| QM/MM calculations with deMon2k University of Calgary, The University of Calgary | Publication | 2015-01-01 | D. Salahub, S. Noskov, B. Lev, R. Zhang, V. Ngo, A. Goursot, P. Calaminici, A. M. Köster, A. Alvarez-Ibarra, D. Mejía-Rodríguez, J. Řezáč, F. Cailliez, A. d. Lande |
| Progress with density functional theory and other tools for the multiscale modeling of catalysis University of Calgary | Presentation | 2013-05-06 | D. Salahub |
| Computational chemistry and biology in the real world: from the hohenberg-kohn theorems to health, wealth and happiness University of Calgary | Presentation | 2013-05-08 | D. Salahub |
| Computational chemistry and biology in the real world: from the hohenberg-kohn theorems to health, wealth and happiness University of Calgary | Presentation | 2013-05-11 | D. Salahub |
| Computational chemistry and biology in the real world: from the hohenberg-kohn theorems to health, wealth and happiness University of Calgary | Presentation | 2013-05-13 | D. Salahub |
| Progress with density functional theory and other tools for the multiscale modeling of catalysis University of Calgary | Presentation | 2013-05-15 | D. Salahub |
| Computational chemistry and biology in the real world – from the Hohenberg-Kohn Theorem to health, wealth and happiness, University of Calgary | Presentation | 2014-05-06 | D. Salahub |
| Multiscale modeling of (bio)chemical reactions in complex environments – RNA Polymerase University of Calgary | Presentation | 2014-05-06 | D. Salahub |
| Cluster models in the multiscale modeling of nano-catalyzed reactions University of Calgary | Presentation | 2013-02-10 | D. Salahub |
| deMon quo vadis? University of Calgary | Presentation | 2013-06-25 | D. Salahub |
| Towards the multiscale modeling of chemical reactions in complex environments University of Calgary | Presentation | 2013-07-08 | D. Salahub |
| Towards the multiscale modeling of catalysis University of Calgary | Presentation | 2013-08-26 | D. Salahub |
| Multiscale modeling of (bio)chemical reactions in complex environments University of Calgary | Presentation | 2014-03-20 | D. Salahub |
| deMon, quo vadis? University of Calgary | Presentation | 2014-04-28 | D. Salahub |
| Computational chemistry and biology in the real world – from the Hohenberg-Kohn Theorem to health, wealth and happiness University of Calgary | Presentation | 2014-05-08 | D. Salahub |
| Multiscale modeling of (bio)chemical reactions in complex environments – RNA Polymerase University of Calgary | Presentation | 2014-05-08 | D. Salahub |
| Multiscale modeling of (bio)chemical reactions in complex environments – RNA Polymerase University of Calgary | Presentation | 2014-05-09 | D. Salahub |
| DFT in the context of multi-scale modeling, quo vadis? University of Calgary | Presentation | 2014-06-17 | D. Salahub |
| Challenges of oil sands exploitation in Canada – multiscale modeling of heterogeneous catalysis University of Calgary | Presentation | 2014-06-20 | D. Salahub |
| Multiscale modeling of chemical reactions in complex environments University of Calgary | Presentation | 2014-06-26 | D. Salahub |
| Towards the multiscale modeling of reactions in biology University of Calgary | Presentation | 2014-06-05 | D. Salahub |
| A theoretical study of the mechanism of the nucleotidyl transfer reaction catalyzed by yeast RNA polymerase II University of Calgary | Publication | 2012-08-01 | Y. Zhang, D. Salahub |
| Dioxygen Activation by Mononuclear Copper Enzymes: Insights from a Tripodal Ligand Mimicking Their Cu M Coordination Sphere University of Calgary | Publication | 2009-08-01 | A. d. Lande, D. Salahub, V. Moliner, H. Gérard, J. Piquemal, O. Parisel |
| Delay stochastic simulation of single-gene expression reveals a detailed relationship between protein noise and mean abundance University of Calgary | Publication | 2008-08-01 | R. Zhu, D. Salahub |
