Computation based on molecular models is playing an increasingly important role in biology, biological chemistry, and biophysics. Since only a very limited number of properties of biomolecular systems is actually accessible to measurement by experimental means, computer simulation can complement experiment by providing not only averages, but also distributions and time series of any definable quantity, for example, conformational distributions or interactions between parts of systems. Present day biomolecular modeling is limited in its application by four main problems: 1) the force-field problem, 2) the search (sampling) problem, 3) the ensemble (sampling) problem, and 4) the experimental problem. These four problems are discussed and illustrated by practical examples. Perspectives are also outlined for pushing forward the limitations of biomolecular modeling.

The subject of this report is the calibration of a model of the liquid state of acetonitrile (methyl cyanide). The model describes the liquid in terms of molecular mechanics with each molecule of the liquid treated as a rigid body that is composed of three interaction sites, between which Coulomb and dispersion interactions are computed. A brief overview of the literature on such models is given and a set of parameters for the model is presented. The representation of liquid acetonitrile produced by the parameters is compared to that produced by several other parameter sets available in the literature. It is concluded that, of the parameter sets for the three-site molecular mechanics model that currently are available, under the simulation conditions used, the one presented produces the most rounded representation of the properties of liquid acetonitrile.

Computerverfahren auf der Grundlage von Molekülmodellen gewinnen in Biologie, biologischer Chemie und Biophysik zunehmend an Bedeutung. Da nur wenige Eigenschaften biomolekularer Systeme durch Messungen zugänglich sind, können Computersimulationen experimentelle Daten ergänzen, indem sie nicht nur Durchschnittswerte, sondern auch Verteilungen und Zeitreihen jeder bestimmbaren Größe liefern, z. B. Konformationsverteilungen oder Wechselwirkungen zwischen Teilen eines Systems. Die Anwendung moderner biomolekularer Modellierungsverfahren wird zurzeit durch vier grundlegende Probleme eingeschränkt: 1) das Kraftfeldproblem, 2) das Suchproblem, 3) das Ensembleproblem und 4) das Experimentalproblem. Diese vier Probleme werden anhand praktischer Beispiele erläutert, außerdem werden Lösungsperspektiven aufgezeigt.

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It has been suggested that the stability of a beta-peptide helical fold is affected by the interplay between the electrical charge of terminal groups and the dipole due to the helical conformation, the so-called charge-dipole stabilization; the numerical simulations presented herein test that suggestion. The motions of two beta-peptide oligomers, each of which has been shown by NMR spectroscopy to fold into a different helical conformation, have been simulated. The simulated motions bear out empirical observations as to the effect of chemical protection of terminal groups on the stability of beta-peptide helical folds and they support the hypothesis of charge-dipole stabilization.