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Publications by D. R. Salahub

Refereed Journal Publications

    2018

  1. S. Ahmadi, L. Barrios, M. Chehelamirani, J. Hostas, S. Jalife and D. R. Salahub, Multiscale modeling of enzymes: QM-cluster, QM/MM, and QM/MM/MD – a tutorial review, International Journal of Quantum Chemistry 118(9): e25558 (34 pp.), 17 January 2018. (Special issue in honour of Nino Russo, Early View (2017)).

  2. 2017

  3. H. R. Zhekova, V. Ngo, M. C. da Silva, D. R. Salahub and S. Y. Noskov, Selective ion binding and transport by membrane proteins – A computational perspective, Coordination Chemistry Reviews 345: 108 - 136, 15 August 2017. (Special issue on Chemical Bonding in Inorganic Specials "State of Art" Coordination Chemistry Review, 50 Years of Progress).

  4. P. Piazzetta, T. Marino, N. Russo and D. R. Salahub, The role of metal substitution in the promiscuity of natural and artificial carbonic anhydrases, Coordination Chemistry Reviews 345: 73 - 85, 15 August 2017. (Special issue on Chemical Bonding in Inorganic Specials "State of Art" Coordination Chemistry Review, 50 Years of Progress).

  5. X.-J. Wu, J.-M. Teuler, F. Cailliez, C. Clavaguéra, D. R. Salahub and A. de la Lande, Simulating electron dynamics in polarizable environments, Journal of Chemical Theory and Computation 13(9): 3985 - 4002, 24 July 2017.

  6. M. Chehelamirani and D. R. Salahub, Effect of dispersion corrections on Covalent and Non-covalent Interactions in DFTB Calculations, Structural Chemistry 28(5): 1399 - 1407, 8 June 2017.

  7. X.-H. Li, M. C. da Silva and D. R. Salahub, First-principles calculations of the structural, mechanical, electronic and bonding properties of (CrB2)n CrAl with n = 1, 2, 3, Journal of Alloys and Compounds 698: 291 - 303, 25 March 2017.

  8. P. Piazzetta, T. Marino, N. Russo and D. R. Salahub, Explicit water molecules play a key role in the mechanism of rhodium-substituted human carbonic anhydrase, ChemCatChem 9: 1047 - 1053, 15 February 2017.

  9. M. Chehelamirani, M. C. da Silva and D. R. Salahub, Electronic properties of carbon nanotubes complexed with a DNA nucleotide, Physical Chemistry Chemical Physics 19(10): 7333 - 7342, 13 February 2017.

  10. 2016

  11. X.-C. Liu, M. Wahiduzzaman, A. F. Oliveira, T. Heine and D. R. Salahub, Density-functional-based tight-binding parameterization of Mo, C, H, O and Si for studying hydrogenation reactions on molybdenum carbide, Theoretical Chemistry Accounts 135: 168 (14 pp.), 20 June 2016.

  12. W. Li, S. G. Srinivasan, D. R. Salahub and T. Heine, Ni on the CeO2 (110) and (100) surfaces: adsorption vs. substitution effects on the electronic and geometric structures and oxygen vacancies, Physical Chemistry Chemical Physics 18(16): 11139 - 11149, 20 March 2016.

  13. 2015

  14. N. Manin, I. Zdravkovic, M. C. da Silva, O. Eliseeva, A. Dyshin, O. Yasar, D. R. Salahub, A. M. Kolker, M. G. Kiselev and S. Y. Noskov, LiCl solvation in N-methyl-Acetamide (NMA) as a model for understanding of Li+ binding to amide plane, Physical Chemistry Chemical Physics 18(5): 4191 - 4200, 7 December 2015.

  15. V. Ngo, M. Silva, M. Kubilius, H. Li, M. Elstner, B. Roux, Q. Cui, D. R. Salahub and S. Y. Noskov, Quantum effects in cation interactions with first and second coordination shell ligands in metalloproteins, Journal of Chemical Theory and Computation 11(10): 4992 - 5001, 22 September 2015.

