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Zdenek Havlas

Publications and source records attributed to Zdenek Havlas.

10 recordsLinked to original sources
PubMed2006

Interaction of carboranes with biomolecules: formation of dihydrogen bonds.

Noncovalent interactions of the polyhedral carborane 1-carba-closo-dodecaborane (CB(11)H(12))(-) with building blocks of biomolecules, modelled by glycine (GLY), serine (SER), phenylalanine (PHE), glutamic acid (GLU), lysine (LYS) and arginine (ARG), were investigated in vacuo by molecular dynamics simulations with the UFF empirical potential. Selected structures were further studied by accurate ab initio quantum chemical procedures. Interactions with a peptide bond (GLY-SER dipeptide) and a nucleic acid building block (guanine) were also considered. The RESP and NPA charges of carboranes and small model systems are compared and their use is discussed. The dominant interaction between carboranes and biomolecules is the formation of unconventional proton-hydride hydrogen bonds (dihydrogen bonds) characterized by a short distance between hydrogen atoms (as close as 1.8 A) and an average strength in the range of 4.2-5.8 kcal mol(-1). The total stabilization energy of complexes investigated is rather large, and the largest value (approximately 15 kcal mol(-1)) was found for the carborane complexes with ARG and the GLY-SER dipeptide. These interactions are ubiquitous under geometrical constraints influencing the strength of the interaction. The carborane forms dihydrogen bonds with biomolecules preferably with the hydrogen atoms of its lower hemisphere (i.e. the part of the cage opposite to the carbon atom). These two geometrical factors can be used to explain the specificity of inhibition of HIV protease by carboranes.

Biophysics↗
PubMed2006

CB11Me11 boronium ylides: carba-closo-dodecaboranes with a naked boron vertex.

In pentane solution, 2 equiv of the icosahedral CB(11)Me(12)(*) radical cleaves the Si-Si bond of hexaalkyldisilanes by boron to silicon methyl transfer with formation of 2 equiv of methyltrialkylsilanes. The loss of a methyl radical converts the CB(11)Me(12)(*) radical into an internally charge-compensated "boronium ylide" CB(11)Me(11) with a naked vertex, which can be formally viewed as a deprotonated hypercloso carborane. It has been isolated as an air-sensitive solid, stable only below approximately -60 degrees C. The naked vertex appears to be in position 12 since the material reacts instantaneously with alcohols and ethers to form the 12-alkoxy anions 12-CB(11)Me(11)OR. It reacts with many other nucleophiles to yield more complex mixtures containing similar products. DFT calculations for the four CB(11)Me(11) isomers give closed-shell ground-state electronic structures. For the isomer with naked vertex 12, a DFT computational search failed to reveal any skeletal dimers, apparently due to excessive methyl-methyl repulsions, and only a cyclic dimer bound through weak interactions of one of the 7-methyl hydrogen atoms on each cage with the empty exocyclic orbitals on B12 of the other cage was found. Natural hybrid orbital populations suggest that the three possible isomers of monomeric boronium ylides are close to true singlet ylides, with triplet states approximately 50 kcal/mol higher. The calculated electronic structure of the carbonium ylide is close to a singlet carbene, with a triplet state approximately 16 kcal/mol higher. An attempted preparation of Me(3)C(+)CB(11)Me(12)(-) yielded neopentane and products consistent with a sequential loss of methyl groups from the carborane cage with a transient formation of similar boronium ylides. Probable mechanisms of these methyl transfer reactions are considered, and the possibly quite general role of "ylide" structures in Lewis acid induced substitution reactions on the boron vertices of carboranes and boranes is noted.

Journal Article↗
PubMed2005

An experimental and theoretical study of stereoselectivity of furan-maleic anhydride and furan-maleimide diels-alder reactions.

