Library

feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
  • 2000-2004  (3)
  • 1995-1999  (6)
  • 1
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 105 (1996), S. 4289-4293 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: An investigation into the effects of the anisotropic nature of the Ewald potential for the treatment of long range electrostatic interactions in liquid solutions has been performed. The rotational potential energy surface for two simple charge distributions, and a small protein, have been studied under conditions typically implemented in current biomolecular simulations. A transition between hindered and free rotation is observed which can be modeled quantitatively for simple charge distributions. For most systems in aqueous solution, the transition involves an energy change well below kBT. It is argued that, for solvents with a reasonably high relative permittivity, Ewald artifacts will be small and in many cases may be safely ignored. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 2
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 5451-5459 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Molecular dynamics simulations of ionic systems require the inclusion of long-range electrostatic forces. We propose an expression for the long-range electrostatic forces based on an analytical solution of the Poisson–Boltzmann equation outside a spherical cutoff, which can easily be implemented in molecular simulation programs. An analytical solution of the linearized Poisson–Boltzmann (PB) equation valid in a spherical region is obtained. From this general solution special expressions are derived for evaluating the electrostatic potential and its derivative at the origin of the sphere. These expressions have been implemented for molecular dynamics (MD) simulations, such that the surface of the cutoff sphere around a charged particle is identified with the spherical boundary of the Poisson–Boltzmann problem. The analytical solution of the Poisson–Boltzmann equation is valid for the cutoff sphere and can be used for calculating the reaction field forces on the central charge, assuming a uniform continuum of given ionic strength beyond the cutoff. MD simulations are performed for a periodic system consisting of 2127 SPC water molecules with 40 NaCl ions (1 molar). We compare the structural and dynamical results obtained from MD simulations in which the long range electrostatic interactions are treated differently; using a cutoff radius, using a cutoff radius and a Poisson–Boltzmann generalized reaction field force, and using the Ewald summation. Application of the Poisson–Boltzmann generalized reaction field gives a dramatic improvement of the structure of the solution compared to a simple cutoff treatment, at no extra computational cost. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 3
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 114 (2001), S. 426-435 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: 2,2,2-trifluoroethanol (TFE) is a commonly used cosolvent in experimental studies of peptides and proteins. Although concentration-dependent TFE effects have been well studied experimentally, the exact mechanism by which TFE affects the solubility and stability of peptides is still unclear. Here we report molecular dynamics simulations of TFE/water mixtures of different composition in an attempt to improve our atomic level understanding of the properties of TFE/water mixtures. The trends in most properties—densities, diffusion constants, dielectric constants, and enthalpies of mixing—were well reproduced, although quantitative agreement with experiment was poor. Other thermodynamic properties of the solutions—partial molar volumes, derivatives of activity coefficients, and isothermal compressibilities—were also determined using the Kirkwood–Buff theory of mixtures. The Kirkwood–Buff analysis indicated significant aggregation of TFE molecules in the mixtures, especially at low mole fractions, in agreement with experiment. However, the aggregation of TFE molecules was exaggerated using the current TFE and water models. The results suggest that the combination of simulation data and Kirkwood–Buff theory provides a powerful tool for the investigation of the thermodynamic properties of hydrogen bonding mixtures. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 4
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Biochemistry 34 (1995), S. 16269-16278 
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 5
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 117 (1995), S. 2147-2158 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 6
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 5568-5579 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Molecular dynamics (MD) simulations have been used to determine the two dimensional free energy surface of the alanine dipeptide in solution. The intramolecular dipeptide interactions were described by the CHARMM22 force field. Three models of solvation were considered; (i) a simple scaling of electrostatic interactions, (ii) solvation energies determined by finite difference Poisson–Boltzmann calculations, and (iii) inclusion of explicit TIP3P solvent molecules. All three solvation models produced qualitatively similar effects, but differed significantly in their quantitative values. In particular, the continuum based models predicted the β (extended) conformation to be most stable, whereas the explicit solvent model favored the αR (folded) conformation. Comparison with experimental data for the H–N–Cα-Hα coupling constant, helix–coil transition thermodynamics, and polypeptide infinite chain length characteristic ratios was performed. The explicit solvent surface produced the strongest agreement with experiment, although there is no unambiguous data to support any of the solvent models. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 7
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 115 (2001), S. 5521-5530 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: It is necessary to evaluate the quality of a force field by comparison with known experimental properties before it can be used with confidence in a simulation. Here, such a study is reported for pure 2,2,2-trifluoroethanol (TFE) solutions and for TFE/water mixtures at two different compositions. Six literature force fields were examined using molecular dynamics simulations. It is found that none of the currently available force fields describe all the properties of pure liquid TFE. The models of van Buren and Berendsen, Duffy and Jorgensen, and Fioroni et al. produce properties that are in reasonable agreement with experiment. The ability to adequately describe properties of TFE/water mixtures varied with the property of interest. The heat of mixing is too unfavorable for all the models. The aggregation properties of the mixtures were well described by the model of Duffy and Jorgensen at the lower composition (30% by volume of TFE), while the Fioroni et al. model performed better at higher TFE concentrations. The activity coefficient derivative from the Fioroni et al. model was in very good agreement with experiment for all compositions studied here. Consequently, the choice of the most appropriate force field will depend on the major properties of interest. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 8
    ISSN: 1430-4171
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 9
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 27 (1997), S. 227-233 
    ISSN: 0887-3585
    Keywords: peptide conformation ; ramachandran plot ; PDB search ; peptide dynamics ; BPTI ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A simple method is presented for projecting the conformation of extended secondary structure elements of peptides and proteins that extend over four Cαatoms onto a simple two-dimensional surface. A new set of two degrees of freedom is defined, a pseudo-dihedral involving four sequential Cαatoms, as well as the triple scalar product for the vectors describing the orientation of the three intervening peptide groups. The method provides a reduction in dimensionality, from the usual combination of multiple φ,ψ pairs to a single pair, yielding valuable information concerning the structure and dynamics of these important elements. The new two-dimensional surface is explored by reference to 63 selected protein crystal structures together with a comparison of model built peptides representing the common secondary structural elements. Dynamical aspects on this new surface are examined using a molecular dynamics trajectory of Basic Pancreatic Trypsin Inhibitor. © 1997 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...