József Csontos

High-accuracy thermochemistry of atmospherically important fluorinated and chlorinated methane derivatives.

High-precision quantum chemical calculations have been performed for atmospherically important halomethane derivatives including CF, CF(3), CHF(2), CH(2)F, CF(2), CF(4), CHF, CHF(3), CH(3)F, CH(2)F(2), CCl, CCl(3), CHCl(2), CH(2)Cl, CCl(2), CCl(4), CHCl, CHCl(3), CH(3)Cl, CH(2)Cl(2), CHFCl, CF(2)Cl, CFCl(2), CFCl, CFCl(3), CF(2)Cl(2), CF(3)Cl, CHFCl(2), CHF(2)Cl, and CH(2)FCl. Theoretical estimates for the standard enthalpy of formation at 0 and 298.15 K as well as for the entropy at 298.15 K are presented. The determined values are mostly within the experimental uncertainty where accurate experimental results are available, while for the majority of the considered heat of formation and entropy values the present results represent the best available estimates.

High-Accuracy Theoretical Thermochemistry of Atmospherically Important Sulfur-Containing Molecules

In this study, several sulfur-containing molecules with atmospherical importance were investigated by means of high-accuracy quantum chemical calculations including: HSO, HOS, HOSO2, HSNO, SH, CH2SO, CH2SH, S2COH, and SCSOH. After identifying the stable conformers of the molecules, a coupled-cluster-based composite model chemistry, which includes contributions up to quadruple excitations as well as corrections beyond the nonrelativistic and Born–Oppenheimer approximations, was applied to calculate the corresponding heat of formation (Δ(f)H(0)° and Δ(f)H(298)°) and entropy (S(298)°) values. In most of the cases, this study delivers more reliable estimates for the investigated thermodynamic properties than those reported in previous investigations. Our data also suggest that the experimental heats of formation associated with the HSO molecule are very likely to belong to its structural isomer, HOS. It is also confirmed by the calculated thermodynamic properties including standard reaction entropies, enthalpies, and equilibrium constants that, in the reaction CS2 + OH CS2OH, the SCSOH structural isomer is produced. It is also noted that the currently accepted Δ(f)H(0)°(S(gas)) = 274.73 ± 0.3 kJ/mol value is in need of revision, and based on a recent measurement, which is also confirmed by our computations, it is advised to update it to Δ(f)H(0)°(S(gas)) = 277.25 ± 0.3 kJ/mol.

Aromatic‐backbone interactions in model α‐helical peptides

The effects on helical stability of weak polar interactions between aromatic side‐chains and the peptide backbone were examined. α‐Helical model peptides, hexa‐Ala, with sequential Tyr replacement, were investigated computationally to obtain the geometries and energetics of the interactions. Geometries were obtained with the B3LYP/6‐31G* level of theory. Interaction energies were calculated using BHandHLYP/cc‐pVTZ and an improved method to correct for basis set superposition error when fragmentation caused steric clashes. Both i, i + 1 and i, i − 4 interactions were observed when Tyr was in position i = 5. The position of the aromatic residue in the amino acid sequence was crucial in facilitating aromatic‐backbone interactions. The distance between the center of the aromatic ring of Tyr and the individual interacting backbone atoms ranged from 3.65 to 5.50 Å. The interactions have energies of the same order as hydrogen bonds and, thus, could have a significant impact on the stability of the helix.

On the protonation of water

Imaging photoelectron photoion coincidence (iPEPICO) spectroscopy on isolated water molecules and water dimers establishes a new route to determining the water proton affinity (PA) with unprecedented accuracy. A floating thermochemical cycle constructed from the OH+ and H3O+ appearance energies and three other spectroscopic values establishes the water PA as 683.22 ± 0.25 kJ mol−1 at 0 K, which converts to 688.81 ± 0.25 kJ mol−1 at room temperature. The experimental results are corroborated by a hierarchy of coupled-cluster calculations up to pentuple excitations and septuple-ζ basis set. Combined with diagonal Born–Oppenheimer and Dirac–Coulomb–Gaunt relativistic corrections, they provide the best theoretical estimate for both the hydronium ions geometry and a water PA of 683.5 ± 0.4 kJ mol−1 and 689.1 ± 0.4 kJ mol−1 at 0 K and 298.15 K, respectively.

