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Tag qmmm [68 articles]

Recent papers classified by the tag qmmm.
  • Interfacing ab Initio Quantum Mechanical Method with Classical Drude Osillator Polarizable Model for Molecular Dynamics Simulation of Chemical Reactions
    J. Chem. Theory Comput., Vol. 4, No. 8. (12 August 2008), pp. 1237-1248.
    by Zhenyu Lu, Yingkai Zhang
    posted to shellmodel qmmm polarizable by yzlab on 2008-09-19 03:34:03 as read
  • Computational photochemistry of retinal proteins.
    Journal of computer-aided molecular design, Vol. 20, No. 7-8. (g 2006), pp. 511-518.
    by M Wanko, M Hoffmann, T Frauenheim, M Elstner
    posted to structure spectrum rhodopsin qmmm protein md gpcr by vahmurk on 2008-09-16 23:09:25 as **
  • The role of intersection topography in bond selectivity of cis-trans photoisomerization
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 4. (19 February 2002), pp. 1769-1773.
    by M Ben-Nun, F Molnar, K Schulten, Todd J Martínez
    posted to structure retinal qmmm photoisomeration by vahmurk on 2008-09-28 10:16:21 as **
  • Computational studies of the primary phototransduction event in visual rhodopsin.
    Accounts of chemical research, Vol. 39, No. 3. (March 2006), pp. 184-193.
    by JA Gascón, EM Sproviero, VS Batista
    posted to structure rhodopsin qmmm gpcr by vahmurk on 2008-09-16 22:59:38 as **
  • Calculating absorption shifts for retinal proteins: computational challenges.
    The journal of physical chemistry. B, Vol. 109, No. 8. (3 March 2005), pp. 3606-3615.
    by M Wanko, M Hoffmann, P Strodel, A Koslowski, W Thiel, F Neese, T Frauenheim, M Elstner
    posted to retinal qmmm protein method by vahmurk on 2008-09-26 23:55:34 as **
  • Accurate evaluation of the absorption maxima of retinal proteins based on a hybrid QM/MM method
    Journal of Computational Chemistry, Vol. 27, No. 14. (2006), pp. 1623-1630.
    by Azuma Matsuura, Hiroyuki Sato, Hirohiko Houjou, Shino Saito, Tomohiko Hayashi, Minoru Sakurai
    posted to structure spectrum rhodopsin qmmm protein prediction pigments method md gpcr bacteriorhodopsin by vahmurk on 2008-09-26 23:47:03 as *****
  • Nature of the Surface Crossing Process in Bacteriorhodopsin: Computer Simulations of the Quantum Dynamics of the Primary Photochemical Event
    J. Phys. Chem. B, Vol. 105, No. 40. (11 October 2001), pp. 9857-9871.
    by A Warshel, ZT Chu
    posted to qmmm photoisomeration mechanism md light_absorption bacteriorhodopsin by vahmurk on 2008-09-28 10:23:44 as **
  • Hybrid molecular dynamics-quantum mechanics simulations of solute spectral properties in the condensed phase: evaluation of simulation parameters.
    Journal of computational chemistry, Vol. 28, No. 9. (15 July 2007), pp. 1572-1581.
    by MC Zwier, JM Shorb, BP Krueger
    posted to spectrum qmmm method by vahmurk on 2008-09-26 23:57:43 as **
  • An opsin shift in rhodopsin: retinal S0-S1 excitation in protein, in solution, and in the gas phase.
    Journal of the American Chemical Society, Vol. 129, No. 43. (31 October 2007), pp. 13035-13042.
    by K Bravaya, A Bochenkova, A Granovsky, A Nemukhin
    posted to rhodopsin retinal qmmm opsin_shift md gpcr by vahmurk on 2008-09-27 00:09:09 as **
  • Computational evidence in favor of a two-state, two-mode model of the retinal chromophore photoisomerization
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 97, No. 17. (2000), pp. 9379-9384.
