Inter-atom force fields

An improved united atom force field for simulation of mixed lipid bilayers has been introduced and compared to X-ray and NMR structures. The dynamics of hydration-water in several phospholipids membranes of different compositions was studied by 2D H P heteronuclear correlation NMR under MAS using a H T2 filter before and a H mixing time after the evolution period and P detection so that inter-bilayer water is selectively... 

A united atom CHARMm-based parameter set for carbohydrates has been introduced that offers a unique method for overcoming the multiple minima problem associated with inter-residue hydrogen bonding. In analogy with united atom force fields that treat C-H atomic pairs as extended atoms, the CHEAT approach unites O-H atomic pairs. The default... 

Ludovice, Jaffe, and Yoon have used the same approach to characterize the inter- and intramolecular energy surface of polyvinyl chloride (PVC) model compounds.2-Chloropropane and 1,3-dichloropropane were studied, and a classical force field was fitted to their quantum chemically derived energy surfaces. The ultimate goals were to obtain a new force field for molecular mechanics and stochastic dynamics simulations and to analyze the atomic level morphology of this particular polymer. 

In many force fields, truncation schemes are often used to reduce the number of non-bonded electrostatic and Lennard-Jones interactions that need to be calculated. Such schemes, are readily incorporated into the.inter-action Hamiltonian either by omitting all interactions that have a distance greater than some cutoff or by multiplying the appropriate interactions by a tapering function that reduces the interactions to zero beyond a certain distance. It is to be noted that in some hybrid force fields (see, for example, [35]) the electrostatic interaction terms are not included and the QM/MM interaction is due solely to the Lennard-Jones terms (and link-atoms if they are present). This could be a reasonable approximation in non-polar systems (such as the transition metal complexes for which some of these force fields were developed) but it will not be sufficiently accurate in the general case. 

An attempt has been made to correlate deviations from predicted C shifts in hydroxyandrostanes with geometric distortion. Allinger s molecular force field was used to calculate geometries of the molecules. Although some correlation of C shifts with non-bonded interactions can be achieved, it seems unwise to postulate geometric distortion alone as the cause of observed n.m.r. deviations. A computer-based method for prediction of C chemical shifts in saturated mono-and poly-cyclic frameworks gives, inter alia, a close fit with data for the individual carbon atoms in 5a-androstane. ... 

Abstract Atomic force spectroscopy (AFM)-based single-molecule force spectroscopy (SMFS) was invented in the 1990s. Since then, SMFS has been developed into a powerful tool to study the inter- and intra-molecular interactions of macro-molecules. Using SMFS, a number of problems in the field of supramolecular chemistry and mechanochemistry have been studied at the single-molecule level, which are not accessible by traditional ensemble characterization methods. In this review, the principles of SMFS are introduced, followed by the discussion of several problems of contemporary interest at the interface of supramolecular chemistry and mechanochemistry of macromolecules, including single-chain elasticity of macromolecules, interactions between water and macromolecules, interactions between macromolecules and solid surface, and the interactions in supramolecular polymers. 

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