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Concordia University Concordia celebrates 50 years!
Concordia University Concordia celebrates 50 years!

Centre for Research in Molecular Modeling

Centre de recherche en modélisation moléculaire

Centre for Research in Molecular Modeling

Centre de recherche en modélisation moléculaire

Publications

Access some of our research publications, including journal papers, conference papers, and theses.

 
  1. Narayana, S.D.S., Premkumar, T., Sundararajan, V., Ravindran, R., Gunasekaran, S., Madathil, D., Kaliamurthi, S., Peslherbe, G.H., Selvaraj, G*., Lulu, S.S., 2024. Insights of dietary phytochemicals targeting Parkinson's disease key genes and pathways: A network pharmacology approach. Computers in Biology and Medicine, p.108195.
  2. Wei, D., Peslherbe, G.H., Selvaraj, G., Wang, Y., 2023. Advances in Drug Design and Development for Human Therapeutics Using Artificial Intelligence-II. Biomolecules, 13, 1735.
  3. Kaliamurthi, S., Selvaraj, G., Cho, W., Wei, DQ., Peslherbe, GH., “The Implication of miRNA signature in the characteristic features and diagnosis of lung cancer”, In: Interdisciplinary Cancer Research. Springer, 1-26. (2023). (Book Chapter).
  4. Wei, DQ.; Peslherbe, GH., Selvaraj, G., Wang, Y., “Advances in Drug Design and Development for Human Therapeutics Using Artificial Intelligence”, Biomolecules 12(12), 1846 (2022).
  5. Kaliamurthi, S.; Selvaraj, G.; Selvaraj, C.; Singh, S.K.; Wei, D.-Q.; Peslherbe, G.H., “Structure-Based Virtual Screening Reveals Ibrutinib and Zanubrutinib as Potential Repurposed Drugs against COVID-19”. International Journal of Molecular Sciences 22, 7071 (2021).
  6. Selvaraj, G.; Kaliamurthi, S.; Peslherbe, GH.; Wei DQ., “Are the allergic reactions of COVID-19 Vaccines caused by mRNA constructs or Nanocarriers? An Immunological Insight”, Interdisciplinary Sciences: Computational Life Sciences 13(2), 344-347 (2021).
  7. Selvaraj, G.; Kaliamurthi, S.; Peslherbe, GH., Wei DQ., “Identifying potential drug targets and candidate drugs for COVID-19: biological networks and structural modeling approaches” F1000Research 10, 127 (2021).
  8. Selvaraj, G.; Kaliamurthi, S.; Peslherbe, GH.; Wei DQ., “Application of artificial intelligence in drug repurposing: a mini-review”, Current Chinese Science, 1 (3), 334-345 (2021).
  9. Huang, S.; Wei, Y.K.; Kaliamurthi, S.; Cao, Y.; Nangraj, A.S.; Sui, X.; Chu, D; Wang, H.; Wei, D.Q.; Peslherbe, G.H.; Selvaraj, G.; Shi, J., “Circulating miR-1246 targeting UBE2C, TNNI3, TRAIP, UCHL1 Genes and key pathways as a potential biomarker for lung adenocarcinoma: Integrated biological network analysis”,  Journal of Personalized Medicine, 10(4), 162 (2020).
  10. Simbrunner, J.; Hofer, S.; Schrode, B.; Garmshausen, Y.; Hecht, S.; Resel, R.; Salzmann, I., "Indexing grazing-incidence X-ray diffraction patterns of thin films: lattices of higher symmetry", Journal of Applied Crystallography 52, 428 (2019).
  11. T. N.; Lamoureux, G., "Ion Permeation through ORAI Proteins", Biophysical Journal 116, 433A (2019).
  12. Orabi, E. A.; Peslherbe, G. H. , "Computational insight into hydrogen persulfide and a new additive model for chemical and biological simulations", Physical Chemistry Chemical Physics 21, 15988 (2019).
  13. Orabi, E. A.; English, A. M., "Expanding the range of binding energies and oxidizability of biologically relevant S-aromatic interactions: imidazolium and phenolate binding to sulfoxide and sulfone", Physical Chemistry Chemical Physics 21, 14620 (2019).
  14. Maiti, S.; Sedrakyan, T., "Fermionization of bosons in a flat band", Physical Review B  99 (2019).
  15. Issack, B. B.; Peslherbe, G. H., "Accuracy and precision of simulated free energies: water permeation of hydrated DPPC bilayers as a paradigm", Molecular Simulation 45, 466 (2019).
