Solution conformation of tripeptides by NMR spectroscopy and force-field calculations

The solution conformation of three linear tripeptides Boc-Ala-Val-Val-OMe1, Boc-Ala-Pro-Val-OMe2, and Boc-Ala-(D)Pro-Val-OMe3 was studied by NMR spectroscopy and accompanying force-field calculations. In one case,2, as preferred conformation the-turnall trans conformer was found.     

Guidelines for the analysis of free energy calculations

Journal of Computer-Aided Molecular Design - Free energy calculations based on molecular dynamics simulations show considerable promise for applications ranging from drug discovery to prediction of...     

The geometry and vibrational frequency shift of CO molecules in an argon matrix studied by force-field calculations

In this paper, the CO·Ar interaction potential including pairwise and three-body contributions which reproduces the experimental CO vibrational frequency shift, Δω = ?4.7 cm^?1 in a static force-field approximation, is presented. The geometry of the COAr solid system is described in detail. The frequency shift is obtained when the CO molecule is oriented along the (0, 0, 1) crystal axis, with its center of mass shifted by 0.25 Å from the center of interaction, and with the surrounding first shell argon atoms relaxed into an approximately ellipsoidal cage. The semi-axes of the ellipsoid deviate from the radius of the undistorted first shell, 3.756 Å, by only 0.06 Å. The second shell of the argon atoms is also distorted into an ellipsoidal cage but the deviations from the sphere in this case are an order of magnitude smaller than for the first shell. Distortions of more distant crystal sites are negligible. Substitution of an Ar atom by a CO molecule with subsequent lattice relaxations into the minimum potential energy configuration results in a decrease in potential energy of 0.16 kJ mol^?1. The three-body contributions to the CO·Ar potential have only a negligible influence on the geometry of the COAr system (including the lattice relaxations) but a strong influence on the vibrational frequency shift.     

Structure-parameter and force-field refinement for lead dihalide molecules

Conclusions It has been shown for PbF₂ that one can process electron-diffraction data for molecules containing heavy atoms on the basis of atomic scattering amplitudes calculated with a relativistic approximation for the atomic electron density. The errors in calculating the atomicscattering amplitudes explain the previous discrepancies in the observed values for the Pb-Cl amplitudes in PbCl₂ derived in two independent researches. The differences between those values are now not so considerable, and they may be explained as due to experimental error or to the processing of the measurements in Hungary for most of the scattering angles having been performed without the relativistic corrections to the electron density.Our mean-square vibration amplitudes and the measured frequencies can be used with our semiempirical relationships for the force constants to determine the potential-energy parameters for those molecules and to estimate the vibrational frequencies for PbI₂, which have not been measured.I am indebted to Professor V. P. Spiridonov and staff at the vapor electron-diffraction laboratory at Moscow University for providing the observed values for the reduced molecular component of the scattering intensities for lead dihalides and for valuable comments in discussion on the draft.High-Temperature Institute, Academy of Sciences of the USSR. Translated from Zhurnal Strukturnoi Khimii, Vol. 32, No. 1, pp. 54–59, January–February, 1991.     

Molecular mechanics force-field development for amino acid zwitterions

Understanding the conformational flexibility of amino acid zwitterions (ZWs) and their associated conformational energies is crucial for predicting their interactions in biological systems. Gas-phase ab initio calculations of ZWs are intractable. Molecular mechanics (MM), on the other hand, is able to handle large systems but lacks the necessary force field parameters to model ZWs. To develop force field parameters that are able to correctly model ZW geometries and energetics we used a novel combinatorial approach: amino acid ZWs were broken down structurally into key functional components, which were parameterized separately. M?ller-Plesset second-order perturbation calculations on small carboxylates, on the glycine cation, and on novel hydrogen bonded systems, coupled with available experimental data, were used to generate MM3(2000) ZW parameters (Allinger N. L.; Yuh, Y. H.; Lii, J.-H. J Am Chem Soc 1989, 111, 8551). The MM3 results from this combinatorial approach gave geometries that are in good agreement with neutron diffraction experiments, plus their frequencies and energies appear to be reasonably modeled. Current limitations and future development of MM force fields are discussed briefly.     

