PERFORM Publications

Keyword search (4,163 papers available)

Title		Authors	PubMed ID
1	Comprehensive DFT investigation of small-molecule adsorption on the paradigm M-MOF-74 family of metal-organic frameworks	Jodaeeasl N; Wang S; Hu A; Peslherbe GH;	39829319 CERMM
2	Modeling predicts facile release of nitrite but not nitric oxide from the thionitrate CH3SNO2 with relevance to nitroglycerin bioactivation	Parmar V; Orabi EA; English AM; Peslherbe GH;	39738238 CERMM
3	Core charge of imidazolium annulated triphenylene derivatives induces discotic columnar mesomorphism	Chen S; Taing H; Ahmida M; He HY; Carr A; Muchall HM; Eichhorn SH;	39315415 CERMM
4	Theoretical evidence that Cu(I) complexation promotes degradation of S-nitrosothiols	Toubin C; Yeung DY; English AM; Peslherbe GH;	12475301 CERMM
5	Further insight into the relaxation dynamics of photoexcited I-(H2O)n clusters	Qadir K Timerghazin	12914436 CERMM
6	The electronic structure of nitrilimines revisited	Robert C Mawhinney	15306921 CERMM
7	Substituent effects and the role of negative hyperconjugation in siloxycarbene rearrangements	Paul G Loncke	15917909 CERMM
8	Nonadiabatic trajectory studies of NaI(H2O)n photodissociation dynamics	Denise M Koch	16435804 CERMM
9	On the statistical nature of collision and surface-induced dissociation: a theoretical investigation of aluminum clusters	Pascal Larrégaray	16435829 CERMM
10	Accurate ab initio potential for the Na+...I* complex	Qadir K Timerghazin	16438589 CERMM
11	Calculations of the C2 fragmentation energies of higher fullerenes C80 and C82	Grygoriy A Dolgonos	17588181 CERMM
12	Resonance description of S-nitrosothiols: insights into reactivity	Qadir K Timerghazin	17616141 CERMM
13	Non-nuclear attractor of electron density as a manifestation of the solvated electron	Qadir K Timerghazin	17705589 CERMM
14	Electronic structure of the acetonitrile and acetonitrile dimer anions: a topological investigation	Qadir K Timerghazin	18154288 CERMM
15	Microsolvation of the sodium and iodide ions and their ion pair in acetonitrile clusters: a theoretical study	Tao-Nhân V Nguyen	18183958 CERMM
16	Quantum effects on the free energy of ionic aqueous clusters evaluated by nonequilibrium computational methods	Hernández de la Peña L; Peslherbe GH;	20377185 CERMM
17	Mechanically induced generation of highly reactive excited-state oxygen molecules in cluster scattering	Nguyen TN; Timerghazin QK; Vach H; Peslherbe GH;	21322678 CERMM
18	From inert to explosive, the hydrolytic reactivity of R-NSO compounds understood: a computational study	Ivanova EV; Muchall HM;	21428403 CERMM
19	Conformational analysis of 18-azacrown-6 and its bonding with late first transition series divalent metals: insight from DFT combined with NPA and QTAIM analyses	Varadwaj PR; Varadwaj A; Peslherbe GH; Marques HM;	21961695 CERMM
20	Ammonium transporters achieve charge transfer by fragmenting their substrate	Wang S; Orabi EA; Baday S; Bernèche S; Lamoureux G;	22631217 CERMM
21	Effective simulations of gas diffusion through kinetically accessible tunnels in multisubunit proteins: O2 pathways and escape routes in T-state deoxyhemoglobin	Shadrina MS; English AM; Peslherbe GH;	22690872 CERMM
22	An electronic structure theory investigation of the physical chemistry of the intermolecular complexes of cyclopropenylidene with hydrogen halides	Varadwaj PR; Varadwaj A; Peslherbe GH;	22696309 CERMM
23	Can a single molecule of water be completely isolated within the subnano-space inside the fullerene C60 cage? A quantum chemical prospective	Varadwaj A; Varadwaj PR;	23090782 CERMM
24	Identification of a cholesterol-binding pocket in inward rectifier K(+) (Kir) channels	Fürst O; Nichols CG; Lamoureux G; D' Avanzo N;	25517146 CERMM
25	Molecular model of hemoglobin N from Mycobacterium tuberculosis bound to lipid bilayers: a combined spectroscopic and computational study	Jean-François Rhéault	25723781 CERMM
26	Mechanism of NH4(+) Recruitment and NH3 Transport in Rh Proteins	Sefer Baday	26190573 CERMM
27	Quaternary-Linked Changes in Structure and Dynamics That Modulate O2 Migration within Hemoglobin's Gas Diffusion Tunnels	Maria S Shadrina	26226318 CERMM
28	O2 and Water Migration Pathways between the Solvent and Heme Pockets of Hemoglobin with Open and Closed Conformations of the Distal HisE7	Maria S Shadrina	26226401 CERMM