  16. Chen, M. T.; Hofmann, O. T.; Gerlach, A.; Broker, B.; Burker, C.; Niederhausen, J.; Hosokai, T.; Zegenhagen, J.; Vollmer, A.; Riegel, R.; Mullen, K.; Schreiber, F.; Salzmann, I.; Koch, N.; Zojer, E.; Duhm, S., "Energy-level alignment at strongly coupled organic-metal interfaces", Journal of Physics-Condensed Matter 31, 10 (2019).
  17. Sacre, L.; O'Flaherty, D. K.; Archambault, P.; Copp, W.; Peslherbe, G. H.; Muchall, H. M.; Wilds, C. J., "O-4-Alkylated-2-Deoxyuridine Repair by O-6-Alkylguanine DNA Alkyltransferase Is Augmented by a C5-Fluorine Modification". Chembiochem  19, 575-582 (2018).
  18. Orabi, E. A.; Lamoureux, G., "Cation-Pi Interactions between Quaternary Ammonium Ions and Amino Acid Aromatic Groups in Aqueous Solution". Journal of Physical Chemistry B  122, 2251-2260 (2018).
  19. Orabi, E. A.; English, A. M., "Modeling Protein S-Aromatic Motifs Reveals Their Structural and Redox Flexibility". Journal of Physical Chemistry B  122, 3760-3770 (2018).
  20. Orabi, E. A.; English, A. M., "A Simple Additive Potential Model for Simulating Hydrogen Peroxide in Chemical and Biological Systems". Journal of Chemical Theory and Computation  14, 2808-2821 (2018).
  21. Jahangiri, S.; Timerghazin, Q. K.; Jiang, H.; Peslherbe, G. H.; English, A. M., "Dramatic C-C Bond Activation on Protonation of the Persistent Nitroxyl Radical Tempo Center Dot". International Journal of Mass Spectrometry  429, 182-188 (2018).
  22. Parmar, V.; English, A. M.; Peslherbe, G. H., "Distinct Structural Dynamics of Monomeric, Dimeric and Tetrameric Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) Illuminate Its Multiple Functions". Protein Science  26, 52-53 (2017).
  23. Ozturk, T. N.; Lamoureux, G., "Molecular Modelling of Hexamer and Tetramer Forms of the Orai Calcium Channel". Biophysical Journal  112, 506A-506A (2017).
  24. Ozturk, T. N.; Lamoureux, G., "Molecular Modelling of the Orai Calcium Channels". Protein Science  26, 48-48 (2017).
  25. Orabi, E.; English, A., "Modeling Cysteine and Methionine Binding to Aromatic Residues". Protein Science  26, 52-52 (2017).
  26. Ebert, M.; Espinola, J. G.; Lamoureux, G.; Pelletier, J. N., "Substrate-Specific Screening for Mutational Hotspots Using Biased Molecular Dynamics Simulations". Acs Catalysis  7, 6786-6797 (2017).
  27. Ebert, M.; Durr, S.; Houle, A. A.; Lamoureux, G.; Pelletier, J., "Shifting the Boundaries of Experimental Studies in Engineering Enzymatic Functions: Combining the Benefits of Computational and Experimental Methods". Protein Science  26, 58-58 (2017).
  28. Derevyanko, G.; Lamoureux, G.; Grudinin, S., "Deep Convolutional Networks for Protein Structure Quality Assessment". Protein Science  26, 111-111 (2017).
  29. Sivakumar, R.; Askari, M. S.; Woo, S.; Madwar, C.; Ottenwaelder, X.; Bohle, D. S.; Cuccia, L. A., "Homochiral Crystal Generation Via Sequential Dehydration and Viedma Ripening". Crystengcomm  18, 4277-4280 (2016).
  30. Shadrina, M. S.; English, A. M.; Peslherbe, G. H., "Benchmarking Rapid Tles Simulations of Gas Diffusion in Proteins: Mapping O-2 Migration and Escape in Myoglobin as a Case Study". Journal of Chemical Theory and Computation  12, 2038-2046 (2016).
  31. Ramos, A. P.; Lague, P.; Lamoureux, G.; Lafleur, M., "Effect of Saturated Very Long-Chain Fatty Acids on the Organization of Lipid Membranes: A Study Combining H-2 Nmr Spectroscopy and Molecular Dynamics Simulations". Journal of Physical Chemistry B  120, 6951-6960 (2016).
  32. Noce, A. A.; Peslherbe, G. H., "Transitioning to a Hydrogen Economy: Kinetic Isotope Effects of Stratospheric Monodeuterated Hydrogen Accumulation". International Journal of Hydrogen Energy  41, 15373-15387 (2016).
