VAMP Scientific References

2010

• Stanislav R. Stoyanov et al.,
  Computational and Experimental Study of the Structure, Binding Preferences, and Spectroscopy of Nickel(II) and Vanadyl Porphyrins in Petroleum,
  J. Phys. Chem. B 114 (2010) 2180–2188 ( abstract )
• Hakan Kayi,
  AM1* parameters for gold,
  Journal of Molecular Modeling 16 (2010) 1029–1038 ( abstract )
• Hakan Kayi and Timothy Clark,
  AM1* parameters for manganese and iron,
  Journal of Molecular Modeling 16 (2010) 1109–1126 ( abstract )
• Hakan Kayi and Timothy Clark,
  AM1* parameters for cobalt and nickel,
  Journal of Molecular Modeling 16 (2010) 29–47 ( abstract )

2009

• Hakan Kayi and Timothy Clark,
  AM1* parameters for vanadium and chromium,
  Journal of Molecular Modeling 15 (2009) 1253–1269 ( abstract )
• Hakan Kayi and Timothy Clark,
  AM1* parameters for bromine and iodine,
  Journal of Molecular Modeling 15 (2009) 295–308 ( abstract )
• Yu Lin Zhong, Wibowo Ng, Jia-Xiang Yang and Kian Ping Loh,
  Electrostatically Self-Assembled Polyoxometalates on Molecular-Dye-Functionalized Diamond,
  Journal of the American Chemical Society 131 (2009) 18293–18298 ( abstract )

2008

• James A. Elliott and Yasushi Shibuta,
  A semi-empirical molecular orbital study of freestanding and fullerene-encapsulated Mo nanoclusters,
  Molecular Simulation 34 (2008) 891–903 ( abstract )
• Francesco Mercuri,
  Semiempirical calculations on the electronic properties of finite-length models of carbon nanotubes based on Clar sextet theory,
  Molecular Simulation 34 (2008) 905–908 ( abstract )
• E. Vaganova, N. Berestetsky, S. Yitzchaik, A. Goldberg,
  Modelling of poly(4-vinyl pyridine) and poly(4-vinyl pyridine)/pyridine composites: structural and optical properties,
  Molecular Simulation 34 (2008) 981–987 ( abstract )

2007

• Matthias O. Schmitt, Siegfried Schneider, Mark L. Nelson,
  Novel Insight into the Protonation.Deprotonation Equilibria of Tetracycline and Several Derivatives in Aqueous Solution. II. Analysis of the pH-Dependent Fluorescence Spectra by the SVD Technique,
  Zeitschrift fur Physikalische Chemie 221 (2007) 235-271 ( abstract )
• Ismail Salama et al.,
  Structure-Selectivity Investigations of D₂-Like Receptor Ligands by CoMFA and CoMSIA Guiding the Discovery of D₃ Selective PET Radioligands,
  J. Med. Chem. 50 (2007) 489-500 ( abstract )
• Anselm H. C. Horn and Timothy Clark,
  Multipole electrostatic potential derived atomic charges in NDDO-methods with spd-basis sets,
  Journal of Molecular Modeling 13 (2007) 381-392 ( abstract )
• Cheolbeom Bae, Gwanghoon Kwag and Malcolm E. Kenney,
  Synthesis and characterization of near-infrared absorption tin octabutoxy naphthalocyanines,
  Polyhedron 26 (2007) 2810–2816 ( abstract )
• Bingshe Xu, Yuying Hao, Xiaohong Fang, Hua Wang, and Xuguang Liu,
  Optical and electrical properties of [N,N-bis(salicylidene)-ethylenediamine]zinc as an electroluminescent material,
  Applied Physics Letters 90 (2007) 053903 ( abstract )

2006

• Stephen F. Nelsen, Asgeir E. Konradsson, and Yoshio Teki,
  Charge-Localized Naphthalene-Bridged Bis-hydrazine Radical Cations,
  J. Am. Chem. Soc. 128 (2006) 2902-2910 ( abstract )
• Frank R. Beierlein, Olaf G. Othersen, Harald Lanig, Siegfried Schneider, and Timothy Clark,
  Simulating FRET from Tryptophan: Is the Rotamer Model Correct?,
  J. Am. Chem. Soc. 128 (2006) 5142-5152 ( abstract )
• Andreas H. Goller, Matthias Hennemann, Jorg Keldenich, and Timothy Clark,
  In Silico Prediction of Buffer Solubility Based on Quantum-Mechanical and HQSAR- and Topology-Based Descriptors,
  J. Chem. Inf. Model. 46 (2006) 648-658 ( abstract )
• Karin Schlotter, Frank Boeckler, Harald Hubner and Peter Gmeiner,
  Fancy Bioisosteres: Novel Paracyclophane Derivatives As Super-Affinity Dopamine D3 Receptor Antagonists,
  J. Med. Chem. 49 (2006) 3628-3635 ( abstract )
• Ismail Salama et al.,
  CoMFA and CoMSIA investigations of dopamine D3 receptor ligands leading to the prediction, synthesis, and evaluation of rigidized FAUC 365 analogues,
  Bioorganic & Medicinal Chemistry 14 (2006) 5898-5912 ( abstract )
• Olaf G. Othersen, Harald Lanig and Timothy Clark,
  The structure of 5a,6-anhydrotetracycline and its Mg²⁺ complexes in aqueous solution,
  Journal of Molecular Modeling 12 (2006) 953-963 ( abstract )
• Michael Galle, Ralph Puchta, Nico J. R. van Eikema Hommes, Rudi van Eldik,
  Rational Design of Cation Hosts - Prediction of Cation Selectivity by Quantum Chemical Calculations,
  Zeitschrift fur Physikalische Chemie 220 (2006) 511-523 ( abstract )
• Harald Lanig et al.,
  Molecular Dynamics Simulations of the Tetracycline-repressor Protein: The Mechanism of Induction,
  Journal of Molecular Biology 359 (2006) 1125-1136 ( abstract )

