: an alternative to general acid catalysis.

General acid catalysis is a powerful and widely used strategy in enzymatic nucleophilic displacement reactions. For example, hydrolysis/phosphorolysis of the N-glycosidic bond in nucleosides and nucleotides commonly involves the protonation of the leaving nucleobase concomitant with nucleophilic attack. However, in the nucleoside hydrolase of the parasite Trypanosoma vivax, crystallographic and mutagenesis studies failed to identify a general acid. This enzyme binds the purine base of the substrate between the aromatic side-chains of Trp83 and Trp260. Here, we show via quantum chemical calculations that face-to-face stacking can raise the pKa of a heterocyclic aromatic compound by several units. Site-directed mutagenesis combined with substrate engineering demonstrates that Trp260 catalyzes the cleavage of the glycosidic bond by promoting the protonation of the purine base at N-7, hence functioning as an alternative to general acid catalysis.

Acids↗
PubMed2004

Quantum chemical study of the reactivity of C60HR and C60(CHR) derivatives.

In the present work a quantum chemical study of a series of substituted hydrofullerenes, C(60)HR, and a series of methanofullerenes, C(60)(CHR), is presented. Their reactivity and geometrical, energetic, electronic, and magnetic properties, as well as the influence of the substituent, are discussed. As a probe of the reactivity, the acidic properties of these fullerene derivatives were predicted, based on the calculated deprotonation energies, with a previously set up scheme. The electronic delocalization upon deprotonation was described, and the global (magnetizabilities) and local aromaticity (nucleus-independent chemical shifts) was analyzed and compared with respect to the group properties for the series of functional groups. The geometries of both acidic and basic forms were fully optimized at the AM1 level, and all property calculations were performed at the HF/3-21G and the B3LYP/6-31G* level of theory.

Journal Article↗
PubMed2004

Ring currents as probes of the aromaticity of inorganic monocycles : P5-, As5-, S2N2, S3N3-, S4N3+, S4N42+, S5N5+, S42+ and Se42+.

Current-density maps were calculated by the ipsocentric CTOCD-DZ/6-311G** (CTOCD-DZ=continuous transformation of origin of current density-diamagnetic zero) approach for three sets of inorganic monocycles: S(4) (2+), Se(4) (2+), S(2)N(2), P(5) (-) and As(5) (-) with 6 pi electrons; S(3)N(3) (-), S(4)N(3) (+) and S(4)N(4) (2+) with 10 pi electrons; and S(5)N(5) (+) with 14 pi electrons. Ipsocentric orbital analysis was used to partition the currents into contributions from small groups of active electrons and to interpret the contributions in terms of symmetry- and energy-based selection rules. All nine systems were found to support diatropic pi currents, reinforced by sigma circulations in P(5) (-), As(5) (-), S(3)N(3) (-), S(4)N(3) (+), S(4)N(4) (2+) and S(5)N(5) (+), but opposed by them in S(4) (2+), Se(4) (2+) and S(2)N(2). The opposition of pi and sigma effects in the four-membered rings is compatible with height profiles of calculated NICS (nucleus-independent chemical shifts).

Journal Article↗
PubMed2003

Ab initio study of the binding of Trichostatin A (TSA) in the active site of histone deacetylase like protein (HDLP).

Histone deacetylase (HDAC) inhibitors have recently attracted considerable interest because of their therapeutic potential for the treatment of cell proliferative diseases. An X-ray structure of a very potent inhibitor, Trichostatin A (TSA), bound to HDLP (an HDAC analogue isolated from Aquifex aeolicus), is available. From this structure, an active site model (322 atoms), relevant for the binding of TSA and structural analogues, has been derived, and TSA has been minimized in this active site at HF 3-21G* level. The resulting conformation is in excellent accordance with the X-ray structure, and indicates a deprotonation of the hydroxamic acid in TSA by His 131. Also, a water molecule was minimized in the active site. In addition to a similar deprotonation, in accordance with a possible catalytic mechanism of HDAC as proposed by Finnin et al. (M. S. Finnin, J. R. Donigian, A. Cohen, V. M. Richon, R. A. Rifkind and P. A. Marks, Nature, 1999, 401, 188-193), a displacement of the resulting OH- ion in the active site was observed. Based on these results, the difference in energy of binding between TSA and water was calculated. The resulting value is realistic in respect to experimental binding affinities. Furthermore, the mechanism of action of the His 131-Asp 166 charge relay system was investigated. Although the Asp residue in this motif is known to substantially increase the basicity of the His residue, no proton transfer from His 131 to Asp 166 was observed on binding of TSA or water. However, in the empty protonated active site, this proton transfer does occur.

