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  1. No Access

    Article

    Using Molecular Dynamics to Predict Factors Affecting Binding Strength and Magnetic Relaxivity of MRI Contrast Agents

    We demonstrate the use of molecular dynamics and molecular mechanics methods to calculate properties and behavior of metal-chelate complexes that can be used as MRI contrast agents. Static and dynamic properti...

    Yen T. Tan, Richard S. Judson, Carl F. Melius, John Toner… in Molecular modeling annual (1996)

  2. No Access

    Article

    PM3 and AM1 Study on β-N-acetyl-muramic Acid and 3 Murein Related Derivatives

    The energetically favoured conformations of β-N-acetyl-Muramic acid, its C6-O-acetylated form, the methylamide and the methyl-glycoside have been investigated using the semiempirical PM3 and AM1 methods. All t...

    Peter Keller, Hans Bradaczek in Molecular modeling annual (1996)

  3. No Access

    Article

    Modeling of Platinum Clusters in H-Mordenite

    The size, location and structure of Pt clusters in H-mordenite have been investigated by molecular mechanics energy minimization and molecular dynamics simulation techniques using the Catalysis software of Molecu...

    Maria E. Grillo, Maria M. Ramirez de Agudelo in Molecular modeling annual (1996)

  4. No Access

    Article

    Molecular Dynamics Simulation of a Micellar System

    We present the results of an atomistic molecular dynamics simulation based on the AMBER/OPLS force field applied to segments of isolated one-dimensional micelles, 2,3,6,7,10,11-Hexa-(1,4,7-Trioxaoctyl)-Triphen...

    Tim Bast, Reinhard Hentschke in Molecular modeling annual (1996)

  5. No Access

    Article

    Ab initio Calculation of the Conformations and Vibrational Spectra of 2-Phenylbutane

    Molecules with internal degrees of rotation are of particular interest to understand the behavior of synthetic or natural polymers. With the extremely rapid increase in floating point performance of modern com...

    Christian Borsdorf, Thomas Dorfmüller in Molecular modeling annual (1996)

  6. No Access

    Article

    Theoretical Study of the Water Exchange Reaction on Divalent Zinc Ion using Density Functional Theory

    Recent ab initio studies reported in the literature have challenged the mechanistic assignments made on the basis of volume of activation data [1,2]. In addition to that ab initio molecular orbital calculations o...

    Michael Hartmann, Timothy Clark, Rudi van Eldik in Molecular modeling annual (1996)

  7. No Access

    Article

    Quadrupole Relaxation of the 7Li+ Ion in Dilute Aqueous Solution Determined by Experimental and Theoretical Methods

    A combination of molecular dynamics simulations (MD), ab initio selfconsistent field (SCF) calculations and nuclear magnetic resonance relaxation time experiments (NMR) is a powerful battery of techniques to inve...

    Ralf Baumert, Ralf Ludwig, Alfons Geiger in Molecular modeling annual (1996)

  8. No Access

    Article

    Exploring the Conformational Behavior of Rigid Porphyrin-Quinone Systems by High-Temperature MD Simulations and Temperature-Dependent 1H-NMR Experiments

    Photoinduced electron transfer reactions play an important role in the primary step of the biological photosynthesis process. In an attempt to understand better the mechanism of the charge separation organic d...

    Martin Frank, Katrin Peraus, Heinz A. Staab in Molecular modeling annual (1996)

  9. No Access

    Article

    Peptides and Peptoids - A Systematic Structure Comparison

    A systematic analysis of the conformational space of the basic structure unit of peptoids in comparison to the corresponding peptide unit was performed based on ab initio MO theory and complemented by molecular m...

    Kerstin Möhle, Hans-Jörg Hofmann in Molecular modeling annual (1996)

  10. No Access

    Article

    Characterization of a Novel Reverse-orientation Model for a Peptide/MHC Complex Putatively Associated with Type I Diabetes Mellitus

    Molecular modeling techniques were used to generate structures of several HLA-DQ proteins associated with insulin-dependent diabetes mellitus (IDDM). A peptide fragment from glutamic acid decarboxylase (GAD), ...