The stereoselectivity of the reaction of furan (1) with maleic anhydride (2) and maleimide (3) was studied experimentally and theoretically. Although the two reactions are highly similar with regard to their preference for endo and exo steroisomers, notable differences were experimentally observed and explained on the basis of calculated reaction-free energies and transition-state barriers. The experimental values of rate constants (k(1+2endo) = (1.75 +/- 0.48) x 10(-5); mol(-1) l s(-1); k(1+2exo) = (3.10 +/- 0.55) x 10(-5); mol(-1) l s(-1); k(1+3endo) = (1.93 +/- 0.082) x 10(-5); mol(-1) l s(-1), k(1+3exo) = (1.38 +/- 0.055) x 10(-5); mol(-1) l s(-1) all at 300 K) and the observed reaction course clearly confirm that neither of these reactions are prototypical examples of Diels-Alder [4 + 2] cycloadditions, whose dominant preference is for endo isomers. However, only by comparing their energetics-calculated at the CCSD(T) level of theory-with the analogous reactions involving cyclopentadiene (8) as a diene can these observations be understood. The low thermodynamic stability of furan [4 + 2] adducts opens retro-Diels-Alder reaction channels and overrules the very small kinetic preference (calculated and measured here) of initial formation for endo stereoisomers. On a macroscopic scale "an irregular"-thermodynamically more stable-exo stereoisomer was consequently observed as a dominant species.

Journal Article↗
PubMed2004

Metal cation-methyl interactions in CB11Me12(-) salts of Me3Ge+, Me3Sn+, and Me3Pb+.

Oxidation of Me(6)M(2) (M = Ge, Sn) and Me(4)Pb with the CB(11)Me(12)(*) radical in alkane solvents produced the insoluble salts Me(3)M(+)CB(11)Me(12)(-), characterized by CP-MAS NMR and EXAFS. The cations interact with methyl groups of CB(11)Me(12)(-) with coordination strength increasing from Pb to Ge. Density functional theory (DFT) calculations for the isolated ion pairs, Me(3)M(+)CB(11)Me(12)(-) (M = Ge, Sn), revealed three isomers with the cation above methyl 2, 7, or 12, and not above a BB edge or a BBB triangle. The interaction has a considerable covalent component, with the cation attempting to perform a backside S(E)2 substitution on the methyl carbon. In a fourth less favorable isomer the cation is near methyl 1, inclined toward methyl 2, and interacts with hydrogens. DFT atomic charge distributions and plots of the electrostatic potential on the surface of spheres centered at the CB(11)H(12)(-) and CB(11)Me(12)(-) icosahedra display the effects of uneven charge distribution within the anion and contradict the common belief that the negative charge of the cage anion is concentrated primarily on the cage boron atoms 7-12; in CB(11)Me(12)(-), roughly half is on the cage carbon and the rest on methyls 7-12.

Boron Compounds↗
PubMed2004

Higher metal-ligand coordination in the catalytic site of cobalt-substituted Thermoanaerobacter brockii alcohol dehydrogenase lowers the barrier for enzyme catalysis.

Thermoanaerobacter brockii alcohol dehydrogenase (TbADH) is a zinc-dependent NADP(+)/H-linked class enzyme that reversibly catalyzes the oxidation of secondary alcohols to their corresponding ketones. Cobalt substitution studies of other members of the alcohol dehydrogenase (ADH) family showed that the cobalt-containing ADHs have a similar active site structure but slightly decreased activity compared to wild-type zinc ADHs. In contrast, the cobalt-substituted TbADH (Co-TbADH) exhibits an increase in specific activity compared to the native enzyme [Bogin, O., Peretz, M., and Burstein, Y. (1997) Protein Sci. 6, 450-458]. However, the structural basis underlying this behavior is not yet clear. To shed more light on this issue, we studied the local structure and electronics at the catalytic metal site in Co-TbADH by combining X-ray absorption (XAS) and quantum chemical calculations. Importantly, we show that the first metal-ligand coordination shell of Co-TbADH is distorted compared to its native tetrahedral coordination shell and forms an octahedral structure. This is mediated presumably by the addition of two water molecules and results in more positively charged catalytic metal ions. Recently, we have shown that the metal-ligand coordination number of the zinc ion in TbADH changes dynamically during substrate turnover. These structural changes are associated with a higher coordination number of the native catalytic zinc ion and the consequent buildup of a positive charge. Here we propose that the accumulation of a higher coordination number and positive charge at the catalytic metal ion in TbADH stabilizes the structure of the catalytic transition state and hence lowers the barrier for enzyme catalysis.

