Water-Mediated Proton Transfer: A Mechanistic Investigation on the Example of the Hydration of Sulfur Oxides

The sulfur dioxide-water complex: CCSD(T)/CBS anharmonic vibrational spectroscopy of stacked and hydrogen-bonded dimers

This study examines the structures, energies, and IR vibrational spectra of the sulfur dioxide-water SO2(H2O) complexes by employing coupled cluster theory CCSD(T) with Dunning style correlation consistent type basis sets aug-cc-pV(n+d)Z (n = D, T, Q, 5). Complete basis set (CBS) extrapolations have been carried out to predict binding energies for two isomers of the SO2(H2O) complex: a stacked global minimum (1A) structure and a hydrogen-bonded local minimum (1B) structure. The CCSD(T)/CBS extrapolation predicts an intermolecular S-O distance rS⋯O = 2.827 Å for the stacked isomer, which is in excellent agreement with an experimental measurement of 2.824 Å [K. Matsumura et al., J. Chem. Phys., 91, 5887 (1989)]. The CCSD(T)/CBS binding energy for the stacked dimer 1A and hydrogen-bonded form 1B is De = -4.37 kcal/mol and De = -2.40 kcal/mol, respectively. This study also employs anharmonic VPT2 MP2/aug-cc-pV(n+d)Z level corrections to CCSD(T)/aug-cc-pV(n+d)Z vibrational frequencies in both forms of SO2(H2O). The anharmonic CCSD(T)/aug-cc-pV(Q+d)Z OH stretching frequencies in the stacked structure 1A are 3743 cm-1 (ν3) and 3647 cm-1 (ν1), and these align well with the recorded IR spectroscopic values of 3745 and 3643 cm-1, respectively [C. Wang et al., J. Phys. Chem. Lett., 13, 5654 (2022)]. If we combine CCSD(T)/aug-cc-pV(n+d)Z De values with VPT2 vibrational frequencies, we obtain a new CCSD(T)/aug-cc-pV(Q+d)Z anharmonic dissociation energy D0 = -3.48 kcal/mol for 1A and D0 = -1.74 kcal/mol for 1B. In summary, the results presented here demonstrate that the application of CCSD(T) calculations with aug-cc-pV(n+d)Z basis sets and CBS extrapolations is critical in probing the structure and IR spectroscopic properties of the sulfur dioxide-water complex.

Computational chemistry of cluster: Understanding the mechanism of atmospheric new particle formation at the molecular level

New particle formation (NPF), which exerts significant influence over human health and global climate, has been a hot topic and rapidly expands field of research in the environmental and atmospheric chemistry recent years. Generally, NPF contains two processes: formation of critical nucleus and further growth of the nucleus. However, due to the complexity of the atmospheric nucleation, which is a multicomponent process, formation of critical clusters as well as their growth is still connected to large uncertainties. Detection limits of instruments in measuring specific gaseous aerosol precursors and chemical compositions at the molecular level call for computational studies. Computational chemistry could effectively compensate the deficiency of laboratory experiments as well as observations and predict the nucleation mechanisms. We review the present theoretical literatures that discuss nucleation mechanism of atmospheric clusters. Focus of this review is on different nucleation systems involving sulfur-containing species, nitrogen-containing species and iodine-containing species. We hope this review will provide a deep insight for the molecular interaction of nucleation precursors and reveal nucleation mechanism at the molecular level.

A computational study of the HO2 + SO3 → HOSO2 + 3O2 reaction catalyzed by water monomer, water dimer and small clusters of sulfuric acid: kinetics and atmospheric implications

Herein, the reaction mechanisms and kinetics for the HO2 + SO3 → HOSO2 + 3O2 reaction catalyzed by water monomer, water dimer and small clusters of sulfuric acid have been...

CHAL336 Benchmark Set: How Well Do Quantum-Chemical Methods Describe Chalcogen-Bonding Interactions?

