Benchmark Structures and Binding Energies of Small Water Clusters with Anharmonicity Corrections

For (H2O)n where n = 1–10, we used a scheme combining molecular dynamics sampling with high level ab initio calculations to locate the global and many low lying local minima for each cluster. For each isomer, we extrapolated the RI-MP2 energies to their complete basis set limit, included a CCSD(T) correction using a smaller basis set and added finite temperature corrections within the rigid-rotor-harmonic-oscillator (RRHO) model using scaled and unscaled harmonic vibrational frequencies. The vibrational scaling factors were determined specifically for water clusters by comparing harmonic frequencies with VPT2 fundamental frequencies. We find the CCSD(T) correction to the RI-MP2 binding energy to be small (<1%) but still important in determining accurate conformational energies. Anharmonic corrections are found to be non-negligble; they do not alter the energetic ordering of isomers, but they do lower the free energies of formation of the water clusters by as much as 4 kcal/mol at 298.15 K.

Benchmark Structures and Binding Energies of Small Water Clusters with Anharmonicity Corrections

For (H2O)n where n = 1–10, we used a scheme combining molecular dynamics sampling with high level ab initio calculations to locate the global and many low lying local minima for each cluster. For each isomer, we extrapolated the RI-MP2 energies to their complete basis set limit, included a CCSD(T) correction using a smaller basis set and added finite temperature corrections within the rigid-rotor-harmonic-oscillator (RRHO) model using scaled and unscaled harmonic vibrational frequencies. The vibrational scaling factors were determined specifically for water clusters by comparing harmonic frequencies with VPT2 fundamental frequencies. We find the CCSD(T) correction to the RI-MP2 binding energy to be small (

Doubly-charged ethane ions: Solution to the dilemma of stability predicted by theory and instability observed in experiment

Potential energy curves have been computed for [C2H6]2+ ions and the results used to interpret the conspicuous absence of these ions in 2E mass spectra and in charge-stripping experiments. The energies and structures of geometry-optimized ground-state singlet and excited-state triplet [C2H6]2+ ions have been determined along with energies for different decomposition barriers and dissociation asymptotes. Although singlet and triplet [C2H6]2+ ions can exist as stable entities, they possess low energy barriers to decomposition. Vertical Franck-Condon transitions, involving electron impact ionization of ethane as well as charge-stripping collisions of [C2H6]+ ions, produce [C2H6]2+ ions which promptly dissociate since they are formed with energies in excess of various decomposition barriers. Appearance energies computed for doubly-charged ethane fragment ions are in accordance with experimental values.

Charge transfer reactions of organic ions containing oxygen: Correlation between reaction energetics and cross sections

Cross sections for charge transfer reactions of organic ions containing oxygen have been obtained using time-of-flight techniques. Charge transfer cross sections have been determined for reactions of 2.0 to 3.4 keV ions produced by electron impact ionization of oxygen containing molecules such as methanol, ethanal and ethanol. Experimental cross section magnitudes have been correlated with reaction energy defects computed from ion recombination energies and target ionization energies. Large cross sections are observed for reacting systems with small energy defects.

Hydration of the Bisulfate Ion: Atmospheric Implications

Using molecular dynamics configurational sampling combined with ab initio energy calculations, we determined the low energy isomers of the bisulfate hydrates. We calculated the CCSD(T) complete basis set (CBS) binding electronic and Gibbs free energies for 53 low energy isomers of HSO4–(H2O)n=1–6 and derived the thermodynamics of adding waters sequentially to the bisulfate ion and its hydrates. Comparing the HSO4–/H2O system to the neutral H2SO4/H2O cluster, water binds more strongly to the anion than it does to the neutral molecules. The difference in the binding thermodynamics of HSO4–/H2O and H2SO4/H2O systems decreases with increasing number of waters. The thermodynamics for the formation of HSO4–(H2O)n=1–5 is favorable at 298.15 K, and that of HSO4–(H2O)n=1–6 is favorable for T < 273.15 K. The HSO4– ion is almost always hydrated at temperatures and relative humidity values encountered in the troposphere. Because the bisulfate ion binds more strongly to sulfuric acid than it does to water, it is expected to play a role in ion-induced nucleation by forming a strong complex with sulfuric acid and water, thus facilitating the formation of a critical nucleus.

