Quantum mechanical treatment of biopolymers as solids: Possible implications for carcinogenesis

After briefly reviewing the results of ab initio band structure calculations on periodic polynucleotides, it is shown how these band structures can be corrected for correlation (quasi particle band structures). Some new results on the electronic structure of aperiodic polypeptides (having up to four different amino acids as components) obtained with the help of the matrix block negative factor counting technique are then presented. They are supplemented by similar results calculated for nonperiodic nucleotide base stacks. Some plausible long-range effects for the activation of oncogenes through carcinogens are then reviewed. Finally, the preparation of much better defined samples of biopolymers (on which reliable physical measurements could be performed) is discussed.     

Theoretical study on reaction mechanism of sulfuric acid and ammonia and hydration of (NH4)2SO4

In order to understand the mechanism of nucleation of (NH₄)₂SO₄ aerosol, the reaction between sulfuric acid and ammonia in the absence of water molecule is performed at M06/6-311++G(d,p) level. The results show that the (NH₄)₂SO₄ and NH₄HSO₄ units may exist instantaneously in gas phase without water molecule, which is a theoretical prediction that needs detection by further experiment. To further study the growth of the primary nuclei, the geometries, energies, and harmonic frequencies of (NH₄)₂SO₄ · (H₂O) _n (n = 0–9) are calculated both at M06/6-311++G(d,p) and B3LYP/6-311++G(d,p) levels. The tendency of the theoretical vibration frequencies is in accordance with the experimental results. The influence of the water molecule on the properties of (NH₄)₂SO₄ is also analyzed. Our results indicate that M06 is more accurate than B3LYP for this kind of system. Moreover, the first principle molecular dynamics method is used to simulate the structural transformation for two representative isomers whose energies are close, to understand the relationship between solvent-shared ion pairs and contact ion pairs.     

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.     

Quantum mechanical investigation of the atmospheric reaction CH3O2 + NO

The important stationary points on the potential energy surface of the reaction CH(3)O(2) + NO have been investigated using ab initio and density functional theory techniques. The optimizations were carried out at the B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) levels of theory while the energetics have been refined using the G2MP2, G3//B3LYP, and CCSD(T) methodologies. The calculations allow the proper characterization of the transition state barriers that determine the fate of the nascent association conformeric minima of methyl peroxynitrite. The main products, CH(3)O + NO(2), are formed through either rearrangement of the trans-conformer to methyl nitrate and its subsequent dissociation or via the breaking of the peroxy bond of the cis-conformer to CH(3)O + NO(2) radical pair. The important consequences of the proposed mechanism are (a) the allowance on energetic grounds for nitrate formation parallel to radical propagation under favorable external conditions and (b) the confirmation of the conformational preference of the homolytic cleavage of the peroxy bond, discussed in previous literature.     

A study of the chemical stability of beryl and of the product of its mechanical activation against sulfuric acid

Effect of the concentration of sulfuric acid used for beryl sulfatization, degree of beryl grinding, temperature and duration of beryl sulfatization, and other technological parameters of sulfuric acid decomposition on the extent of beryl recovery was studied. The results obtained made it possible to suggest a method for preparation of beryl concentrates for sulfatization. The method is based on a mechanochemical activation of this kind of raw materials and can serve as an alternative to the conventionally employed beryl activation techniques.     

Quantum mechanical/molecular mechanical study of anthrax lethal factor catalysis

We report a hybrid quantum mechanical and molecular mechanical study of the catalysis of anthrax lethal factor. The calculations suggest that the zinc peptidase uses the same general base-general acid mechanism as in thermolysin and carboxypeptidase A, in which a zinc-bound water is activated by Glu687 to nucleophilically attack the scissile carbonyl carbon in the substrate. The catalysis is aided by an oxyanion hole formed by the zinc ion and the side chain of Tyr728, which provide stabilization for the fractionally charged carbonyl oxygen. The assigned role of Tyr728 differs from previous suggestions but is consistent with the established mechanism of other zinc proteases.     