We present the CHAL336 benchmark set-the most comprehensive database for the assessment of chalcogen-bonding (CB) interactions. After careful selection of suitable systems and identification of three high-level reference methods, the set comprises 336 dimers each consisting of up to 49 atoms and covers both σ- and π-hole interactions across four categories: chalcogen-chalcogen, chalcogen-π, chalcogen-halogen, and chalcogen-nitrogen interactions. In a subsequent study of DFT methods, we re-emphasize the need for using proper London dispersion corrections when treating noncovalent interactions. We also point out that the deterioration of results and systematic overestimation of interaction energies for some dispersion-corrected DFT methods does not hint at problems with the chosen dispersion correction but is a consequence of large density-driven errors. We conclude this work by performing the most detailed DFT benchmark study for CB interactions to date. We assess 109 variations of dispersion-corrected and dispersion-uncorrected DFT methods and carry out a detailed analysis of 80 of them. Double-hybrid functionals are the most reliable approaches for CB interactions, and they should be used whenever computationally feasible. The best three double hybrids are SOS0-PBE0-2-D3(BJ), revDSD-PBEP86-D3(BJ), and B2NCPLYP-D3(BJ). The best hybrids in this study are ωB97M-V, PW6B95-D3(0), and PW6B95-D3(BJ). We do not recommend using the popular B3LYP functional nor the MP2 approach, which have both been frequently used to describe CB interactions in the past. We hope to inspire a change in computational protocols surrounding CB interactions that leads away from the commonly used, popular methods to the more robust and accurate ones recommended herein. We would also like to encourage method developers to use our set for the investigation and reduction of density-driven errors in new density functional approximations.

Barrierless HONO and HOS(O)2-NO2 Formation via NH3-Promoted Oxidation of SO2 by NO2

In the troposphere, the knowledge about nitrous acid (HONO) sources is incomplete. The missing source of sulfate and fine particles cannot be explained during haze events. Air quality models cannot predict high levels of secondary fine-particle pollution. Despite extensive studies, one challenging issue in atmospheric chemistry is identifying the source of HONO. Here, we present direct ab initio molecular dynamics simulation evidence and typical air pollution events of the formation of gaseous HONO, nitrogen dioxide/hydrogen sulfite (HOS(O)2-NO₂ or NO₂-HSO₃) from nitrogen dioxide (NO₂), sulfur dioxide (SO₂), water (H₂O), and ammonia (NH₃) molecules in a proportion of 2:1:3:3. The reactions show a new mechanism for the formation of HONO and NO₂-HSO₃ in the troposphere, especially when the concentration of NO₂, SO₂, H₂O, and NH₃ is high (e.g., 2:1:3:3 or higher) in the air. Contrary to the proportion NO₂, SO₂, H₂O, and NH₃ equaling to 1:1:3:1 and 1:1:3:2, the proportion (2:1:3:3) enables barrierless reactions and weak interactions between molecules via the formation of HONO, NO₂-HSO₃, and NH₃/H₂O. In addition, field observations are carried out, and the measured data are summarized. Correlation analysis supported the conversion of NO₂ to HONO during observational studies. The weak interactions promote proton transfer, resulting in the generation of HONO, NO₂-HSO₃, and NH₃/H₂O pairs.

A Density Functional Theory Study toward Ring-Opening Reaction Mechanisms of 2,4,6-Trinitrotoluene's Meisenheimer Complex for the Biodegradation of Old Yellow Enzyme Flavoprotein Reductase

The subsequent degradation pathway of the dihydride-Meisenheimer complex (2H^--TNT), which is the metabolite of 2,4,6-trinitrotoluene (TNT) by old yellow enzyme flavoprotein reductases of yeast and bacteria, was investigated computationally at the SMD/TPSSH/6-311+G(d,p) level of theory. Combining the experimentally detected products, a series of protonation, addition, substitution (dearomatization), and ring-opening reaction processes from 2H^--TNT to alkanes were proposed. By analyzing reaction free energies, we determined that the protonation is more advantageous thermodynamically than the dimerization reaction. In the ring-opening reaction of naphthenic products, the water molecule-mediated proton transfer mechanism plays a key role. The corresponding activation energy barrier is 37.7 kcal·mol^-1, which implies the difficulty of this reaction. Based on our calculations, we gave an optimum pathway for TNT mineralization. Our conclusions agree qualitatively with available experimental results. The details on transition states, intermediates, and free energy surfaces for all proposed reactions are given and make up for a lack of experimental knowledge.