  16. A. de la Lande, V. Moliner and D. R. Salahub, Editorial - Measurement and prediction of quantum coherence effects in biological processes, Physical Chemistry Chemical Physics 17: 30772 - 30774, 17 September 2015.

  17. A. de la Lande, N. Gillet, S.-F. Chen and D. R. Salahub, Progress and challenges in simulating and understanding electron transfer in proteins, Archives of Biochemistry and Biophysics 582: 28 - 41, 15 September 2015. special issue on “Computer simulations of proteins, from structure to function”.

  18. P. Piazzetta, T. Marino, N. Russo and D. R. Salahub, Direct hydrogenation of carbon dioxide by an artificial reductase obtained by substituting rhodium for zinc in the carbonic anhydrase catalytic center. A mechanistic study, ACS Symposium Series 5(9): 5397 - 5409, 5 August 2015.

  19. X.-C. Liu and D. R. Salahub, Application of topological analysis of the electron localization function to the complexes of molybdenum carbide nanoparticles with unsaturated hydrocarbons, Canadian Journal of Chemistry 94(4): 282 - 292, 10 July 2015. (Calgary Special Issue).

  20. D. R. Salahub, S. Y. Noskov, B. B. Lev, R. Zhang, V. Ngo, A. Goursot, P. Calaminici, A. M. Köster, A. Alvarez-Ibarra, D. Mejía-Rodríguez, J. Řezáč, F. Cailliez and A. de la Lande, QM/MM calculations with deMon2k, Molecules 20(3): 4780 - 4812, 16 March 2015.

  21. X.-C. Liu and D. R. Salahub, Molybdenum carbide nanocatalysts at work in the in-situ environment: a DFTB and QM(DFTB)/MM study, Journal of the American Chemical Society 137(12): 4249 - 4259, 16 March 2015.

  22. H. Li, V. Ngo, M. C. da Silva, D. R. Salahub, K. Kallahan, B. Roux and S. Y. Noskov, Representation of ion-protein interactions using the Drude polarizable force-field, Journal of Physical Chemistry B special issue: A - P, 10 January 2015.

  23. 2014

  24. R. Zhang, A. Bhattacharjee, M. J. Field and D. R. Salahub, Multiple proton relay routes in the reactionmechanism of RNAP II: Assessing the effect of structural model, Proteins 83(2): 268 - 281, 18 December 2014.

  25. C. de Oliviera, D. R. Salahub, H. de Abreu and H. A. Duarte, Native defects in α-Mo2C: Insights from first-principles calculations, Journal of Physical Chemistry C 118(44): 25517 - 25524, 9 October 2014.

  26. 2013

  27. X.-C. Liu, A. Tkalych, B. Zhou and D. R. Salahub, Adsorption of hexacyclic C6H6, C6H8, C6H10 and C6H12 on a Mo-terminated α-Mo2C (0001) surface, Journal of Physical Chemistry C 117(14): 7069 - 7080, 19 March 2013.

  28. F. Ahmed, R. Miura, N. Hatakeyama, H. Takaba, A. Miyamoto and D. R. Salahub, Quantum chemical molecular dynamics study of the water-gas shift reaction on a Pd/MgO(100) catalyst surface, Journal of Physical Chemistry C 117(10): 5051 - 5066, 18 February 2013.

  29. A. de la Lande, N. S. Babcock, J. Řezáč, B. C. Sanders and D. R. Salahub, Correction: Surface residues dynamically organize water bridges to enhance electron transfer between proteins (PNAS, vol 107, pg 11799, 2010), Proceedings of the National Academy of Sciences of the United States of America 110(3): 1136 - 1137, 15 January 2013.