  33. Huang, Z.; Askari, M. S.; Esguerra, K. V. N.; Dai, T. Y.; Kwon, O.; Ottenwaelder, X.; Lumb, J. P., "A Bio-Inspired Synthesis of Oxindoles by Catalytic Aerobic Dual C-H Functionalization of Phenols". Chemical Science  7, 358-369 (2016).
  34. Hebert, M.; Petiot, P.; Benoit, E.; Dansereau, J.; Ahmad, T.; Le Roch, A.; Ottenwaelder, X.; Gagnon, A., "Synthesis of Highly Functionalized Triarylbismuthines by Functional Group Manipulation and Use in Palladium- and Copper-Catalyzed Arylation Reactions". Journal of Organic Chemistry  81, 5401-5416 (2016).
  35. Ebert, M. C. C. J. C.; Durr, S. L.; Houle, A. A.; Lamoureux, G.; Pelletier, J. N., "Evolution of P450 Monooxygenases toward Formation of Transient Channels nad Exclusion of Nonproductive Gases", Acs Catalysis 6, 7426 (2016).
  36. Dolgonos, G. A.; Peslherbe, G. H., "Can two H-2 molcules be inserted into C-60 - an accurate first-principles exploration of structural, energetic and vibrational properties of the 2H(2)@C-60 complex". Chemical Physics Letters 663, 104-110 (2016).
  37. Khavryuchenko, O. V.; Peslherbe, G. H., "Spin Catalysis over Conductive Solids: Enhancing the Rate of Model C-C Bond Cracking over Carbon Nanoparticles". CHEMCATCHEM 8, 3156-3160 (2016).
  38. Huang, Z.; Askari, M. S.; Esguerra, K. V. N.; Dai, T. Y.; Kwon, O.; Ottenwaelder, X.; Lumb, J. P., “A Bio-Inspired Synthesis of Oxindoles by Catalytic Aerobic Dual C-H Functionalization of Phenols”. Chemical Science 7, 358-369 (2016).
  39. Noce, A. A.; Peslherbe, G. H., “Transitioning to a Hydrogen Economy: Kinetic Isotope Effects of Stratospheric Monodeuterated Hydrogen Accumulation”. International Journal of Hydrogen Energy 41, 15373-15387 (2016).
  40. Ramos, A. P.; Lague, P.; Lamoureux, G.; Lafleur, M., “Effect of Saturated Very Long-Chain Fatty Acids on the Organization of Lipid Membranes: A Study Combining H2 Nmr Spectroscopy and Molecular Dynamics Simulations”. Journal of Physical Chemistry B 120, 6951-6960 (2016).
  41. Shadrina, M. S.; English, A. M.; Peslherbe, G. H., “Benchmarking Rapid Tles Simulations of Gas Diffusion in Proteins: Mapping O2 Migration and Escape in Myoglobin as a Case Study”. Journal of Chemical Theory and Computation 2016, 12, 2038-2046 (2016).
  42. Baday, S.; Orabi, E. A.; Wang, S.; Lamoureux, G.; Berneche, S., “Mechanism of Nh4+ Recruitment and Nh3 Transport in Rh Proteins”. Structure 23, 1550-1557 (2015).
  43. Issack, B. B.; Peslherbe, G. H., “Effects of Cholesterol on the Thermodynamics and Kinetics of Passive Transport of Water through Lipid Membranes”. Journal of Physical Chemistry B 119, 9391-9400 (2015).
  44. Jahangiri, S.; Legris-Falardeau, V.; Peslherbe, G. H., “Computational Investigation of the Hydration of Alkyl Diammonium Cations in Water Clusters”. Chemical Physics Letters 621, 85-90 (2015).
  45. Khavryuchenko, O. V.; Peslherbe, G. H.; Hagelberg, F., “Spin Filter Circuit Design Based on a Finite Single-Walled Carbon Nanotube of the Zigzag Type”. Journal of Physical Chemistry C 119, 3740-3745 (2015).
  46. Khavryuchenko, O. V.; Wang, L. D.; Mitoraj, D.; Peslherbe, G. H.; Beranek, R., “Enabling Visible-Light Water Photooxidation by Coordinative Incorporation of Co(Ii/Iii) Cocatalytic Sites into Organic-Inorganic Hybrids”: Quantum Chemical Modeling and Photoelectrochemical Performance. Journal of Coordination Chemistry 68, 3317-3327 (2015).
