The remarkably invariant interaction energies of lithium first-row compounds with water and with ammonia

Solvation energies of lithium first-row compounds LiX (X ? H, Li, BeH, BH₂, CH₃, NH₂, OH, F) and of the lithium cation with the model solvents, water and ammonia, have been calculated ab inito (MP2/6-31 + G^*//6-31G^* with zero-point vibrational energy corrections at 3-21G//3-21G). The solvation energies are found to be remarkably constant: ?18.0 ± 1.2 and ?21.5 ± 1.3 kcal/mol for the hydrates and ammonia solvates, respectively. This independence on the nature of X is due largely to the ionic character of the LiX compounds (dipole moments 4.7–6.6 debye). The unexpectedly high solvation energies of the lithium molecule (?14.3 and ?17.8 kcal/mol, respectively) are due to the polarizability of Li₂. At the same level, the lithium cation has interaction energies with H₂O and NH₃ of ?34.1 and ?39.7 kcal/mol, respectively. For the hydrates of LiOH and LiF cyclic structures with hydrogen bonds and somewhat increased solvation energies also are described.     

Theoretical study of the adsorption of ethylene on alkali‐exchanged zeolites

The structures of alkali‐exchanged faujasite (X–FAU, X = Li⁺ or Na⁺ ion) and ZSM‐5 (Li–ZSM‐5) zeolites and their interactions with ethylene have been investigated by means of quantum cluster and embedded cluster approaches at the B3LYP/6‐31G(d, p) level of theory. Inclusion of the Madelung potential from the zeolite framework has a significant effect on the structure and interaction energies of the adsorption complexes and leads to differentiation of different types of zeolites (ZSM‐5 and FAU) that cannot be drawn from a typical quantum cluster model, H₃SiO(X)Al(OH)₂OSiH₃. The Li–ZSM‐5 zeolite is predicted to have a higher Lewis acidity and thus higher ethylene adsorption energy than the Li–FAU zeolites (16.4 vs. 14.4 kcal/mol), in good agreement with the known acidity trend of these two zeolites. On the other hand, the cluster models give virtually the same adsorption energies for both zeolite complexes (8.9 vs. 9.1 kcal/mol). For the larger cation‐exchanged Na–FAU complex, the adsorption energy (11.6 kcal/mol) is predicted to be lower than that of Li–FAU zeolites, which compares well with the experimental estimate of about 9.6 kcal/mol for ethylene adsorption on a less acidic Na–X zeolite. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 333–340, 2003     

Ab initio studies of RO− … HOR′ complexes. Solvent effects on the relative acidities of water and methanol

Ab initio molecular orbital calculations are reported for complexes of hydroxide and methoxide anions with water and methanol. The basis set dependence of the results is carefully considered for HO^? ? H₂O. 4-31G and 6-31G* calculations yield similar geometrical predictions; however, the 6-31G* basis set is superior for computing dissociation energies. Further extension to the 6-31G** level provides little change. The dissociation energies for the complexes range from 25 to 37 kcal/mole with hydroxide ion and methanol acting as the strongest base and acid. The difference in gas phase acidities of water and methanol is halved by the introduction of one solvent molecule.     

Analysis of the intermolecular interaction between CH(3)OCH(3), CF(3)OCH(3), CF(3)OCF(3), and CH(4): high level ab initio calculations

The intermolecular interaction energies of the CH₃OCH₃? CH₄, CF₃OCH₃? CH₄, and CF₃OCF₃? CH₄ systems were calculated by ab initio molecular orbital method with the electron correlation correction at the second order Møller–Plesset perturbation (MP2) method. The interaction energies of 10 orientations of complexes were calculated for each system. The largest interaction energies calculated for the three systems are ?1.06, ?0.70, and ?0.80 kcal/mol, respectively. The inclusion of electron correlation increases the attraction significantly. It gains the attraction ?1.47, ?1.19, and ?1.27 kcal/mol, respectively. The dispersion interaction is found to be the major source of the attraction in these systems. In the CH₃OCH₃? CH₄ system, the electrostatic interaction (?0.34 kcal/mol) increases the attraction substantially, while the electrostatic energies in the other systems are not large. Fluorine substitution of the ether decreases the electrostatic interaction, and therefore, decreases the attraction. In addition the orientation dependence of the interaction energy is decreased by the substitution. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1472–1479, 2002     