  30. 2012

  31. A. Goursot, T. Mineva, J. M. Vásquez-Pérez, P. Calaminici, A. M. Köster and D. R. Salahub, Contribution of high-energy conformations to NMR chemical shifts, a DFT-BOMD study, Physical Chemistry Chemical Physics 15(3): 860 - 867, 14 November 2012.

  32. A. Alvarez-Ibarra, A. M. Köster, R. Zhang and D. R. Salahub, Asymptotic expansion for electrostatic embedding integrals in QM/MM calculations, Journal of Chemical Theory and Computation 8(11): 4232 - 4238, 30 August 2012.

  33. Y. Zhang and D. R. Salahub, A theoretical study of the mechanism of the nucleotidyl transfer reaction catalyzed by yeast RNA polymerase II, Science China Chemistry 55(9): 1887 - 1894, 3 August 2012.

  34. B. Zhou, X.-C. Liu, J. Cuervo and D. R. Salahub, Density functional study of benzene adsorption on the α-Mo 2C(0001) surface, Structural Chemistry 23(5): 1459 - 1466, 4 June 2012.

  35. A. de la Lande, N. S. Babcock, J. Řezáč, B. Lévy, B. C. Sanders and D. R. Salahub, Quantum effects in biological electron transfer, Physical Chemistry Chemical Physics 14(17): 5902 - 5918, 20 March 2012.

  36. 2011

  37. G. Geudtner, P. Calaminici, J. Carmona-Espíndola, J. M. del Campo, V. D. Domínguez-Soria, R. F. Moreno, G. U. Gamboa, A. Goursot, A. M. Köster, J. U. Reveles, T. Mineva, J. M. Vásquez-Pérez, A. Vela, B. Zúñinga-Gutierrez and D. R. Salahub, deMon2k, Wiley Interdisciplinary Reviews: Computational Molecular Science 2(4): 548 - 555, 21 November 2011.

  38. A. de la Lande, J. Řezáč, B. Lévy, B. C. Sanders and D. R. Salahub, Transmission coefficients for chemical reactions with multiple states: Role of quantum decoherence, Journal of the American Chemical Society 133(11): 3883 - 3894, 23 March 2011.

  39. 2010

  40. A. de la Lande, D. R. Salahub, J. Maddaluno, A. Scemama, J. Pilme, O. Parisel, H. Gérard, M. Caffarel and J.-P. Piquemal, Spin-driven activation of dioxygen in various metalloenzymes and their inspired models, Journal of Computational Chemistry 32(6): 1178 - 1182, 29 November 2010.

  41. A. Goursot, T. Mineva, C. Bissig, J. Gruenberg and D. R. Salahub, Structure, dynamics, and energetics of lysobisphosphatidic acid (LBPA) isomers, Journal of Physical Chemistry B 114(47): 15712 - 15720, 5 November 2010.

  42. A. de la Lande, N. S. Babcock, J. Řezáč, B. C. Sanders and D. R. Salahub, Surface residues dynamically organize water bridges to enhance electron transfer between proteins, Proceedings of the National Academy of Sciences 107(26): 11799 - 11804, 29 June 2010.

  43. A. de la Lande and D. R. Salahub, Derivation of interpretative models for long range electron transfer from constrained density functional theory, Journal of Molecular Structure: THEOCHEM 943(41277): 115 - 120, 15 March 2010.

  44. B. B. Lev, D. R. Salahub and S. Y. Noskov, Na(+), K (+) and Tl(+) hydration from QM/MM computations and MD simulations with a polarizable force field., Interdisciplinary sciences, computational life sciences 2(1): 12 - 20, 28 January 2010.

  45. 2009

  46. L. E. V. Bogdan, R. Zhang, A. de la Lande, D. R. Salahub and S. Y. Noskov, The QM-MM interface for CHARMM-deMon, Journal of Computational Chemistry 31(5): 1015 - 1023, 21 December 2009.

