Prediction of Aqueous Reduction Potentials of X•, ChH•, and XO• Radicals with X = Halogen and Ch = Chalcogen.

The aqueous electron affinity and aqueous reduction potentials for F•, Cl•, Br•, I•, OH•, SH•, SeH•, TeH•, ClO•, BrO•, and IO• were calculated using electronic structure methods for explicit cluster models coupled with a self-consistent reaction field (SMD) to treat the aqueous solvent. Calculations were conducted using MP2 and correlated molecular orbital theory up to the CCSD(T)-F12b level for water tetramer clusters and MP2 for octamer cluster. Inclusion of explicit waters was found to be important for accurately predicting the redox potentials in a number of cases. The calculated reduction potentials for X• and ChH• were predicted to within ∼0.1 V of the reported literature values. Fluorine is anomalous due to abstraction of a hydrogen from one of the surrounding water molecules to form a hydroxyl radical and hydrogen fluoride, so its redox potential was calculated using only an implicit model. Larger deviations from experiment were predicted for ClO• and BrO•. These deviations are due to the free energy of solvation of the anion being too negative, as found in the pKa calculations, and that for the neutral being too positive with the current approach.

Absolute Hydration Free Energy of Small Anions and the Aqueous pKa of Simple Acids.

Heats of formation and gas phase acidities for the simple acids and their deprotonated anions (A- = F-, Cl-, Br-, I-, OH-, SH-, SeH-, TeH-, OCl-, OBr-, and OI-) were calculated using the Feller-Peterson-Dixon (FPD) method with large basis sets including Douglass-Kroll scalar relativistic corrections. Hydration of the neutral and anionic species was predicted using the supermolecule-continuum approach, resulting in absolute hydration free energies that, when combined with calculated gas phase acidities, produce aqueous acidities and pKa values for these simple acids that are, in general, in excellent agreement with experimental literature values. Absolute hydration free energy values converged quickly in terms of the experimental values for neutral species, requiring only four explicit H2O molecules. HI is anomalous in that it fully dissociates ionically in a water tetramer and was treated without explicit water molecules. The hydration energies of anionic species converged more slowly and were modeled with up to 16 explicit H2O molecules. Calculated values for ΔHf and ΔGgas agree with experimental values within ca. 1.2 kcal/mol, and ΔGaq and ΔΔGhyd agree with experimental values within ca. 2 kcal/mol in most cases.

Synergistic Coupling of CO2 and H2O during Expansion of Clays in Supercritical CO2-CH4 Fluid Mixtures.

We used IR and XRD, with supporting theoretical calculations, to investigate the swelling behavior of Na+-, NH4+-, and Cs+-montmorillonites (SWy-2) in supercritical fluid mixtures of H2O, CO2, and CH4. Building on our prior work with Na-clay that demonstrated that H2O facilitated CO2 intercalation at relatively low RH, here we show that increasing CO2/CH4 ratios promote H2O intercalation and swelling of the Na-clay at progressively lower RH. In contrast to the Na-clay, CO2 intercalated and expanded the Cs-clay even in the absence of H2O, while increasing fluid CO2/CH4 ratios inhibited H2O intercalation. The NH4-clay displayed intermediate behavior. By comparing changes in the HOH bending vibration of H2O intercalated in the Cs-, NH4-, and Na-clays, we posit that CO2 facilitated expansion of the Na-clay by participating in outer-sphere solvation of Na+ and by disrupting the H-bond network of intercalated H2O. In no case did the pure CH4 fluid induce expansion. Our experimental data can benchmark modeling studies aimed at predicting clay expansion in humidified fluids with varying ratios of CO2 and CH4 in real reservoir systems with implications for enhanced hydrocarbon recovery and CO2 storage in subsurface environments.

Polarizabilities of neutral atoms and atomic ions with a noble gas electron configuration.

Atomic polarizabilities play an important role in the development of force fields for molecular simulations, as well as for the development of qualitative concepts of atomic and molecular behavior. Coupled cluster theory at the coupled cluster singles doubles triples level with very large correlation-consistent basis sets with extended diffuse functions has been used to predict the polarizabilities of the atomic neutrals, mono-cations and mono-anions with a noble gas configuration. Additional corrections for scalar relativistic and spin-orbit effects were also included for the electron configurations of Kr, Xe, and Rn. The results are in excellent agreement with experiment or with other high level calculations where available. The current results for most of these species represent the best available values for the polarizabilities. The results show that the polarizability of H- is very difficult to calculate without extremely diffuse functions. The polarizability of H- is the largest value, 34.05 Å3, calculated for all species in the current study. The polarizabilities of the remaining halogen anions are also the best available values. The polarizabilities of the halogen anions (excluding F-) and H- have a linear correlation with the electron affinity of the neutral atom. Spin-orbit effects, even for closed shell species, cannot be ignored for quantitative accuracy, and the inclusion of spin-orbit effects for Fr+, Rn, and At- increases the polarizability by 4%, 6%, and 15%, respectively.

