Theoretical study of light-metal tetrahydroborates

Ab initio calculations of the structural, energetic, vibrational, and magnetic characteristics of the lowest-lying structures for isolated molecules and ions of light-metal tetrahydroborates (Li, Na, Be, Mg, and Al) have been performed by the perturbation theory (MP2), quadratic configuration interaction (QCISD(T)), coupled cluster (CCSD(T)), and density functional theory (B3LYP) methods using the 6-31G*, 6-31G**, 6-311+G**, and 6-311++G** basis sets. The trends in the behavior of the structural parameters, the energies of different decomposition pathways, barriers to internal rotation of BH₄ groups, normal mode frequencies, magnetic shielding constants, and spin density distribution (in radicals) have been analyzed in various related series of these compounds. The results obtained by ab initio methods and at the DFT level are compared. The economical approximation B3LYP/6-311++G**//B3LYP/6-311+G** adequately reproduces the results obtained at the higher level of theory CCSD(T)/6-311++G*s*//MP2/6-31G* even though it requires considerably shorter CPU times and smaller amounts of memory.     

Theoretical study of ibuprofen phototoxicity

The photochemical properties and degradation of the common nonsteroid anti-inflammatory drug ibuprofen is studied by means of hybrid density functional theory. Computed energies and properties of various species show that the deprotonated form dominates at physiological pH, and that the species will not be able to decarboxylate from a singlet excited state. Instead, decarboxylation will occur, with very high efficiency, provided the deprotonated compound can undergo intersystem crossing from an excited singlet to its excited triplet state. In the triplet state, the C-C bond connecting the carboxyl group is elongated, and the CO2 moiety detaches with a free energy barrier of less than 0.5 kcal/mol. Depending on the local environment, the decarboxylated product can then either be quenched through intersystem crossing (involving the possible formation of singlet oxygen) and protonation, or serve as an efficient source for superoxide anions and the formation of a peroxyl radical that will initiate lipid peroxidation.     

Theoretical study of free-radical migrations

Free-radical migrations have been investigated by ab initio molecular orbital theory to account for the facts that 1,2-migrations are observed for Cl-atoms, aryl or vinyl groups, whereas for H atoms only 1,5- and 1,6-migrations have been seen in contrast to the easy 1,2-hydride shifts in cations. The optimum geometry and energy models of the transition states of 1,2- and 1,5-migrations, and of their corresponding initial states have been determined using the Gaussian 70 STO-3G RHF method. The calculated activation energies ΔE are in agreement with experimental observations. The main features of the 1,2-migration reactions are (i) ΔE is more important for elements of the first and second row of the periodic classification than for those belonging to the third row; (ii) protonation strongly reduces ΔE. For both 1,2- and 1,5-migrations a correlation exists between ΔE and the energetic change of the frontier orbital, Δ?_somo: the reactions are under frontier orbital control.     

Theoretical study of hyaluronan oligosaccharides

The structure and energetics of hyaluronan oligomers from di- to decasaccharides have been studied by density functional theory calculations at the B3LYP/6-31G** level. The study covered selected conformers of the sodium salt, anionic disaccharides, and neutral acids in the isolated state and in aqueous solution using the PCM model approach. We investigated the structural changes of the hyaluronan chain when the Na⁺ ion is removed or replaced by proton. These processes result in some characteristic changes in the glycosidic torsional angles and hydrogen bonding interactions. We evaluated the folding for the hyaluronan chains and obtained values between 2.2 and 3.2, somewhat smaller than reported for the crystals. We found a contraction of the hyaluronan chains upon enlargement in most derivatives attributed partly to the helical character of hyaluronan. The energy consequences of the enlargement have been modeled by isodesmic reactions. The enlargement processes proved to be exothermal and the energies consistent within the gradual enlargement.     

Theoretical study of single-bubble sonochemistry

Numerical simulations of bubble oscillations in liquid water irradiated by an ultrasonic wave are performed under the experimental condition for single-bubble sonochemistry reported by Didenko and Suslick [Nature (London) 418, 394 (2002)]. The calculated number of OH radicals dissolving into the surrounding liquid from the interior of the bubble agrees sufficiently with the experimental data. OH radicals created inside a bubble at the end of the bubble collapse gradually dissolve into the surrounding liquid during the contraction phase of an ultrasonic wave although about 30% of the total amount of OH radicals that dissolve into the liquid in one acoustic cycle dissolve in 0.1 micros at around the end of the collapse. The calculated results have indicated that the oxidant produced by a bubble is not only OH radical but also O atom and H2O2. It is suggested that an appreciable amount of O atom is produced by bubbles inside a standing-wave-type sonochemical reactor filled with water in which oxygen is dissolved as in the case of air.     