| An efficient Monte Carlo method for calculating ab initio transition state theory reaction rates in solution University of Calgary | Publication | 2003-01-01 | R. Iftimie, D. Salahub, J. Schofield |
| DFT study of hyperconjugation effects on the charge distribution in pyrogallol University of Calgary | Publication | 2003-11-01 | I. Vedernikova, D. Salahub, E. Proynov |
| Using a classical potential as an efficient importance function for sampling from an ab initio potential University of Calgary | Publication | 2000-01-01 | R. Iftimie, D. Salahub, D. Wei, J. Schofield |
| Self-consistent implementation of nonlocal exchange and correlation in a Gaussian density-functional method University of Calgary | Publication | 1991-01-01 | P. Mlynarski, D. Salahub |
| Theoretical determination of work functions and adsorption energies of atoms on metal surfaces from small-cluster calculations: A local-spin-density approach University of Calgary | Publication | 1990-09-01 | V. Russier, D. Salahub, C. Mijoule |
| Molybdenum carbide nanocatalysts at work in the in-situ environment: a DFTB and QM(DFTB)/MM study University of Calgary | Publication | 2015-01-01 | X. Liu, D. Salahub |
| Native defects in α-Mo2C: Insights from first-principles calculations University of Calgary | Publication | 2014-01-01 | C. d. Oliviera, D. Salahub, H. d. Abreu, H. A. Duarte |
| Molybdenum carbide nanoparticles as catalysts for hydrogenation reactions, between the cluster and bulk perspectives University of Calgary | Publication | 2014-01-01 | X. Liu, D. Salahub |
| Molybdenum carbide nanoparticles as catlalysts for hydrogenation reactions, between the cluster and bulk perpsectives University of Calgary | Presentation | 2014-07-03 | X. Liu, D. Salahub |
| Molybdenum carbide nanoparticles as catlalysts for hydrogenation reactions, between clusters and the bulk University of Calgary | Presentation | 2014-08-17 | X. Liu, D. Salahub |
| Unexpected quantumcriticality in proteins and other biomolecules. University of Calgary | Publication | 2015-07-01 | G. Vattay, D. Salahub, I. Csabai, A. Nassimi |
| Derivation of Interpretive Models for Long Range Electron Transfer from Constrained Density Functional Theory University of Calgary | Publication | 2010-06-01 | A. d. Lande, D. Salahub |
| Dioxygen activation by mononuclear copper enzymes: insights from a tripodal ligand mimicking their Cu(M) coordination sphere. University of Calgary | Publication | 2009-08-01 | A. l. de, D. Salahub, V. Moliner, H. Gérard, J. P. Piquemal, O. Parisel |
| Extending the domain of constrained Density Functional Theory to large molecular systems University of Calgary | Publication | 2013-05-01 | A. d. Lande, D. Salahub |
| Mercury 6(3P1) photosensitization of mono- and difluoroethylenes. Correlation of mechanism with calculated molecular orbital energy levels University of Calgary | Publication | 1970-11-01 | O. P. Strausz, R. J. Norstrom, D. Salahub, R. K. Gosavi, H. E. Gunning, I. G. Csizmadia |
| Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes University of Calgary | Publication | 2009-07-01 | J. Řezáč, J. Fanfrlík, D. Salahub, P. Hobza |
| Studying genetic regulatory networks at the molecular level: Delayed reaction stochastic models University of Calgary | Publication | 2007-06-01 | R. Zhu, A. S. Ribeiro, D. Salahub, S. A. Kauffman |
| Changes of local electronic structure of perfect (VO)2P2O7() surface in response to oxygen vacancy formation: effect of electron trapping University of Calgary | Publication | 2002-07-01 | A. Haras, H. A. Duarte, D. Salahub, M. Witko |
| Excitation processes in alkali-cationized esters: a molecular orbital study University of Calgary | Publication | 2001-09-01 | I. Vedernikova, M. Claeysa, D. Salahub, M. E. Casida |