    by Remedios González-Luque, Marco Garavelli, Fernando Bernardi, Manuela Merchán, Michael A Robb, Massimo Olivucci
    posted to retinal qmmm photoisomeration membrane mechanism by vahmurk on 2008-09-28 10:08:13 as **
  • notes Mechanism of color tuning in retinal protein: SAC-CI and QM/MM study
    Chemical Physics Letters, Vol. 414, No. 1-3. (03 October 2005), pp. 239-242.
    by K Fujimoto, J Hasegawa, S Hayashi, S Kato, H Nakatsuji
    posted to spectrum retinal qmmm pigments photoisomeration mechanism light_absorption bacteriorhodopsin 081002 by vahmurk on 2008-10-02 21:45:04 as *****
  • Study on the prediction of visible absorption maxima of azobenzene compounds.
    Journal of Zhejiang University. Science. B, Vol. 6, No. 6. (June 2005), pp. 584-589.
    by JN Liu, ZR Chen, SF Yuan
    posted to qmmm method by vahmurk on 2008-09-27 00:23:56 as **
  • QM/MM study of energy storage and molecular rearrangements due to the primary event in vision.
    Biophysical journal, Vol. 87, No. 5. (November 2004), pp. 2931-2941.
    by JA Gascon, VS Batista
    posted to vision rhodopsin retinal qmmm mechanism md bacteriorhodopsin 081006 by vahmurk on 2008-09-27 00:06:20 as *****
  • Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints
    Journal of Computational Chemistry, Vol. 24, No. 6. (2003), pp. 760-769.
    by Thom Vreven, Keiji Morokuma, Ödön Farkas, Bernhard H Schlegel, Michael J Frisch
    posted to uv spectrum retinal qmmm method bacteriorhodopsin 081118 by vahmurk on 2008-11-17 23:45:03 as *****
  • Flexible effective fragment QM/MM method: validation through the challenging tests.
    Journal of computational chemistry, Vol. 24, No. 12. (September 2003), pp. 1410-1420.
    by AV Nemukhin, BL Grigorenko, IA Topol, SK Burt
    posted to qmmm method by vahmurk on 2008-09-27 00:20:58 as **
  • Investigation of the S0S1 excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid method
    Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), Vol. 109, No. 3. (18 April 2003), pp. 125-132.
    by T Vreven, K Morokuma
    posted to uv spectrum retinal qmmm opsin_shift method bacteriorhodopsin 081118 by vahmurk on 2008-11-17 23:40:25 as *****
  • On the color-tuning mechanism of Human-Blue visual pigment: SAC-CI and QM/MM study
    Chemical Physics Letters, Vol. 432, No. 1-3. (4 December 2006), pp. 252-256.
    by Kazuhiro Fujimoto, Jun-Ya Hasegawa, Shigehiko Hayashi, Hiroshi Nakatsuji
    posted to vision structure rhodopsin qmmm protein pigments by vahmurk on 2008-09-16 23:10:43 as **
  • Exploring the Molecular Mechanism for Color Distinction in Humans
    J. Phys. Chem. B, Vol. 110, No. 34. (31 August 2006), pp. 17230-17239.
    by RJ Trabanino, N Vaidehi, WA Goddard
    posted to rhodopsin qmmm protein membrane md gpcr by vahmurk on 2008-09-16 23:08:46 as **
  • Spectral tuning in visual pigments: an ONIOM(QM:MM) study on bovine rhodopsin and its mutants.
    The journal of physical chemistry. B, Vol. 112, No. 22. (5 June 2008), pp. 6814-6827.
    by A Altun, S Yokoyama, K Morokuma
    posted to rhodopsin qmmm md by vahmurk on 2008-09-16 11:30:47 as *****
  • Retinal Photoisomerization in Rhodopsin: Electrostatic and Steric Catalysis
    AIP Conference Proceedings, Vol. 963, No. 2. (2007), pp. 727-730.
    by Gaia Tomasello, Piero Altoè, Marco Stenta, Gloria O González, Marco Garavelli, Giorgio Orlandi
    edited by Theodore E Simos, George Maroulis
    posted to structure rhodopsin qmmm protein photoisomeration md gpcr by vahmurk on 2008-09-16 23:00:37 as **
  • Photoexcited breathers in conjugated polyenes: An excited-state molecular dynamics study
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 5. (4 March 2003), pp. 2185-2190.
