Virgil E. Jackson
Other affiliations: University of California, Davis
Bio: Virgil E. Jackson is an academic researcher from University of Alabama. The author has contributed to research in topics: Solvation & Density functional theory. The author has an hindex of 12, co-authored 20 publications receiving 711 citations. Previous affiliations of Virgil E. Jackson include University of California, Davis.
TL;DR: In this paper, density-functional electronic structure calculations are used to compute the equilibrium constants for 26Mg/24Mg and 44Ca/40Ca isotope exchange between carbonate minerals and uncomplexed divalent aquo ions.
Abstract: Density-functional electronic structure calculations are used to compute the equilibrium constants for 26Mg/24Mg and 44Ca/40Ca isotope exchange between carbonate minerals and uncomplexed divalent aquo ions. The most reliable calculations at the B3LYP/6-311++G(2d,2p) level predict equilibrium constants K, reported as 103ln (K) at 25 °C, of −5.3, −1.1, and +1.2 for 26Mg/24Mg exchange between calcite (CaCO3), magnesite (MgCO3), and dolomite (Ca0.5Mg0.5CO3), respectively, and Mg2+(aq), with positive values indicating enrichment of the heavy isotope in the mineral phase. For 44Ca/40Ca exchange between calcite and Ca2+(aq) at 25 °C, the calculations predict values of +1.5 for Ca2+(aq) in 6-fold coordination and +4.1 for Ca2+(aq) in 7-fold coordination. We find that the reduced partition function ratios can be reliably computed from systems as small as M ( CO 3 ) 6 10 - and M ( H 2 O ) 6 2 + embedded in a set of fixed atoms representing the second-shell (and greater) coordination environment. We find that the aqueous cluster representing the aquo ion is much more sensitive to improvements in the basis set than the calculations on the mineral systems, and that fractionation factors should be computed using the best possible basis set for the aquo complex, even if the reduced partition function ratio calculated with the same basis set is not available for the mineral system. The new calculations show that the previous discrepancies between theory and experiment for Fe3+–hematite and Fe2+–siderite fractionations arise from an insufficiently accurate reduced partition function ratio for the Fe3+(aq) and Fe2+(aq) species.
TL;DR: The calculated results confirm the crucial role of direct participation of three water molecules in the eight-member cyclic TS for the CO 2 hydration reaction and are consistently higher in energy than the corresponding CO 2 complexes and can undergo more facile water-assisted dehydration processes.
Abstract: Thermochemical parameters of carbonic acid and the stationary points on the neutral hydration pathways of carbon dioxide, CO 2 + nH 2O --> H 2CO 3 + ( n - 1)H 2O, with n = 1, 2, 3, and 4, were calculated using geometries optimized at the MP2/aug-cc-pVTZ level. Coupled-cluster theory (CCSD(T)) energies were extrapolated to the complete basis set limit in most cases and then used to evaluate heats of formation. A high energy barrier of approximately 50 kcal/mol was predicted for the addition of one water molecule to CO 2 ( n = 1). This barrier is lowered in cyclic H-bonded systems of CO 2 with water dimer and water trimer in which preassociation complexes are formed with binding energies of approximately 7 and 15 kcal/mol, respectively. For n = 2, a trimeric six-member cyclic transition state has an energy barrier of approximately 33 (gas phase) and a free energy barrier of approximately 31 (in a continuum solvent model of water at 298 K) kcal/mol, relative to the precomplex. For n = 3, two reactive pathways are possible with the first having all three water molecules involved in hydrogen transfer via an eight-member cycle, and in the second, the third water molecule is not directly involved in the hydrogen transfer but solvates the n = 2 transition state. In the gas phase, the two transition states have comparable energies of approximately 15 kcal/mol relative to separated reactants. The first path is favored over in aqueous solution by approximately 5 kcal/mol in free energy due to the formation of a structure resembling a (HCO 3 (-)/H 3OH 2O (+)) ion pair. Bulk solvation reduces the free energy barrier of the first path by approximately 10 kcal/mol for a free energy barrier of approximately 22 kcal/mol for the (CO 2 + 3H 2O) aq reaction. For n = 4, the transition state, in which a three-water chain takes part in the hydrogen transfer while the fourth water microsolvates the cluster, is energetically more favored than transition states incorporating two or four active water molecules. An energy barrier of approximately 20 (gas phase) and a free energy barrier of approximately 19 (in water) kcal/mol were derived for the CO 2 + 4H 2O reaction, and again formation of an ion pair is important. The calculated results confirm the crucial role of direct participation of three water molecules ( n = 3) in the eight-member cyclic TS for the CO 2 hydration reaction. Carbonic acid and its water complexes are consistently higher in energy (by approximately 6-7 kcal/mol) than the corresponding CO 2 complexes and can undergo more facile water-assisted dehydration processes.
