Quantum chemical modelling of the rate determining step for oxygen reduction on quinones

Two inner-sphere electrocatalytic channels for quinone-mediated reduction of molecular oxygen to form hydrogen peroxide have been addressed by means of density functional theory. Each of the channels comprises an initial rate determining chemical step and a subsequent electrochemical reduction step by which peroxide is produced. The reduction mechanism was determined for 9,10-anthraquinone and 9,10-phenanthrenequinone and the quantum chemical results are compared with experimental results. Two distinctly different structures were determined for the critical chemical step depending on whether the catalytic site is present as HQ* or Q*-. While a superoxo species is formed on HQ*, a van der Waals (vdW) type compound is formed on Q*-. It is shown that the Gibbs energy of activation for the semiquinone/oxygen reaction is largely determined by the entropy term. The results explain the experimentally observed pH dependence of the O2 reduction rate on quinone functionalised electrodes.     

Synthesis of a cyclic peptide containing norlanthionine: effect of the thioether bridge on peptide conformation

Two diastereomeric analogues of ring C of nisin incorporating a novel norlanthionine residue have been synthesized via a triply orthogonal protecting group strategy. A full structural study was carried out by NMR, which elucidated the conformational properties of the two peptides and enabled the identity of each diastereoisomer to be proposed.     

Quantum chemical calculation for the inhibitory effect of compounds

The effects of the molecular structure on the corrosion inhibition efficiency are investigated by nine methods of calculations. The selected thio compounds were previously identified as corrosion inhibitors for mild steel in the 1.0 M HCl solution. The electronic properties such as highest occupied molecular orbital (EHOMO) energy, lowest unoccupied molecular orbital (ELUMO) energy, dipole moment (μ), and Fukui indices are calculated and discussed. Results show that the corrosion inhibition efficiency increase with the increase in both EHOMO and μ values, respectively, and decrease in ELUMO. QSAR approach is utilized in this study; a good relationship is found between the experimental corrosion inhibition efficiency (IE_exp, %) and the theoretical corrosion inhibition efficiency (IE_theor, %). The calculated inhibition efficiency is found closer to the experimental inhibition efficiency with a coefficient of correlation (R ²) of 0.875.     

Quantum chemical aspects of the chelate effect in complexes

A typical “chelate” effect is demonstrated by means of all-electron ab initio LCGO SCF calculations on the [Li(HCONH₂)₂]⁺ complex in different geometrical arrangements. Energetic factors and the electronic structure of the complexes are discussed, showing the chelate effect to be connected with striking changes in bonding, density distribution and electronic energy.     

Puckering transition of 4-substituted proline residues

The puckering transition of 4-substituted proline residues by electron-withdrawing groups, i.e., 4(R)-hydroxy-L-proline (Hyp) and 4(R)-fluoro-L-proline (Flp) residues, with trans and cis prolyl peptide bonds was studied by adiabatic optimizations along the torsion angle chi1 of the prolyl ring at the HF/6-31+G(d) level. By analyzing the potential energy surface and local minima, it is observed that the puckering transition of the prolyl ring for Hyp and Flp residues proceeds from a down-puckered conformation to an up-puckered one through the transition state with an envelope form having the N atom at the top of envelope and not a planar one for both trans and cis conformers, which is the same as found for the unsubstituted proline residue. At HF/6-31+G(d) and B3LYP/6-311++G(d,p) levels, the structures of the backbone and prolyl ring for local minima of Ac-Hyp-NHMe and Ac-Flp-NHMe are quite similar to those of Ac-Pro-NHMe. However, the relative stability of the up-puckered conformation to the down-puckered one is increased for Ac-Hyp-NHMe with the cis imide bond and for Ac-Flp-NHMe with the trans and cis imide bonds. In particular, the 4(R)-substitution by hydroxy and fluorine groups has brought some structural changes in the prolyl ring of the transition states and the changes in barriers for the puckering transition. The puckering transitions for Ac-Hyp-NHMe and Ac-Flp-NHMe are proven to be predominantly electronically driven by analyzing the electronic and enthalpic contributions to the barriers, as seen for Ac-Pro-NHMe.     