A possible unaccounted source of atmospheric sulfate formation: amine-promoted hydrolysis and non-radical oxidation of sulfur dioxide

Numerous field and laboratory studies have shown that amines, especially dimethylamine (DMA), are crucial to atmospheric particulate nucleation. However, the molecular mechanism by which amines lead to atmospheric particulate formation is still not fully understood. Herein, we show that DMA molecules can also promote the conversion of atmospheric SO2 to sulfate. Based on ab initio simulations, we find that in the presence of DMA, the originally endothermic and kinetically unfavourable hydrolysis reaction between gaseous SO2 and water vapour can become both exothermic and kinetically favourable. The resulting product, bisulfite NH2(CH3)2 +·HSO3 -, can be readily oxidized by ozone under ambient conditions. Kinetic analysis suggests that the hydrolysis rate of SO2 and DMA with water vapour becomes highly competitive with and comparable to the rate of the reaction between SO2 and OH·, especially under the conditions of heavily polluted air and high humidity. We also find that the oxidants NO2 and N2O5 (whose role in sulfate formation is still under debate) appear to play a much less significant role than ozone in the aqueous oxidation reaction of SO2. The newly identified oxidation mechanism of SO2 promoted by both DMA and O3 provides another important new source of sulfate formation in the atmosphere.

Equilibrium Structure, Hydrogen Bonding, and Proton Conductivity in Half-Neutralized Diamine Ionic Liquids

Recent experiments on proton conducting ionic liquids point to half-neutralized diamine-triflate salts as promising candidates for applications in power generation and energy conversion electrochemical devices. Structural and dynamical properties of the simplest among these compounds are investigated by a combination of density functional theory (DFT) and molecular dynamics (MD) simulations based on an empirical force field. Three different cations have been considered, consisting of a pair of amine-ammonium terminations joined by a short aliphatic segment -(CH₂) _n- with n = 2, 3, and 4. First, the ground state structure, vibrational eigenstates, and hydrogen-bonding properties of single ions, neutral ion pairs, small neutral aggregates of up to eight ions, and molecularly thin hydrogen bonded wires have been investigated by DFT computations. Second, structural and dynamical properties of homogeneous liquid and amorphous phases are investigated by MD simulations over the temperature range of 200 ≤ T ≤ 440 K. Structure factors, radial distribution functions, diffusion coefficient, and electrical conductivity are computed and discussed, highlighting the inherent structural heterogeneity of these compounds. The core investigation, however, is the characterization of connected paths consisting of cation chains that could support proton transport via a Grotthuss-type mechanism. Since simulations are carried out using a force field of fixed bonding topology, this analysis is based on the equilibrium structure only, using geometrical criteria to identify potential paths for proton conduction. Paths of connected cations can reach a length of 80 cations and 30 Å, provided that bridging oxygen atoms from triflate anions are taken into account. The effects of water contamination at 1% weight concentration on the structure, dynamics, and paths for proton transport are discussed.

A theoretical insight into the reaction mechanisms of a 2,4,6-trinitrotoluene nitroso metabolite with thiols for toxic effects

2,4,6-Trinitrotoluene (TNT) is a class C carcinogen as rated by the Environmental Protection Agency. One of the toxicity mechanisms of TNT is the covalent binding of its metabolites to critical proteins. However, knowledge about their molecular reaction mechanisms is scarce. Herein, we have provided density functional theory (DFT) simulation evidences for the reaction mechanisms of the nitroso metabolite of TNT with the sulfhydryl group of model thiols for the first time. The results show that the solvent-mediated proton-transfer mechanism plays a significant role in the entire process. For the formation of semimercaptal, the mechanism is slightly different from the previous one where the thiolate anion attacks the nitroso group. The rearrangement of semimercaptal needs to be triggered by an acid or hydrated ion (H₃O⁺), which is consistent with the previous assumption. The other pathway, the conversion of semimercaptal to hydroxylamine, has to overcome a higher barrier, although it does not need the participation of an acid or a hydrated ion. In addition, the details on transition states, intermediates and free energy surfaces for three reactions are given, which make up for the lack of experimental knowledge. These conclusions can help to deeply understand the toxic effects of TNT and other nitroaromatic explosives.