Bacterial Proteins↗
PubMed2002

Magnetic properties and aromaticity of o-, m-, and p-benzyne.

The relative aromaticities of the three singlet benzyne isomers, 1,2-, 1,3-, and 1,4-didehydrobenzenes have been evaluated with a series of aromaticity indicators, including magnetic susceptibility anisotropies and exaltations, nucleus-independent chemical shifts (NICS), and aromatic stabilization energies (all evaluated at the DFT level), as well as valence-bond Pauling resonance energies. Most of the criteria point to the o-benzyne<m-benzyne<p-benzyne aromaticity order, whereas the relative aromaticity of each isomer with respect to benzene depends on the aromaticity criterion. An additional aromaticity evaluation involved the transition state of the Bergman cyclization of (Z)-hexa-1,5-diyn-3-ene which yields p-benzyne. Dissected NICS calculations reveal an aromatic transition state with a larger total NICS but a smaller NICS(pi) component and thus lower aromaticity than benzene.

Journal Article↗
PubMed2002

A nucleophile activation dyad in ribonucleases. A combined X-ray crystallographic/ab initio quantum chemical study.

Ribonucleases (RNases) catalyze the cleavage of the phosphodiester bond in RNA up to 10(15)-fold, as compared with the uncatalyzed reaction. High resolution crystal structures of these enzymes in complex with 3'-mononucleotide substrates demonstrate the accommodation of the nucleophilic 2'-OH group in a binding pocket comprising the catalytic base (glutamate or histidine) and a charged hydrogen bond donor (lysine or histidine). Ab initio quantum chemical calculations performed on such Michaelis complexes of the mammalian RNase A (EC ) and the microbial RNase T(1) (EC ) show negative charge build up on the 2'-oxygen upon substrate binding. The increased nucleophilicity results from stronger hydrogen bonding to the catalytic base, which is mediated by a hydrogen bond from the charged donor. This hitherto unrecognized catalytic dyad in ribonucleases constitutes a general mechanism for nucleophile activation in both enzymic and RNA-catalyzed phosphoryl transfer reactions.

Binding Sites↗
PubMed1998

The Basicity of p-Substituted Phenolates and the Elimination-Substitution Ratio in p-Nitrophenethyl Bromide: A HSAB Theoretical Study.

The influence of basicity in a set of para-substituted phenolates on the elimination-substitution ratio obtained upon reaction with p-nitrophenethyl bromide has been studied. A correlation between experimental equilibrium data (pK(a)) and reactivity indices obtained from density functional theory (DFT) was looked for in order to show that the hard and soft acids and bases principle (HSAB) is well suited to describe the basicity properties of the para-substituted phenolates. When the basicity of para-substituted phenolates increases, their global hardness and their condensed softness at the oxygen atom increase; the negative net charge, condensed nucleophilic fukui function, and condensed nucleophilic softness of the oxygen atom increase. The proposal that the alkyl halide substrate possesses a hard beta-hydrogen atom and a soft alpha-carbon was studied for p-nitrophenethyl bromide; it turns out that the beta-hydrogen atom is soft, even softer than the carbon atom. The experimental results for the elimination-substitution ratio for p-nitrophenethyl bromide can be explained from a local-local HSAB viewpoint for the para-substituted phenolates and p-nitrophenethyl bromide and not from a global-local level viewpoint as suggested before. The results suggest that para-substituted phenolates with higher basicity (harder), less delocalized negative charge into the fragment R-C(6)H(4), and a more polarizable oxygen atom (softer) do have a lower (relative) attraction toward an alkyl carbon atom (soft) than toward a hydrogen atom (softer) from p-nitrophenethyl bromide. The beta-hydrogen and alpha-carbon atoms can be considered to act as a Lewis acid toward the para-substituted phenolate nucleophile considered as a base.

Journal Article↗