Author(s): Chen S; Taing H; Ahmida M; He HY; Carr A; Muchall HM; Eichhorn SH;

Thermotropic ionic liquid crystals have remained a relatively little studied group of materials despite their many potential applications as anisotropic ionic liquids and charge (ion and electron/hole) transporting materials. Particularly rare are core char...

Article GUID: 39315415

Author(s): Toubin C; Yeung DY; English AM; Peslherbe GH;

The degradation of S-nitrosothiols (RSNOs) to release NO is believed to be catalyzed by CuI ions, but the mechanism remains unclear. Kinetic experiments have shown that decomposition rates vary significantly with the chemical nature of the RSNO considered. ...

Article GUID: 12475301

Author(s): Qadir K Timerghazin

First-principles molecular dynamics simulations of the excited-state dynamics of I-(H2O)3 have been performed to gain some insight into the general features of the relaxation process of photoexcited I-(H2O)n clusters. The relaxation of excited I-(H2O)3 is c...

Article GUID: 12914436

Author(s): Robert C Mawhinney

A combination of density-functional theory and natural resonance theory has been used to show that a complete description of the electronic structure of nitrilimines, R(1)CNNR(2), requires four resonance structures (propargylic, allenic, 1,3-dipolar and car...

Article GUID: 15306921

Author(s): Paul G Loncke

Substituent effects and the role of negative hyperconjugation in 1,2-silyl migration and decarbonylation of methoxy(substituted-siloxy)carbenes have been investigated using quantum chemical calculations and natural bond orbital analysis. It has been found t...

Article GUID: 15917909

Author(s): Denise M Koch

We have investigated the photodissociation dynamics of NaI(H(2)O)(n) [n = 1-4] clusters using the molecular dynamics with quantum transitions method and a quantum mechanics/molecular mechanics description of NaI(H(2)O)(n), which involves a semiempirical val...

Article GUID: 16435804

Author(s): Pascal Larrégaray

The unimolecular dissociation dynamics of aluminum clusters following collision with either a rare gas atom or a surface is investigated by classical trajectory simulations with model potentials. Two conformers of Al(6) with very distinct shapes, i.e., the ...

Article GUID: 16435829

Author(s): Qadir K Timerghazin

High-level ab initio calculations employing the multireference configuration interaction and coupled clusters methods with a correlation-consistent sequence of basis sets have been used to obtain accurate potential energy curves for the complex of the sodiu...

Article GUID: 16438589

Author(s): Grygoriy A Dolgonos

The C2 fragmentation energies of the most stable isolated-pentagon-rule (IPR) isomers of the C80 and C82 fullerenes were evaluated with second-order Møller-Plesset (MP2) theory, density-functional theory (DFT) and the semiempirical self-consistent charge de...

Article GUID: 17588181

Author(s): Qadir K Timerghazin

A resonance representation of the electronic structure of S-nitrosothiols as a combination of the conventional R-S-N=O structure, a zwitterionic structure R-S+=N-O-, and a RS-/NO+ ion pair is proposed. The resonance forms are employed to predict and rationa...

Article GUID: 17616141

Author(s): Qadir K Timerghazin

Two or more polar molecules can trap an excess electron either in a dipole-bound fashion where it is located outside of the cluster (dipole-bound electron) or inside the cluster (solvated electron). The topology of the electron density in dipole-bound and s...

Article GUID: 17705589

Author(s): Qadir K Timerghazin

Acetonitrile molecules are known for their intriguing ability to accommodate an excess electron in either a diffuse dipole-bound orbital, away from the valence electrons, or in its valence orbitals, depending on the environment. In this work, we report a co...

Article GUID: 18154288

Author(s): Tao-Nhân V Nguyen

The structural and thermodynamic properties of Na+(CH3CN)n, I-(CH3CN)n, and NaI(CH3CN)n clusters have been investigated by means of room-temperature Monte Carlo simulations with model potentials developed to reproduce the properties of small clusters predic...

Article GUID: 18183958

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 characteriz...

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-consis...

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 specie...

Article GUID: 21428403

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, i...

Article GUID: 21961695

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, notab...

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...

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 again...

Article GUID: 22696309

Author(s): Varadwaj A; Varadwaj PR;

Based on an experimental observation, it has been controversially suggested in a study (Kurotobi et al., Science 2011, 33, 613) that a single molecule of water can completely be localized within the subnano-space inside the fullerene C(60) cage and, that ne...

