Milán Szőri

Conformation-Dependent •OH/H2O2 Hydrogen Abstraction Reaction Cycles of Gly and Ala Residues: A Comparative Theoretical Study

To determine if (•)OH can initiate the unfolding of an amino acid residue, the elementary reaction coordinates of H abstraction by (•)OH different conformations (β(L), γ(L), γ(D), α(L), and α(D)) of Gly and Ala dimethyl amides were computed using first-principles quantum computations. The MPWKCIS1K/6-311++G(3df,2p)//BHandHLYP/6-311+G(d,p) level of theory was selected after different combinations of functionals and basis sets were compared. The structures of Gly and Ala in the elementary reaction steps were compared to the conformers of the Gly, Gly(•), Ala, and Ala(•) structures in the absence of (•)OH/H(2)O, which were identified by optimizing the minima of the respective potential energy surfaces. A dramatic change in conformation is observed in the Gly and Ala conformers after conversion to Gly(•) and Ala(•), respectively, and this change can be monitored along the minimal energy pathway. The β(L) conformer of Gly (-0.3 kJ mol(-1)) and Ala (-1.6 kJ mol(-1)) form the lowest-lying transition states in the reaction with (•)OH, whereas the side chain of Ala strongly destabilizes the α conformers compared to the γ conformers, which could cause the lower reactivity shown in Ala. This effect shown in Ala could affect the abstraction of hydrogen from Ala and the other chiral amino acid residues in the helices. The energy of subsequent hydrogen abstraction reactions between Ala(•) and Gly(•) and H(2)O(2) remains approximately 90 kJ mol(-1) below the entrance level of the (•)OH reaction, indicating that the (•)OH radical can initiate an α to β transition in an amino acid residue if a molecule such as H(2)O(2) can provide the hydrogen atom necessary to re-form Gly and Ala. This work delineates the mechanism of the rapid (•)OH-initiated unfolding of peptides and proteins which has been proposed in Alzheimers and other peptide misfolding diseases involving amyloidogenic peptides.

Analyses of the large subunit histidine-rich motif expose an alternative proton transfer pathway in [NiFe] hydrogenases.

A highly conserved histidine-rich region with unknown function was recognized in the large subunit of [NiFe] hydrogenases. The HxHxxHxxHxH sequence occurs in most membrane-bound hydrogenases, but only two of these histidines are present in the cytoplasmic ones. Site-directed mutagenesis of the His-rich region of the T. roseopersicina membrane-attached Hyn hydrogenase disclosed that the enzyme activity was significantly affected only by the replacement of the His104 residue. Computational analysis of the hydrogen bond network in the large subunits indicated that the second histidine of this motif might be a component of a proton transfer pathway including Arg487, Asp103, His104 and Glu436. Substitutions of the conserved amino acids of the presumed transfer route impaired the activity of the Hyn hydrogenase. Western hybridization was applied to demonstrate that the cellular level of the mutant hydrogenases was similar to that of the wild type. Mostly based on theoretical modeling, few proton transfer pathways have already been suggested for [NiFe] hydrogenases. Our results propose an alternative route for proton transfer between the [NiFe] active center and the surface of the protein. A novel feature of this model is that this proton pathway is located on the opposite side of the large subunit relative to the position of the small subunit. This is the first study presenting a systematic analysis of an in silico predicted proton translocation pathway in [NiFe] hydrogenases by site-directed mutagenesis.

High accuracy ab initio calculations on reactions of OH with 1-alkenes. The case of propene

The energetics of terminal, central OH-additions as well as allylic H-abstractions by OH in its reaction with propene was studied as proxies for the 1-alkenes + OH reactions using several single and multireference ab initio techniques with basis set extrapolation where possible. Selection of the localized occupied orbitals forming the active space for multireference methods is discussed. Initial geometries of the reactants, prereaction complex (π-complex), and transition states were determined at the [5,5]-CASPT2/cc-pVTZ level of theory. Frequency analysis was also carried out at this level with the introduction of a scale factor. Analyzing the results, it will be concluded that multireference effects are negligible, and from the various single reference models we will opt for UCCSD(T)/cc-pVTZ for final geometry optimizations and vibrational frequency analysis. These results will be compared with those from approximate models yielding information on the reliability of the latter. Triples contributions are found to be very important, except for the π-complex, which has a UCCSD(T)/CBS relative enthalpy of -10.56 kJ/mol compared to infinitely separated propene + OH. The addition transition states are found to have relative enthalpies of -9.93 kJ/mol for the central and -9.84 kJ/mol for the terminal case. Allylic abstraction mechanisms, although lying significantly higher, still have only slightly positive barriers - a value of 3.21 kJ/mol for the direct and 1.67 kJ/mol for the consecutive case. Conventional transition state theory was used as a rough estimation for determining rate constants and turned out to agree well with experimental data.