    by S Tretiak, A Saxena, RL Martin, AR Bishop
    posted to qmmm polyenes method md by vahmurk on 2008-09-28 10:21:57 as **
  • Proton Transfer in Bacteriorhodopsin: Structure, Excitation, IR Spectra, and Potential Energy Surface Analyses by an ab Initio QM/MM Method
    J. Phys. Chem. B, Vol. 104, No. 45. (16 November 2000), pp. 10678-10691.
    by S Hayashi, I Ohmine
    posted to spectrum qmmm proton_pathways protein gpcr bacteriorhodopsin 081006 by vahmurk on 2008-09-28 10:07:02 as *****
  • Absorption of schiff-base retinal chromophores in vacuo.
    Journal of the American Chemical Society, Vol. 127, No. 35. (7 September 2005), pp. 12347-12350.
    by LH Andersen, IB Nielsen, MB Kristensen, MO El Ghazaly, S Haacke, MB Nielsen, MA Petersen
    posted to spectrum retinal qmmm method md light_absorption by vahmurk on 2008-09-26 23:57:07 as **
  • Effects of the protein electrostatic environment on the absorption maximum of bacteriorhodopsin
    Chemical Physics Letters, Vol. 294, No. 1-3. (11 September 1998), pp. 162-166.
    by H Houjou
    posted to spectrum qmmm light_absorption bacteriorhodopsin 081002 by vahmurk on 2008-10-02 21:23:42 as *****
  • Computational analysis of the proton translocation from Asp96 to schiff base in bacteriorhodopsin.
    The journal of physical chemistry. B, Vol. 110, No. 45. (16 November 2006), pp. 22804-22812.
    by Y Sato, M Hata, S Neya, T Hoshino
    posted to retinal qmmm proton_pathways mechanism md isomerisation gpcr bacteriorhodopsin by vahmurk on 2008-09-27 00:17:11 as **
  • Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme.
    Journal of molecular biology, Vol. 103, No. 2. (15 May 1976), pp. 227-249.
    by A Warshel, M Levitt
    posted to qmmm warshel by sim82 on 2008-07-12 17:45:55 as **
  • COMPUTER SIMULATIONS OF ENZYME CATALYSIS: Methods, Progress, and Insights
    Annual Review of Biophysics and Biomolecular Structure, Vol. 32, No. 1. (2003), pp. 425-443.
    by Arieh Warshel
    posted to qmmm review warshel by sim82 on 2008-07-12 14:29:59 as **
  • Exploring Structure and Dynamics of the Diaquotriamminezinc(II) Complex by QM/MM MD Simulation
    J. Phys. Chem. B, Vol. 112, No. 18. (8 May 2008), pp. 5788-5794.
    by MQ Fatmi, TS Hofer, BR Randolf, BM Rode
    posted to hartree-fock md qmmm simulation zinc by qaiser_fatmi on 2008-07-23 20:15:44 as ** along with 1 group group
  • A QM/MM MD simulation study of hydrated Pd2+
    Chemical Physics Letters, Vol. 426, No. 4-6. (4 August 2006), pp. 301-305.
    by Shah, Thomas S Hofer, Qaiser M Fatmi, Bernhard R Randolf, Bernd M Rode
    posted to hartree-fock md pd qmmm simulation by qaiser_fatmi on 2008-07-23 20:17:15 as ** along with 1 group group
  • Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical (QM/MM) approach
    Journal of Computational Chemistry, Vol. 26, No. 9. (2005), pp. 915-931.
    by Art E Cho, Victor Guallar, Bruce J Berne, Richard Friesner
    posted to dft docking lead-optimization protein qmmm by qaiser_fatmi on 2008-08-16 22:45:34 as ** along with 1 person and 1 group boris_aguilar group
  • Structure and dynamics of the [Zn(NH3)(H2O)5]2+ complex in aqueous solution obtained by an ab initio QM/MM molecular dynamics study
    Phys. Chem. Chem. Phys., Vol. 8, No. 14. (2006), pp. 1675-1681.