  47. Mak, C. C.; Peslherbe, G. H., “New Developments in First-Principles Excited-State Dynamics Simulations: Unveiling the Solvent Specificity of Excited Anionic Cluster Relaxation and Electron Solvation”. Molecular Simulation 41, 156-167 (2015).
  48. Moreira, S.; Noutahi, E.; Lamoureux, G.; Burger, G., “Three-Dimensional Structure Model and Predicted Atp Interaction Rewiring of a Deviant Rna Ligase 2”. Bmc Structural Biology 15 (2015).
  49. Rheault, J. F.; Gagne, E.; Guertin, M.; Lamoureux, G.; Auger, M.; Lague, P., “Molecular Model of Hemoglobin N from Mycobacterium Tuberculosis Bound to Lipid Bilayers: A Combined Spectroscopic and Computational Study”. Biochemistry 54, 2073-2084 (2015).
  50. Shadrina, M. S.; Peslherbe, G. H.; English, A. M., “Quaternary-Linked Changes in Structure and Dynamics That Modulate O2 Migration within Hemoglobin's Gas Diffusion Tunnels”. Biochemistry 54, 5268-5278 (2015).
  51. Shadrina, M. S.; Peslherbe, G. H.; English, A. M., “O2 and Water Migration Pathways between the Solvent and Heme Pockets of Hemoglobin with Open and Closed Conformations of the Distal Hise7”. Biochemistry 54, 5279-5289 (2015).
  52. G. A. Dolgonos and G. H. Peslherbe, "Encapsulation of diatomic molecules in fullerene C-60: implications for their main properties", Physical Chemistry Chemical Physics 16, 26294 (2014).
  53. S. Baday, S. Wang, G. Lamoureux, and S. Berneche, "Different hydration patterns in the pores of AmtB and RhCG could determine their transport mechanisms", Biochemistry 52, 7091 (2013).
  54. S. Jahangiri, G. Dolgonos, T. Frauenheim, and G. H. Peslherbe, "Parameterization of halogens for the density-functional tight-binding description of halide hydration", Journal of Chemical Theory and Computation 9, 3321 (2013).
  55. S. Jahangiri, S. M. Mercer, P. G. Jessop, and G. H. Peslherbe, "Computational investigation of the hydration of alkyl diammonium chlorides and their effect on THF/water phase separation", Journal of Physical Chemistry B 117, 8010 (2013).
  56. C. C. Mak, Q. K. Timerghazin, and G. H. Peslherbe, "Photoexcitation and charge-transfer-to-solvent relaxation dynamics of the I (CH3CN) Complex", Journal of Physical Chemistry A 117, 7595 (2013).
  57. A. G. Moiseev, E. A. Margulies, J. A. Schneider, F. Belanger-Gariepy, and D. F. Perepichka, "Protecting the triplet excited state in sterically congested platinum porphyrin", Dalton Transactions 43, 2676 (2014).
  58. L. Zhang, H. M. Muchall, and G. H. Peslherbe, "Substituent effects in the absorption spectra of phenol radical species: Origin of the redshift caused by 3,5-dimethoxyl substitution", Photochemistry and Photobiology 89, 536 (2013).
  59. E. A. Orabi and G. Lamoureux, “Molecular dynamics investigation of alkali metal ions solvated in liquid and aqueous ammonia”. Journal of Chemical Theory and Computation 9, 2324–2338 (2013).
  60. M.S. Shadrina, A.M. English and G.H. Peslherbe, “Effective simulations of gas diffusion through kineticlly accessible tunnels in multi-subunit proteins: O2 pathways and escape routes in T-state deoxyhemoglobin”, Journal of the American Chemical Society 134, 11177−11184 (2012).
  61. O.V. Khavryuchenko, N.V. Stus and G.H. Peslherbe, “Structural and spin properties of (PO2)4(WO3)8 model bronzes from density-functional theory calculations”, Solid State Communications 152, 2138-2141 (2012).
  62. E. A. Orabi and G. Lamoureux, “Polarizable interaction model for liquid, supercritical, and aqueous ammonia”. Journal of Chemical Theory and Computation 9, 2035–2051 (2013).
  63. G. Lamoureux and E.A. Orabi, ”Molecular modeling of cation–π interactions”. Molecular Simulation 38, 704–722 (2012).
  64. P.R. Varadwaj, A. Varadwaj and G.H. Peslherbe, “An electronic structure theory investigation of the physical chemistry of the intermolecular complexes of cyclopropenylidene with hydrogen halides”, Journal of Computational Chemistry 33, 2073 (2012).