Photophysical Properties of Gilvocarcins V and M and Their Binding Constant to Calf Thymus DNA

Abstract— Absorption and emission techniques were used to characterize the ground (S₀), singlet (S|) and triplet states (T₁) of gilvocarcin V (GV) and gilvocarcin M (GM) in different solvents. Aggregation of GV with dimerization constant equal to 7800 M^?1is observed in 10% dimethyl-sulfoxide (DMSO)/water. The photophysical properties of the S, state of these molecules are more sensitive to changes in solvent characteristics than the corresponding ground states. The absorption of visible light by GV and GM results in a higher dipole moment of the excited state causing a red shift in the fluorescence spectra with increasing solvent polarity. The fluorescence quantum yield remains practically unchanged with changes in solvent properties unless water is present as a co-solvent. Both φ_f and φ_f values corresponding to GV in DMSO are larger than those of GM, whereas in 10% DMSO/H₂O the opposite is observed. Thus, GV is more susceptible to other deactivation pathways besides emission in the presence of water than GM. The relative phosphorescence quantum yield (φ_p= 0.03) and the triplet energy (E_T= 52 kcal/mol) of GV and GM are similar. The S₀-S₁ energy difference is 63 kcal/mol for GV, whereas for GM it is 67. Thus, the singlet-triplet energy difference is 11 and 15 kcal/mol, respectively. The PM3/CI calculated electronic structures of these compounds are consistent with the observed photophysical properties. The dark binding constants of GV to calf thymus DNA ([1.1–0.08] × 10⁶M^?1) are about an order of magnitude larger than those of GM ([0.24–0.018] × 10⁶M^?1) at different ionic strengths (0–2.00 M NaCl). Also, the number of gilvocarcin molecules bound per base pair is smaller for GM than for GV. These differences in dark DNA binding parameters between GV and GM could have implications in the large photocytotoxic ability of GV as compared to GM.     

Gas-phase acidities of cysteine-polyglycine peptides: The effect of the cysteine position

The sequence and conformational effects on the gas-phase acidities of peptides have been studied by using two pairs of isomeric cysteine-polyglycine peptides, CysGly_3,4NH₂ and Gly_3,4CysNH₂. The extended Cooks kinetic method was employed to determine the gas-phase acidities using a triple quadrupole mass spectrometer with an electrospray ionization source. The ion activation was achieved via collision-induced dissociation experiments. The deprotonation enthalpies (Δ_acid H) were determined to be 323.9 ± 2.5 kcal/mol (CysGly₃NH₂), 319.2 ± 2.3 kcal/mol (CysGly₄NH₂), 333.8 ± 2.1 kcal/mol (Gly₃CysNH₂), and 321.9 ± 2.8 kcal/mol (Gly₄CysNH₂), respectively. The corresponding deprotonation entropies (Δ_acid S) of the peptides were estimated. The gas-phase acidities (Δ_acid G) were derived to be 318.4 ± 2.5 kcal/mol (CysGly₃NH₂), 314.9 ± 2.3 kcal/mol (CysGly₄NH₂), 327.5 ± 2.1 kcal/mol (Gly₃CysNH₂), and 317.4 ± 2.8 kcal/mol (Gly₄CysNH₂), respectively. Conformations and energetic information of the neutral and anionic peptides were calculated through simulated annealing (Tripos), geometry optimization (AM1), and single point energy calculations (B3LYP/6-31+G(d)), respectively. Both neutral and deprotonated peptides adopt many possible conformations of similar energies. All neutral peptides are mainly random coils. The two C-cysteine anionic peptides, Gly_3,4(Cys-H)⁻NH₂, are also random coils. The two N-cysteine anionic peptides, (Cys-H)⁻Gly_3,4NH₂, may exist in both random coils and stretched helices. The two N-cysteine peptides, CysGly₃NH₂ and CysGly₄NH₂, are significantly more acidic than the corresponding C-terminal cysteine ones, Gly₃CysNH₂ and Gly₄CysNH₂. The stronger acidities of the former may come from the greater stability of the thiolate anion resulting from the interaction with the helix-macrodipole, in addition to the hydrogen bonding interactions.     

Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes

The structures and interaction energies of guanine and uracil quartets have been determined by B3LYP hybrid density‐functional calculations. The total interaction energy ΔE^T of the C_4h‐symmetric guanine quartet consisting of Hoogsteen‐type base pairs with two hydrogen bonds between two neighbor bases is −66.07 kcal/mol at the highest level. The uracil quartet with C6 H6O4 interactions between the individual bases has only a small interaction energy of −20.92 kcal mol⁻¹, and the interaction energy of −24.63 kcal/mol for the alternative structure with N3 H3O4 hydrogen bonds is only slightly more negative. Cooperative effects contribute between 10 and 25% to all interaction energies. Complexes of metal ions with G‐quartets can be classified into different structure types. The one with Ca²⁺ in the central cavity adopts a C_4h‐symmetric structure with coplanar bases, whereas the energies of the planar and nonplanar Na⁺ complexes are almost identical. The small ions Li⁺, Be²⁺, Cu⁺, and Zn²⁺ prefer a nonplanar S₄‐symmetric structure. The lack of coplanarity prevents probably a stacking of these base quartets. The central cavity is too small for K⁺ ions and, therefore, this ion favors in contrast to all other investigated ions a C₄‐symmetric complex, which is 4.73 kcal/mol more stable than the C_4h‐symmetric one. The distance 1.665 Å between K⁺ and the root‐mean‐square plane of the guanine bases is approximately half of the distance between two stacked G‐quartets. The total interaction energy of alkaline earth ion complexes exceeds those with alkali ions. Within both groups of ions the interaction energy decreases with an increasing row position in the periodic table. The B3LYP and BLYP methods lead to similar structures and energies. Both methods are suitable for hydrogen‐bonded biological systems. Compared with the before‐mentioned methods, the HCTH functional leads to longer hydrogen bonds and different relative energies for two U‐quartets. Finally, we calculated also structures and relative energies with the MMFF94 forcefield. Contrary to all DFT methods, MMFF94 predicts bifurcated C HO contacts in the uracil quartet. In the G‐quartet, the MMFF94 hydrogen bond distances N2 H22N7 are shorter than the DFT distances, whereas the N1 H1O6 distances are longer. © 2000 John Wiley & Sons, Inc. J Comput Chem 22: 109–124, 2001     

Reaction between U(IV) and H2O2 in hydrochloric acid medium

Kinetic investigations on the reaction between U(IV) and H₂O₂ have been carried out at different acidities in chloride medium at an ionic strength of 2M. The observed bimolecular rate constant has been found to be dependant on [H⁺]^?1.3. The activation energy of the overall reaction has been found to vary from 13.4 ± 0.7 to 18.0 ± 0.8 kcal/mol in the range of acidity from 0.3 to 1.5M. The results have been explained on the basis of three parallel rate-controlling reactions involving unhydrolyzed species of U(IV) and hydrolyzed species UCl(OH)²⁺ and UO²⁺. The values of the rate constants for these three reaction paths have been found to be of the order of 3.95, 5.59 × 10³, and 1.49 × 10⁵M^?1 min^?1, respectively.     

A multilayered representation,quantum mechanical and molecular mechanics study of the CH3F + OH− reaction in water

The bimolecular nucleophilic substitution (S_N2) reaction of CH₃F + OH^? in aqueous solution was investigated using a combined quantum mechanical and molecular mechanics approach. Reactant complex, transition state, and product complex along the reaction pathway were analyzed in water. The potentials of mean force were calculated using a multilayered representation with the DFT and CCSD(T) level of theory for the reactive region. The obtained free energy activation barrier for this reaction at the CCSD(T)/MM representation is 18.3 kcal/mol which agrees well with the experimental value at ～21.6 kcal/mol. Both the solvation effect and solute polarization effect play key roles on raising the activation barrier height in aqueous solution, with the former raising the barrier height by 3.1 kcal/mol, the latter 1.5 kcal/mol. © 2013 Wiley Periodicals, Inc.     

