Metal-histidine-glutamate as a regulator of enzymatic cycles: a case study of carbonic anhydrase.

International audienceHistidine is a very common metal ligand in metalloenzymes. Besides being an efficient Lewis base, its electronic properties are essential to shape the metal ability to catalyze the reaction. Here we show that histidine's properties can be tuned, in turn, by an easy proton transfer to a nearby glutamate. We study this situation in Human Carbonic Anhydrase II (HCA II) in which one of the three histidines bound to zinc (His119) interacts also with a glutamate residue (Glu117). Proton transfer from His119 to Glu117 has been hypothesized in the past, however realistic modeling is performed here for the first time. We show that the carboxylate group of Glu117 behaves only as a hydrogen bond acceptor in the hydroxy form of HCA II. On the other hand, our results suggest that Glu117 could exist either as a hydrogen bond acceptor or as a proton acceptor in the aqua form of HCA II, the two isomers having almost the same thermodynamic stability. We propose that this proton shift may be used by the enzyme to facilitate the final displacement of bicarbonate by water

A comparative study of semiempirical, ab initio, and DFT methods in evaluating metal-ligand bond strength, proton affinity, and interactions between first and second shell ligands in Zn-biomimetic complexes

International audienceAlthough theoretical methods are now available which give very accurate results, often comparable to the experimental ones, modeling chemical or biological interesting systems often requires less demanding and less accurate theoretical methods, mainly due to computer limitations. Therefore, it is crucial to know the precision of such less reliable methods for relevant models and data. This has been done in this work for small zinc-active site models including O- (H2O and OH-) and N-donor (NH3 and imidazole) ligands. Calculations using a number of quantum mechanical methods were carried out to determine their precision for geometries, coordination number relative stability, metal–ligand bond strengths, proton affinities, and interaction energies between first and second shell ligands. We have found that obtaining chemical accuracy can be as straightforward as HF geometry optimization with a double-f plus polarization basis followed by a B3LYP energy calculation with a triple-f quality basis set including diffuse and polarization functions. The use of levels as low as PM3 geometry optimization followed by a B3LYP single-point energy calculation with a double-tzeta quality basis including polarization functions already yields useful trends in bond length, proton affinities or bond dissociation energies, provided that appropriate caution is taken with the optimized structures. The reliability of these levels of calculation has been successfully demonstrated for real biomimetic cases

Comparison between alpha- and beta-carbonic anhydrases: can Zn(His)3(H2O) and Zn(His)(Cys)2(H2O) sites lead to equivalent enzymes?

International audienceLarge models of alpha- and beta-carbonic anhydrases were compared using DFT calculations. They indicate similar acidity of coordinated water molecule and zinc affinity. This explains their similar mechanism of action, despite the wide difference in their first coordination sphere

Guiding the synthesis of pentazole derivatives and their mono- and di-oxides with quantum modeling

International audienceThere is high prospect that derivatives of pentazole can lead to high energy density materials. However these molecules are potentially hazardous because of their high formation enthalpies and weak N-N bonds. In order to devise efficient protocols, possible schemes for the synthesis of nitro and azido derivatives of pentazole, and their mono- and di-oxides, have been explored using quantum chemical methods. Reaction pathways have been investigated in detail, with particular emphasis on locating transition states and on obtaining a reliable treatment of solvent effects. Oxidation by ozone is found to be a favorable process, leading to some regioselectivity in favor of b-mono-oxides. Nitration by NO2+BF4- is also predicted to be favorable. In contrast the electrochemical azidation of N5- and its oxidized derivatives is found to be energetically inaccessible. Combination of the individual addition and oxidation steps leads to recommendations for future synthetic work. Finally the kinetic stability of products with respect to N2 and N2O elimination is assessed

Thermodynamic stability versus kinetic lability of ZnS4 core

International audienceDensity Functional Theory and post-Hartree Fock calculations reveal an unusual energy profile for Zn-S and Zn-N bond dissociation reactions in several Zn(SR)4(2–) and Zn(Im)(SR)3(–) complexes. The Zn-S bond dissociation in tetrathiolate dianions, which is highly exothermic in the gas phase, proceeds through a late transition state which can be rationalised on the basis of an avoided-crossing resulting from Coulomb repulsion between the anionic fragments and ligand-to-metal charge-transfer in the Zn(SR)4(2–) complexes. When solvation models for water, DMSO or acetonitrile are included, some complexes become stable while others are metastable, so this constitutes the first theoretical model which is in full agreement with the experimental data for various Zn(SR)4(2–), Zn(SR)3(–) and Zn(Im)(SR)3(–) complexes. The analysis given here indicates that the Zn(Cys)4 and Zn(His)(Cys)3 cores of numerous proteins are metastable with respect to Zn-S and Zn-N bond dissociation respectively; this is consistent with the kinetic lability at the zinc-centres and illustrates that, in nature, thermodynamic stability is imparted upon the zinc cores by the protein environment

Acid-base thermochemistry of gaseous oxygen and sulfur substituted amino acids (Ser, Thr, Cys, Met)