High-Throughput Analysis of Ammonia Oxidiser Community Composition via a Novel, amoA-Based Functional Gene Array

Advances in microbial ecology research are more often than not limited by the capabilities of available methodologies. Aerobic autotrophic nitrification is one of the most important and well studied microbiological processes in terrestrial and aquatic ecosystems. We have developed and validated a microbial diagnostic microarray based on the ammonia-monooxygenase subunit A (amoA) gene, enabling the in-depth analysis of the community structure of bacterial and archaeal ammonia oxidisers. The amoA microarray has been successfully applied to analyse nitrifier diversity in marine, estuarine, soil and wastewater treatment plant environments. The microarray has moderate costs for labour and consumables and enables the analysis of hundreds of environmental DNA or RNA samples per week per person. The array has been thoroughly validated with a range of individual and complex targets (amoA clones and environmental samples, respectively), combined with parallel analysis using traditional sequencing methods. The moderate cost and high throughput of the microarray makes it possible to adequately address broader questions of the ecology of microbial ammonia oxidation requiring high sample numbers and high resolution of the community composition.

Quantum Chemical Quantification of Weakly Polar Interaction Energies in the TC5b Miniprotein

The tertiary structure of the TC5b miniprotein is stabilized by inter-residue interactions of the Trp-cage, which is composed of a Tyr and several Pro residues surrounding a central Trp residue. The interactions include Ar-Ar (aromatic side-chain-aromatic side-chain), Ar-NH (aromatic side-chain-backbone amide), and CH-pi (aromatic side-chain-aliphatic hydrogen) interactions. In the present work, the strength of the weakly polar interactions found in the TC5b miniprotein was quantified using all of the available 38 NMR structures (1L2Y) from the Protein Data Bank with DFT quantum chemical calculations at the BHandHLYP/cc-pVTZ level of theory and molecular fragmentation with capping of the partial structures. The energies of interaction between the individual residues of the Trp-cage range between -5.85+/-1.41 and -21.30+/-0.88 kcal mol(-1), leading to a significant total structural stabilization energy of -52.13+/-2.56 kcal mol(-1) of which about 50% is from the weakly polar interactions. Furthermore, the strengths of the individual weakly polar interactions are between -2.32+/-0.17 and -2.93+/-0.12 kcal mol(-1) for the CH-pi interactions, between -2.48+/-0.97 and -3.09+/-1.02 kcal mol(-1) for the Ar-NH interaction and -2.74+/-1.06 kcal mol(-1) for the Ar-Ar interaction.

High-accuracy theoretical study on the thermochemistry of several formaldehyde derivatives.

In the case of several formaldehyde derivatives, with importance in atmospheric and combustion chemistry, the currently available thermochemical values suffer from considerably large uncertainties. In this study a high-accuracy theoretical model chemistry has been used to provide accurate thermochemical data including heats of formation at 0 and 298 K and standard molar entropies at 298 K for CF(2)O, FCO, HFCO, HClCO, FClCO, HOCO, and NH(2)CO. For most of the thermochemical quantities studied here, this investigation delivers the best available estimate.

Dissociation of the fluorine molecule.