| New τ-dependent correlation functional combined with a modified Becke exchange University of Calgary | Publication | 2000-01-01 | E. Proynov, H. Chermette, D. Salahub |
| Time-dependent density-functional theory investigation of excitation spectra of open-shell molecules University of Calgary | Publication | 2000-08-01 | J. Guan, M. E. Casida, D. Salahub |
| Density functional study of the NO dimer using GGA and LAP functionals University of Calgary | Publication | 1998-01-01 | H. A. Duarte, E. Proynov, D. Salahub |
| Bonding in C2 and Be2: Broken symmetry and correlation in DFT solutions University of Calgary | Publication | 1995-05-01 | A. Goursot, J. P. Malrieu, D. Salahub |
| Gradient-free exchange-correlation functional beyond the local-spin-density approximation University of Calgary | Publication | 1994-11-01 | E. I. Proynov, A. Vela, D. Salahub |
| Bioelectric motors: bridging the gapA series of membrane-bound proteins called the cellular respiratory chain (or "electron transport chain") serves as the power system sustaining all known oxygen-breathing life on Earth. This system is essentially a chain of electric motors, powered by the flow of tunneling electrons. Thanks to the advent of sophisticated experimental and numerical techniques, biological molecules have become a particularly attractive medium in which to study quantum transport.
The bacterium Paracoccus denitrificans is believed to share a common ancestor with the modern mitochondrion (the "powerhouse of the cell"). I present numerical characterizations of molecular motion at an inter-protein electron transfer interface in the respiratory chain of Paracoccus denitrificans. I am motivated by a recent experiment in which anomalous electron transfer rates were measured for this tunneling step [Ma et al., Biochemistry 46, 11137 (2007)]. I argue that specific amino acids are likely to harness nearby water molecules to bridge the inter-protein gap, enhancing the tunneling rate. University of Calgary | Presentation | 2009-03-25 | N. Babcock, A. l. De, D. Salahub, B. C. Sanders |
| Coherent & incoherent electron transfer in biological systemsIntermolecular electron transport is vital to the life of all respiring organisms (i.e., the vast majority of Earth's biomass). During electron transfer, any structures between the donor and acceptor molecules are collectively referred to as the "bridge." Interferences between multiple tunneling pathways through the bridge can enhance or reduce electronic coupling. A clear picture of decoherence due to dynamic bridge effects is therefore necessary to understand electron transport in biological systems. In respiring organisms, adenosine-5'-triphosphate (ATP) is recycled at a membrane-bound complex called the "electron transport chain," which in turn is powered by electricity produced from the oxidation of food (chemosynthesis) or the absorption of sunlight (photosynthesis). In this work, we examine a single bridging step in the electron transport chain of Paracoccus denitrificans. Recent experiments have shown this process to be extremely sensitive to the change of just a few atoms in the surrounding protein structure. We hypothesize that this reaction is mediated by a bridge of water molecules stabilized by nearby amino acid residues, effectively suppressing the decoherence of the through-water coupling term. We test this hypothesis using molecular mechanics and density functional theory to calculate the electronic coupling matrix elements for a variety of configurations. We believe the mathematical tools and intuition of quantum information theory will help provide deeper insight into the role of decoherence in this intriguing phenomenon. University of Calgary | Presentation | 2008-06-17 | N. Babcock, A. l. De, D. Salahub, B. C. Sanders |