    Carol DeWeese, William W. Kwok, Gerald T. Nepom… in Molecular modeling annual (1996)

  11. No Access

    Article

    Gibbs-Ensemble Molecular Dynamics: A New Method for Simulations Involving Particle Exchange

    We discuss a novel simulation method suitable for simulating phenomena involving particle exchange. The method is a molecular dynamics version of the Gibbs-Ensemble Monte Carlo technique, which has been develo...

    Reinhard Hentschke, Tim Bast, Ewald Aydt, Michael Kotelyanskii in Molecular modeling annual (1996)

  12. No Access

    Article

    Investigation of the Uncatalyzed Hydration of CO2 and First Approximations to the Active Site of Carbonic Anhydrase - A Combined Ab initio and DFT Study -

    Michael Hartmann, Timothy Clark, Rudi van Eldik in Molecular modeling annual (1996)

  13. No Access

    Article

    Computer-Aided Receptor Modelling of Human Opioid Receptors: (Mu, Kappa & Delta)

    Opioid receptors (OPRs) are important agents in the centeral nervous system (CNS) function. These receptors belong to “G-Protein Coupled Receptors (GPCRs)” which have structural similarity with the BACTERIORHODOP...

    Bahram Habibi-Nezhad, Mahindokht Hanifian, Massoud Mahmoudian in Molecular modeling annual (1996)

  14. No Access

    Article

    Elastic Properties of Polymer Networks

    Many fundamental questions for the understanding of polymer melts and networks are more suitably addressed by current computer simulations than by experiments. The reason is that simulations have simultaneous ...

    Ralf Everaers, Kurt Kremer in Molecular modeling annual (1996)

  15. No Access

    Article

    Ab Initio and Molecular Mechanics Calculations of Various Substituted Ureas - Rotational Barriers and a New Parametrization for Ureas

    High-level ab initio calculations have been performed on urea, methylurea, tetramethylurea and three isomers of dimethylurea to obtain accurate rotational barriers. Results of MP2(fc)/6-31 G(d) calculations are c...

    Thomas Strassner in Molecular modeling annual (1996)

  16. No Access

    Article

    Interaction Energies and Dynamics of Alkali and Alkaline-Earth Cations in Quadruplex-DNA-Structures

    We have investigated the nonbonded interaction energies and dynamical properties of different types of cations in quadruplex DNA structures using the GROMOS force field [1]. Quadruplex structures consist of pl...

    Jutta Töhl, Wolfgang Eimer in Molecular modeling annual (1996)

  17. No Access

    Article

    VRML in Cancer Research Local Molecular Properties of the p53 Tumor Suppressor Protein-DNA Interface

    The three-dimensional structure information of the p53 core domain-DNA complex is presented. The Virtual Reality Modeling Language (VRML), a new concept of information transfer is used for this biochemical app...

    Gerd Moeckel, Matthias Keil, Bertold Spiegelhalder… in Molecular modeling annual (1996)

  18. No Access

    Article

    The Photodissociation/Recombination Dynamics of I2 in an Ar Matrix: Wave Packet Propagation in a Mixed Quantum-Classical Picture

    The theoretical description of photodissociation processes of molecules after short time laser excitations is essentially based on the formalism of quantum mechanics, i.e. both the product formation and the en...

    Udo Schmitt, Jürgen Brickmann in Molecular modeling annual (1996)

  19. No Access

    Article

    Sedimentation of Clusters of Spheres

    We describe a numerical method for calculating hydrodynamic interactions between spherical particles efficiently and accurately, both for particles immersed in an infinite liquid and for systems with periodic ...

    Konrad Hinsen, Gerald Reinhard Kneller in Molecular modeling annual (1996)

  20. No Access

    Article

    Reparametrisation of Force Constants in MOPAC 6.0/7.0 for Better Description of the Activation Barrier of Peptide Bond Rotations

    We have reparametrised the force constants in AM1 and PM3 for better description of activation barriers of peptide bond rotations. A new keyword MMOP was introduced for special recognition of peptide bonds pre...

    Olaf Ludwig, Heiko Schinke, Wolfgang Brandt in Molecular modeling annual (1996)

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