  47. J. Řezáč and D. R. Salahub, Multilevel fragment-based approach (MFBA): A novel hybrid computational method for the study of large molecules, Journal of Chemical Theory and Computation 6(1): 91 - 99, 16 December 2009.

  48. A. Goursot, T. Mineva, S. Krishnamurty and D. R. Salahub, Structural analysis of phosphatidyl choline lipids and glycerol precursors, Canadian Journal of Chemistry 87(10): 1261 - 1267, 29 July 2009.

  49. A. de la Lande, D. R. Salahub, V. Moliner, H. Gérard, J.-P. Piquemal and O. Parisel, Dioxygen activation by mononuclear copper enzymes: Insights from a tripodal ligand mimicking their CuM coordination sphere, Inorganic Chemistry 48(15): 7003 - 7005, 8 July 2009.

  50. J. Řezáč, J. Fanfrlík, D. R. Salahub and P. Hobza, Semiempirical quantum chemical PM6 method augmented by dispersion and H-bonding correction terms reliably describes various types of noncovalent complexes, Journal of Chemical Theory and Computation 5(7): 1749 - 1760, 26 May 2009.

  51. R. Zhu, A. de la Lande, R. Zhang and D. R. Salahub, Exploring the molecular origin of the high selectivity of multisubunit RNA polymerases by stochastic kinetic models., Interdisciplinary sciences, computational life sciences 1(2): 91 - 98, 19 February 2009.

  52. 2008

  53. S. Krishnamurty, M. Stefanov, T. Mineva, S. Bégu, J. M. Devoisselle, A. Goursot, R. Zhu and D. R. Salahub, Lipid thermodynamics: Melting is molecular, ChemPhysChem 9(16): 2321 - 2324, 1 November 2008.

  54. S. Krishnamurty, M. Stefanov, T. Mineva, S. Bégu, J. M. Devoisselle, A. Goursot, R. Zhu and D. R. Salahub, Density functional theory-based conformational analysis of a phospholipid molecule (dimyristoyl phosphatidylcholine), Journal of Physical Chemistry B 112(42): 13433 - 13442, 23 October 2008.

  55. R. Zhu and D. R. Salahub, Delay stochastic simulation of single-gene expression reveals a detailed relationship between protein noise and mean abundance, FEBS Letters 582(19): 2905 - 2910, 20 August 2008.

  56. R. Zhu, F. Janetzko, Y. Zhang, A. C. T. Van Duin, W. A. Goddard III and D. R. Salahub, Characterization of the active site of yeast RNA polymerase II by DFT and ReaxFF calculations, Theoretical Chemistry Accounts 120(4-6): 479 - 489, 1 July 2008.

  57. 1970

  58. O. Strausz, R. J. Norstrom, D. R. Salahub, R. K. Gosavi, H. E. Gunning and I. G. Csizmadia, Mercury 6(3P1) photosensitization of mono- and difluoroethylenes. Correlation of mechanism with calculated molecular orbital energy levels, Journal of the American Chemical Society 92(22): 6395 - 6402, 4 November 1970.

Conference Publications

    2015

  1. G. Vattay, D. R. Salahub, I. Csabai, A. Nassimi and S. A. Kauffman, Quantum criticality at the origin of life, 3 July 2015, Proceedings of 7th International Workshop DICE 2014 Spacetime - Matter - Quantum Mechanics , H T Elze, L Diósi, L Fronzoni, J J Halliwell, C Kiefer, E Prati and G Vitiello, eds. 626: 012023 (10 pp.), Castiglioncello, Italy, 15 Sep 2014 - 19 Sep 2014, Published by IOP Publishing (ISBN 9781510808010). Journal of Physics: Conference Series.


  2. X.-C. Liu and D. R. Salahub, Molybdenum carbide nanoparticles as catalysts for oil sands upgrading – dynamics and free-energy profiles, 23 March 2015, Proceedings of 11th International Conference on Computational Methods in Sciences and Engineering (ICCMSE 2015), Athens, Greece, 20 Mar 2015 - 23 Mar 2015.