TL;DR: Carbon-isotope fractionation factors for gas, aqueous, and mineral phases are integrated into a single theoretical/computational framework and a new method is introduced on the basis of conservation of Pauling bond strength.
Abstract: Quantum chemical calculations on large supermolecular carbonate−water and carbonate mineral clusters are used to predict equilibrium constants for 13,12C-isotope-exchange reactions between CO2(g), aqueous carbonate species, and the common carbonate minerals. For the aqueous species, we evaluate the influence of the size and conformational variability of the solvation shell, the exchange−correlation functional, and the basis set. The choice of exchange−correlation functional (PBE vs B3LYP), the basis set (6-31G* vs aug-cc-pVDZ), and solvation shell size (first shell only vs first shell and a partial second shell) each produce changes of ∼5−10 per mil in the reduced partition function ratio. Conformational variability gives rise to a standard error of ∼0.5 per mil using ∼10 solute−solvent conformations. The best results are obtained with the B3LYP/aug-cc-pVDZ combination, but because the improvements in the basis set and exchange correlation functional drive the reduced partition function ratios in opposite...
TL;DR: In this article, density functional and correlated molecular orbital calculations (MP2) were carried out on B(OH) 3 · n H 2 O clusters (n ǫ = 0, 6, 32), and B( OH ) 4 - · nH 2 O ( n Â= 0, 8, 11, 32) to estimate the equilibrium distribution of 10 B and 11 B isotopes between boric acid and borate in aqueous solution.
Abstract: Density functional and correlated molecular orbital calculations (MP2) are carried out on B(OH) 3 · n H 2 O clusters ( n = 0, 6, 32), and B ( OH ) 4 - · n H 2 O ( n = 0, 8, 11, 32) to estimate the equilibrium distribution of 10 B and 11 B isotopes between boric acid and borate in aqueous solution. For the large 32-water clusters, multiple conformations are generated from ab initio molecular dynamics simulations to account for the effect of solvent fluctuations on the isotopic fractionation. We provide an extrapolated value of the equilibrium constant α 34 for the isotope exchange reaction 10 B(OH) 3 (aq) + 11 B ( OH ) 4 - (aq) = 11 B(OH) 3 (aq) + 11 B ( OH ) 4 - (aq) of 1.026–1.028 near the MP2 complete basis set limit with 32 explicit waters of solvation. With some exchange-correlation functionals we find potentially important contributions from a tetrahedral neutral B(OH) 3 ·H 2 O Lewis acid–base complex. The extrapolations presented here suggest that DFT calculations give a value for 10 3 ln α 34 about 15% higher than the MP2 calculations.
TL;DR: The gas-phase acidities of the 20 L-amino acids have been predicted at the composite G3(MP2) level and it is predicted that tyrosine is deprotonated at the CO(2)H site, and the calculated values are within experimental error.
Abstract: The gas-phase acidities of the 20 l-amino acids have been predicted at the composite G3(MP2) level. A broad range of structures of the neutral and anion were studied to determine the lowest energy conformer. Excellent agreement is found with the available experimental gas-phase deprotonation enthalpies, and the calculated values are within experimental error. We predict that tyrosine is deprotonated at the CO2H site. Cysteine is predicted to be deprotonated at the SH but the proton on the CO2H is shared with the S– site. Self-consistent reaction field (SCRF) calculations with the COSMO parametrization were used to predict the pKa’s of the non-zwitterion form in aqueous solution. The differences in the non-zwitterion pKa values were used to estimate the free energy difference between the zwitterion and nonzwitterion forms in solution. The heats of formation of the neutral compounds were calculated from atomization energies and isodesmic reactions to provide the first reliable set of these values in the gas...