    by Qaiser M Fatmi, Thomas S Hofer, Bernhard R Randolf, Bernd M Rode
    posted to hartree-fock md qmmm simulation zinc by qaiser_fatmi on 2008-07-23 20:14:57 as ** along with 1 group group
  • Temperature Effects on the Structural and Dynamical Properties of the Zn(II)-Water Complex in Aqueous Solution: A QM/MM Molecular Dynamics Study
    J. Phys. Chem. B, Vol. 110, No. 1. (12 January 2006), pp. 616-621.
    by MQ Fatmi, TS Hofer, BR Randolf, BM Rode
    posted to hartree-fock md qmmm simulation temperature-effect zinc by qaiser_fatmi on 2008-07-23 20:16:18 as ** along with 1 group group
  • Stability of Different Zinc(II)-Diamine Complexes in Aqueous Solution with Respect to Structure and Dynamics: A QM/MM MD Study
    J. Phys. Chem. B, Vol. 111, No. 1. (11 January 2007), pp. 151-158.
    by MQ Fatmi, TS Hofer, BR Randolf, BM Rode
    posted to hartree-fock md qmmm simulation zinc by qaiser_fatmi on 2008-07-23 20:14:19 as ** along with 1 group group
  • An extended ab initio QM/MM MD approach to structure and dynamics of Zn(II) in aqueous solution
    The Journal of Chemical Physics, Vol. 123, No. 5. (2005)
    by Qaiser M Fatmi, Thomas S Hofer, Bernhard R Randolf, Bernd M Rode
    posted to hartree-fock md qmmm simulation zinc by qaiser_fatmi on 2008-07-18 00:24:22 as *****
  • Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules
    The Journal of Chemical Physics, Vol. 123, No. 1. (2005)
    by Patricia Schaefer, Demian Riccardi, Qiang Cui
    posted to qmmm multiscale electrostatics by onufriev on 2008-11-12 04:42:23 as **
  • The implementation of a fast and accurate QM/MM potential method in Amber
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2007), NA.
    by Ross C Walker, Michael F Crowley, David A Case
    posted to qmmm gb by onufriev on 2008-11-01 23:50:15 as ** along with 2 people RamuAnandakrishnan softsimu
  • A Generalized-Born Solvation Model for Macromolecular Hybrid-Potential Calculations
    J. Phys. Chem. A, Vol. 106, No. 7. (21 February 2002), pp. 1316-1326.
    by E Pellegrini, MJ Field
    posted to qmmm gb by onufriev on 2008-11-02 00:02:48 as **
  • Hepatitis C Virus NS5B Polymerase: QM/MM Calculations Show the Important Role of the Internal Energy in Ligand Binding
    J. Phys. Chem. B (14 February 2008)
    by JM Parks, RK Kondru, H Hu, DN Beratan, W Yang
    posted to docking internal_energy polarization qmmm by middledomain on 2008-02-14 10:32:51 as **
  • Flooding in <TT>GROMACS</TT>: Accelerated barrier crossings in molecular dynamics
    Journal of Computational Chemistry, Vol. 27, No. 14. (2006), pp. 1693-1702.
    by Oliver F Lange, Lars V Schäfer, Helmut Grubmüller
    posted to qmmm gromacs by loison on 2007-01-10 13:16:33 as ** along with 2 people softsimu daevans
  • Ionization Potentials of Fluoroindoles and the Origin of Nonexponential Tryptophan Fluorescence Decay in Proteins<sup><img src="http://pubs.acs.org/images/entities/bottom.gif" border="0"></sup>
    J. Am. Chem. Soc., Vol. 127, No. 11. (23 March 2005), pp. 4104-4113.
    by T Liu, PR Callis, BH Hesp, M Degroot, WJ Buma, J Broos
    posted to peptide qmmm trp by loison on 2006-12-04 09:33:13 as **
  • Computer Simulation of the Linear and Nonlinear Optical Susceptibilities of <i>p</i>-Nitroaniline in Cyclohexane, 1,4-Dioxane, and Tetrahydrofuran in Quadrupolar Approximation. II. Local Field Effects and Optical Susceptibilitities
