Structures and thermochemistry of calcium-containing molecules

A variety of theoretical procedures, including the high-level ab initio methods G3, G3[CC](dir,full), and W2C//ACQ, have been used to predict the structures and heats of formation of several small calcium-containing molecules (CaH, CaH2, CaO, CaOH, Ca(OH)2, CaF, CaF2, CaS, CaCl, and CaCl2). B3-LYP and CCSD(T) with both the (aug-)cc-pWCVQZ and (aug-)cc-pWCVQ+dZ basis sets are found to give molecular geometries that agree well with the experimental results. The CCSD(T)(riv)/(aug-)cc-pWCVQ+dZ results are found to be the most accurate, with a mean absolute deviation from experiment of just 0.008 angstroms. Zero-point vibrational energies (ZPVEs) and thermochemical corrections are found to be relatively insensitive to the level of theory, except in the case of molecules with highly anharmonic calcium-centered bending modes (CaH2, Ca(OH)2, CaF2, CaCl2), where special procedures need to be employed in order to obtain satisfactory results. Several potential improvements to the W2C method were investigated, most of which do not produce significant changes in the heats of formation. It was observed, however, that for CaO and CaS the scalar relativistic corrections are unexpectedly large and highly basis set dependent. In these cases, Douglas-Kroll CCSD(T)/(aug-)cc-pWCV5Z calculations appear to give a converged result. The G3[CC](dir,full) and best W2C-type heats of formation are both found generally to agree well with experimental values recommended in recent critical compendia. However, in some cases (CaO, Ca(OH)2, and CaF2), they differ from one another by more than their predicted error margins. The available experimental data are not sufficiently precise to distinguish definitively between the two sets of results although, in general, when discrepancies exist the W2C heats of formation are lower in energy and tend to be in better agreement with experiment. In the case of CaO, the W2C heat of formation (20.7 kJ mol(-1)) is approximately 20 kJ mol(-1) lower than the G3[CC](dir, full) result and most of the experimental data. Extensive investigation of possible refinements of the W2C method has failed to reveal any weaknesses that could account for this discrepancy. We therefore believe that the heat of formation of CaO is likely to lie closer to the more recent direct experimental determination of 27 kJ mol(-1) than to the value of approximately 40 kJ mol(-1) recommended in recent thermochemical reviews.     

Trapping and structural elucidation of a very advanced intermediate in the lesion-extrusion pathway of hOGG1

Here we present the first structure of a very advanced intermediate in the lesion-extrusion pathway of a DNA glycosylase, human 8-oxoguanine DNA glycosylase (hOGG1), and a substrate DNA containing a mutagenic lesion, 8-oxoguanine (oxoG). The structure was obtained by irradiation and flash-freezing of a disulfide-cross-linked (DXLed) complex of hOgg1 bound to DNA containing a novel photocaged derivative of oxoG. The X-ray structure reveals that, upon irradiation, the oxoG lesion has transited from the exosite to the active site pocket, but has not undergone cleavage by the enzyme. Furthermore, all but one of the specificity-determining interactions between the lesion and the enzyme are unformed in the flashed complex (FC), because active site functionality and elements of the DNA backbone are mispositioned. This structure thus provides a first glimpse into the structure of a very late-stage intermediate in the lesion-extrusion pathway--the latest observed to date for any glycosylase--in which the oxoG has undergone insertion into the enzyme active site following photodeprotection, but the enzyme and DNA have not yet completed the slower process of adjusting to the presence of the lesion in the active site.     

The elusive 5'-deoxyadenosyl radical in coenzyme-B12-mediated reactions

Vitamin B(12) and its biologically active counterparts possess the only examples of carbon-cobalt bonds in living systems. The role of such motifs as radical reservoirs has potential application in future catalytic and electronic nanodevices. To fully understand radical generation in coenzyme B(12) (dAdoCbl)-dependent enzymes, however, major obstacles still need to be overcome. In this work, we have used Car-Parrinello molecular dynamics (CPMD) simulations, in a mixed quantum mechanics/molecular mechanics (QM/MM) framework, to investigate the initial stages of the methylmalonyl-CoA-mutase-catalyzed reaction. We demonstrate that the 5'-deoxyadenosyl radical (dAdo(?)) exists as a distinct entity in this reaction, consistent with the results of extensive experimental and some previous theoretical studies. We report free energy calculations and first-principles trajectories that help understand how B(12) enzymes catalyze coenzyme activation and control highly reactive radical intermediates.     

Many-valued quantum algebras

We deal with algebras of the same signature as MV-algebras which are a common extension of MV-algebras and orthomodular lattices, in the sense that (i) A bears a natural lattice structure, (ii) the elements a for which is a complement in the lattice form an orthomodular sublattice, and (iii) subalgebras whose elements commute are MV-algebras. We also discuss the connections with lattice-ordered effect algebras and prove that they form a variety. Supported by the Research and Development Council of the Czech Government via the project MSM6198959214.     