  65. S. Wang, E. A. Orabi, S. Baday, S. Bernèche and G. Lamoureux, “Ammonium transporters achieve charge transfer by fragmenting their substrate”, Journal of the American Chemical Society 134, 10419–10427 (2012).
  66. E. A. Orabi and G. Lamoureux. “Cation–π and π–π interactions in aqueous solutions studied using polarizable potential models”. Journal of Chemical Theory and Computation 8, 182–193 (2012).
  67. L. Zhang, H.M. Muchall, G.H. Peslherbe, “Substituent effects in the absorption spectra of phenol radical species: Origin of the red shift caused by 3,5-dimethoxyl substitution”, Photochemistry Photobiology 89, 536-544 (2012).
  68. C.C. Mak, Q.K. Timerghazin and G.H. Peslherbe, “Photoinduced electron transfer and solvation dynamics in aqueous clusters: Comparison of the photoexcited iodide-water pentamer and the water pentamer anion”, Physical Chemistry Chemical Physics 14, 6250 (2012).
  69. S.M. Mercer, T. Robert, D.V. Dixon, C.-S. Chen, Z.G. Rahami, J.R. Harjani, S. Jahangiri, G.H. Peslherbe and P.G. Jessop, “Design, synthesis, and solution behavior of small polyamines as switchable water additives”, Green Chemistry 14, 832 (2012).
  70. S. Wang, E.A. Orabi, S. Baday, S. Bernèche, and G. Lamoureux, "Ammonium Transporters Achieve Charge Transfer by Fragmenting Their Substrate". Journal of the American Chemical Society, Article ASAP (2012).
  71. E A. Orabi and G. Lamoureux, " Cation–π and π–π interactions in aqueous solutions studied using polarizable potential models", Journal of Chemical Theory and Computation 8, 182–193 (2012).
  72. P.R. Varadwaj, A. Varadwaj and G.H. Peslherbe, “An Electronic Structure Theory Investigation of the Physical Chemistry of the Intermolecular Complexes of Cyclopropenylidene with Hydrogen Halides”, Journal of Computational Chemistry 33, 2073-2082 (2012).
  73. M. Shadrina, A.M. English and G.H. Peslherbe, "Effective Simulations of Gas Diffusion Through Kinetically Accessible Tunnels in Multisubunit Proteins: O2 Pathways and Escape Routes in T-state Deoxyhemoglobin", Journal of the American Chemical Society 134, 11177-11184 (2012).
  74. C.C. Mak, Q.K. Timerghazin and G.H. Peslherbe, “Photoinduced Electron Transfer and Solvation Dynamics in Aqueous Clusters: Comparison of the Photoexcited  Iodide-Water Pentamer and the Water Pentamer Anion”, special issue on Ultrafast Chemical Dynamics, Physical Chemistry Chemical Physics 14, 6250-6258 (2012).
  75. S M. Mercer, T. Robert, D.V. Dixon, C.-S. Chen, Z.G. Rahami, J.R. Harjani, S. Jahangiri, G.H. Peslherbe and P.G. Jessop, “Design, Synthesis, and Solution Behavior of Small Polyamines as Switchable Water Additives”, Green Chemistry 14, 832-839 (2012).
  76. G. Lamoureux and E. A. Orabi, " Molecular modeling of cation–π interactions", Molecular Simulation, in press (2012).
  77. Q.K. Timerghazin, I. Rizvi and G.H. Peslherbe, “Can a Dipole-Bound Electron Form a Pseudo-Atom? An Atoms-In-Molecules Study of the Hydrated Electron”, special issue honoring Richard Bader, Journal of Physical Chemistry A 115, 13201–13209 (2011).
  78. P.R. Varadwaj, A. Varadwaj, G H. Peslherbe and H.M. Marques, “A 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”, special issue honoring Richard Bader, Journal of Physical Chemistry A 115, 13180–13190 (2011).
  79. Y. Fang, P. Nguyen, O. Ivasenko, M.P. Aviles, E. Kebede, M.S. Askari, X. Ottenwaelder, U. Ziener, O. Siri, L.A. Cuccia, “Charge-Assisted Hydrogen Bond-Directed Self-Assembly of an Amphiphilic Zwitterionic Quinonemonoimine at the Liquid-Solid Interface”, Chemical Communications  47, 11255-11257 (2011).
  80. O.V. Khavryuchenko, V.D. Khavryuchenko, V.V. Lisnyak and G.H. Peslherbe, “A Density-Functional Theory Investigation of the Electronic Structure of the Active Carbon Graphite-like and Amorphous Domains”, Chemical Physics Letters 513, 261–266 (2011).