Theoretical study of I2O

We present high-level density functional calculations (DFT) on the unknown I₂O molecule. The results suggest that the compound may be sufficiently stable for detection and synthesis. Our results also suggest that the DFT method is a reliable and computationally cheap alternative to G2, for estimating thermodynamic properties. The trends in relative stabilities within the HOX and X₂O series are discussed (X=halogen). © 1998 John Wiley & Sons, Inc. Heteroatom Chem 9:383–385, 1998     

Theoretical study of acridane oxidation reactions

The interactions of acridanes with oxidants were modeled using combined methods of quantum chemistry (DFT B3LYP/6-311G(d,p)), molecular mechanics, MERA model, and MOPS algorithm. The results of simulation are compared with XRD data, oxidation potentials of acridanes, and the reduction potentials of the products of the oxidation reaction. It is shown that elimination of the hydride anion by the reactions of acridanes with oxidants is a consequence of a two-step process; the first step is the transfer of electron density from the HOMO of acridane to the LUMO of the oxidant; the second step is hydrogen elimination from the acridane molecule due to hydrogen bonding with the oxygen atom of the oxidant. The details of the mechanism were established by modeling the acridane-oxidant complexes using the MOPS algorithm including the continuum model of the solvent. The logarithms of the rate constants of the processes depend on the structure parameters of the model complexes with correlation coefficients of at least 0.93.     

Theoretical study of cooperativity in biotin

To give a deeper insight into the widely discussed catalytic mechanism of biotin, four representative model molecules and their aggregates hydrogen bonding (H-bonding) to water molecules were investigated by means of ab initio calculations and compared with molecular dynamics simulations. The roles of the ureido group, the sulfur atom, and the side chain of biotin are examined and discussed, respectively. Some significant H-bonding cooperativities are theoretically demonstrated in the ureido group of biotin. The pi-electron delocalization of the ureido group makes the system a good candidate for the H-bonding cooperativities, which in turn increases the covalent character of the corresponding H-bonds and facilitates the electrophilic substitution of the nitrogen atoms in the ureido group. The sulfur of biotin may participate in the delocalized pi-electron system of the ureido group via special sulfur-nitrogen bonding interactions, which reinforces the H-bonding cooperativities of the ureido group. The side chain of biotin not only reduced the accessibility of 3-NH due to steric hindrance but also enhanced the H-bonding cooperativities of the ureido group by folding over to hydrogen bond to more water molecules. The folded states are a probable way of activating 1-NH by strong cooperative effects. In addition, the H-bonding cooperativities may be a significant reason for the strong and specific binding between biotin and streptavidin.     

Theoretical study of formamide decomposition pathways

The chemical transformations of formamide (NH(2)CHO), a molecule of prebiotic interest as a precursor for biomolecules, are investigated using methods of electronic structure computations and Rice-Rampserger-Kassel-Marcus (RRKM) theory. Specifically, quantum chemical calculations applying the coupled-cluster theory CCSD(T), whose energies are extrapolated to the complete basis set limit (CBS), are carried out to construct the [CH(3)NO] potential energy surface. RRKM theory is then used to systematically examine decomposition channels leading to the formation of small molecules including CO, NH(3), H(2)O, HCN, HNC, H(2), HNCO, and HOCN. The energy barriers for the decarboxylation, dehydrogenation, and dehydration processes are found to be in the range of 73-78 kcal/mol. H(2) loss is predicted to be a one-step process although a two-step process is competitive. CO elimination is found to prefer a two-step pathway involving the carbene isomer NH(2)CHO (aminohydroxymethylene) as an intermediate. This CO-elimination channel is also favored over the one-step H(2) loss, in agreement with experiment. The H(2)O loss is a multistep process passing through a formimic acid conformer, which subsequently undergoes a rate-limiting dehydration. The dehydration appears to be particularly favored in the low-temperature regime. The new feature identifies aminohydroxymethylene as a transient but crucial intermediate in the decarboxylation of formamide.     