Article GUID: 23090782

Author(s): Fürst O; Nichols CG; Lamoureux G; D' Avanzo N;

Cholesterol is the major sterol component of all mammalian plasma membranes. Recent studies have shown that cholesterol inhibits both bacterial (KirBac1.1 and KirBac3.1) and eukaryotic (Kir2.1) inward rectifier K(+) (Kir) channels. Lipid-sterol interactions...

Article GUID: 25517146

Author(s): Jean-François Rhéault

A singular aspect of the 2-on-2 hemoglobin structures of groups I and II is the presence of tunnels linking the protein surface to the distal heme pocket, supporting the storage and the diffusion of small apolar ligands to/from the buried active site. As th...

Article GUID: 25723781

Author(s): Sefer Baday

In human cells, membrane proteins of the rhesus (Rh) family excrete ammonium and play a role in pH regulation. Based on high-resolution structures, Rh proteins are generally understood to act as NH3 channels. Given that cell membranes are permeable to gases...

Article GUID: 26190573

Author(s): Maria S Shadrina

Atomistic molecular dynamics simulations of diffusion of O2 from the hemes to the external solvent in the a- and ß-subunits of the human hemoglobin (HbA) tetramer reveal transient gas tunnels that are not seen in crystal structures. We find here that the tu...

Article GUID: 26226318

Author(s): Maria S Shadrina

Hemoglobin transports O2 by binding the gas at its four hemes. Hydrogen bonding between the distal histidine (HisE7) and heme-bound O2 significantly increases the affinity of human hemoglobin (HbA) for this ligand. HisE7 is also proposed to regulate the rel...

Article GUID: 26226401

Author(s): Sandrine Moreira

CONCLUSION: Homology modeling and molecular dynamics simulations strongly suggest that DpRNL is an RNA ligase 2. The predicted innovative reshaping of DpRNL's catalytic pocket is worthwhile to be tested experimentally.

Article GUID: 26449279

Author(s): Esam A Orabi

A polarizable model for ammonia is optimized based on the ab initio properties of the NH3 molecule and the NH3-NH3 and NH3-H2O dimers calculated at the MP2 level. For larger (NH3)m, NH3(H2O)n, and H2O(NH3)n clusters (m = 2-7 and n = 1-4), the model yields s...

Article GUID: 26583551

Author(s): Esam A Orabi

A polarizable potential model for M(+)-NH3 interactions (M(+) = Li(+), Na(+), K(+), Rb(+), Cs(+)) is optimized based on the ab initio properties of the ion-ammonia dimers calculated at the MP2 level of theory. The optimized model reproduces the ab initio bi...

Article GUID: 26583725

Author(s): Esam A Orabi

A polarizable model for hydrogen sulfide (H2S) is optimized based on the experimental properties of the monomer and of the bulk liquid. The model is characterized by rigid SH bonds but flexible HSH angle and the polarizability is based on the Drude oscillat...

Article GUID: 26588292

Author(s): Esam A Orabi

Polarizable potential models for the interaction of Li(+), Na(+), K(+), and NH4(+) ions with benzene are parametrized based on ab initio quantum mechanical calculations. The models reproduce the ab initio complexation energies and potential energy surfaces ...

Article GUID: 26592880

Author(s): Jardali F; Tran J; Liège F; Florea I; Leulmi ME; Vach H;

The outstanding properties of silicon nanoparticles have been extensively investigated during the last few decades. Experimental evidence and applications of their theoretically predicted permanent electric dipole moment, however, have only been reported fo...

Article GUID: 37570492

Author(s): Selvaraj G; Kaliamurthi S; Peslherbe GH; Wei DQ;

ackground: Coronavirus (CoV) is an emerging human pathogen causing severe acute respiratory syndrome (SARS) around the world. Earlier identification of biomarkers for SARS can facilitate detection and reduce the mortality rate of the disease. Thus, by integ...

Article GUID: 33968364

Author(s): Ozturk TN; Culham DE; Tempelhagen L; Wood JM; Lamoureux G;

Osmosensing transporter ProP detects the increase in cytoplasmic cation concentration associated with osmotically induced cell dehydration and mediates osmolyte uptake into bacteria. ProP is a 12-transmembrane helix protein with an a-helical, cytoplasmic C-...