The interrelation between transfer and relaxation processes in aqueous solutions of electrolytes and hydration numbers and activation energies of molecular motions

The influence of transfer processes and activation energies on the electrical conductivity and nuclear magnetic relaxation rate of a reference aqueous solution of KCl and sea water at 15°C was studied. The closest agreement between the calculated and experimental conductivity values was obtained with the coordination numbers n _S of the K⁺ and Cl^? ions equal to 4 and 1, respectively, and the activation energy close to E _a for vapor (3.38 kcal/mol). According to nuclear magnetic relaxation rate, viscosity, diffusion, and self-diffusion measurements, the n _S values of these ions are 8 and 4, respectively, and E _a ≈ 4.6 kcal/mol. The main reasons for the difference in the n _S and E _a values for transfer processes in aqueous solutions of strong electrolytes are discussed. The temperature and concentration dependences of NMR relaxation rates and the other parameters related to molecular mobility are best described by a function which is the sum of exponential functions whose number depends on solution concentration.     

Oxidation of formic acid by bromine in aqueous,strongly acid media

Spectrophotometric methods were used to investigate the rate of the reaction of Br₂ with HCOOH in aqueous, acidic media. The reaction products are Br^? and CO₂. The kinetics of this reaction are complicated by both the formation of Br₃^? as Br^? is formed and the dissociation of HCOOH into HCOO^? and H⁺. Previous work on this reaction was carried out at acidities lower than the highest used here and led to the conclusion that only HCOO^? reacts with Br₂. It is agreed that this is by far the principal reaction. However, at the highest acidity experiments, an added small component of reaction was found, and it is suggested that it results from the direct reaction of Br₂ with HCOOH itself. On this assumption, values of the rate constants for both reactions are derived here. The rate constant for the reaction of HCOO^? with Br₂ agrees with values previously reported, within a factor of 2 on the low side. The reaction involving HCOOH is more than 2000 times slower than the reaction involving HCOO^?, but it does contribute to the overall rate as [H⁺] approaches 1M. These derived rate constants are able to simulate quantitatively the authors' absorbance-versus-time data, demonstrating the validity of their data treatment methods, if not mechanistic assignments. Finally, activation parameters were determined for both rate constants. The values obtained are: ΔE^?(HCOOH + Br₂) = 13.3 ± 1.1 kcal/mol, ΔS^? (HCOOH + Br₂) = ?28 ± 3 cal/deg mol, ΔE^? (HCOO^? + Br₂) = 13.1 ± 0.9 kcal/mol, and ΔS^?(HCOO^? + Br₂) = ?12 ± 1 cal/deg mol. That the activation energies of the two reactions turn out to be essentially identical does not support the authors' suggestion that both HCOOH and HCOO^? react with Br₂.     

Free energy calculations involving NH4+ in water

The analysis of the hydration of NH₄⁺ and the estimation of relative or absolute free energies of hydration by means of Monte Carlo computer simulations using different 1-6-12 potential functions is reported. Two electrostatic representations of NH₄⁺ (used respectively by W.L. Jorgensen and P.A. Kollman) in conjunction with two common water models (TIP3P and TIP4P) are considered. A change in relative hydration free energies of 1.7 kcal/mol is found when the NH₄⁺ models are mutated into each other in either TIP3P or TIP4P. The NH₄⁺ → Na⁺ mutation in both solvent models leads to similar but overestimated relative hydration energies of about ?28.7 kcal/mol. Similarly, the NH₄⁺ annihilation significantly overestimates the absolute free energy of hydration.     

Demetallation of α,β,γ,δ-tetrakis(p-sulfophenyl) porphiniron(III) in mineral acid–alcohol–water media

Demetallation rates of α,β,γ,δ-tetrakis(p-sulfophenyl)porphiniron(III) in hydrochloric acid–ethanol–water, perchloric acid–ethanol–water, and sulfuric acid–alcohol–water media were determined. For a given acidity value H₀ the order of the rates for the three acids was HCl > H₂SO₄ > HClO₄. This is also the order for complex formation between acid anion and iron(III). Consequently ligands as well as protons are involved in the breaking of bonds between the metal and the porphyrin leading to the formation of the activated complex. The log k values for HCl and HClO₄ media were not linearly related to the Hammett acidity function as they were for sulfuric acid–ethanol–water media. The average ΔH? and ΔS?values for the HCl media were 18.4 ± 1.4 kcal/mol and ? 19 ± 3 cal K mol, respectively, in very close agreement with those for H₂SO₄ media despite the difference in H ₀ dependence. For H₂SO₄–alcohol–water media the order of the rates was butanol > propanol > ethanol with little difference between isomeric alcohols.     