    J. Phys. Chem. B, Vol. 110, No. 37. (21 September 2006), pp. 18537-18552.
    by H Reis, MG Papadopoulos, A Grzybowski
    posted to theory solvent qmmm hyperpolarizability by loison on 2007-01-11 13:50:19 as ***
  • Automated Parametrization of Biomolecular Force Fields from Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations through Force Matching
    J. Chem. Theory Comput. (20 January 2007)
    by P Maurer, A Laio, H Hugosson, MC Colombo, U Rothlisberger
    posted to forcematching qmmm by loison on 2007-05-04 14:29:01 as ** along with 1 person daevans
  • Dependence of Tryptophan Emission Wavelength on Conformation in Cyclic Hexapeptides
    J. Phys. Chem. B, Vol. 110, No. 13. (6 April 2006), pp. 7009-7016.
    by CP Pan, PR Callis, MD Barkley
    posted to peptide qmmm trp by loison on 2006-12-04 09:25:22 as **
  • Electronic Structure of Compound I in Human Isoforms of Cytochrome P450 from QM/MM Modeling
    J. Am. Chem. Soc., Vol. 127, No. 37. (21 September 2005), pp. 12900-12908.
    by CM Bathelt, J Zurek, AJ Mulholland, JN Harvey
    posted to porphyrin qmmm by loison on 2007-05-15 13:59:37 as **
  • Quantum capping potentials with point charges: A simple QM/MM approach for the calculation of large-molecule NMR shielding tensors
    The Journal of Chemical Physics, Vol. 120, No. 19. (2004), pp. 9080-9086.
    by Seongho Moon, Phillip A Christiansen, Gino A Dilabio
    posted to qmmm by loison on 2008-07-23 14:37:29 as **
  • Spectroscopic Properties of Porphyrin-Like Photosensitizers: Insights from Theory
    J. Phys. Chem. B, Vol. 110, No. 5. (9 February 2006), pp. 2398-2404.
    by L Petit, A Quartarolo, C Adamo, N Russo
    posted to porphyrin qmmm by loison on 2007-06-12 10:26:55 as **
  • QM/MM calculations with DFT for taking into account protein effects on the EPR and optical spectra of metalloproteins. Plastocyanin as a case study.
    J Comput Chem, Vol. 27, No. 12. (September 2006), pp. 1463-1475.
    by S Sinnecker, F Neese
    posted to dft qmmm by kimikazu on 2007-06-29 03:18:35 as read along with 2 people hlwoodcock loison
  • Color Tuning in Rhodopsins: The Mechanism for the Spectral Shift between Bacteriorhodopsin and Sensory Rhodopsin II
    J. Am. Chem. Soc., Vol. 128, No. 33. (23 August 2006), pp. 10808-10818.
    by M Hoffmann, M Wanko, P Strodel, PH Konig, T Frauenheim, K Schulten, W Thiel, E Tajkhorshid, M Elstner
    posted to qm-mm qmmm sccdftb by hlwoodcock on 2006-08-16 18:51:32 as ** along with 1 person vahmurk
  • QM/MM Boundaries Across Covalent Bonds: A Frozen Localized Molecular Orbital-Based Approach for the Effective Fragment Potential Method
    J. Phys. Chem. A, Vol. 104, No. 28. (20 July 2000), pp. 6656-6665.
    by V Kairys, JH Jensen
    posted to qmmm by hlwoodcock on 2006-03-30 23:04:54 as **
  • A DFT-Based QM-MM Approach Designed for the Treatment of Large Molecular Systems: Application to Chorismate Mutase
    J. Phys. Chem. B, Vol. 107, No. 49. (11 December 2003), pp. 13728-13736.
    by A Crespo, DA Scherlis, MA Marti, P Ordejon, AE Roitberg, DA Estrin
    posted to qmmm by hlwoodcock on 2006-03-30 23:07:11 as ** along with 1 person loison
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