| First-principles calculations of the structural, mechanical, electronic and bonding properties of (CrB2)n CrAl with n = 1, 2, 3 University of Calgary | Publication | 2017-03-01 | X. -. Li, M. C. Silva, D. Salahub |
| Electronic properties of carbon nanotubes complexed with a DNA nucleotide University of Calgary | Publication | 2017-02-01 | M. Chehelamirani, M. C. Silva, D. Salahub |
| The QM-MM interface for CHARMM-deMon University of Calgary | Publication | 2009-01-01 | B. Lev, R. Zhang, A. d. Lande, D. Salahub, S. Y. Noskov |
| Dissociation, solvation, and dynamics of HBr in small water clusters University of Calgary | Publication | 2005-05-01 | A. Goursot, G. Fischer, C. C. Lovallo, D. Salahub |
| Solvation of formic acid and proton transfer in hydrated clusters University of Calgary | Publication | 2002-01-01 | D. Wei, J. Truchon, S. Sirois, D. Salahub |
| Molecular structure of mono- and dicarbonyls of rhodium and palladium University of Calgary | Publication | 1992-11-01 | I. P�pai, A. Goursot, A. St-Amant, D. Salahub |
| Representation of ion-protein interactions using the Drude polarizable force-field University of Calgary, The University of Calgary | Publication | 2015-01-01 | H. Li, V. Ngo, M. C. Silva, D. Salahub, K. Kallahan, B. Roux, S. Noskov |
| Multiple proton relay routes in the reactionmechanism of RNAP II: Assessing the effect of structural model University of Calgary | Publication | 2014-01-01 | R. Zhang, A. Bhattacharjee, M. J. Field, D. Salahub |
| Adsorption of hexacyclic C6H6, C6H8, C6H10 and C6H12 on a Mo-terminated α-Mo2C (0001) surface University of Calgary | Publication | 2013-01-01 | X. Liu, A. Tkalych, B. Zhou, D. Salahub |
| Electron superhighways and bridges in protein complexesDoes Natural Selection optimize biomachinery at the quantum level? Does quantum coherence play a role in biochemical electron transport? We show
that a particular redox protein complex is configured so that metastable water bridges act as "superhighways" for coherent electron transport between its constituent protein molecules. The bridge enables fast coherent electron transport across the gap instead of dooming the electron to slow thermal hopping through the interprotein medium. Although our study focuses on a particular protein complex
that has been frozen and characterized by crystallography, we conjecture that bridge-building is ubiquitous for redox processes.
University of Calgary | Presentation | 2009-06-19 | B. C. Sanders, N. Babcock, A. l. De, D. Salahub |
| Integrating out the quantum nature of electron transfer processes at the macromolecular scales University of Calgary | Presentation | 2012-10-08 | A. l. De, N. Babcock, B. C. Sanders, D. Salahub, E. H. El, C. Houée-Levin, B. Lévy, I. Demachy |
| QM-MM interface for CHARMM-DeMON: Application to ion solvation problem University of Calgary | Publication | 2010-04-01 | B. Lev, R. Zhang, A. D. Lande, D. Salahub, S. Y. Noskov |
| The QM-MM interface for CHARMM-deMon. University of Calgary, The University of Calgary | Publication | 2010-04-01 | B. Lev, R. Zhang, A. l. de, D. Salahub, S. Noskov |
| Explicit water molecules play a key role in the mechanism of rhodium-substituted human carbonic anhydrase University of Calgary | Publication | 2017-02-01 | P. Piazzetta, T. Marino, N. Russo, D. Salahub |
| Structure, Dynamics, and Energetics of Lysobisphosphatidic Acid (LBPA) Isomers University of Calgary | Publication | 2010-12-01 | A. Goursot, T. Mineva, C. Bissig, J. Gruenberg, D. Salahub |
| A density functional study of the hydrogen-bond network within the HIV-1 protease catalytic site cleft University of Calgary | Publication | 2003-05-01 | S. Sirois, E. I. Proynov, J. -. Truchon, C. M. Tsoukas, D. Salahub |