The primary purpose of the present study is to resolve the discrepancy that exists between the two most recently published dissociation energies for the fluorine molecule [D0(F2)] and, consequently, for the associated heats of formation of the fluorine atom [ΔfH0°(F)]. We hope to provide a reliable, well-established theoretical estimate for these thermochemical quantities. To this end, a high-accuracy coupled-cluster-based composite ab initio model chemistry has been utilized. The protocol involves contributions of up to pentuple excitations in coupled-cluster theory augmented with basis set extrapolation techniques and additional corrections beyond the nonrelativistic and Born–Oppenheimer approximations. The augmented core–valence correlation consistent basis set families, aug-cc-pCVXZ, have been successively used, in some cases, up to octuple-ζ quality. Our best theoretical results for D0(F2) and ΔfH0°(F) obtained in this study are 154.95 ± 0.48 and 77.48 ± 0.24 kJ/mol, respectively. Because conflicting theoretical results are also reported about the existence of a barrier along the dissociation curve of F2, extensive multireference configuration interaction and coupled-cluster calculations have been performed using reference orbitals taken from all-electron complete active space self-consistent field computations. Extrapolations from the results obtained with the aug-cc-pCVXZ (X = T, Q, 5) basis sets clearly indicate that the barrier indeed exists. It is located at 3.80 ± 0.20 Å along the dissociation curve with a height of 42 ± 10 μEh (∼0.11 ± 0.03 kJ/mol). Because of the neglect of this effect during the evaluation of the raw experimental data used to obtain D0(F2) = 154.52 ± 0.12 kJ/mol and ΔfH0°(F) = 77.26 ± 0.06 kJ/mol [Stevens; et al. J. Phys. Chem. A 2010, 114, 13134], an additional error should be attached to these latter values. Obviously, the barrier does not affect either the experimental results, D0(F2) = 154.92 ± 0.10 kJ/mol and ΔfH0°(F) = 77.46 ± 0.05 kJ/mol [Yang; et al. J. Chem. Phys. 2005, 122, 134308; 2007, 127, 209901], which are based on the ion-pair dissociation of the molecule, or the data calculated theoretically. It is also noteworthy that our best estimates are in excellent agreement with those obtained from the ion-pair dissociation experiment.

High-accuracy theoretical thermochemistry of atmospherically important nitrogen oxide derivatives

High-accuracy quantum chemical calculations were performed for several atmospherically important nitrogen oxide derivatives, such as HOONO, HOONO(2), NH(2)NO(2), FNO, FNO(2), FONO, FONO(2), ClNO, ClONO, ClONO(2), and ClOONO. The stable conformers of the molecules were identified, and the corresponding heats of formation (Δ(f)H(0)° and Δ(f)H(298)°) and entropy values (S(298)°) were computed. On the basis of the thermodynamic functions, equilibrium constants were also calculated for a couple of reactions with importance in the chemistry of the atmosphere. In a number of cases this study provides more reliable estimates for the investigated thermodynamic properties than those can be collected from previous reports.

Benchmarking Experimental and Computational Thermochemical Data: A Case Study of the Butane Conformers.

Due to its crucial importance, numerous studies have been conducted to determine the enthalpy difference between the conformers of butane. However, it is shown here that the most reliable experimental values are biased due to the statistical model utilized during the evaluation of the raw experimental data. In this study, using the appropriate statistical model, both the experimental expectation values and the associated uncertainties are revised. For the 133-196 and 223-297 K temperature ranges, 668 ± 20 and 653 ± 125 cal mol(-1), respectively, are recommended as reference values. Furthermore, to show that present-day quantum chemistry is a favorable alternative to experimental techniques in the determination of enthalpy differences of conformers, a focal-point analysis, based on coupled-cluster electronic structure computations, has been performed that included contributions of up to perturbative quadruple excitations as well as small correction terms beyond the Born-Oppenheimer and nonrelativistic approximations. For the 133-196 and 223-297 K temperature ranges, in exceptional agreement with the corresponding revised experimental data, our computations yielded 668 ± 3 and 650 ± 6 cal mol(-1), respectively. The most reliable enthalpy difference values for 0 and 298.15 K are also provided by the computational approach, 680.9 ± 2.5 and 647.4 ± 7.0 cal mol(-1), respectively.