Quantum chemical study of the effect of complexation on the acetonitrile→amindine transformation

The electronic structures of acetonitrile CH₃CN and amidine CH₃C(NH)NH₂ in the free states and in the coordinated states in the Pt(II) and Pt(IV) complexes are studied by the semiempirical CNDO method and by the ab initio Hartree-Fock-Roothaan method with the effective core potential for the Pt atom using the GAUSSLAN-92 software. It is shown that the complexation of acetonitrile with platinum(II) and particularly with platinum(IV) increases the positive charge on the acetonitrile carbon atom, making it more accessible to the nucleophilic attack. In these complexes, a decrease in the energies of the unoccupied MOs of acetonitrile also favors the nucleophilic attack. St. Petersburg State Technological Institute (Technical University). Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 2, pp. 225–230, March–April, 1996. Translated by I. Izvekova     

Electronic CD study of a helical peptide incorporating Z-dehydrophenylalanine residues: conformation dependence of the simulated CD spectra

Electronic circular dichroism (CD) spectra as well as transitions from ground to excited states were predicted for a helical nonapeptide based on alternative sequence--[Z-alpha,beta-dehydrophenylalanine (Delta(Z)Phe)-X]--through semiempirical molecular orbital computation combined with time-dependent (TD) method. The simulation was performed for its various conformers that differ in helix type, helix sense, and Delta(Z)Phe side-chain orientation. These conformational variations have been shown to depend largely on its CD spectra. Comparison between simulated and observed CD profiles reveals that peptide 1 in solution favors a right-handed 3(10)-helix that adopts phenyl (Delta(Z)Phe) planes basically in a vertical orientation with respect to the helix axis. These predictions were essentially supported from CD simulation of a shorter helical analogue at ab inito or density functional TD levels. The theoretical CD-conformation relationship should provide us useful guideline for determination of helix sense in the dehydropeptide, and for estimation of its conformations statistically averaged in solution.     

Quantum chemical modelling of ethene epoxidation with hydrogen peroxide: role of catalytic sites

Ethene epoxidation with hydrogen peroxide was studied on hydroxylated binuclear metal sites, using DFT calculations at the B3LYP/6-311+G(d,p) level of theory. A decrease of the activation enthalpy of approximately 100 kJ mol(-1) was observed compared to the gas phase reaction between hydrogen peroxide and ethene. It was previously shown that micro-solvation with water reduces the activation enthalpy by approximately 77 kJ mol(-1) and only the additional 24 kJ mol(-1) can be attributed to the binuclear site. Three different metal centres were tested, Ti(iv), Si(iv) and Ge(iv), in order to investigate any specific role of the metal centre on the activation enthalpy. The results clearly show that the activation enthalpy is independent on the nature of the metal centre. This emphasises the role of the hydrogen bonded network provided by the hydroxylated metal sites, on the stabilisation of the transitions state. In ref. 1 (A. Lundin, I. Panas and E. Ahlberg, J. Phys. Chem. A, 2007, 111, 9080) it was demonstrated that, at the transition state and upon micro-solvation, the hydrogen peroxide entity becomes polarized within the hydrogen bonding network, forming a negatively-charged fragment distant from the ethene molecule and a positively-charged fragment directly involved in the oxygen insertion step. The same mechanism was found to hold also for the reaction at the binuclear catalytic site, since the required hydrogen bonding is effectively provided by the hydroxylated metal centres. This mechanism is compared to the two-step pathway which employs a metal peroxide intermediate. Both reaction channels were found to be plausible in confined environments.     

Quantum chemical studies on structure, conformation and isomerization of nitroso, nitro substituted benzene and 1,3-cyclopentadiene

The molecular structure, conformational stability and isomerization of nitroso, nitro substituted benzene and 1,3-cyclopentadiene in gas phase have been investigated using ab initio and density functional theory methods. The molecular geometries and energetics of possible conformers were obtained by employing MP2, B3LYP and B3PW91 levels of theory implementing 6-31G* basis set. The relative stabilities of the conformations were evaluated from the energy differences of the structure. Chemical hardness (η) and chemical potential (μ) were calculated at HF/6-31G* level of theory for all the positional and geometrical isomers to study the maximum hardness principle. Each optimized structure has been tested against the imaginary frequencies at MP2/6-31G* level of theory in order to be sure they are located at energy minimum.     