Catalytic conversions of atmospheric sulfur dioxide and formation of acid rain over mineral dusts: Molecular oxygen as the oxygen source

Sulfur dioxide (SO₂) ranks as a major air pollutant and is likely to generate acid rain. When molecular oxygen is the oxygen source, the regular surfaces of gibbsite (one of the most abundant mineral dusts) show no reactivity for SO₂ conversions to H₂SO₄, while the partially dehydrated (100) surface with coordination-unsaturated Al sites becomes catalytically effective. Because of the easy availability of molecular oxygen, results manifest that acid rain can form under all atmospheric conditions and may account for the high conversion ratio of atmospheric SO₂. The (100) and (001) surfaces show divergent catalytic effects, and hydrolysis is always the rate-limiting step. Path A (hydrolysis and then oxidation) is preferred for (100) surface, whereas a third path with obviously lower activation barriers is presented for (001) surface, which is non-existent for (100) surface. Atomic oxygen originating from the dissociation of molecular oxygen is catalytically active for (100) surface, while the active site of (001) surface fails to be recovered, suggesting that SO₂ conversions over gibbsite surfaces are facet-controlled. This work also offers an environmentally friendly route for production of H₂SO₄ (one of the essential compounds in chemical industry), directly using molecular oxygen as the oxygen source.

Insights into the roles of water on the aqueous phase reforming of glycerol

Microkinetic modeling using energies from DFT and scaling relations to reveal roles of water in aqueous phase reforming of glycerol.

Towards understanding the role of amines in the SO2 hydration and the contribution of the hydrated product to new particle formation in the Earth's atmosphere

By theoretical calculations, the gas-phase SO₂ hydration reaction assisted by methylamine (MA) and dimethylamine (DMA) was investigated, and the potential contribution of the hydrated product to new particle formation (NPF) also was evaluated. The results show that the energy barrier for aliphatic amines (MA and DMA) assisted SO₂ hydration reaction is lower than the corresponding that of water and ammonia assisted SO₂ hydration. In these hydration reactions, nearly barrierless reaction (only a barrier of 0.1 kcal mol^-1) can be found in the case of SO₂ + 2H₂O + DMA. These lead us to conclude that the SO₂ hydration reaction assisted by MA and DMA is energetically facile. The temporal evolution for hydrated products (CH₃NH₃⁺-HSO₃^--H₂O or (CH₃)₂NH₂⁺-HSO₃^--H₂O) in molecular dynamics simulations indicates that these complexes can self-aggregate into bigger clusters and can absorb water and amine molecules, which means that these hydrated products formed by the hydration reaction may serve as a condensation nucleus to initiate the NPF.

The hydrolysis of 6-phosphogluconolactone in the second step of pentose phosphate pathway occurs via a two-water mechanism

Hydrolysis reaction marks the basis of life yet the mechanism of this crucial biochemical reaction is not completely understood. We recently reported the mechanisms of hydrolysis of nucleoside triphosphate and phosphate monoester. These two reactions hydrolyze P-O-P and P-O-C linkages, respectively. Here, we present the mechanism of hydrolysis of δ-6-phosphogluconolactone, which is an important precursor in the second step of the pentose phosphate pathway. Its hydrolysis requires the cleavage of C-O-C linkage and its mechanism is hitherto unknown. We report three mechanisms of hydrolysis of δ-6-phosphogluconolactone based on density functional computations. In the energetically most favorable mechanism, two water molecules participate in the hydrolysis reaction and the mechanism is sequential, i.e., activation of the attacking water molecule (OH bond breaking) precedes that of the cleavage of the CO bond of the C-O-C linkage. The rate-limiting energy barrier of this mechanism is comparable to the reported experimental free energy barrier. This mechanism has similarities with the mechanism of triphosphate hydrolysis and that of hydrolytic cleavage of DNA in EcoRV enzyme. This two-water sequential hydrolysis mechanism could be the unified mechanism required for the hydrolysis of other hydrolysable species in living cells.

Platinum-mediated monohydration of SO2

The monohydration of SO₂ has been achieved in solution mediated by a platinum-aquo complex.

