Shlomo Nir

Polarizability calculations on water, hydrogen, oxygen, and carbon dioxide

Based on the semiclassical model of damped oscillators, a procedure is developed for the calculation of the dispersion of refractive index, polarizability, and dielectric permeability, which are treated as complex quantities. Using experimental values of refractive indices and employing the frequencies of strong absorption bands, a least squares fit is used to determine oscillator strengths and damping factors. The absorption coefficient and the imaginary part of the refractive index are also calculated at the corresponding wavelengths. The procedure is applied for the cases of water, hydrogen, and oxygen in both the liquid and gaseous states and for gaseous carbon dioxide, and a good agreement is obtained between calculated and observed values of refractive indices. Results are also compared with those of previous calculations. Calculated absorption coefficients agree well with experimental values in the region of absorption bands. The calculated values of oscillator strengths and damping factors are dis...

On the applicability of certain approximations of the Lifshitz theory to thin films

Abstract In an attempt to evaluate the attractive interaction energies between cells, the van der Waals forces between two semi-infinite media composed of substance A and separated by a thin film of substance B are considered on the basis of the Lifshitz theory. An improved approximation is proposed, whereby some previously neglected terms are included in the final expression for forces and interaction energies. The symmetry behavior of forces under interchan e of media is treated. Numerical investigations show that the proposed corrections become important in certain situations. The problem of a correct representation of dielectric coefficients for biological systems for the purpose of calculating dispersion forces is also discussed. A proposed representation of dielectric permeability for the case of liquid water is shown to well represent experimental data. Calculations of the van der Waals forces with the improved representation of dielectric permeabilities for a water-hydrocarbon system show significant changes from previously obtained results.

Long range intermolecular forces between macroscopic bodies: Macroscopic and microscopic approaches☆

Abstract Van der Waals energies of interaction are calculated by two methods, the macroscopic method of Lifshitz and the microscopic method of London-Casimir and Polder-Hamaker for the case of two semi-infinite slabs separated by a thin film. When retardation effects may be neglected, the London-Hamaker approach yields values of dispersion interactions which almost coincide with those of the Lifshitz approach, the magnitude of the former values being larger by approximately 10–25%, which is attributed to the effect of the molecular environment in condensed media. At 50–100 A film thicknesses where retardation effects are small, dispersion terms are generally the major part of van der Waals forces in the Lifshitz formulation. Hence, for 50–100 A film thicknesses the Hamaker approach, which only includes dispersion interactions is generally adequate. By accounting for retardation effects, which significantly reduce the magnitude of dispersion interactions at several hundred A, there is a reasonable agreement between the values obtained by the macroscopic and microscopic approaches. When polar substances are present and for film thicknesses of several hundred A, where dispersion interactions are significantly reduced, the major contribution to van der Waals forces may arise from orientation and induction terms. For such cases the Hamaker approach may lead to critical underestimates of the calculated magnitude of van der Waals forces. An ad hoc way to overcome this difficulty which is applicable to any geometry is proposed. This study presents a simple procedure for the determination of free energies of interaction between macroscopic bodies of various shapes. The procedure, which is applicable when the molecules of bodies and surrounding medium are isotropic, yields results which closely approximate those obtained with the Lifshitz theory.

Simulation and display of macromolecular complexes

Abstract An interactive program for building, manipulating and displaying molecules has been written. The program provides perspective, planar, and stereoscopic views on a computer terminal display. The views are given both for standard observer locations relative to the object and for locations determined and varied by the user. The user can rotate the whole molecule or parts of it relative to any axis in space, which can also be one of the bonds. The whole molecule or parts of it can be translated in a given direction and bond connections can be added or eliminated by the user. One of the subroutines enables juxtaposition of two molecular fragments in such a fashion that two given bonds are aligned and two planes and two corresponding points coincide. Hence the user can join two molecular fragments at a sought relative orientation and location. Another option includes a duplication of a given unit, e.g. an amino-acid or a DNA base. The program is running on the Roswell Park Univac 70 Computer which employs a time sharing system, but it has been written with an emphasis on flexibility and an easy adaptability to any computer. The display at the Roswell Park computer is supported by a hard copy unit, but plotter drawings can also be generated. The program is written in FORTRAN. In our laboratory the program is employed as one of the tools in the study of template properties of polynucleotides and their specific interactions with polypeptides. Few examples are illustrated.