29	Three-dimensional structure model and predicted ATP interaction rewiring of a deviant RNA ligase 2	Sandrine Moreira	26449279 CERMM
30	Polarizable Interaction Model for Liquid, Supercritical, and Aqueous Ammonia	Esam A Orabi	26583551 CERMM
31	Molecular Dynamics Investigation of Alkali Metal Ions in Liquid and Aqueous Ammonia	Esam A Orabi	26583725 CERMM
32	Simulation of Liquid and Supercritical Hydrogen Sulfide and of Alkali Ions in the Pure and Aqueous Liquid	Esam A Orabi	26588292 CERMM
33	Cation-π and π-π Interactions in Aqueous Solution Studied Using Polarizable Potential Models	Esam A Orabi	26592880 CERMM
34	Electric Field-Induced Nano-Assembly Formation: First Evidence of Silicon Superclusters with a Giant Permanent Dipole Moment	Jardali F; Tran J; Liège F; Florea I; Leulmi ME; Vach H;	37570492 CERMM
35	Identifying potential drug targets and candidate drugs for COVID-19: biological networks and structural modeling approaches	Selvaraj G; Kaliamurthi S; Peslherbe GH; Wei DQ;	33968364 CERMM
36	Salt-Dependent Interactions between the C-Terminal Domain of Osmoregulatory Transporter ProP of Escherichia coli and the Lipid Membrane	Ozturk TN; Culham DE; Tempelhagen L; Wood JM; Lamoureux G;	32838524 CERMM
37	An efficient method for indexing grazing-incidence X-ray diffraction data of epitaxially grown thin films	Simbrunner J; Schrode B; Domke J; Fritz T; Salzmann I; Resel R;	32356785 CERMM
38	Singlet exciton fission via an intermolecular charge transfer state in coevaporated pentacene-perfluoropentacene thin films	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 R;	31675857 CERMM
39	Genetic, Structural, and Functional Evidence Link TMEM175 to Synucleinopathies	Krohn L; Öztürk TN; Vanderperre B; Ouled Amar Bencheikh B; Ruskey JA; Laurent SB; Spiegelman D; Postuma RB; Arnulf I; Hu MTM; Dauvilliers Y; Högl B; Stefani A; Monaca CC; Plazzi G; Antelmi E; Ferini-Strambi L; Heidbreder A; Rudakou U; Cochen De Cock V; Young P; Wolf P; Oliva P; Zhang XK; Greenbaum L; Liong C; Gagnon JF; Desautels A; Hassin-Baer S; Montplaisir JY; Dupré N; Rouleau GA; Fon EA; Trempe JF; Lamoureux G; Alcalay RN; Gan-Or Z;	31658403 CERMM
40	Drude polarizable force field for cation-π interactions of alkali and quaternary ammonium ions with aromatic amino acid side chains	Orabi EA; Davis RL; Lamoureux G;	31652004 CERMM
41	Development of Semiempirical Models for Proton Transfer Reactions in Water	Shihao Wang	26588263 CERMM
42	Effect of Saturated Very Long-Chain Fatty Acids on the Organization of Lipid Membranes: A Study Combining (2)H NMR Spectroscopy and Molecular Dynamics Simulations	Adrian Paz Ramos	27351151 CERMM
43	Do Mammalian Cells Really Need to Export and Import Heme?	Prem Ponka	28254242 CERMM
44	Mechanism of the Nitric Oxide Dioxygenase Reaction of Mycobacterium tuberculosis Hemoglobin N	Lavinia A Carabet	28835102 CERMM
45	O4 -Alkylated-2-Deoxyuridine Repair by O6 -Alkylguanine DNA Alkyltransferase is Augmented by a C5-Fluorine Modification	Lauralicia Sacre	29243336 CERMM
46	Cation-π Interactions between Quaternary Ammonium Ions and Amino Acid Aromatic Groups in Aqueous Solution	Esam A Orabi	29397727 CERMM
47	Modeling Protein S-Aromatic Motifs Reveals Their Structural and Redox Flexibility	Esam A Orabi	29533644 CERMM
48	A Simple Additive Potential Model for Simulating Hydrogen Peroxide in Chemical and Biological Systems	Esam A Orabi	29630362 CERMM
49	Deep convolutional networks for quality assessment of protein folds	Georgy Derevyanko	29931128 CERMM
50	Indexing grazing-incidence X-ray diffraction patterns of thin films: lattices of higher symmetry	Simbrunner J; Hofer S; Schrode B; Garmshausen Y; Hecht S; Resel R; Salzmann I;	30996719 CERMM

Title:	Molecular Dynamics Investigation of Alkali Metal Ions in Liquid and Aqueous Ammonia
Authors:	Esam A Orabi
Link:	https://pubmed.ncbi.nlm.nih.gov/26583725/
DOI:	10.1021/ct4001069
Publication:	Journal of chemical theory and computation
Keywords:
PMID:	26583725	Category:	Date Added:	2015-11-20
Dept Affiliation:	CERMM 1 Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.

Description:

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 binding energies of M(+)(NH3)n (n = 2-4) and M(+)(NH3)n(H2O)m (n, m = 1-3 and n + m = 4) clusters and gives relative solvation free energies in liquid ammonia in good agreement with experimental data, without further adjustments. It also...

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