Ammonia Catalyzed Formation of Sulfuric Acid in Troposphere: The Curious Case of a Base Promoting Acid Rain

Electronic structure calculations have been performed to investigate the role of ammonia in catalyzing the formation of sulfuric acid through hydrolysis of SO₃ in Earth's atmosphere. The uncatalyzed process involves a high activation barrier and, until date, is mainly known to occur in Earth's atmosphere only when catalyzed by water and acids. Here we show that hydrolysis of SO₃ can be very efficiently catalyzed by ammonia, the most abundant basic component in Earth's atmosphere. It was found, based on magnitude of relative potential energies as well as rate coefficients, that ammonia is the best among all the catalysts studied until now (water and acids) and could be a considerable factor in formation of sulfuric acid in troposphere. The calculated rate coefficient (at 298 K) of ammonia catalyzed reaction has been found to be ∼10⁵-10⁷ times greater than that for water catalyzed ones. It was found, based on relative rates of ammonia and water catalyzed processes, that in troposphere ammonia, together with water, could be the key factor in determining the rate of formation of sulfuric acid. In fact, ammonia could surpass water in catalyzing sulfuric acid formation via hydrolysis of SO₃ at various altitudes in troposphere depending upon their relative concentrations.

Proton transfer in acetaldehyde–water clusters mediated by a single water molecule

Bridging molecules: a single water molecule enhances the stability of symmetric acetaldehyde water clusters, and acts as a bridge for the transport of a proton between two acetaldehyde molecules.

Hydrolysis of Sulfur Dioxide in Small Clusters of Sulfuric Acid: Mechanistic and Kinetic Study

The deposition and hydrolysis reaction of SO2 + H2O in small clusters of sulfuric acid and water are studied by theoretical calculations of the molecular clusters SO2-(H2SO4)n-(H2O)m (m = 1,2; n = 1,2). Sulfuric acid exhibits a dramatic catalytic effect on the hydrolysis reaction of SO2 as it lowers the energy barrier by over 20 kcal/mol. The reaction with monohydrated sulfuric acid (SO2 + H2O + H2SO4 - H2O) has the lowest energy barrier of 3.83 kcal/mol, in which the cluster H2SO4-(H2O)2 forms initially at the entrance channel. The energy barriers for the three hydrolysis reactions are in the order SO2 + (H2SO4)-H2O > SO2 + (H2SO4)2-H2O > SO2 + H2SO4-H2O. Furthermore, sulfurous acid is more strongly bonded to the hydrated sulfuric acid (or dimer) clusters than the corresponding reactant (monohydrated SO2). Consequently, sulfuric acid promotes the hydrolysis of SO2 both kinetically and thermodynamically. Kinetics simulations have been performed to study the importance of these reactions in the reduction of atmospheric SO2. The results will give a new insight on how the pre-existing aerosols catalyze the hydrolysis of SO2, leading to the formation and growth of new particles.

The gas-phase reaction of methane sulfonic acid with the hydroxyl radical without and with water vapor

The gas phase reaction between methane sulfonic acid (CH3SO3H; MSA) and the hydroxyl radical (HO), without and with a water molecule, was investigated with DFT-B3LYP and CCSD(T)-F12 methods. For the bare reaction we have found two reaction mechanisms, involving proton coupled electron transfer and hydrogen atom transfer processes that produce CH3SO3 and H2O. We also found a third reaction mechanism involving the double proton transfer process, where the products and reactants are identical. The computed rate constant for the oxidation process is 8.3 × 10(-15) cm(3) s(-1) molecule(-1). CH3SO3H forms two very stable complexes with water with computed binding energies of about 10 kcal mol(-1). The presence of a single water molecule makes the reaction between CH3SO3H and HO much more complex, introducing a new reaction that consists in the interchange of H2O between HO and CH3SO3H. Our kinetic calculations show that 99.5% of the reaction involves this interchange of the water molecule and, consequently, water vapor does not play any role in the oxidation reaction of methane sulfonic acid by the hydroxyl radical.

Adenosine triphosphate hydrolysis mechanism in kinesin studied by combined quantum-mechanical/molecular-mechanical metadynamics simulations