Alcohol Dehydrogenase↗
PubMed2003

Racemization barriers of 1,1'-binaphthyl and 1,1'-binaphthalene-2,2'-diol: a DFT study.

Density functional theory has been applied to the study of various pathways and transition states for the configurational inversion of 1,1'-binaphthyl (1) and 1,1'-binaphthalene-2,2'-diol (2). The preferred pathway is found to be anti with centrosymmetric transition state. Whereas the reaction path of 1 goes downhill from transition to ground state, in the case of 2 it contains one unexpected local minimum. Very satisfactory agreement with available experimental values of activation Gibbs energies is achieved.

Journal Article↗
PubMed2002

Study of the nature of improper blue-shifting hydrogen bonding and standard hydrogen bonding in the X3CH...OH2 and XH...OH2 complexes (X = F, Cl, Br, I): A correlated Ab initio study.

Weak hydrogen bonding was studied in the XH...OH2 and X3CH...OH2 complexes (X = F, Cl, Br, I) using the correlated MP2 ab initio method with relativistic Stuttgart/Dresden pseudopotentials and basis set (SDD). The accuracy of the method was tested for selected nonrelativistic complexes by performing MP2 calculations with all-electron basis sets (6-311G** and TZVPP). The characteristics of bonding in the hydrogen halide complexes correspond to the standard H-bonding (an elongation of the X-H bond and red shift of its stretch frequency), whereas those in the X3CH...OH2 complexes (X = F, Cl) are typical of improper blue-shifting H-bonding (a contraction of the CH bond and blue shift of the respective stretch frequency). A natural bond orbital analysis revealed some important differences between both classes of complexes: a) the electron density transfer (EDT) in the former complexes is considerably larger than that in the latter complexes: b) the EDT in the former complexes is almost completely directed to the sigma*-antibonding orbital of the XH bond, which causes a weakening of this bond, its elongation, and a concomitant decrease of the XH stretch frequency. In the latter complexes, only a small portion of the EDT goes to the sigma*-antibonding orbital of the CH bond of the proton donor and a larger part is transferred to the remote (nonparticipating) part of the proton donor. As a consequence, the structural reorganization of the proton donor occurred, leading to the contraction of the C-H bond. The fact that a small red shift of the C-H stretch frequency was found in bromoform-water and iodoform-water complexes was explained by the competition of both the above-mentioned mechanisms with dominating passage of electron density to the sigma*-antibonding orbital of the C-H bond. For an explanation of all the geometric features of both types of complexes, it is however necessary to consider both charge transfer and electrostatic effects. The electrostatic effects fail sometimes to interpret the geometry changes in the proton donor.

Journal Article↗
PubMed2002

Prediction of an inverse heavy-atom effect in H-C-CH(2)Br: bromine substituent as a pi acceptor.

A comparison of spin-orbit coupling calculated [CASSCF(6,6)/(cc-pVDZ on C,H and VDZ+P on Br] for bromomethylcarbene and methylcarbene predicts a highly unusual inverse heavy-atom effect by the Br substituent, particularly at geometries near the syn conformation. This behavior is due to a vacant 4d orbital on the Br atom acting as a weak pi-electron acceptor and overwhelming the even weaker effect of the pi-symmetry lone pair donor 4p orbital, which in itself would cause a small normal heavy-atom effect.

Journal Article↗