Heterogeneous chemistry of butanol and decanol with sulfuric acid: implications for secondary organic aerosol formation

Recent environmental chamber studies suggest that acid-catalyzed reactions between alcohols and aldehydes in the condensed phase lead to the formation of hemiacetals and acetals, enhancing secondary organic aerosol (SOA) growth. We report measurements of heterogeneous uptake of butanol and decanol on liquid H2SO4 in the range of 62-84 wt % and between 273 and 296 K. Both alcohols exhibit two distinct types of uptake behaviors (partially irreversible vs totally irreversible uptake), depending on the acid concentration and temperature. For the partially irreversible uptake, a fraction of the alcohol was physically absorbed while the other fraction underwent irreversible reaction. For the totally irreversible uptake, the alcohols were completely lost onto the sulfuric acid. The Henry's law solubility constant (H*) was determined from the time-dependent uptake, while the reactive uptake coefficients were calculated from the time-independent irreversible loss. Coexistence of butanol or decanol with octanal or decanal did not show enhanced uptake of the aldehydes in the sulfuric acid. Protonation and dissolution likely account for the reversible uptake, while formation of alkyl sulfate or dialkyl sulfate explains irreversible uptake of the alcohols. The results suggest that heterogeneous uptake of larger alcohols is unlikely of significant importance in the lower atmosphere except in the case of freshly nucleated aerosols that may have high acid concentrations.     

First-principles molecular dynamics study on aqueous sulfuric acid solutions

The properties of aqueous sulfuric acid have been studied employing density functional theory-based molecular dynamics simulations in conjunction with norm-conserving pseudopotentials. The simulations were carried out for two different concentrations whose molar concentrations were fixed at 0.84 and 10.2 mol/l. The structural features of aqueous sulfuric acid solutions show a strong dependency on the concentration. The Gr?tthuss-type proton transfer mechanism is not effectively operative at the higher concentration because of the broken hydrogen bond network of water induced by ions generated by the dissociation of sulfuric acid. In addition, to evaluate electrical properties, we carried out a simulation that takes an electric field into account. Results are compared with those of the simulation undertaken with no external electric field.     

Kinetics and mechanism of hydration of 3-methyl-3-buten-1-ol in aqueous solutions of sulfuric acid

Conclusions The kinetic regularities of hydration of 3-methyl-3-buten-1-ol in 9.6 to 34% aqueous solutions of sulfuric acid at 25°C were studied. An equation was found for describing the influence of the medium on the value of the effective rate constant of hydration of 3-methyl-3-buten-1-ol.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 5, pp. 1016–1019, May, 1988.     

Formic acid catalyzed hydrolysis of SO3 in the gas phase: a barrierless mechanism for sulfuric acid production of potential atmospheric importance

Computational studies at the B3LYP/6-311++G(3df,3pd) and MP2/6-311++G(3df,3pd) levels are performed to explore the changes in reaction barrier height for the gas phase hydrolysis of SO(3) to form H(2)SO(4) in the presence of a single formic acid (FA) molecule. For comparison, we have also performed calculations for the reference reaction involving water assisted hydrolysis of SO(3) at the same level. Our results show that the FA assisted hydrolysis of SO(3) to form H(2)SO(4) is effectively a barrierless process. The barrier heights for the isomerization of the SO(3)···H(2)O···FA prereactive collision complex, which is the rate limiting step in the FA assisted hydrolysis, are found to be respectively 0.59 and 0.08 kcal/mol at the B3LYP/6-311++G(3df,3pd) and MP2/6-311++G(3df,3pd) levels. This is substantially lower than the ~7 kcal/mol barrier for the corresponding step in the hydrolysis of SO(3) by two water molecules--which is currently the accepted mechanism for atmospheric sulfuric acid production. Simple kinetic analysis of the relative rates suggests that the reduction in barrier height facilitated by FA, combined with the greater stability of the prereactive SO(3)···H(2)O···FA collision complex compared to SO(3)···H(2)O···H(2)O and the rather plentiful atmospheric abundance of FA, makes the formic acid mediated hydrolysis reaction a potentially important pathway for atmospheric sulfuric acid production.     

Quantum mechanical study of a reaction path bifurcation model

The feasibility of close coupling techniques for bifurcation processes is investigated using a simple model. Density contours and a flux map illustrate the bifurcation process. The relevance of this study to the theory of three-dimensional chemical reactions is discussed.     

Equilibrium structure of sulfuric acid

The equilibrium structure of the more stable conformer of H2SO4, of C2 symmetry, has been calculated ab initio using the CCSD(T) method and taking into account the core correlation correction. The accuracy of this structure has been checked by comparing it to that of similar molecules and by estimating the effects of basis set enlargement and of diffuse functions. Furthermore, the quadratic, cubic, and quartic force fields have been calculated at the MP2 level of theory using a basis set of triple-zeta quality. The spectroscopic constants derived from the force field are in satisfactory agreement with the experimental ones. The resulting band origins are compared to literature infrared values, including those for overtone and combination bands. Normal modes of vibration are pictured. Using this force field, semiexperimental equilibrium rotational constants are determined which allows us to check the accuracy of the ab initio structure and to refine it using a mixed regression method.     