  3. 2014

  4. X.-C. Liu and D. R. Salahub, Molybdenum carbide nanoparticles as catalysts for hydrogenation reactions, between the cluster and bulk perspectives, 3 July 2014, Proceedings of 14th International Conference on Computational and Mathematical Methods in Science and Engineering (2014 CMMSE), Cadiz, Spain, 3 Jul 2014 - 7 Jul 2014.


  5. 2012

  6. T. Mineva, S. Krishnamurty, D. R. Salahub and A. Goursot, Temperature dependence of the molecular conformations of dilauroyl phosphatidylcholine: A density functional study, International Journal of Quantum Chemistry, 13 February 2012 113(5): 631 - 636.


Books, Chapters in Books and Booklets

    2017

  1. P. Calaminici, A. Alvarez-Ibarra, D. Cruz-Olvera, V. D. Domínguez-Soria, R. Flores-Moreno, G. U. Gamboa, G. Geudtner, A. Goursot, D. Mejía-Rodríguez, D. R. Salahub, B. Zuniga-Gutierrez and A. M. Köster, Auxiliary density functional theory: from molecules to nanostructures, section in book: Handbook of Computational Chemistry, Jerzy Leszczynski, Anna Kaczmarek-Kedziera, Tomasz Puzyn, Manthos G. Papadopoulos, Heribert Reis, Manoj K. Shukla , eds.: 795 - 860, 2017 (ISBN 978-3-319-27281-8). Springer.


  2. 2016

  3. A. de la Lande, F. Cailliez and D. R. Salahub, Electron transfer reactions in enzymes: Seven things that might break down in vanilla Marcus theory and how to fix them if they do, section in book: Simulating Enzyme Reactivity: Computational Methods in Enzyme Catalysis, Inaki Tunon, Vicent Moliner, eds., Chapter 4: 89 - 149, 2016. Royal Society of Chemistry.


  4. 2015

  5. X.-C. Liu, B. Zhou, F. Ahmed, A. Tkalych, A. Miyamoto and D. R. Salahub, Multiscale modelling of in-situ oil sands upgrading with molybdenum carbide nanoparticles, J.-L. Rivail, X. Assfeld and Manuel Ruiz, eds. 21: 415 - 446, Published by Springer International Publishing, Switzerland, 2015 (ISBN 978-3-319-21625-6). (online ISBN: 978-3-319-21626-3).


  6. A. Alvarez-Ibarra, P. Calaminici, A. Goursot, C. Z. Gómez-Castro, R. Grande-Aztatzi, T. Mineva, D. R. Salahub, J. M. Vásquez-Pérez, A. Vela, B. Zúñinga-Gutierrez and A. M. Köster, First principles computational biochemistry with deMon2k, section in book: Frontiers in Computational Chemistry (eBook), Zaheer ul Haq and J. D. Madura (Eds), eds. 1: 281 - 325, 2015 (ISBN 978-1-60805-865-5). Bentham Science Publishers.


  7. 2014

  8. A. de la Lande, D. R. Salahub and A. M. Köster, Extending the domain of constrained Density Functional Theory to large molecular systems, section in book: Concepts and Methods in Modern Theoretical Chemistry: Electronic Structure and Reactivity, Swapan Kumar Ghosh, Pratim Kumar Chattaraj, eds.: 201 - 219, 2014. Book Series: Atoms, Molecules, and Clusters.


  9. 2013

  10. D. R. Salahub, A. de la Lande, A. Goursot, R. Zhang and Y. Zhang, Recent progress in density functional methodology for biomolecular modeling, section in book: Applications of Density Functional Theory to Biological and Bioinorganic Chemistry, Mihai V. Putz, D. Michael P. Mingos , eds. 150: 1 - 46, 2013 (ISBN 978-3-642-32749-0). Book Series: Structure and Bonding.




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Last updated Jan 12, 2019