Author(s): Kamya PR; Muchall HM;

We have evaluated the performance of three (TD-)DFT functionals with the 6-31+G(d,p) basis set for the reproduction of experimental geometries, vertical ionization potentials, and low excitation energies of a selection of [2.2] and [3.3]paracyclophanes. Overall, (TD-)BH& H outperforms both (TD-)B3LYP and (TD-)PBE0. Some shortcomings are shown by B3LYP ...

Article GUID: 19055395

Author(s): Hernández de la Peña L; Peslherbe GH;

Nonequilibrium simulation methods and rigid-body path-integral techniques are combined to estimate the relevance of protonic quantum effects in the free energy of ion-water clusters. The Crooks' fluctuation relation is used to quantitatively characterize the impact of quantum effects on the dissociation free energy of the paradigm I(-)(H(2)O)(5). By u ...

Article GUID: 20377185

Author(s): Nguyen TN; Timerghazin QK; Vach H; Peslherbe GH;

Molecular electronic excitation in (O(2))(n) clusters induced by mechanical collisions via the "chemistry with a hammer" is investigated by a combination of molecular dynamics simulations and quantum chemistry calculations. Complete active space self-consistent field augmented with triple-zeta polarizable basis set quantum chemistry calculations of a comp ...

Article GUID: 21322678

Author(s): Ivanova EV; Muchall HM;

We present a computational study on the concerted hydrolysis of several classes of N-sulfinylamines of generic formula R-N-S-O, such as the -amines themselves (R-NSO), -hydrazines (R-NH-NSO), -hydrazides (R-CO-NH-NSO) and -amides (R-CO-NSO), as these species are known to possess a wide range of hydrolytic reactivity. Two possible mechanisms of hydrolysis, ...

Article GUID: 21428403

Author(s): Varadwaj PR; Varadwaj A; Marques HM;

A density functional theory study of the structure of the title compounds with the divalent metal ions in their high-spin ground state, obtained using B3LYP/6-311++G(d,p) in vacuo and in aqueous solution simulated using a polarized continuum medium, is reported for the first time. The modeling reproduces the pseudo pentagonal bipyramidal crystallographic ...

Article GUID: 21568260

Author(s): Kamya PR; Muchall HM;

Calculated electron densities from PBE0/6-31+G(d,p) were analyzed with respect to the hydrogen bonding within a nucleic acid base pair and the p-stacking between sets of base pairs. From published X-ray crystallographic data, base pairs were isolated from a total of 11 DNA and RNA duplexes, and their experimental geometry was maintained throughout the ana ...

Article GUID: 21721560

Author(s): Varadwaj PR; Varadwaj A; Peslherbe GH; Marques HM;

Density functional theory calculations, together with quantum theory of atoms in molecules (QTAIM) analyses, have been performed to investigate 18-azacrown-6 complexes of the high-spin late first transition series divalent metal ions in the gas phase and, in some cases, in aqueous solution simulated by a polarizable continuum model. Six intramolecular H-H ...

Article GUID: 21961695

Author(s): Heidi M Muchall

Nitrilimines (R-CNN-R) can be described through a carbenic valence bond structure, and although intermolecular carbenic reactions from nitrilimines are unknown, intramolecular reaction products from ortho-vinyl MeCOO-CNN-Ph (1) and Ph-CNN-Ph (2) that seem to have followed two typical carbene reaction mechanisms, [1+2] cycloaddition and C-H insertion, have ...

Article GUID: 21974693

Author(s): Mak CC; Timerghazin QK; Peslherbe GH;

Upon photoexcitation of iodide-water clusters, I(-)(H(2)O)(n), an electron is transferred from iodide to a diffuse cluster-supported, dipole-bound orbital. Recent femtosecond photoelectron spectroscopy experiments have shown that, for photoexcited I(-)(H(2)O)(n) (n= 5), complex excited-state dynamics ultimately result in the stabilization of the transferr ...

Article GUID: 22466252

Author(s): Wang S; Orabi EA; Baday S; Bernèche S; Lamoureux G;

Proteins of the Amt/MEP family facilitate ammonium transport across the membranes of plants, fungi, and bacteria and are essential for growth in nitrogen-poor environments. Some are known to facilitate the diffusion of the neutral NH(3), while others, notably in plants, transport the positively charged NH(4)(+). On the basis of the structural data for Amt ...

Article GUID: 22631217

Author(s): Shadrina MS; English AM; Peslherbe GH;

The diffusion of small gases to special binding sites within polypeptide matrices pivotally defines the biochemical specificity and reactivity of proteins. We investigate here explicit O(2) diffusion in adult human hemoglobin (HbA) as a case study employing the recently developed temperature-controlled locally enhanced sampling (TLES) method and vary the ...

Article GUID: 22690872

Author(s): Varadwaj PR; Varadwaj A; Peslherbe GH;

The proton accepting and donating abilities of cyclopropenylidene (c-C(3)H(2)) on its complexation with hydrogen halides H-X (X = F, Cl, Br) are analyzed using density-functional theory with three functionals (PBE0, B3LYP, and B3LYP-D) and benchmarked against second-order Møller-Plesset (MP2) theory. Standard signatures including, inter alia, dipole momen ...

Article GUID: 22696309