Mixed micelles of sodium cholate and sodium dodecylsulphate 1:1 binary mixture at different temperatures--experimental and theoretical investigations.

Micellisation process for sodium dodecyl sulphate and sodium cholate in 1∶1 molar ratio was investigated in a combined approach, including several experimental methods and coarse grained molecular dynamics simulation. The critical micelle concentration (cmc) of mixed micelle was determined by spectrofluorimetric and surface tension measurements in the temperature range of 0–50°C and the values obtained agreed with each other within the statistical error of the measurements. In range of 0–25°C the cmc values obtained are temperature independent while cmc values were increased at higher temperature, which can be explained by the intensive motion of the monomers due to increased temperature. The evidence of existing synergistic effect among different constituent units of the micelle is indicated clearly by the interaction parameter (β1,2) calculated from cmc values according to Rubingh. As the results of the conductivity measurements showed the negative surface charges of the SDS-NaCA micelle are not neutralized by counterions. Applying a 10 µs long coarse-grained molecular dynamics simulation for system including 30-30 SDS and CA (with appropriate number of Na+ cations and water molecules) we obtained semi-quantitative agreement with the experimental results. Spontaneous aggregation of the surfactant molecules was obtained and the key steps of the micelle formation are identified: First a stable SDS core was formed and thereafter due to the entering CA molecules the size of the micelle increased and the SDS content decreased. In addition the size distribution and composition as well as the shape and structure of micelles are also discussed.

Critical evaluation of the potential energy surface of the CH3 + HO2reaction system

The CH3 + HO2 reaction system was studied theoretically by a newly developed, HEAT345-(Q) method based CHEAT1 protocol and includes the combined singlet and triplet potential energy surfaces. The main simplification is based on the CCSDT(Q)/cc-pVDZ calculation which is computationally inexpensive. Despite the economic and black-box treatment of higher excitations, the results are within 0.6 kcal/mol of the highly accurate literature values. Furthermore, the CHEAT1 surpassed the popular standard composite methods such as CBS-4M, CBS-QB3, CBS-APNO, G2, G3, G3MP2B3, G4, W1U, and W1BD mainly due to their poor performance in characterizing transition states (TS). For TS structures, various standard DFT and MP2 method have also been tested against the resulting CCSD/cc-pVTZ geometry of our protocol. A fairly good agreement was only found in the cases of the B2PLYP and BHandHLYP functionals, which were able to reproduce the structures of all TS studied within a maximum absolute deviation of 7%. The complex reaction mechanism was extended by three new low lying reaction channels. These are indirect water elimination from CH3OOH resulted formaldehyde, H2 elimination yielded methylene peroxide, and methanol and reactive triplet oxygen were formed via H-shift in the third channel. CHEAT1 protocol based on HEAT345-(Q) method is a robust, general, and cheap alternative for high accurate kinetic calculations.

Atropisomerism of the Asn α radicals revealed by ramachandran surface topology

C radicals are typically trigonal planar and thus achiral, regardless of whether they originate from a chiral or an achiral C-atom (e.g., C-H + (•)OH → C• + H2O). Oxidative stress could initiate radical formation in proteins when, for example, the H-atom is abstracted from the Cα-carbon of an amino acid residue. Electronic structure calculations show that such a radical remains achiral when formed from the achiral Gly, or the chiral but small Ala residues. However, when longer side-chain containing proteogenic amino acid residues are studied (e.g., Asn), they provide radicals of axis chirality, which in turn leads to atropisomerism observed for the first time for peptides. The two enantiomeric extended backbone structures, •βL and •βD, interconvert via a pair of enantiotopic reaction paths, monitored on a 4D Ramachandran surface, with two distinct transition states of very different Gibbs-free energies: 37.4 and 67.7 kJ/mol, respectively. This discovery requires the reassessment of our understanding on radical formation and their conformational and stereochemical behavior. Furthermore, the atropisomerism of proteogenic amino acid residues should affect our understanding on radicals in biological systems and, thus, reframes the role of the D-residues as markers of molecular aging.

Glutathione as a prebiotic answer to α-peptide based life.

The energetics of peptide bond formation is an important factor not only in the design of chemical peptide synthesis, but it also has a role in protein biosynthesis. In this work, quantum chemical calculations at 10 different levels of theory including G3MP2B3 were performed on the energetics of glutathione formation. The strength of the peptide bond is found to be closely related to the acid strength of the to-be N-terminal and the basicity of the to-be C-terminal amino acid. It is shown that the formation of the first peptide activates the amino acid for the next condensation step, manifested in bacterial protein synthesis where the first step is the formation of an N-formylmethionine dipeptide. The possible role of glutathione in prebiotic molecular evolution is also analyzed. The implications of the thermodynamics of peptide bond formation in prebiotic peptide formation as well as in the preference of α- instead of β- or γ-amino acids are discussed. An empirical correction is proposed for the compensation of the error due to the incapability of continuum solvation models in describing the change of the first solvation shell when a peptide bond is formed from two zwitterions accompanied by the disappearance of one ion pair.