Crystallographic evidence of Watson-Crick connectivity in the base pair of anionic adenine with thymine.

Utilizing an ionic liquid strategy, we report crystal structures of salts of free anionic nucleobases and base pairs previously studied only computationally and in the gas phase. Reaction of tetrabutylammonium ([N4444]+) or tetrabutylphosphonium ([P4444]+) hydroxide with adenine (HAd) and thymine (HThy) led to hydrated salts of deprotonated adenine, [N4444][Ad]·2H2O, and thymine, [P4444][Thy]·2H2O, as well as the double salt cocrystal, [P4444]2[Ad][Thy]·3H2O·2HThy. The cocrystal includes the anionic [Ad-(HThy)] base pair which is a stable formation in the solid state that has previously not even been suggested. It exhibits Watson-Crick connectivity as found in DNA but which is unusual for the free neutral base pairs. The stability of the observed anionic bases and their supramolecular formations and hydrates has also been examined by electronic structure calculations, contributing to more insight into how base pairs can bind when a proton is removed and highlighting mechanisms of stabilization or chemical transformation in the DNA chains.

The H•/H- Redox Couple and Absolute Hydration Energy of H.

A supermolecule-continuum approach with water clusters up to n = 16 H2O molecules has been used to predict the absolute hydration free energies at 298 K (ΔGhyd) of both hydrogen (H•) and hydride (H-) to be 4.6 ± 1 and -78 ± 3 kcal/mol, respectively. These values are combined with a high accuracy prediction of the gas-phase electron affinity (ΔGgas,298K = -16.9 kcal/mol) to determine the aqueous electron affinity of H• of 99.5 ± 3 kcal/mol, which yields a reduction potential for H• vs SHE of -0.03 ± 0.15 V. This value is in agreement within 0.2 V with most estimates obtained using a wide variety of approaches. These results can be used to improve the absolute hydricity scale in water which provides additional insights into how a putative hydride interacts with solvent but do not change the ability to predict the relative reactivity of two species using relative hydricity scales.

Elucidation of Bottom-Up Growth of CaCO3 Involving Prenucleation Clusters from Structure Predictions and Decomposition of Globally Optimized (CaCO3)n Nanoclusters.

Low-energy minima structures for (CaCO3)n, n ≤ 28, are predicted using bottom-up genetic algorithms in conjunction with density functional theory electronic structure calculations, in comparison with the frozen and relaxed top-down clusters generated by cuts from the calcite, vaterite, and aragonite crystal structures. Similarities in structural motifs for the bottom-up and relaxed top-down are revealed using a fragment recognition technique. Fragment energy decomposition analysis shows that the bottom-up and relaxed top-down clusters belong to two classes of amorphous clusters with distinct intracluster energy distributions, despite their structural similarity. The bottom-up clusters with >20 formula units are surface stabilized with negative surface energy densities. In contrast, the top-down clusters are interior stabilized with positive surface energy densities. We prove that the sign of the surface energy density determines whether the nucleation reaction energy as a function of nuclear size has a maximum or a minimum. The surface-stabilized bottom-up clusters are proposed to be a type of prenucleation cluster at the minimum of the nucleation reaction energy. A mechanism for mineralization of CaCO3 involving prenucleation clusters and nonclassical growth pathway is proposed on the basis of our theoretical findings, which is consistent with previous titration experiments.

Reaction Energetics and 13C Fractionation of Alanine Transamination in the Aqueous and Gas Phases.