Calculated electronic transitions in sulfuric acid and implications for its photodissociation in the atmosphere

We have calculated electronic transitions for sulfuric acid in the ultraviolet region using a hierarchy of coupled cluster response functions and correlation consistent basis sets. Our calculations indicate that the lowest energy singlet transition occurs at 8.42 eV with an oscillator strength of 0.01. The lowest energy triplet state occurs at 8.24 eV. Thus, the cross section of sulfuric acid in the actinic region is likely to be very small and smaller than the upper limit put on this cross section by previous experimental investigations. We estimate the cross section of sulfuric acid in the atmospherically relevant Lyman-alpha region ( approximately 10.2 eV) to be approximately 6 x 10 (-17) cm (2) molecule (-1), a value approximately 30 times larger than the speculative value used in previous atmospheric simulations. We have calculated the J values for photodissociation of sulfuric acid with absorption of visible, UV, and Lyman-alpha radiation, at altitudes between 30 and 100 km. We find that the dominant photodissociation mechanism of sulfuric acid below 70 km is absorption in the visible region by OH stretching overtone transitions, whereas above 70 km, absorption of Lyman-alpha radiation by high energy Rydberg excited states is the favored mechanism. The low lying electronic transitions of sulfuric acid in the UV region do not contribute significantly to its dissociation at any altitude.     

Methanesulfinic acid reaction with OH: mechanism, rate constants, and atmospheric implications

The mechanism for the atmospheric oxidation of methanesulfinic acid (MSIA) has been studied. This is the first theoretical study of the reaction between MSIA and the OH radical. All the possible channels in this reaction have been studied theoretically, and their corresponding rate constants have been evaluated under the variational transition-state theory (VTST) formalism. Two different products can be formed: the CH3S(O)2 radical (which had been experimentally proposed as the only one), and sulfurous acid (H2SO3). The CH3S(O)2 radical can be formed directly or can form via an intermediate adduct, which yields to the radical through the elimination of a water molecule. For the first time, it is theoretically demonstrated that SO2 is formed in the addition channel of the DMS + OH reaction. The consequences of this result in the interpretation of the T-dependence of the SO4(2-)/MSA (methanesulfonic acid) quocient are analyzed. The competition between the unimolecular dissociation of the CH3S(O)2 radical and OH-addition to yield MSA is proposed as one of the possible multiple branching points (along the DMS + OH degradation scheme) influencing the T-dependence of the SO4(2-)/MSA relation.     

Citric acid oxidation by vanadium(V) in sulfuric acid medium: Kinetic and mechanistic study

The citric acid oxidation by vanadium(V) in sulfuric acid medium at 303 K is reported. The reaction rate was determined spectrophotometrically by monitoring the formation of vanadium(IV) at 760 nm. The oxidation showed a first‐order dependence with respect to vanadium(V) concentration and fractional order with respect to citric acid concentrations, with no control and with constant ionic strength. The reaction is also first order with respect to sulfuric acid concentration with no control and of fractional order at constant ionic strength. The reaction rate is enhanced by an increase of ionic strength and increased by a decrease of the dielectric constant. The activation parameters were calculated based on the rate constants determined in the 293 to 313 K interval. The proposed oxidation mechanisms and the derived rate laws are consistent with the experimental rate laws. © 2000 John Wiley & Sons, Inc. Int J Chem Kinet 32: 566–572, 2000     

Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis

The molecular mechanism of hairpin ribozyme catalysis is studied with molecular dynamics simulations using a combined quantum mechanical and molecular mechanical (QM/MM) potential with a recently developed semiempirical AM1/d-PhoT model for phosphoryl transfer reactions. Simulations are used to derive one- and two-dimensional potentials of mean force to examine specific reaction paths and assess the feasibility of proposed general acid and base mechanisms. Density-functional calculations of truncated active site models provide complementary insight to the simulation results. Key factors utilized by the hairpin ribozyme to enhance the rate of transphosphorylation are presented, and the roles of A38 and G8 as general acid and base catalysts are discussed. The computational results are consistent with available experimental data, provide support for a general acid/base mechanism played by functional groups on the nucleobases, and offer important insight into the ability of RNA to act as a catalyst without explicit participation by divalent metal ions.     

A study of the reaction of pentacyclic triterpenoids with concentrated sulfuric acid

Summary The conditions for the reaction of triterpenoids with concentrated sulfuric acid have been studied by the method of mathematical planning, and the optimum conditions for performing this reaction have been found.Pyatigorsk Pharmaceutical Institute. Translated from Khimiya Prirodnykh Soedinenii, No. 3, pp. 294–296, May–June, 1971.