| Spin Densities and Polymerizabilities of Aniline Derivatives Deduced from Density Functional Calculations University of Calgary | Publication | 1996-01-01 | G. D’Aprano, E. Proynov, M. Lebœuf, M. Leclerc, D. Salahub |
| Correction: Surface residues dynamically organize water bridges to enhance electron transfer between proteins (PNAS, vol 107, pg 11799, 2010) University of Calgary | Publication | 2013-01-01 | A. d. Lande, N. Babcock, J. Řezáč, B. C. Sanders, D. Salahub |
| A molecular breakwater enhances electron transfer between proteinsDoes natural selection optimize molecular biomachinery at the quantum level? We present statistical characterizations of molecular dynamics at an interprotein electron transfer (ET) interface. In simulations of the wild-type protein complex, we find that the most frequently occurring molecular configurations afford superior electronic coupling due to the consistent presence of a single water molecule hydrogen-bonded between the donor and acceptor sites. We attribute the persistence of this water bridge to a ``molecular breakwater'' composed of several hydrophobic residues surrounding the acceptor site. The breakwater supports the function of solvent-organizing residues by limiting the exchange of water molecules between the sterically constrained ET region and the surrounding bulk. When the breakwater is affected by a mutation, bulk solvent molecules disrupt the water bridge, resulting in reduced electronic coupling. These results suggest that protein surface residues may stabilize interprotein solvent dynamics to enable coherent ET along a single molecular pathway. University of Calgary | Presentation | 2011-03-23 | N. Babcock, A. l. De, J. Řezáč, B. C. Sanders, D. Salahub |
| A guide to QM/MM methodology and applications University of Calgary, The University of Calgary | Publication | 2010-06-01 | R. Zhang, B. Lev, J. E. Cuervo, S. Noskov, D. Salahub |
| A molecular breakwater enhances electron transfer between proteins University of Calgary | Publication | 2011-03-01 | N. Babcock, A. l. De, J. Rezác, B. C. Sanders, D. Salahub |
| Contribution of high-energy conformations to NMR chemical shifts, a DFT-BOMD study University of Calgary | Publication | 2013-01-01 | A. Goursot, T. Mineva, J. M. Vásquez-Pérez, P. Calaminici, A. M. Köster, D. Salahub |
| Binary Iron−Dinitrogen Compounds Synthesized by Co-deposition of Mass-Selected Fe, Fe 2 , and Fe 3 with N 2 University of Calgary | Publication | 2000-06-01 | T. L. Haslett, S. Fedrigo, K. Bosnick, M. Moskovits, H. A. Duarte, D. Salahub |
| Calculation of 29 Si and 27 Al MAS NMR Chemical Shifts in Zeolite-β Using Density Functional Theory: Correlation with Lattice Structure University of Calgary | Publication | 1998-11-01 | G. Valerio, A. Goursot, R. Vetrivel, O. Malkina, V. Malkin, D. Salahub |
| First Principles Computational Biochemistry with deMon2k University of Calgary | Publication | 2015-03-01 | A. Alvarez-Ibarra, P. Calaminici, A. Goursot, C. Z. Gómez-Castro, R. Grande-Aztatzi, T. Mineva, D. Salahub, J. M. Vásquez-Pérez, A. Vela, B. Zuniga-Gutierrez |
| Auxiliary Density Functional Theory: From Molecules to Nanostrucutres University of Calgary | Publication | 2011-06-01 | P. Calaminici, V. D. Dominguez, R. FLores, G. U. Gamboa, G. Geudtner, A. Goursot, D. Salahub |
| Cluster Structures: Bridging Experiment and Theory University of Calgary | Publication | 2010-06-01 | F. Janetzko, A. Goursot, T. Mineva, P. Calaminici, R. Flores-Moreno, A. M. Koster, D. Salahub |
| Electronic Polarization Effects in Cation Interactions with First and Second Coordination Shell Ligands in Metalloproteins University of Calgary | Publication | 2015-07-01 | V. Ngo, M. d. Silva, M. Kubilius, H. Li, M. Elstner, B. Roux, Q. Cui, D. Salahub |