The Conformations of cis-cyclododecene. Evidence from dynamic NMR spectroscopy and iterative force-field calculations

$\text{cis}$-Cyclododecene shows conformations barriers of 7 and 9.6 kcal/mol and exists as a mixture of two unsymmetrical conformations, labelled [1_ene2333] and [1_ene2342].     

Monte Carlo and modified Tanford-Kirkwood results for macromolecular electrostatics calculations

The understanding of electrostatic interactions is an essential aspect of the complex correlation between structure and function of biological macromolecules. It is also important in protein engineering and design. Theoretical studies of such interactions are predominantly done within the framework of Debye-Hückel theory. A classical example is the Tanford-Kirkwood (TK) model. Besides other limitations, this model assumes an infinitesimally small macromolecule concentration. By comparison to Monte Carlo (MC) simulations, it is shown that TK predictions for the shifts in ion binding constants upon addition of salt become less reliable even at moderately macromolecular concentrations. A simple modification based on colloidal literature is suggested to the TK scheme. The modified TK models suggested here satisfactorily predict MC and experimental shifts in the calcium binding constant as a function of protein concentration for the calbindin D(9k) mutant and calmodulin.     

Gatekeeping patterns in the publication of analytical chemistry research

An analysis has been made of the nationalities of the members of advisory and editorial boards of analytical chemistry journals. Correlations were sought between their number and citation rates and between their number and the number of analytical papers published by scientists from the country in question. A comparison is given for the gatekeepers of organic and inorganic chemistry journals.     

A force-field study of alkenyl radical ring closure

In accord with stereoelectronic considerations there is a good correlation between the relative rates, regiochemistry, and stereochemistry of ring closure of ω-alkenyl radicals, and the strain energies of transition structures determined by force field calculations.     

An evaluation of force-field treatments of aromatic interactions

Experimental measurements of edge-to-face aromatic interactions have been used to test a series of molecular mechanics force fields. The experimental data were determined for a range of differently substituted aromatic rings using chemical double mutant cycles on hydrogen-bonded zipper complexes. These complexes were truncated for the purposes of the molecular mechanics calculations so that problems of conformational searching and the optimisation of large structures could be avoided. Double-mutant cycles were then carried out in silico using these truncated systems. Comparison of the experimental aromatic interaction energies and the X-ray crystal structures of these truncated complexes with the calculated data show that conventional molecular mechanics force fields (MM2, MM3, AMBER and OPLS) do not perform well. However, the XED force field which explicitly represents electron anisotropy as an expansion of point charges around each atom reproduces the trends in interaction energy and the three-dimensional structures exceedingly well. Collapsing the XED charges onto atom centres or the use of semi-empirical atom-centred charges within the XED force field gives poor results. Thus the success of XED is not related to the methods used to assign the atomic charge distribution but can be directly attributed to the use of off-atom centre charges.     

Some results from 50 years' research on surface forces

A review is presented about research on surface forces and surface interactions conducted over the past half-century, with some emphasis on the pioneering contributions of the Department of Surface Phenomena at the Institute of Physical Chemistry of the USSR Academy of Sciences.     

AMBER force-field parameters for guanosine triphosphate and its imido and methylene analogs

Parameters were derived for guanosine triphosphate (GTP) and GTP analogs suitable for the AMBER force field. Electrostatically derived net atomic charges and force parameters were extracted from MNDO semiempirical calculations. The later parameters came from fitting MNDO and AMBER atom–atom forces in a manner that is extensible to other compounds that lack sufficient vibrational spectral data. The geometric parameters for these compounds were obtained from model compounds in the Cambridge crystallographic data base. Dynamic simulations of Na₄ GTP and Na₂ Mg GTP of 140 and 100 ps, respectively, indicated a strong preference for a syn C2′ exo conformation in solution. © 1993 John Wiley & Sons, Inc.