Alteration in 5HT1A Receptor Activity from a Prenatal Exposure to Dexamethasone in a Stressed and Non-Stressed Adult Male Rat

Synthetic glucocorticoids (GC) are used as a clinical therapeutic to stimulate lung development in fetuses that present the risk of preterm delivery. Previous studies have shown that a prenatal exposure to Dexamethasone (DEX) causes a disturbance in normal GC mediation of neuritic outgrowth, cell signaling, and serotonergic systems. Our hypothesis is that a prenatal exposure to DEX during the third trimester of pregnancy alters 5HT1A receptor function. Pregnant dams were injected daily with 150μg/ml/kg of DEX from gestation day 14 through 19. Control dams were treated with and equal volume of saline. Swim stress followed by elevated plus maze testing was conducted on male rats an hour and a half prior to being sacrificed to induce postnatal acute stress. The non-stressed group was also tested and allowed to return to baseline before sacrifice. Hippocampi were analyzed using a radioligand-receptor binding assay and GTPγS35 incorporation (3H-MPPF antagonist and 8-OH-DPAT agonist, respectively). A significant increase in Kd was found in non-stressed DEX-exposed animals compared to non-stressed controls (p

Study Of The Binding Of Substrate By The Phe557Val Mutant Soybean Lipoxygenase-1

Lipoxygenases are a class of enzymes which consist of non-heme iron dioxygenases that are produced by fungi, plants, and mammals and catalyze the oxygenation of polyunsaturated fatty acid substrates to unsaturated fatty acid hydroperoxide products. The unsaturated fatty acid hydroperoxide products are stereo- and regiospecific. One such lipoxygenase, soybean lipoxygenase-1 (SBLO-1), catalyzes the conversion of linoleate to 13-hydroperoxy-9(Z),11(E)-octadecadienoate (13-HPOD) and a small amount of 9-hydroperoxy-10(E),12(Z)-octadecadienoate (9-HPOD). Although the structure of SBLO-1 is known and it is the most widely studied lipoxygenase, how it binds to substrate is still poorly understood. Two competing binding hypotheses that have been used to understand and explain the binding are the head first binding model and the tail first binding model. The head first binding model predicts linoleate binds with its polar carboxylate group in the binding pocket and the methyl terminus at the surface of the binding pocket. The tail first binding model predicts that linoleate binds with its methyl terminus end in the binding pocket and the polar carboxylate group at the surface of the binding pocket. Both binding models have been used in the explanation of previous work. In previous work the replacement of phenylalanine with valine has been performed to produce the phe557val mutant SBLO-1. The mutant SBLO-1 was then used in the enzymatic oxygenation of linoleate. With this mutant, the amount of 9-HPOD that is formed increases. This result has been interpreted using the head-first binding model in which the smaller valine residue allows linoleate to bind with the polar carboxylate group of linoleate interacting with arginine-707. The work presented in this thesis confirms the regiochemical results of the previous work and further tests the head-first binding model. If head-first binding occurs, the 9-HPOD is expected to have primarily S configuration. Utilizing chiral-phase HPLC, it was found that the 9-HPOD produced by the phe557val mutant SBLO-1 is primarily S, consistent with head-first binding. The head-first binding model was also tested using linoleyl dimethylamine (LDMA), which has been shown to be a good substrate for SBLO-1 at pH 7.0, where LDMA is thought to be positively charged. This model predicts that less of the 9-peroxide should be produced with this substrate. Through the use of gas chromatography/mass spectrometry, it was found that the conversion of LDMA by the phe557val mutant SBLO-1 resulted in the formation of a 46:54 mixture of the 13-peroxide:9-peroxide. The higher amount of 9-peroxide is the opposite of what is expected for the currently proposed model suggesting that the proposed model may not be entirely correct. The results thus far have been consistent with reverse binding but not with the proposed interaction of the polar end of the substrate with arginine-707.