  81. H.M. Muchall, “Computational Insight into the Carbenic Character of Nitrilimines from a Reactivity Perspective”, Journal of Physical Chemistry A 115, 13694-13705 (2011).
  82. G A. Dolgonos and G H. Peslherbe, “Conventional and Density-Fitting Local Møller–Plesset Theory Calculations of C60 and its Endohedral H2@C60 and 2H2@C60 Complexes”, Chemical Physics Letters 513, 236-240 (2011).
  83. T.-N.V. Nguyen, Q.K. Timerghazin, H. Vach and G.H. Peslherbe, “Mechanically-Induced Generation of Highly Reactive Excited-State Oxygen Molecules in Clusters”, Journal of Chemical Physics 134, 064305 (2011).
  84. L. Chaloner, M.S. Askari, A. Kutteh, S. Schindler, X. Ottenwaelder, "Formation and Reactivity of a Biomimetic Hydroperoxocopper(II) Cryptate", European Journal of Inorganic Chemistry  27, 4204-4211 (2011).
  85. M.S. Askari, B. Girard, M. Murugesu, X. Ottenwaelder, "The Two Spin States of an End-On Copper(II)-Superoxide Mimic", Chemical Communications 28, 8055-8057 (2011).
  86. P.R.N. Kamya and H.M. Muchall, “Revisiting the Effects of Sequence and Structure on the Hydrogen Bonding and pi-Stacking Interactions in Nucleic Acids”, Journal of Physical Chemistry A 115, 12800-12808 (2011).
  87. Lei Zhang,* Gilles H. Peslherbe and Heidi M. Muchall, “A General Measure of Conjugation in Biphenyls and Their Radical Cations”, special issue Honoring Russ Boyd, Canadian Journal of Chemistry 88, 1175-1185 (2010).
  88. Samir H. Mushrif,* Alejandro D. Rey and Gilles H. Peslherbe, “Energetics and Dynamics of Hydrogen Adsorption, Desorption and Migration on a Carbon-Supported Palladium Cluster”, Journal of Materials Chemistry 20, 10503-10510 (2010).
  89. Samir H. Mushrif,* Alejandro D. Rey and Gilles H. Peslherbe, “Towards Understanding Palladium Doping of Carbon Supports: a First-Principles Molecular Dynamics Investigation”, Communication, Journal of Materials Chemistry 20, 6859-6862 (2010).
  90. Lisandro Hernández de la Peña* and Gilles H. Peslherbe, “Quantum Effects on the Free Energy of Ionic Aqueous Clusters Evaluated by Nonequilibrium Computational Methods”, Journal of Physical Chemistry B 114, 5404-5411 (2010).
  91. Samir H. Mushrif,* Alejandro D. Rey and Gilles H. Peslherbe, “First-Principles Calculation of the Palladium (II) Acetylacetonate Crystal Structure”, Chemical Physics Letters 465, 63-66 (2008).
  92. R. van Zon, L. Hernandez de la Pena, G. H. Peslherbe and J. Schofield, "Quantum free-energy differences from nonequilibrium path integrals. I. Methods and numerical application." Phys. Rev. E, 78, 041103/1-041103/11, (2008).
  93. S. M. Mushrif, A. D. Rey and G. H. Peslherbe, "First-principles calculations of the palladium(II) acetylacetonate crystal structure." Chem. Phys. Lett., 465, 63-66, (2008).
  94. Q. K. Timerghazin, G. H. Peslherbe and A. M. English, "Structure and stability of HSNO, the simplest S-nitrosothiol." Phys. Chem. Chem. Phys., 10, 1532-1539, (2008).
  95. Q. K. Timerghazin, A. M. English and G. H. Peslherbe, "On the multireference character of S-nitrosothiols: A theoretical study of HSNO." Chem. Phys. Lett., 454, 24-29, (2008).
  96. D. M. Koch, C. Toubin, G. H. Peslherbe and J. T. Hynes, "A Theoretical Study of the Formation of the Aminoaetonitrile Precursor of Glycine on Icy Grain in the Interstellar Medium." J. Phys. Chem. C, 112, 2972-2980, (2008).
  97. D. M. Koch and G. H. Peslherbe, "Importance of Polarization in Quantum Mechanics/Molecular Mechanics Descriptions of Electronic Excited States: NaI(H2O)n Photodissociation Dynamics as a Case Study." J. Phys. Chem. B, 112, 636-649, (2008).
