Gas-phase Quantum Chemical Calculations Research Articles

Proton Hopping Mechanisms in a Protic Organic Ionic Plastic Crystal

We elucidate the dynamics and mechanism of proton transport in a protic organic ionic plastic crystal (POIPC) [TAZ][pfBu] by means of Born–Oppenheimer molecular dynamics simulations at 400 K and zero humidity. The arrangement of ionic species in the crystal offers a two-dimensional hydrogen bond network along which an acidic proton can travel from one cation to another through a sequence of molecular reorientations. The results suggest spontaneous autodissociation of the N–HN bond in the cation and multiple proton shuttle events from the cation’s nitrogen to the anion’s oxygen site in a native crystal. A complete proton transfer event is observed in simulations of a defective crystal with a single proton hole created in the cation. The barrier for proton transfer is determined using ab initio metadynamics simulations to be 7 kcal/mol, in agreement with experimental conductivity data. Using gas phase quantum chemical calculations, we propose [TAZ][CF3CF2CH2CF2SO3] as a compound that can show enhanced conductivity compared to that of [TAZ][pfBu].

Encapsulated Guests in the Smallest Spaces: Shrinking Guests by Compression and Investigations under Solvent-Free Conditions.

Noncovalent interactions play a pivotal role in a variety of biological and chemical processes. The experimental determination and quantum chemical calculations of the forces driving these interactions are of utmost importance. Of special interest are interactions of molecules in small spaces which show phenomena different from conventional behavior in solution. An extension is the encapsulation of guests in smallest spaces: The guests are too large to be included under standard conditions and hence must be forced to intrude into the cavity. Here, we show the design of such a host-guest system which allows to directly compare the measured thermodynamic values to gas-phase quantum chemical calculations. Structural investigation of the complexes reveals that the encapsulation process causes not only an extension of the hollow space of the host but also a shrinking of the included guest by compression.

Quantum Chemical Calculations with the Inclusion of Nonspecific and Specific Solvation: Asymmetric Transfer Hydrogenation with Bifunctional Ruthenium Catalysts

Details of the mechanism of asymmetric transfer hydrogenation of ketones catalyzed by two chiral bifunctional ruthenium complexes, (S)-RuH[(R,R)-OCH(Ph)CH(Ph)NH(2)](η(6)-benzene) (Ru-1) or (S)-RuH[(R,R)-p-TsNCH(Ph)CH(Ph)NH(2)](η(6)-mesitylene) (Ru-2), were studied computationally by density functional theory, accounting for the solvation effects by using continuum, discrete, and mixed continuum/discrete solvation models via "solvated supermolecules" approach. In contrast to gas phase quantum chemical calculations, where the reactions were found to proceed via a concerted three-bond asynchronous process through a six-membered pericyclic transition state, incorporation of the implicit and/or explicit solvation into the calculations suggests that the same reactions proceed via two steps in solution: (i) enantio-determining hydride transfer and (ii) proton transfer through the contact ion-pair intermediate, stabilized primarily by ionic hydrogen bonding between the cation and the anion. The calculations suggest that the proton source for neutralizing the chiral RO(-) anion may be either the amine group of the cationic Ru complex or, more likely, a protic solvent molecule. In the latter case, the reaction may not necessarily proceed via the 16e amido complex Ru[(R,R)-XCH(Ph)CH(Ph)NH](η(6)-arene). The origin of enantioselectivity is discussed in terms of the newly formulated mechanism.

Vibrational Spectra of Linear Oligomers of Carbonic Acid: A Quantum Chemical Study

Gas phase quantum chemical calculations of linear, hydrogen bonded oligomers of carbonic acid have been carried out to examine the feasibility for such species to be the building blocks of crystalline carbonic acid. Infrared and Raman vibrational spectra have been calculated and are compared against experimentally known spectra for two polymorphs of carbonic acid. The calculated anharmonic frequencies of the linear oligomer agree well with the experimental data for the centrosymmetric β-carbonic acid, rather than with that for the α polymorph. These calculations strongly suggest that β-carbonic acid should consist of one-dimensional hydrogen bonded carbonic acid molecules in the anti-anti conformation.

Electrophile affinity and positional selectivity in electrophilic substitution reactions of N-substituted pyrroles

In terms of the density functional theory (DFT) using B3LYP/6-31G(d) method with full geometry optimization, gas-phase quantum chemical calculations were performed for σ-complexes formed upon the attack of electrophiles E (E = H+, Me+, Me3Si+, Br+, NO2 +, MeCO+, SO3) on α- and β-positions of furan, thiophene, selenophene, pyrrole, and N-substituted pyrroles (NR-pyrroles, R = Me, But, SiMe3, SiPri 3, C6H4NO2-p, SO2Ph, CHO, COOMe) and for respective α- and β-substituted electrophilic substitution products. The energy differences between the α- and β-isomers of the σ-complexes characterize the preferred direction of the electrophilic attack, while the energy differences between the isomeric products make it possible to estimate the energy preference of a particular product. An analysis of the results obtained demonstrates the effect of the structure of heterocycle, the nature of electrophile, and thermodynamic and steric factors on the positional selectivity (α/β ratio) in electrophilic substitution reactions of π-electron rich five-membered heteroaromatics.

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

Single crystal x-ray diffraction study of dioxane, pyrazine, and pyridine complexes of 3-(1-amino-2,2,2-trifluoroethylidene)-2-imino-1,1,4,5,6,7-hexafluoroindan

Single crystals of complexes of 3-(1-amino-2,2,2-trifluoroethylidene)-2-imino-1,1,4,5,6,7-hexafluoroindan (1) with 1,4-dioxane, pyrazine, and pyridine have been synthesized. Their structure was investigated by X-ray analysis. In crystals of the dioxane complex, compound 1 is present together with its tautomer — 2-amino-3-(1-imino-2,2,2-trifluoroethyl)-1,1,4,5,6,7-hexafluoroindene (1a), and these compounds are in an equilibrium ratio of ∼60:40. Gas-phase quantum chemical calculations have been performed to examine the possibility of a tautomeric equilibrium of enaminoimine 1 in the corresponding complexes.

Force Field Validation Using Protein Side Chain Prediction

The prediction of protein side chain conformations is used to evaluate the accuracy of force field parameters. Specifically, new torsional parameters have recently been reported for the OPLS-AA force field, which achieved substantially better accuracy with respect to high level gas-phase quantum chemical calculations [J. Phys. Chem. B 2001, 105, 6474]. Here we demonstrate that these new parameters also lead to qualitatively improved side chain prediction accuracy. The primary emphasis is on the prediction of single side chain conformations, with the rest of the protein held fixed at the native configuration. Errors due to incomplete sampling can thus be essentially eliminated, using a combination of rotamer search and energy minimization. In addition, the protein environment is modeled realistically using implicit solvation and an explicit representation of crystal packing effects. Aided by the development of new algorithms, these calculations have been performed with modest computational requirements (a cluster of PCs) on a database of 36 proteins (∼5000 total residues). The side chain prediction tests that we employ are quite general and can be used to evaluate nonbonded or solvation parameters as well. As such, they provide a useful complement to decoy studies for force field validation.

Quantum mechanical calculations on some 4-methyl-5-substituted imidazole derivatives as acidic corrosion inhibitor for zinc

Gas phase quantum chemical calculations for the efficiency of some imidazole derivatives as corrosion inhibitors, along with the relative stability and proton affinity determination were performed by means of the AM1, PM3, MINDO/3 and MNDO semi-empirical SCF molecular orbital methods. The agreement with the experimental data was found to be satisfactory.