Kinesin is a molecular motor that hydrolyzes adenosine triphosphate (ATP) and moves along microtubules against load. While motility and atomic structures have been well-characterized for various members of the kinesin family, not much is known about ATP hydrolysis inside the active site. Here, we study ATP hydrolysis mechanisms in the kinesin-5 protein Eg5 by using combined quantum mechanics/molecular mechanics metadynamics simulations. Approximately 200 atoms at the catalytic site are treated by a dispersion-corrected density functional and, in total, 13 metadynamics simulations are performed with their cumulative time reaching ~0.7 ns. Using the converged runs, we compute free energy surfaces and obtain a few hydrolysis pathways. The pathway with the lowest free energy barrier involves a two-water chain and is initiated by the Pγ-Oβ dissociation concerted with approach of the lytic water to PγO3-. This immediately induces a proton transfer from the lytic water to another water, which then gives a proton to the conserved Glu270. Later, the proton is transferred back from Glu270 to HPO(4)2- via another hydrogen-bonded chain. We find that the reaction is favorable when the salt bridge between Glu270 in switch II and Arg234 in switch I is transiently broken, which facilitates the ability of Glu270 to accept a proton. When ATP is placed in the ADP-bound conformation of Eg5, the ATP-Mg moiety is surrounded by many water molecules and Thr107 blocks the water chain, which together make the hydrolysis reaction less favorable. The observed two-water chain mechanisms are rather similar to those suggested in two other motors, myosin and F1-ATPase, raising the possibility of a common mechanism.

Investigation of simple and water assisted tautomerism in a derivative of 1,3,4-oxadiazole: a DFT study

Investigation of tautomerism and transition states in a derivative of 1,3,4-oxadiazole (A, B, C and D) in the gas phase and in solution and in a micro hydrated environment with 1-3 water molecules was performed by calculations at the DFT-B3LYP/6-311++G(d,p) level of theory. The solvent effect is taken into account via the self-consistent reaction field (SCRF) method. The geometries of four possible tautomers of 5-amino-1,3,4-oxadiazole-2(3H)-one were optimized in the gas phase and solution with polarized continuum model (PCM). It was found that in the gas phase and different solvents, A and C tautomers are the most stable and unstable forms, respectively. The results show that the tautomeric interconversion C to D has the lowest Gibbs free energy changes and so the highest equilibrium constant in the gas phase and solution. The equilibrium and rate constants of intermolecular tautomerism in the absence and presence of 1-3 molecules of water were also calculated. The calculated results show that the presence of water molecules considerably reduces the barrier energy of the various reactions. Therefore, this water-assisted tautomerism can be performed fast, especially, with the assistance of two molecules of water.

Quantum proton transfer in hydrated sulfuric acid clusters: a perspective from semiempirical path integral simulations

We have carried out path-integral molecular dynamics simulations for hydrated sulfuric acid clusters to understand acid-dissociation and hydrogen-bonded structural rearrangement processes in these clusters from a quantum mechanical viewpoint. The simulations were performed using the PM6 semiempirical electronic structure level whose parameters were modified on the basis of the specific reaction parameters strategy so that relative energies of optimized structures, as well as water binding energies reproduce ab initio and density-functional theory calculations. We have found that the acid dissociation processes, first and second deprotonation, effectively occur in a hydrated cluster with a specific cluster size. The mechanisms of the proton-transfer processes were analyzed in detail and it was found that the distance between O in sulfuric acid and O in the proton-accepting water is playing an important role. We also found that the water coordination number of the poton-accepting water is important in the proton-transfer processes.

Water-assisted proton transfer in ferredoxin I

The role of water molecules in assisting proton transfer (PT) is investigated for the proton-pumping protein ferredoxin I (FdI) from Azotobacter vinelandii. It was shown previously that individual water molecules can stabilize between Asp(15) and the buried [3Fe-4S](0) cluster and thus can potentially act as a proton relay in transferring H(+) from the protein to the μ(2) sulfur atom. Here, we generalize molecular mechanics with proton transfer to studying proton transfer reactions in the condensed phase. Both umbrella sampling simulations and electronic structure calculations suggest that the PT Asp(15)-COOH + H(2)O + [3Fe-4S](0) → Asp(15)-COO(-) + H(2)O + [3Fe-4S](0) H(+) is concerted, and no stable intermediate hydronium ion (H(3)O(+)) is expected. The free energy difference of 11.7 kcal/mol for the forward reaction is in good agreement with the experimental value (13.3 kcal/mol). For the reverse reaction (Asp(15)-COO(-) + H(2)O + [3Fe-4S](0)H(+) → Asp(15)-COOH + H(2)O + [3Fe-4S](0)), a larger barrier than for the forward reaction is correctly predicted, but it is quantitatively overestimated (23.1 kcal/mol from simulations versus 14.1 from experiment). Possible reasons for this discrepancy are discussed. Compared with the water-assisted process (ΔE ≈ 10 kcal/mol), water-unassisted proton transfer yields a considerably higher barrier of ΔE ≈ 35 kcal/mol.