2005

• Klaus B. Stark et al.,
  Effect of Stacking and Redox State on Optical Absorption Spectra of Melanins- Comparison of Theoretical and Experimental Results,
  J. Phys. Chem. B 109 (2005) 1970-1977 ( abstract )
• Kathrin Meindl and Timothy Clark,
  Conformations and Tautomers of 5a,6-Anhydrotetracycline,
  J. Phys. Chem. B 109 (2005) 4279-4284 ( abstract )
• Jr-Hung Lin and Timothy Clark,
  An Analytical, Variable Resolution, Complete Description of Static Molecules and Their Intermolecular Binding Properties,
  J. Chem. Inf. Model. 45 (2005) 1010-1016 ( abstract )
• Frank Boeckler et al.,
  CoMFA and CoMSIA Investigations Revealing Novel Insights into the Binding Modes of Dopamine D3 Receptor Agonists,
  J. Med. Chem. 48 (2005) 2492-2508 ( abstract )
• Hartmut Schirok et al.,
  Efficient Regioselective Synthesis of 6-Amino-5-benzoyl-1-Substituted 2(1H)-Pyridinones,
  J. Org. Chem. 70 (2005) 9463-9469 ( abstract )
• Florian Wartha, Anselm H. C. Horn, Heike Meiselbach, and Heinrich Sticht,
  Molecular Dynamics Simulations of HIV-1 Protease Suggest Different Mechanisms Contributing to Drug Resistance,
  J. Chem. Theory Comput. 1 (2005) 315-324 ( abstract )
• A.H.C. Horn, Jr-H. Li and T. Clark,
  Multipole electrostatic model for MNDO-like techniques with minimal valence spd-basis sets,
  Theoretical Chemistry Accounts 114 (2005) 159-168 ( abstract )
• Hongzhou Zhang, Xianggui Qu and Howard Ando,
  A simple method for reaction rate prediction of ester hydrolysis,
  Journal of Molecular Structure: THEOCHEM 725 (2005) 31–37 ( abstract )

2004

• Xin Lu et al.,
  Properties of Fullerene[50] and D_5h Decachlorofullerene[50]: A Computational Study,
  J. Am. Chem. Soc. 126 (2004) 14871-14878 ( abstract )
• Stephen F. Nelsen et al.,
  Electron Transfer within 2,7-Dinitronaphthalene Radical Anion,
  J. Am. Chem. Soc. 126 (2004) 15431-15438 ( abstract )
• A. O. Aptula, M. T. D. Cronin,
  Prediction of hERG K⁺ blocking potency: application of structural knowledge,
  SAR and QSAR in Environmental Research 15 (2004) 399-411 ( abstract )
• Gudrun Schurer, Harald Lanig, and Timothy Clark,
  Aeromonas proteolytica Aminopeptidase: An Investigation of the Mode of Action Using a Quantum Mechanical/Molecular Mechanical Approach,
  Biochemistry 43 (2004) 5414-5427 ( abstract )

2003

• Stark, K. B., Gallas, J.M., Zajac, G. W., Eisner, M., and Golab, T. J.
  Spectroscopic Study and Simulation from Recent Structural Models for Eumelanin: II. Oligomers;
  J. Phys. Chem. B 2003, 107(13), 11558-11562.
  
• Stark, K. B., Gallas, J.M., Zajac, G. W., Eisner, M., and Golab, T. J.,
  Spectroscopic Study and Simulation from Recent Structural Models for Eumelanin: I Monomers, Dimers
  J. Phys. Chem. B 2003, 107(13), 3061.

2002

• Brustle, M., Beck, B., Schindler, T., King, W., Mitchell, T., and Clark, T.,
  Descriptors, Physical Properties, and Drug-Likeness,
  J. Med. Chem., 2002, 45, 3345-3355.
  
• Clark, T.,
  Quantum Cheminformatics: An Oxymoron? Part 2, submitted.
  
• Schurer, G., Horn, A. H. C., Gedeck, P., and Clark, T.,
  The Reaction Mechanism of Bovine Lens Leucine Aminopeptidase,
  J. Phys. Chem. B, 2002, 106, 8815-8830.

2000

• Clark, T.,
  Quantum Cheminformatics: an Oxymoron?,
  in Chemical Data Analysis in the Large: The Challenge of the Automation Age,
  ed. M.Hicks, Beilstein Institute, Frankfurt, 2000, in press.
• Andreas Goller, Ulrich-Walter Grummt,
  Implementation of an NDDO/CI/SOS approach for second-order hyperpolarizabilities,
  International Journal of Quantum Chemistry 77 (2000) 727-760 ( abstract )

1998

• Beck, B., Horn, A., Carpenter, J. E., and Clark, T.,
  Enhanced 3D Database: A Fully Electrostatic Database of AM1-Optimized Structures,
  J. Chem. Inf. Comput. Sci. 38 (1998) 1214-1217 ( abstract )
• Bernd Beck and U.-W. Grummt,
  Semiempirical Calculations of First-Order Hyperpolarizabilities: Testing the Performance of Different Methods in Comparison to Experiment ,
  J. Phys. Chem. B 102 (1998) 664-670 ( abstract )