  98. T.-N. V. Nguyen, S. R. Hughes and G. H. Peslherbe, "Microsolvation of the sodium and iodide ions and their ion pair in acetonitrile clusters: a theoretical study." J. Phys. Chem. B, 112, 621-635, (2008).
  99. Q. K. Timerghazin and G. H. Peslherbe, "Electronic Structure of the Acetonitrile and Acetonitrile Dimer Anions: A Topological Investigation." J. Phys. Chem. B, 112, 520-528, (2008).
  100. R. C. Mawhinney, G. H. Peslherbe and H. M. Muchall, "Characterizing Nitrilimines with Nuclear Magnetic Resonance Spectroscopy. A Theoretical Study." J. Phys. Chem. B, 112, 650-655, (2008).
  101. G. A. Dolgonos and G. H. Peslherbe, "Calculations of the C2 fragmentation energies of higher fullerenes C80 and C82." J. Mol. Mod., 13, 981-986, (2007).
  102. D. M. Koch, C. Toubin, S. Xu, G. H. Peslherbe and J. T. Hynes, "Concerted Proton-Transfer Mechanism and Solvation Effects in the HNC/HCN Isomerization on the Surface of Icy Grain Mantles in the Interstellar Medium." J. Phys. Chem.C, 111, 15026-15033, (2007).
  103. Q. K. Timerghazin and G. H. Peslherbe, "Non-nuclear attractor of electron density as a manifestation of the solvated electron." J. Chem. Phys. , 127, 064108/1-064108/4, (2007).
  104. Q. K. Timerghazin, G. H. Peslherbe and A. M. English. "Resonance Description of S-Nitrosothiols: Insights into Reactivity." Org. Lett., 9, 3049-3052, (2007).
  105. H. Vach, T.-N. V. Nguyen, Q. K. Timerghazin and G. H. Peslherbe, "Nonadiabatic Ladder Climbing during Molecular Collisions.", Phys.l Rev. Lett., 97, 143402/1-143402/4, (2006).
  106. G. Dolgonos, O. Lukin, M. Elstner, G. H. Peslherbe and J. Leszczynski. "Toward a Reversible Isolation of a C20 Fullerene Inside a Tetraureacalix[4]arene Dimer. A Theoretical Study.", J. Phys. Chem. A , 110, 9405-9410, (2006).
  107. G. H. Peslherbe, Q. K. Timerghazin, and D. M. Koch, "First-principles molecular and reaction dynamics simulations: application to the structure, thermodynamics and photochemistry of ionic aqueous clusters." Lecture Series on Computer and Computational Sciences, 4 A(Advances in Computational Methods in Sciences and Engineering), 998-1001, (2005).
  108. L. Zhang, G. H. Peslherbe and H. M. Muchall, "Ultraviolet absorption spectra of substituted phenols: a computational study." Photochem. Photobio. 82, 324-331, (2006).
  109. Q. K. Timerghazin, D. M. Koch and G. H. Peslherbe, "Accurate ab initio potential for the Na+I.bul. complex.". J. Chem. Phys. 124, 034313/1-034313/10, (2006).
  110. D.M. Koch, Q. K. Timerghazin, G. H. Peslherbe, B. M. Ladanyi and J. T. Hynes, "Nonadiabatic Trajectory Studies of NaI(H2O)n Photodissociation Dynamics.", J. Phys. Chem. A, 110, 1438-1454, (2006).
  111. R. C. Mawhinney, H. M. Muchall and G. H. Peslherbe, "A computational study of the 1,3-dipolar cycloaddition reaction mechanism for nitrilimines.", Can. J. Chem. 83, 1615-1625, (2005).
  112. P. Larregaray and G. H. Peslherbe, "On the Statistical Nature of Collision and Surface-Induced Dissociation: A Theoretical Investigation of Aluminum Clusters., J. Phys. Chem. A 110, 1658-1665, (2006).
  113. P. G. Loncke and G. H. Peslherbe, "Substituent effects and the role of negative hyperconjugation in siloxycarbene rearrangements.", Org. & Biomol. Chem. 3, 2191-2201 (2005).
  114. S.R. Hughes, T.-N.V. Nguyen, J.A. Capobianco and G. H. Peslherbe, "A theoretical study of trivalent lanthanide ion microsolvation in water clusters from first principles.", Int. J. Mass Spec., 241, 283-294, (2005).
  115. G. A. Dolgonos and G. H. Peslherbe, "The unimolecular C2 fragmentation of C82: a computational study.", Int. J. Mass Spec., 241, 261-269, (2005).