Theoretical Studies on the Conformation of Peptides in Solution

A procedure for a theoretical prediction of most preferred conformations of molecules in solutions is described and applied for N-acetyl L-alanine N-methyl amide in CCI4 and in water and for N-acetyl glycine N-methyl amide in CCI4. The calculation of intrinsic, or intramolecular energies, employs the method of partitioned energy potential, including electrostatic, nonbonded and torsional terms. The intramolecular electrostatic energies include terms up to segmental octopole moments. Convergence of the electrostatic series is always obtained when all distances between interacting groups are not appreciably less than the sum of corresponding van der Waals radii. The calculation of intermolecular interactions with the environment is based on the method of continuum reaction field, including electrostatic, dispersion and cavity terms, which depend on the conformations through molecular dipole moments, molecular volume, and molecular exposed surface area. The most stable conformations predicted and calculated dipole moment are in reasonable agreement with experimental findings. For the case of N-acetyl glycine N-methyl amide calculations of intramolecular energies with ab-initio (STO-3G) and IEHT/2 are also presented. It is concluded that in the cases treated in this study the partitioned potential method yields significantly better predictions for the stable conformations than the molecular orbital methods.

A Phosphorus-31 NMR Study of Monovalent Cation Interactions with the Negatively Charged Surface of Phosphatidylserine Vesicles

The variation of P-31 nmr shifts and spinlattice relaxation times with cation atmosphere has been investigated for phosphatidylserine, present as a model membrane system of sonicated unilamellar vesicles. Two theoretical approaches, the ion condensation theory and a Gouy-Chapman theory modified to include specific binding sites, are used to describe the interaction of cations with the negatively charged PS surface. An important feature of the ion condensation model is the following: the total fraction of negative PS surface charge “neutralized” by cations in a thin “condensation” layer at the interface is independent of cation concentration in bulk solution. A similar result holds approximately for the binding site model, over an experimentally relevant range of concentrations. However the two models differ in their predicted dependence on cation bulk concentrations for the case where one cation species competes weakly against the other for the PS-solution interface. The observed dependence of P-31 nmr shifts on the fraction of Na+ in a NaCl/TEA·Cl bulk solution mixture appears to conform more closely to the behavior predicted by the binding site model than to that given by the ion condensation theory.

Interactive computer graphics for bio-stereochemical modelling

Several computer graphics programs for bio-stereochemical modelling are discussed for display and manipulation of molecules. The RPMI system which is currently running on the Univac 70 computer, is easily adaptable to any computer, with or without sophisticated graphics hardware. Hence, we emphasize the availability of an easy to handle and inexpensive means for building, manipulating, and displaying molecules. The RPMI system also includes an automated, noninteractive program for fast construction of specified molecular structures. The NASA system is running on an Evans and Sutherland display system which has sophisticated hardware and which is capable of continuously rotating the molecule with constant adjustment of perspective and intensity. Details are given for the important geometrical manipulations such as translations, rotations, and juxtapositions, and several procedures for building of molecules are described. A method is described for exploration of the fitting of peptides around DNA by means of isogeometric helices.Several illustrations are presented for the applications of the programs to the study of interactions of proteins with DNA.

Molecular geometries and moments from the maximum overlap criterion

Abstract The maximized overlap population, defined as Σμ≠νPμνSμν, and a related quantity, Σμ,νPμνS2μν are computed for a series of configurations. The extremum of both approximate molecular geometries, the latter with an accuracy suitable for predictive value. The maximum overlap orbitals predict dipole and quadrupole moments that give reasonable agreement with experimental values.