Article GUID: 32838524

Author(s): Simbrunner J; Schrode B; Domke J; Fritz T; Salzmann I; Resel R;

Crystal structure identification of thin organic films entails a number of technical and methodological challenges. In particular, if molecular crystals are epitaxially grown on single-crystalline substrates a complex scenario of multiple preferred orientat...

Article GUID: 32356785

Author(s): Kim VO; Broch K; Belova V; Chen YS; Gerlach A; Schreiber F; Tamura H; Della Valle RG; D' Avino G; Salzmann I; Beljonne D; Rao A; Friend...

Singlet exciton fission is a spin-allowed process in organic semiconductors by which one absorbed photon generates two triplet excitons. Theory predicts that singlet fission is mediated by intermol...

Article GUID: 31675857

Author(s): Krohn L; Öztürk TN; Vanderperre B; Ouled Amar Bencheikh B; Ruskey JA; Laurent SB; Spiegelman D; Postuma RB; Arnulf I; Hu MTM; Dauvilliers Y;...

Objective: The TMEM175/GAK/DGKQ locus is the 3rd strongest risk locus in genome-wide association studies of Parkinson disease (PD). We aimed to identify the specific disease-associated variants in ...

Article GUID: 31658403

Author(s): Orabi EA; Davis RL; Lamoureux G;

Cation-p interactions play important roles in molecular recognition and in the stability and function of proteins. However, accurate description of the structure and energetics of cation-p interactions presents a challenge to both additive and polarizable f...

Article GUID: 31652004

Author(s): Shihao Wang

This letter presents a method for the parametrization of semiempirical models for proton transfer reactions in water clusters. Two new models are developed: AM1-W, which is a reparameterization of the classic AM1 model, and AM1PG-W, which is a modified AM1-...

Article GUID: 26588263

Author(s): Adrian Paz Ramos

Little is known about the interaction of very long-chain saturated fatty acids (VLCFAs) with biological membranes. However, this could play an important role on interleaflet interactions and signal transduction mechanisms in cells. The aim of this work is t...

Article GUID: 27351151

Author(s): Prem Ponka

Heme is a cofactor that is essential to almost all forms of life. The production of heme is a balancing act between the generation of the requisite levels of the end-product and protection of the cell and/or organism against any toxic substrates, intermedia...

Article GUID: 28254242

Author(s): Lavinia A Carabet

Many globins convert ^(•)NO to innocuous NO(3)^(-) through their nitric oxide dioxygenase (NOD) activity. Mycobacterium tuberculosis fights the oxidative and nitrosative stress imposed by its host (the toxic effects of O(2)^(•-) and ^(•)NO species and their...

Article GUID: 28835102

Author(s): Lauralicia Sacre

Oligonucleotides containing various adducts, including ethyl, benzyl, 4-hydroxybutyl and 7-hydroxyheptyl groups, at the O4 atom of 5-fluoro-O4 -alkyl-2'-deoxyuridine were prepared by solid-phase synthesis. UV thermal denaturation studies demonstrated th...

Article GUID: 29243336

Author(s): Esam A Orabi

Cation-p interactions play important roles in the stabilization of protein structures and protein-ligand complexes. They contribute to the binding of quaternary ammonium ligands (mainly RNH(3)^(+) and RN(CH(3))(3)^(+)) to various protein receptors and are l...

Article GUID: 29397727

Author(s): Esam A Orabi

S-aromatic motifs are important noncovalent forces for protein stability and function but remain poorly understood. Hence, we performed quantum calculations at the MP2(full)/6-311++G(d,p) level on complexes between Cys (H(2)S, MeSH) and Met (Me(2)S) models ...

Article GUID: 29533644

Author(s): Esam A Orabi

Hydrogen peroxide (H(2)O(2)) has numerous industrial, environmental, medical, cosmetic, and biological applications. Given its importance, we provide a simple model as an alternative to experiment for studying the properties of pure liquid H(2)O(2) and its ...

Article GUID: 29630362

Author(s): Georgy Derevyanko

MOTIVATION: The computational prediction of a protein structure from its sequence generally relies on a method to assess the quality of protein models. Most assessment methods rank candidate models using heavily engineered structural features, defined as co...

Article GUID: 29931128

Author(s): Simbrunner J; Hofer S; Schrode B; Garmshausen Y; Hecht S; Resel R; Salzmann I;

Grazing-incidence X-ray diffraction studies on organic thin films are often performed on systems showing fibre-textured growth. However, indexing their experimental diffraction patterns is generally challenging, especially if low-symmetry lattices are invol...

Article GUID: 30996719