Theoretical study of ScCO2+

The structure, binding energy, and vibrational frequencies have been determined for ScCO₂⁺. The inserted OSc⁺CO structure in the ¹A′ state is the most stable isomer and lies 43.2 kcal/mol below the ground-state Sc⁺+ CO₂ asymptote. The linear η¹-O Sc⁺(SINGLE BOND)OCO ³Δ state is bound by a charge-quadrupole interaction and has a binding energy of 13.9 kcal/mol. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 63: 523–528, 1997     

Theoretical study of AlC3+

A theoretical study of the AlC₃⁺ species has been carried out. Predictions have been made for some of the molecular properties (geometries, dipole moments, and harmonic vibrational frequencies) which could help in their possible experimental detection. In addition, a topological analysis of the electron density and its associated Laplacian has also been carried out. The global ground state is predicted to be a linear species with ¹Σ electronic state, but a rhombic four‐membered ring (¹A₁) lies close in energy. It seems that both isomers could be accessible to experimental detection. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Theoretical study of hydrogen-bonded formaldehyde complexes

The hydrogen-bonded complexes involving formaldehyde and a series of proton donors of varying strengths, have been investigated at different levels of ab initio MO theory. The structures of the studied complexes were SCF optimized at the 6-31G basis set level. The binding energy was estimated employing basis set superposition correction, zero-point vibrations and MP2 correlation contribution at the different basis set: STO-3G; 6-31G; MP2/6-31G; 6-31G**; MP2/6-31G**; 6-311G(2d, 2p) and MP2/6-311G(2d, 2p). Linear relationships were found of the calculated binding energy with: the calculated shift in the carbonyl stretching frequency, the changes in carbonyl bond length and the optimum value of hydrogen-bond distance; furthermore the calculations confirm a parallel trend between the proton-donor ability and the strength of the hydrogen bond.     

Theoretical study of metallofullerenes M@C32

14 systems of metal atoms, embedded inside the C₃₂ cage, have been calculated and analyzed using the ab initio quantum chemistry Gamess program. We study their electronic structure, compare their stability. The metal atom with even electrons interjected inside the C₃₂ cage is more stable than the metal atom with odd electrons. Ti@C₃₂ system is the most stable in the 14 metallofullerenes.     

Theoretical study of the ammonia trimer

Open-chain (I) and cyclic (II) structures of the ammonia trimer (NH₃)₃ have been optimized using the 4-3IG extended basis set. The- cyclic structure (II) is found to be the most stable, in agreement with recent experimental results.     

Theoretical study of the Diels-Alder reaction

The cycloaddition of ethylene to butadiene has been studied by theab initio LCAO-SCF-MO method of Roothaan using STO-3G and 7s-3p basis sets. The potential energy hypersurface of the supersystem formed by the reactants has been calculated in order to determine the reaction path. It was found that, during the approach of the partners, the planes of the molecules form an angle around 70 °. The activated complex has a geometry which prefigures the half-chair conformation of cyclohexene and exhibits no biradical character. Our theoretical results are in reasonable agreement with the corresponding experimental ones.     

Theoretical study of the alpha-cyclodextrin dimer

The molecular structure, stabilization energy, and thermodynamic properties of the plausible modes of the interaction for the three possible alpha-cyclodextrin (alpha-CD) dimers (head-to-head, tail-to-tail, and head-to-tail) with a water cluster were obtained using quantum chemical methods for the first time. Nine distinct spatial arrangements were investigated. The head-to-head mode of interaction with water is preferred by more than 10 kcal.mol(-1) (BLYP/6-31G(d,p)//PM3 Gibbs free energy difference value at room temperature) in relation to the next stable structure, with a water dimer structure placed inside each cavity and cyclic water tetramers surrounding each tail end. The inter alpha-CD hydrogen bonds play a major role to stabilize the dimeric structures, with no water tetramer being found between the two alpha-CD subunits for the preferred global minimum structure. Therefore, a theoretical model aimed to describe the behavior of alpha-CD dimer, or their inclusion complexes, in the aqueous media should take into account this preference for binding of the water molecules.