Theoretical study of the molecular ions SiH−5 and SiH−3

Ab initio HF and Cl calculations were performed to determine the equilibrium geometry of SiH^?₅ and SiH^?₃, the barrier for internal rotation (SiH^?₅) and inversion (SiH^?₃) and the stability of SiH^?₅ and further to study the effect of electron correlation on reaction energies. The gaussian-type basis included d and f functions on Si and a p set on II. The D_3h structures of SiH^?₅ is lower in energy than the C_4v structure by 2.9(3.2) kcal/mol (corresponding HF results in parentheses). SiH^?₃ has C_3v structure, the inner-ion barrier computed is 26.2 (27.3) kcal/mol. SiH^?₅ turns out to be stable with respect to SiH₄ + H^? by 20.3 (13.8) kcal/mol, but it is unstable with respect to SiH^?₃ ← H₂ by 6.3 (5.6) kcal/mol. These results show that electron correlation has a small effect on barriers of inversion (SiH^?₃) or pseudorotation (SiH^?₅), but may have a pronounced effect on reaction energies even if all systems involved have closed shells. The correlation energy contributions are analyzed in terms of intrapair and interpair terms in order to get a better understanding of the influence of correlation on reaction and activation energies.     

Definitive heat of formation of methylenimine,CH2NH,and of methylenimmonium ion,CH2NH2+, by means of W2 theory

A long‐standing controversy concerning the heat of formation of methylenimine has been addressed by means of the W2 (Weizmann‐2) thermochemical approach. Our best calculated values, ΔH°_f,298(CH₂NH) = 21.1±0.5 kcal/mol and ΔH°_f,298(CH₂NH₂⁺) = 179.4±0.5 kcal/mol, are in good agreement with the most recent measurements but carry a much smaller uncertainty. As a byproduct, we obtain the first‐ever accurate anharmonic force field for methylenimine: upon consideration of the appropriate resonances, the experimental gas‐phase band origins are all reproduced to better than 10 cm^?1. Consideration of the difference between a fully anharmonic zero‐point vibrational energy and B3LYP/cc‐pVTZ harmonic frequencies scaled by 0.985 suggests that the calculation of anharmonic zero‐point vibrational energies can generally be dispensed with, even in benchmark work, for rigid molecules. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1297–1305, 2001     

Determination of the gas-phase acidity of methylthioacetic acid using the Cooks’ kinetic method

We determined the gas-phase acidity of methylthioacetic acid (MTA) in a triple-quadrupole mass spectrometer using the Cooks’ kinetic method with the consideration of entropy effects. The negatively charged proton-bound dimers were generated by electrospray ionization. Collision-induced dissociation was applied to the dimer ions and the product ion ratios were measured at four different collision energies. The gas-phase acidity (ΔH _acid) of MTA was determined to be 340.0±1.7 kcal/mol using the extended kinetic method and 339.8±1.7 kcal/mol using the standard kinetic method. The entropy term is insignificant in this case and can be ignored. The standard kinetic method yielded a free energy of deprotonation of MTA (ΔG _acid) of 333.0±1.7 kcal/mol. The entropy of the acid dissociation, ΔS _acid, was estimated to be 22.8 cal/mol K. Theoretical prediction at the B3LYP/6-31+G* level of theory gives a similar value for ΔH _acid of 338. 9 kcal/mol. In the gas-phase, MTA is a stronger acid than methoxyacetic acid, although in solution, MTA is a weaker one.     