Influence of silaproline on peptide conformation and bioactivity

The analogue gamma-(dimethylsila)-proline, denoted silaproline (Sip), was synthesized in both enantiomerically pure forms by diastereoselective alkylation of a chiral glycine equivalent with use of Sch?llkopf's bis-lactim ether method. The effect of replacing a proline residue in model peptides by this new proline surrogate has been examined in the crystal state by X-ray diffraction and in solution by IR absorption and NMR techniques. Silaproline and proline-containing sequences exhibit very similar conformational properties. Silaproline was also substituted for proline in a neurotensin (8-13) analogue that retained biological activity and exhibited enhanced resistance to biodegradation.     

Quantum chemical studies of peptide nucleic acid monomers and role of cyclohexyl modification on backbone flexibility

Peptide nucleic acids (PNA) bind sequence specifically to DNA/RNA and are of major interest for all fields of molecular biology and could form the basis for gene‐targeted drugs. Modifications are introduced in PNA to overcome problems associated with orientational selectivity in binding, to restrict conformational flexibility of backbone, and to discriminate binding for either DNA or RNA. The addition of geometrical isomers (1R,2S and 1S,2R) of cyclohexyl ring in the backbone of PNA could bring rigidification to PNA backbone and may impart specificity toward RNA. Therefore, quantum chemical studies are aimed to explore the conformational space, to find out preferred stable conformations of PNA and modified (1R,2S and 1S,2R) cyclohexyl PNA monomer. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Quantum chemical calculations on thioridazine

Quantum chemical CNDO /2 calculations for the conformational preference of the side chain of thioridazine as a function of angle indicated the crystallographically determined structure gave the lowest energy. There is also a small region of conformational flexibility within the first 90° of rotation of the side chain. This is commensurate with the results which we had obtained previously for our similar calculations for promazine and its Cl and CF₃ derivatives, perazine and its Cl and CF₃ derivatives, and for the hypothetical hitherto unknown N-piperidinopromazine and its Cl and CF₃ derivatives. The conformational profile of thioridazine resembles that of the perazines. The calculated gross atomic populations on the alkyl nitrogen in thioridazine was within the range we had previously found necessary for neuroleptic activity.     

Quantum chemical study of the effect of hydrogen bromide-water associates on the bromination of 1-heptene

The MNDO method was used to study the extremal points on the potential energy surface of the reaction of bromine and 1-heptene. The formation of 1,2-dibromoheptane is energetically favored relative to formation of 1-bromo-2-heptene. (H₂O)_nHBr associates reduce the activation energy of the transition state and act as a strong catalytic agent for the molecular reaction. Lvov Research Institute of Judicial Examination, 7 Soborna pl., Lvov 290004, Ukraine. Translated from Teoreticheskaya i éksperimental'naya Khimiya, Vol. 34, No. 4, pp. 239–243, July–August, 1998.     

Quantum chemical studies on polythiophenes containing heterocyclic substituents: effect of structure on the band gap

Color tuning by the tailoring of substituents at the 3-position of thiophene is very encouraging, and comparative experimental and theoretical studies proved to be powerful in the search for a suitable design for the above. Since the novel polythiophene-based materials substituted with five-membered/six-membered ring containing sulphur and nitrogen at different positions are proven to be potential candidates for electron-transporting hole blocking functions, the structure-property relationship of these systems have been focused in the present study. Molecular-orbital calculations are applied to obtain the optimized geometries and band gaps of the thiophene oligomers. An oligomeric approach has been implemented for calculating the band gaps, and the theoretically obtained band gaps for the different model compounds are compared. Density-functional theory B3LYP6-31G* predicted band-gap values are compared with the experimental band gaps obtained from optical-absorption edge. The predicted values show little deviations from experimental band gaps, but the trend in band gap is found to be the same in experimental and theoretical results in most of the cases. Hence, this study illustrates the usefulness of quantum-mechanical calculations in understanding the effects of various structural parameters on optical band gap.     