Mechanism for the abiotic synthesis of uracil via UV-induced oxidation of pyrimidine in pure H(2)O ices under astrophysical conditions

The UV photoirradiation of pyrimidine in pure H(2)O ices has been explored using second-order Moller-Plesset perturbation theory and density functional theory methods, and compared with experimental results. Mechanisms studied include those starting with neutral pyrimidine or cationic pyrimidine radicals, and reacting with OH radical. The ab initio calculations reveal that the formation of some key species, including the nucleobase uracil, is energetically favored over others. The presence of one or several water molecules is necessary in order to abstract a proton which leads to the final products. Formation of many of the photoproducts in UV-irradiated H(2)O:pyrimidine=20:1 ice mixtures was established in a previous experimental study. Among all the products, uracil is predicted by quantum chemical calculations to be the most favored, and has been identified in experimental samples by two independent chromatography techniques. The results of the present study strongly support the scenario in which prebiotic molecules, such as the nucleobase uracil, can be formed under abiotic processes in astrophysically relevant environments, namely in condensed phase on the surface of icy, cold grains before being delivered to the telluric planets, like Earth.

Theoretical and experimental sulfur K-edge X-ray absorption spectroscopic study of cysteine, cystine, homocysteine, penicillamine, methionine and methionine sulfoxide

The experimental sulfur K-edge X-ray absorption near-edge structure (XANES) spectra of the amino acids cysteine, homocysteine, penicillamine, methionine, including the oxidation products methionine sulfoxide and the disulfide cystine, have been analyzed by transition potential DFT calculations. The absolute energies and intensities of the main pre-edge sulfur 1s electron transitions have been computed to determine the character of the receiving unoccupied molecular orbitals (MO), and to investigate the influence of external interactions, especially by introducing water molecules hydrogen-bonded to the ionic species present in different pH ranges. When the thiol group deprotonates for cysteine, homocysteine and penicillamine and also for the cysteine residue in glutathione the energy of the main transition, to an MO with antibonding sigma*(S-H) character, reduces by approximately 1.1 eV and the receiving MO obtains sigma*(S-C) character. The changes in transition energy due to hydrogen-bonding were in most cases found to be relatively small, although the transition intensities could vary significantly due to the changes induced in the molecular charge distribution, thereby affecting the shapes of the spectral features. For the cysteine and penicillamine zwitterions deconvolution of the experimental spectra allowed the microscopic acid dissociation constants to be extracted separately for the thiol and the protonated amine groups, pK(a)(S) = 8.5 +/- 0.1 and 8.2 +/- 0.1, and pK(a)(N) = 8.9 +/- 0.1 and 8.8 +/- 0.1, respectively, with the thiol group in both cases being the more acidic. Coordination of cysteine to nickel(II) or mercury(II) introduced a new low energy transition involving metal ion orbitals in the receiving LUMO. The small experimentally observed energy differences between the similar main absorption features of the cysteine and methionine zwitterions, 0.2-0.3 eV in comparable surrounding, as well as a minor difference in their intensities, are reflected in the calculated transitions. The S K-edge XANES spectrum of the disulfide cystine displays a characteristic double peak with the lower energy transition (2469.9 eV) into the antibonding sigma*(S-S) MO. The second peak, at 2471.5 eV in aqueous solution, contains several transitions into MOs with sigma*(S-C) character involving also charge transfer to the water molecules hydrating the protonated amine groups (NH(3)(+)) of cystine. For solid cystine without hydrogen bonding the experimental energy difference between the two peaks is 0.2 eV larger, while no such increase occurs for the oxidized disulfide of glutathione, with a similar -S-S- bond between its cysteine residues as in cystine, because the amine groups are engaged in peptide bonds. This study shows that externally induced changes in the intramolecular bonding, e.g., by coordination, conformation geometry or hydrogen-bonding, can significantly influence the S K-edge spectra, and emphasizes the importance of a similar chemical surrounding when choosing the model compounds for standard spectra of sulfur functional groups, used to deconvolute composite experimental spectra.