Nature of the water/aromatic parallel alignment interactions

The water/aromatic parallel alignment interactions are interactions where the water molecule or one of its O? H bonds is parallel to the aromatic ring plane. The calculated energies of the interactions are significant, up to ΔE_{CCSD(T)(limit)} = ?2.45 kcal mol^?1 at large horizontal displacement, out of benzene ring and CH bond region. These interactions are stronger than CH···O water/benzene interactions, but weaker than OH···π interactions. To investigate the nature of water/aromatic parallel alignment interactions, energy decomposition methods, symmetry‐adapted perturbation theory, and extended transition state‐natural orbitals for chemical valence (NOCV), were used. The calculations have shown that, for the complexes at large horizontal displacements, major contribution to interaction energy comes from electrostatic interactions between monomers, and for the complexes at small horizontal displacements, dispersion interactions are dominant binding force. The NOCV‐based analysis has shown that in structures with strong interaction energies charge transfer of the type π → σ*(O? H) between the monomers also exists. © 2014 Wiley Periodicals, Inc.     

The investigation on the relative stability of different clusters of thiourea dioxide in water using gas phase quantum chemical calculations

The relative stability of different clusters of thiourea dioxide (TDO) in water is examined using gas phase quantum chemical calculations at the MP2 and B3LYP level with 6‐311++G(d,p) basis set. The possible equilibrium structures and other energetic and geometrical data of the thiourea dioxide clusters, TDO‐(H₂O)_n (n is the number of water molecules), are obtained. The calculation results show that a strong interaction exists between thiourea dioxide and water molecules, as indicated by the binding energies of the TDO clusters progressively increased by adding water molecules. PCM model is used to investigate solvent effect of TDO. We obtained a negative hydration energy of ?20.6 kcal mol^?1 and free‐energy change of ?21.0 kcal mol^?1 in hydration process. On the basis of increasing binding energies with adding water molecules and a negative hydration energy by PCM calculation, we conclude thiourea dioxide can dissolve in water molecules. Furthermore, the increases of the C? S bond distance by the addition of water molecules show that the strength of the C? S bonds is attenuated. We find that when the number of water molecules was up to 5, the C? S bonds of the clusters, TDO‐(H₂O)₅ and TDO‐(H₂O)₆ were ruptured. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Investigation of the water exchange mechanism of the Plutonyl(VI) and Uranyl(VI) ions with quantum chemical methods

The water exchange reactions of [PuO₂(OH₂)₅]²⁺ and [UO₂(OH₂)₅]²⁺ were investigated with density functional theory (DFT) and wave function theory (WFT). Geometries and vibrational frequencies were calculated with DFT and CPCM hydration. The electronic energies were evaluated with general multiconfiguration quasi-degenerate second-order perturbation theory (GMC-QDPT2). Spin-orbit (SO) effects, computed with SO configuration interaction (SO–CI), are negligible. Both Actinyl(VI) ions react via an associative exchange mechanism, most likely I_a. The Gibbs activation energies (ΔG^?) at 25 °C are 33–34 and 30–37 kJ mol^?1 for [PuO₂(OH₂)₅]²⁺ and [UO₂(OH₂)₅]²⁺, respectively. ΔG^? for dissociative mechanisms (D, I_d) is higher by more than 15 kJ mol^?1.     

An ONIOM and DFT study of water and ammonia adsorption on anatase TiO2 (001) cluster

Density functional theory (DFT) calculations at ONIOM DFT B3LYP/ 6‐31G**‐MD/UFF level are employed to study molecular and dissociative water and ammonia adsorption on anatase TiO₂ (001) surface represented by partially relaxed Ti₂₀O₃₅ ONIOM cluster. DFT calculations indicate that water molecule is dissociated on anatase TiO₂ (001) surface by a nonactivated process with an exothermic relative energy difference of 58.12 kcal/mol. Dissociation of ammonia molecule on the same surface is energetically more favorable than molecular adsorption of ammonia (?37.17 kcal/mol vs. ?23.28 kcal/mol). The vibration frequency values also are computed for the optimized geometries of adsorbed water and ammonia molecules on anatase TiO₂ (001) surface. The computed adsorption energy and vibration frequency values are comparable with the values reported in the literature. Finally, several thermodynamical properties (ΔH°, ΔS°, and ΔG°) are calculated for temperatures corresponding to the experimental studies. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011