Quantum chemical contributions on the reactivity of solids

The concept of reactivity is reviewed. Various reactivity indices are discussed. Different methods for the simulation of solids are systematically described. Applications for the reactivity of solids can be subdivided into three categories: surfaces, interfaces and bulk. Examples for the categories are presented with a special emphasis on diffusion processes in the bulk.     

Impact of proline and aspartic acid residues on the dissociation of intermolecularly crosslinked peptides

The dissociation of intermolecularly crosslinked peptides was evaluated for a series of peptides with proline or aspartic acid residues positioned adjacent to the crosslinking sites (lysine residues). The peptides were crosslinked with either disuccinimidyl suberate (DSS) or disuccinimidyl L-tartrate (DST), and the influence of proline and aspartic acid residues on the fragmentation patterns were investigated for precursor ions with and without a mobile proton. Collisionally activated dissociation (CAD) spectra of aspartic acid-containing crosslinked peptide ions, doubly-charged with both protons sequestered, were dominated by cleavage C-terminal to the Asp residue, similar to that of unmodified peptides. The proline-containing crosslinked peptides exhibited a high degree of internal ion formation, with the resulting product ions having an N-terminal proline residue. Upon dissociation of the doubly-charged crosslinked peptides, twenty to fifty percent of the fragment ion abundance was accounted for by multiple cleavage products. Crosslinked peptides possessing a mobile proton yielded almost a full series of b- and y-type fragment ions, with only proline-directed fragments still observed at high abundances. Interestingly, the crosslinked peptides exhibited a tendency to dissociate at the amide bond C-terminal to the crosslinked lysine residue, relative to the N-terminal side. One could envision updating computer algorithms to include these crosslinker specific product ions--particularly for precursor ions with localized protons--that provide complementary and confirmatory information, to offer more confident identification of both the crosslinked peptides and the location of the crosslink, as well as affording predictive guidelines for interpretation of the product-ion spectra of crosslinked peptides.     

Effect of ester chemical structure and peptide bond conformation in fragmentation pathways of differently metal cationized cyclodepsipeptides

Fragmentation behavior of two classes of cyclodepsipeptides, isariins and isaridins, obtained from the fungus Isaria, was investigated in the presence of different metal ions using multistage tandem mass spectrometry (MS(n)) with collision induced dissociation (CID) and validated by NMR spectroscopy. During MS(n) process, both protonated and metal-cationized isariins generated product ions belonging to the identical 'b-ion' series, exhibiting initial backbone cleavage explicitly at the β-ester bond. Fragmentation behavior for the protonated and metal-cationized acyclic methyl ester derivative of isariins was very similar. On the contrary, isaridins during fragmentation produced ions belonging to the 'b' or/and the 'y' ion series depending on the nature of interacting metal ions, due to initial backbone cleavages at the α-ester linkage or/and at a specific amide linkage. Interestingly, independent of the nature of the interacting metal ions, the product ions formed from the acyclic methyl ester derivative of isaridins belonged only to the 'y-type'. Complementary NMR data showed that, while all metal ions were located around the β-ester group of isariins, the metal ion interacting sites varied across the backbone for isaridins. Combined MS and NMR data suggest that the different behavior in sequence specific charge-driven fragmentation of isariins and isaridins is predetermined because of the constituent β-hydroxy acid residue in isariins and the cis peptide bond in isaridins.     

Stabilisation of the type I β-turn conformation by a bicyclic analogue of proline

A highly constrained analogue of l-proline, (1S,2S,4R)-2-phenyl-7-azabicyclo[2.2.1]heptane-1-carboxylic acid, has been incorporated into a model dipeptide. X-Ray diffraction analysis has shown that, in the solid state, this constrained peptide adopts a type I β-turn whereas the analogous dipeptide sequence incorporating l-proline has been shown to accommodate a βII-turn disposition. Attractive interactions involving the middle NH group and either the aromatic rings or the pyramidalised bicycle nitrogen seem to play a role in the stabilisation of the βI-turn conformation observed.