Pyrolysis of ethyl iodide as hydrogen atom source: Kinetics and mechanism in the temperature range 950-1200 K

Abstract Ethyl iodide is a well known H atom precursor in shock tube experiments. In the present work, we study peculiarities, when C2H5I is used under conditions, where its decomposition is not longer fast compared to consecutive bimolecular reactions. On the basis of shock tube experiments with detection of H and I atoms by resonance absorption spectrometry, accompanied by quantum chemical (CCSD(T)/6-311G//CCSD/6-311G) and statistical rate theory calculations, we propose a small mechanism (5 reactions, 7 species) and kinetic data, which allow an adequate description of C2H5I pyrolysis as a H atom source down to temperatures between 950 and 1200 K at pressures ranging from 1 to 4 bar: C2H5I→C2H5 + I (1), k1 = 9.9 × 1012 exp(−23200 K/T) s−1; C2H5 + M→C 2H4 + H + M (2), k2 = 1.7 × 10−6 exp(−16800 KT) cm3 s−1 [D. L. Baulch et al., J. Phys. Chem. Ref. Data 34 (2005) 757]; C2H5I→C2H4 + HI (3), k3 = 1.7 × 1013 exp(−26680 KT) s−1; H + HI→H2 + I (4), k4 = 7.9 × 10−11 exp(−330 KT) cm3 s−1 [D. L. Baulch et al., J. Phys. Chem. Ref. Data 10(Suppl. 1) (1981) 1]; C2H5I + H→C2H5 + HI (5), k5 = 7.0 × 10−9 exp(−3940 KT) cm3 s−1. The latter bimolecular abstraction step turned out crucial for an adaquate d escription of the hydrogen atom concentration-time profiles in the above mentioned temperature and pressure range for initial concentrations [C2H5I]0 > 2 × 1013 cm−3 corresponding to mole fractions > 1 ppm.

Adsorption of Methylamine on Amorphous Ice under Interstellar Conditions. A Grand Canonical Monte Carlo Simulation Study

The adsorption of methylamine at the surface of amorphous ice is studied at various temperatures, ranging from 20 to 200 K, by grand canonical Monte Carlo simulations under conditions that are characteristic to the interstellar medium (ISM). The results are also compared with those obtained earlier on crystalline ( Ih) ice. We found that methylamine has a strong ability of being adsorbed on amorphous ice, involving also multilayer adsorption. The decrease of the temperature leads to a substantial increase of this adsorption ability; thus, considerable adsorption is seen at 20-50 K even at bulk gas phase concentrations that are comparable with that of the ISM. Further, methylamine molecules can also be dissolved in the bulk amorphous ice phase. Both the adsorption capacity of amorphous ice and the strength of the adsorption on it are found to be clearly larger than those corresponding to crystalline ( Ih) ice, due to the molecular scale roughness of the amorphous ice surface as well as to the lack of clear orientational preferences of the water molecules at this surface. Thus, the surface density of the saturated adsorption monolayer is estimated to be 12.6 ± 0.4 μmol/m2, 20% larger than the value of 10.35 μmol/m2, obtained earlier for Ih ice, and at low enough surface coverages the adsorbed methylamine molecules are found to easily form up to three hydrogen bonds with the surface water molecules. The estimated heat of adsorption at infinitely low surface coverage is calculated to be -69 ± 5 kJ/mol, being rather close to the estimated heat of solvation in the bulk amorphous ice phase of -74 ± 7 kJ/mol, indicating that there are at least a few positions at the surface where the adsorbed methylamine molecules experience a bulk-like local environment.

Miscibility and Thermodynamics of Mixing of Different Models of Formamide and Water in Computer Simulation

The thermodynamic changes that occur upon mixing five models of formamide and three models of water, including the miscibility of these model combinations itself, is studied by performing Monte Carlo computer simulations using an appropriately chosen thermodynamic cycle and the method of thermodynamic integration. The results show that the mixing of these two components is close to the ideal mixing, as both the energy and entropy of mixing turn out to be rather close to the ideal term in the entire composition range. Concerning the energy of mixing, the OPLS/AA_mod model of formamide behaves in a qualitatively different way than the other models considered. Thus, this model results in negative, while the other ones in positive energy of mixing values in combination with all three water models considered. Experimental data supports this latter behavior. Although the Helmholtz free energy of mixing always turns out to be negative in the entire composition range, the majority of the model combinations tested either show limited miscibility, or, at least, approach the miscibility limit very closely in certain compositions. Concerning both the miscibility and the energy of mixing of these model combinations, we recommend the use of the combination of the CHARMM formamide and TIP4P water models in simulations of water-formamide mixtures.