International audienceAcid-base thermochemistry of isolated amino acids containing oxygen or sulfur in their side chain (serine, threonine, cysteine and methionine) have been examined by quantum chemical computations. Density functional theory (DFT) was used, with B3LYP, B97-D and M06-2X functionals using the 6-31+G(d,p) basis set for geometry optimizations and the larger 6-311++G(3df,2p) basis set for energy computations. Composite methods CBS-QB3, G3B3, G4MP2 and G4 were applied to large sets of neutral, protonated and deprotonated conformers. Conformational analysis of these species, based on chemical approach and AMOEBA force field calculations, has been used to identify the lowest energy conformers and to estimate the population of conformers expected to be present at thermal equilibrium at 298 K. It is observed that G4, G4MP2, G3B3, CBS-QB3 composite methods and M06-2X DFT lead to similar conformer energies. Thermochemical parameters have been computed using either the most stable conformers or equilibrium populations of conformers. Comparison of experimental and theoretical proton affinities and Delta(acid)H shows that the G4 method provides the better agreement with deviations of less than 1.5 kJ mol-1. From this point of view, a set of evaluated thermochemical quantities for serine, threonine, cysteine and methionine may be proposed: PA = 912, 919, 903, 938; GB = 878, 886, 870, 899; Delta(acid)H = 1393, 1391, 1396, 1411; Delta(acid)G = 1363, 1362, 1367, 1382 kJ mol-1. This study also confirms that a non-negligible Delta(p)S° is associated with protonation of methionine and that the most acidic hydrogen of cysteine in the gas phase is that of the SH group. In several instances new conformers were identified thus suggesting a reexamination of several IRMPD spectra

Pincer versus Pseudo-Pincer: Isomerism in Palladium(II) Complexes bearing κ3C,S,C ligands

International audienceIn NHC pincer complexes incorporatig a hemilabile donor site, there exists an equilibrium between the true pincer form and a pseudopincer coordination isomer. The influence of the NHC moieties on this isomerism has been studied by DFT calculations

Unprecedented directed lateral lithiations of tertiary carbons on NHC platforms

International audienceUnexpected and unprecedented directed remote lateral lithiation at one CH(CH3)2 of the 3-(2,6-di-isopropylphenyl) wingtip took place upon the reaction of functionalised N-heterocyclic carbene-type molecules with excess of LiCH2SiMe3, leading to dilithiated dianionic 4-amido-N-heterocyclic carbenes. DFT calculations show that the nature of the isolated species are under thermodynamic control

Electron Capture in Charge-Tagged Peptides. Evidence for the Role of Excited Electronic States

International audienceElectron capture dissociation (ECD) was studied with doubly charged dipeptide ions that were tagged with fixed-charge tris-(2,4,6-trimethoxyphenyl)phosphonium-methylenecarboxamido (TMPP-ac) groups. Dipeptides GK, KG, AK, KA, and GR were each selectively tagged with one TMPP-ac group at the N-terminal amino group while the other charge was introduced by protonation at the lysine or arginine side-chain groups to give (TMPP-ac-peptide + H)2+ ions by electrospray ionization. Doubly tagged peptide derivatives were also prepared from GK, KG, AK, and KA in which the fixed-charge TMPP-ac groups were attached to the N-terminal and lysine side-chain amino groups to give (TMPP-ac-peptide-ac-TMPP)2+ dications by electrospray. ECD of (TMPP-ac-peptide + H)2+ resulted in 72% to 84% conversion to singly charged dissociation products while no intact charge-reduced (TMPP-ac-dipeptide + H)+• ions were detected. The dissociations involved loss of H, formation of (TMPP + H)+, and N–C(alpha) bond cleavages giving TMPP-CH2CONH2+ (c0) and c1 fragments. In contrast, ECD of (TMPP-ac-peptide-ac-TMPP)2+ resulted in 31% to 40% conversion to dissociation products due to loss of neutral TMPP molecules and 2,4,6-trimethoxyphenyl radicals. No peptide backbone cleavages were observed for the doubly tagged peptide ions. Ab initio and density functional theory calculations for (Ph3P-ac-GK + H)2+ and (H3P-ac-GK + H)2+ analogs indicated that the doubly charged ions contained the lysine side-chain NH3+ group internally solvated by the COOH group. The distance between the charge-carrying phosphonium and ammonium atoms was calculated to be 13.1-13.2 Å in the most stable dication conformers. The intrinsic recombination energies of the TMPP+-ac and (GK + H)+ moieties, 2.7 and 3.15 eV, respectively, indicated that upon electron capture the ground electronic states of the (TMPP-ac-peptide + H)+• ions retained the charge in the TMPP group. Ground electronic state (TMPP-ac-GK + H)+• ions were calculated to spontaneously isomerize by lysine H-atom transfer to the COOH group to form dihydroxycarbinyl radical intermediates with the retention of the charged TMPP group. These can trigger cleavages of the adjacent N–C(alpha) bonds to give rise to the c1 fragment ions. However, the calculated transition-state energies for GK and GGK models suggested that the ground-state potential energy surface was not favorable for the formation of the abundant c0 fragment ions. This pointed to the involvement of excited electronic states according to the Utah-Washington mechanism of ECD

Dissociation channel dependence on peptide size observed in electron capture dissociation of tryptic peptides

International audienceElectron capture dissociation (ECD) of a series of five residue peptides led to the observation that these small peptides did not lead to the formation of the usual c/z ECD fragments, but to a, b, y and w fragments. In order to determine how general this behavior is for small sized peptides, the effect of peptide size on ECD fragments using a complete set of ECD spectra from the SwedECD spectra database was examined. Analysis of the database shows that b and w fragments are favored for small peptide sizes and that average fragment size shows a linear relationship to parent peptide size for most fragment types. From these data, it appears that most of the w fragments are not secondary fragments of the major z ions, in sharp contrast with the proposed mechanism leading to these ions. These data also show that c fragment distributions depend strongly on the nature of C-terminal residue basic site: arginine leads to loss of short neutral fragments, whereas lysine leads to loss of longer neutral fragments. It also appears that b ions might be produced by two different mechanisms depending on the parent peptide size. A model for the fragmentation pathways in competition is proposed. These relationships between average fragment size and parent peptide size could be further exploited also for CID fragment spectra and could be included in fragmentation prediction algorithms