01 Feb 1995
TL;DR: In this paper, the unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio using DFT, MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set.
Abstract: : The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg
Lamont–Doherty Earth Observatory1, University of Bristol2, Yale University3, Wesleyan University4, National Oceanography Centre, Southampton5, Utrecht University6, University of Hawaii at Manoa7, Pennsylvania State University8, University of Southern California9, Museum für Naturkunde10, University of North Carolina at Chapel Hill11, University of California, Santa Cruz12, Cardiff University13, Institute of Arctic and Alpine Research14, University of South Florida St. Petersburg15, Autonomous University of Barcelona16, VU University Amsterdam17, Claremont McKenna College18
TL;DR: This paper reviewed events exhibiting evidence for elevated atmospheric CO2, global warming, and ocean acidification over the past ~300 million years of Earth's history, some with contemporaneous extinction or evolutionary turnover among marine calcifiers.
Abstract: Ocean acidification may have severe consequences for marine ecosystems; however, assessing its future impact is difficult because laboratory experiments and field observations are limited by their reduced ecologic complexity and sample period, respectively. In contrast, the geological record contains long-term evidence for a variety of global environmental perturbations, including ocean acidification plus their associated biotic responses. We review events exhibiting evidence for elevated atmospheric CO2, global warming, and ocean acidification over the past ~300 million years of Earth’s history, some with contemporaneous extinction or evolutionary turnover among marine calcifiers. Although similarities exist, no past event perfectly parallels future projections in terms of disrupting the balance of ocean carbonate chemistry—a consequence of the unprecedented rapidity of CO2 release currently taking place.
TL;DR: This work has highlighted the importance of knowing the carrier and removal status of materials before they are exposed to each other in the intermediate stages of decomposition.
Abstract: 3.1. Sc Group 6772 3.2. Ti Group 6773 3.3. V Group 6775 3.4. Cr Group 6776 3.5. Mn Group 6777 3.6. Fe Group 6779 3.7. Co Group 6780 3.8. Ni Group 6782 3.9. Cu Group 6782 3.10. Zn Group 6784 3.11. Lanthanide Group 6784 3.12. Actinide Group 6785 3.13. Periodic Trends on Bonding and Reactivity 6785 4. Ionic Mononuclear Transition Metal Oxide Species 6787 4.1. Cations 6788 4.2. Anions 6790 4.2.1. Monoxide Anions 6790 4.2.2. Dioxide Anions 6791 4.2.3. Oxygen-Rich Anions 6792 5. Multinuclear Transition Metal Oxide Clusters 6792 5.1. Sc Group 6793 5.2. Ti Group 6793 5.3. V Group 6793 5.4. Cr Group 6797 5.5. Mn Group 6798 5.6. Fe Group 6798 5.7. Co Group 6798 5.8. Ni Group 6798 5.9. Cu Group 6799 6. Summary 6800 7. Acknowledgments 6800 8. References 6800
TL;DR: This review presents the application of metal stable isotopes as source and process tracers in environmental studies, in particular by using mixing and Rayleigh model approaches and the extent of natural isotopic variations for different elements is compared.
Abstract: The biogeochemical cycling of metals in natural systems is often accompanied by stable isotope fractionation which can now be measured due to recent analytical advances. In consequence, a new research field has emerged over the last two decades, complementing the traditional stable isotope systems (H, C, O, N, S) with many more elements across the periodic table (Li, B, Mg, Si, Cl, Ca, Ti, V, Cr, Fe, Ni, Cu, Zn, Ge, Se, Br, Sr, Mo, Ag, Cd, Sn, Sb, Te, Ba, W, Pt, Hg, Tl, U) which are being explored and potentially applicable as novel geochemical tracers. This review presents the application of metal stable isotopes as source and process tracers in environmental studies, in particular by using mixing and Rayleigh model approaches. The most important concepts of mass-dependent and mass-independent metal stable isotope fractionation are introduced, and the extent of natural isotopic variations for different elements is compared. A particular focus lies on a discussion of processes (redox transformations, complexation, sorption, precipitation, dissolution, evaporation, diffusion, biological cycling) which are able to induce metal stable isotope fractionation in environmental systems. Additionally, the usefulness and limitations of metal stable isotope signatures as tracers in environmental geochemistry are discussed and future perspectives presented.