The alanine transaminase enzyme catalyzes the transfer of an amino group from alanine to α-ketoglutarate to produce pyruvate and glutamate. Isotope fractionation factors (IFFs) for the reaction +H3NCH(CH3)COO- + -OOCCH2CH2C(O)COO- ↔ CH3C(O)COO- + +H3NCH(CH2CH2COO-)COO- (zwitterionic neutral alanine + doubly deprotonated α-ketoglutarate ↔ pyruvate + zwitterionic glutamate anion) were calculated from the partition functions of explicitly and implicitly solvated molecules at 298 K. Calculations were done for alanine (noncharge separated, zwitterion, deprotonated), pyruvic acid (neutral, deprotonated), glutamic acid (noncharge separated, zwitterion, deprotonated, doubly deprotonated), and α-ketoglutaric acid (neutral, deprotonated, doubly deprotonated). The computational results, calculated from gas phase- and aqueous-optimized clusters with explicit H2O molecules at the MP2/aug-cc-pVDZ and MP2/aug-cc-pVDZ/COSMO levels, respectively, predict that substitution of 13C at the C2 position of alanine and pyruvic acid and their various forms leads to the C2 position of pyruvic acid/pyruvate being enriched in 13C/12C ratio by 9‰. Simpler approaches that estimate the IFFs based solely on changes in the zero-point energies (ZPEs) are consistent with the higher-level model. ZPE-based IFFs calculated for simple analogues formaldehyde and methylamine (analogous to the C2 positions of pyruvate and alanine, respectively) predict a 13C enrichment in formaldehyde of 7-8‰ at the MP2/aug-cc-pVDZ and aug-cc-pVTZ levels. A simple predictive model using canonical functional group frequencies and reduced masses for 13C exchange between R2C═O and R2CH-NH2 predicted enrichment in R2C═O that is too large by a factor of two but is qualitatively accurate compared with the more sophisticated models. Our models are all in agreement with the expectation that pyruvate and formaldehyde will be preferentially enriched in 13C because of the strength of their >C═O bond relative to that of ≡C-NH2 in alanine and methylamine. 13C/12C substitution is also modeled at the methyl and carboxylic acid sites of alanine and pyruvic acid, respectively.

Experimental and Computational Study of the Gas-Phase Acidities of Acidic Di- and Tripeptides.

Gas-phase acidities (GA or Δ Gacid) of acidic di- and tripeptides are determined for the first time. The peptides studied are composed of inert alanine (A) residues and one X residue of either aspartic acid (D) or glutamic acid (E): AX, XA, AAX, AXA, and XAA. Experimental GAs were measured by the thermokinetic method of deprotonation ion/molecule reactions in a Fourier transform ion cyclotron resonance mass spectrometer. Calculated GAs were obtained by composite correlated molecular orbital theory at the G3(MP2) level for deprotonation of carboxylic acid groups both at the C-terminus and at the side chain. Excellent agreement was found between experimental and calculated GA values. There is a slight preference for peptides with D being more acidic than analogous peptides with E, which agrees with the GAs of the corresponding amino acids. Experiments showed that peptides are more acidic (lower numerical GA values) when the acidic residue is located at the C-terminus (i.e., AX or AAX). The lowest energy form of deprotonated AAE has a unique structure where the longer side chain of E allows the two carboxylates, which are in close proximity, to share the proton. The tripeptides are less acidic (higher GA value) by 3-7 kcal/mol when the acidic residue is in the center. The tripeptides are more acidic (by 2-10 kcal/mol) than dipeptides containing the same acidic residue at the same location.

Energetics of CO2- in Aqueous Solution.

Gas-phase and aqueous solution properties of neutral and anionic clusters of CO2 with 3, 4, and 8 explicit H2O molecules are calculated at the coupled cluster (CCSD(T)) level plus a self-consistent reaction field. Anionic clusters with the radical electron density localized on the carbon of the CO2 molecule rather than localized on the H2O molecules are more favorable energetically by 10-20 kcal/mol in the gas phase (Δ Hgas(298 K)) and 20-30 kcal/mol in aqueous solution (Δ Gaq(298 K)). The most favorable structures are those with the largest number of strong hydrogen bonds between the CO2- and the explicit H2O molecules. Adiabatic electron affinities were calculated in the gas phase and in aqueous solution for the microsolvated anion. The adiabatic electron affinity of aqueous CO2- is predicted to be 2.35 ± 0.08 eV and is converged with as few as 3 explicit H2O molecules plus a self-consistent reaction field. The EA of aqueous CO2 is significantly greater than the aqueous solvation free energy of the electron. The vertical attachment energies to CO2 and the vertical detachment energies from CO2- were calculated. The solvated CO2- anion is substantially bent to 135°, which requires 1.52 eV. The large energy required for bending in combination with the vertical detachment and attachment energies shows that substantial local solvent reorganization occurs on detachment or attachment of an electron to solvated CO2. The formation of aqueous C2O42- from CO2- was also explored, and dimerization is predicted to occur.