Approaches for obtaining accurate rate constants for hydrogen abstraction by a chlorine atom

We have assessed computational methodologies for calculating the rate constants for hydrogen abstraction by Cl(?) for a selection of 12 reactions. For the conventional approach of calculating higher-level [B2K-PLYP/aug'-cc-pV[(T+d),(Q+d)]Z] single-point energies at lower-level [BH&H-LYP/6-31+G(d,p)] stationary points, large deviations from experimental rate constants are found in a number of cases in which the activation energy is very low. These discrepancies are due largely to deviations in the calculated activation energies and can be further traced to the inability of the low level to adequately locate the transition structures. We have examined several alternative approaches for calculating rate constants, namely, IRCmax, IRCmax at 0 K (ZK-IRCmax, with zero-point vibration energies (ZPVEs) incorporated), variational transition-state theory (VTST), and VTST with the inclusion of an Eckart tunneling correction (VTST+E). We find that the low level gives reasonable values for the ZPVEs and thermal enthalpy and entropy corrections that are required in such approaches. While the VTST+E approach yields the closest agreement with experimental rate constants for the systems considered, we find that the simpler IRCmax approach gives adequate values and is able to avoid the major shortcomings of the conventional approach in a cost-effective manner.     

Design of effective zeolite catalysts for the complete hydrogenation of CO2

Ab initio molecular orbital calculations have been applied to the study of the three-stage zeolite-catalyzed hydrogenation of CO2 to methanol. The results present strong evidence that appropriate chemical modifications to ZSM-5 can lead to significantly lower energy barriers for the three component reactions, that is, hydrogenation of CO2, HCO2H, and CH2O. Zeolites incorporating either Na+ or Ge are more effective catalysts than conventional acidic zeolites for the hydrogenation of CO2 to give HCO2H, but amine-based zeolites do not lead to significantly lower barriers for any of the three hydrogenation reactions. However, we predict that when all three features, namely, Na+, N, and Ge, are incorporated in the zeolite, there is a dramatic improvement in catalytic activity for all three reactions.     

Independent joins of tolerance factorable varieties

Let Lat denote the variety of lattices. In 1982, the second author proved that Lat is strongly tolerance factorable, that is, the members of Lat have quotients in Lat modulo tolerances, although Lat has proper tolerances. We did not know any other nontrivial example of a strongly tolerance factorable variety. Now we prove that this property is preserved by forming independent joins (also called products) of varieties. This enables us to present infinitely many strongly tolerance factorable varieties with proper tolerances. Extending a recent result of G. Czédli and G. Grätzer, we show that if ${\mathcal{V}}$ is a strongly tolerance factorable variety, then the tolerances of ${\mathcal{V}}$ are exactly the homomorphic images of congruences of algebras in ${\mathcal{V}}$ . Our observation that (strong) tolerance factorability is not necessarily preserved when passing from a variety to an equivalent one leads to an open problem.     

Assessment of theoretical procedures for hydrogen-atom abstraction by chlorine, and related reactions

We have examined a number of hydrogen-abstraction reactions and assessed various theoretical procedures with regard to their performance for geometry optimization and for calculating barriers and reaction energies. We find that the BH&H-LYP and M05-2X procedures with the 6-31+G(d,p) basis set provide reasonable predictions for the geometries of the transition structures and also yield reasonable imaginary frequencies when compared with our benchmark QCISD/6-31+G(d,p) and CCSD(T)/6-311+G(3df,2p) values. For the calculation of barriers and reaction energies, M05-2X appears to be the most accurate of the hybrid functionals. The double-hybrid functionals, B2K-PLYP, UB2-PLYP-09, ROB2-PLYP, and DSD-B-LYP-D3, when used in combination with an augmented triple-zeta basis set, give very good agreement with the benchmark URCCSD(T)/aug-cc-pVQZ energies. We find that for wavefunction procedures, use of CCSD(T) in combination with an augmented triple-zeta quality basis set is required for the accurate prediction of barriers and reaction energies for these reactions.     

A theoretical study of the condensation reactions of methyl cation with ammonia,water, hydrogen fluoride and hydrogen sulphide

Ab initio molecular orbital calculations have been used to study the condensation reactions of CH₃^? with NH₃, H₂O, HF and H₂S. Geometry optimization has been carried out at the Hartree—Fock (HF) level with the split-valence plus d-polarization 6-31G* basis set and improved relative energies obtained from calculations which employ the split-valence plus dp-polarization 6-31G** basis set with electron correlation incorporated via Moller—Plesset perturbation theory terminated at third order (MP3). Zero-point vibrational energies have also been determined and taken into account in deriving relative energies. The structures of the intermediates CH₃XH^? (X = NH₂, OH, F and SH) have been obtained and dissociation of these intermediates into CH₂X⁺ + H₂ on the one hand, and CH₃^? + HX on the other, has been examined. It is found that for those species for which the methyl condensation reaction is observed to have an appreciable rate (X = NH₂ and SH), the transition structure for hydrogen elimination from CH₃XH^? lies significantly lower in energy than the reactants CH₃^? + HX (by 75 and 70 kJ mol^?1 respectively). On the other hand, for those species for which the methyl condensation reaction is not observed (X = OH and F), the transition structure for H₂ elimination lies higher in energy than CH₃^? + HX (by 6 and 87 kJ mol^?1 respectively).