  116. G. A. Dolgonos and G. H. Peslherbe, "A computational study of the C2 fragmentation energy of C80.", Chem. Phys. Lett., 398(1-3), 217-223, (2004).
    R. C. Mawhinney and G.Schreckenbach, "NMR Quantum Computing: Applying Theoretical Methods to Designing Enhanced Systems", Magn. Reson. Chem., 42, S88-S98, (2004).
  117. R. C. Mawhinney, H. M. Muchall and G. H. Peslherbe, "The Electronic Structure of Nitrilimines Revisited", J. Chem. Soc. Chem. Commun., 1862-1863, (2004).
    R. C. Mawhinney, H. M. Muchall and J.Lessard, "A Theoretical Analysis of the Conformational Behaviour of Substituted Methylenecyclohexanes", Can. J. Chem., 81, 1101-1107, (2003).
  118. Q. K. Timerghazin, G. H. Peslherbe, "Further Insight into the Relaxation Dynamics of Photoexcited I-(H2O)n Clusters.", J. Am. Chem. Soc., 125, 9904, (2003).
  119. T.-N. Nguyen, D.M. Koch, G.H. Peslherbe, H. Vach "Molecular dissociation and vibrational excitation in the surface scattering of (N2)n and (O2)n clusters." J. Chem. Phys. 119, 7451-7460, (2003).
  120. T.-N.V. Nguyen, G.H. Peslherbe, "Microsolvation of Alkali and Halide Ions in Acetonitrile Clusters". J. Phys. Chem. A 107, 1540-1550, (2003).
  121. Q. K. Timerghazin, G. H. Peslherbe, "First-Principles Excited-State Molecular Dynamics Simulations: Application To Cluster Photochemistry.", Proceedings of the The 17th Annual International Symposium on High Performance Computing Systems and Applications, Ed. D. Sénéchal, NRC Research Press, Ottawa, 2003.
  122. Q. K. Timerghazin, T.-N. Nguyen, G. H. Peslherbe, "Asymmetric solvation revisited: The importance of hydrogen bonding in iodide-acetonitrile clusters", J. Chem. Phys., 116, 6867, (2002).
  123. Q. K. Timerghazin, G. H. Peslherbe, "Theoretical Investigation of Charge Transfer to Solvent in Photoexcited Iodide-Acetonitrile Clusters", Chem. Phys. Lett., 354, 31, (2002).
  124. N. Chaabane, G. Jundt, H. Vach, D.M. Koch, G.H. Peslherbe, "Cage effects and rotational hindrance in the surface scattering of large (N2)n clusters". Int. J. Mass Spectrom. 220, 159-170, (2002).
  125. P.G. Loncke, T.A. Gadosy and G.H. Peslherbe, "A Theoretical Study of the Mechanism of 1,2-Migrations in Methoxysiloxycarbenes", Can. J. Chem., 80, 302-314 (2002).
  126. D.M. Koch, G.H. Peslherbe, "On the transition from surface to interior solvation in iodide-water clusters" Chem. Phys. Lett. 359, 381-389, (2002).
  127. P.G. Loncke, T.A. Gadosy and G.H. Peslherbe, "Investigation of the Mechanism of 1,2 Migrations in Methoxysiloxycarbenes with the Electron Localization Function", Arkivoc, special issue honoring O.S. Tee, 2001.
  128. N. Chaâbane, H. Vach and G.H. Peslherbe, "Complex Dynamics During the Si+ + H2 Reaction", J. Noncryst. Solids., 299-302, 42-47 (2002).
    D.M. Koch, G.H. Peslherbe and H. Vach, "Mechanism of Translational and Rotational Energy Transfer in (N2)n Cluster Surface Scattering", J. Chem. Phys. 115, 7685-7696 (2001).
  129. N. Chaabane, H. Vach and G.H. Peslherbe, "A Semiempirical Direct Dynamics Trajectory Study of the Si+ (2P) + H2 -> SiH+ + H Reaction", Technical Proceedings of the Fourth International Conference on Modeling and Simulation of Microsystems 4, 434-437 (2001).
  130. D.M. Koch, N.H. Khieu and G.H. Peslherbe, "Ab Initio Studies of the Glyoxal Unimolecular Dissociation Pathways", J. Phys. Chem. A 105, 3598-3604 (2001).
    H.M. Muchall. The Anti-Hydrogen Bond in Aromatic N-Sulfinyl Amines with ortho H atoms. J. Phys. Chem. A, 105, 632 (2001).

 

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