A comparative analysis of various gradient methods for geometry optimization at the ab initio SCF-MO level

Various techniques, already suggested for improving the computational efficiency of the force relaxation method, have been applied here in conjunction with the variable metric algorithms suggested by Murtagh and Sargent and by Fletcher. Various tests have been performed to assess the computational efficiency of the resulting minimization procedures. In addition, procedures where the steps are defined in terms of a parabolic fitting of the forces in approximated normal coordinates have been tested. In all cases the forces are computed analytically.     

Amplified DNA sensing and immunosensing by the rotation of functional magnetic particles

Amplified chemiluminescent detection of DNA-complementary DNA or of antigen-antibody interactions is accomplished in the presence of rotating functionalized magnetic particles.     

A comparative study of effective core potential and full-electron calculations in Mo compounds. I. An analysis of topological properties of bond charge distribution

Effective core potential (ECP) and full-electron (FE) calculations for MoS₄^?2, MoO₄^?2, and MoOCl₄ compounds were analyzed. Geometry parameters, binding energies, charge distributions, and topological properties of the electronic density were studied for Mo? L bonds (L = S, O, Cl). Results clearly indicate that those approaches that include valence plus 4s and 4p electrons (ECP2 methods) are able to reproduce the topological properties of Mo? L bonds, charge distributions, and geometries with respect to those obtained by FE methods. ECP methods that consider only the 4d and 5s valence electrons (ECP1) fail in the calculation of molecular properties. The use of 5p functions in ECP1 approaches produces a negative Mulliken charge on Mo. Bader's charges give more consistent results than Mulliken's ones. A new parameter for measuring the degree of ionicity is proposed. © 1994 by John Wiley & Sons, Inc.     

The Antiepileptic Lamotrigine and Its Analogues: Comparative Theoretical Electronic Properties

Electronic properties of lamotrigine (LTG) and two analogues (A1 and A2) are compared through MOPAC-AM1 calculations. Two stable conformers of LTG are calculated to exist in agreement with X-ray crystallography. In the three compounds and the two conformers for each of them, the more favorable protonation sites are N₂ and N₄; these should then be the sites appropriate for interaction with a receptor, and group valence reinforces the supposition. The molecular electrostatic potentials show that a region between the two chlorine atoms in LTG could be the site for an electrostatic interaction with a corresponding site in the receptor. The fluorine atom in A1 would play an equivalent role. A simple model for LTG-receptor interaction is proposed.     

From Epiraikovenal,an Instrumental Niche-Exploitation Sesquiterpenoid of Some Strains of the Marine Ciliated Protist euplotes raikovi,to an unusual intramolecular tele-dienone-olefin [2+2] photocycloaddition

It is shown that strains of the marine ciliate Euplotes raikovi are subtly variable in their production of secondary metabolites. Strains GA8 and 39W from Mediterranean and SB8 from Californian coasts produce the sesquiterpenoid epiraikovenal ( 3 ), while strains GA8 and SB8 also produce secoepiraikovenal ( 4 ), which play an instrumental niche-exploitation role and have also taxonomic significance. Comparison of 3 and 4 with raikovenal ( 2 ) and its putative biogenetic precursor 1 , which have similar roles in the conspecific strain Morl from Casablanca coast in the Atlantic Ocean, inspired us the first case of intramolecular tele-dienone-olefin [2+2] photocycloaddition, exemplified here by the transformation of 1 into ent- 3 . This served also to unequivocally clarify the stereochemical relationship between 3 and 2 .     

Titanosilicates as Supports for an Enzymatic Alcoholysis Reaction

Novel [Cr^III(amp)(bipy)(Cl)] (1) (H₂amp = N-(hydroxyphenyl)salicyldimine; bipy = 2,2-bipyridyl) and [Cr^III(app)(bipy)(Cl)]⁺ (2) (H₂app = N-(hydroxyphenyl)pyridine-2-carboxaldimine; bipy = 2,2-bipyridyl) complexes have been synthesized and characterized by physico-chemical methods. Complexes 1 and 2 have been employed as catalysts in the oxidation of both saturated and unsaturated hydrocarbons using tert-butylhydroperoxide (t-BuOOH). The significance of the results with respect to oxo-functionalization of C-H bonds both in unsaturated and saturated hydrocarbons is noted.     

Ab initio computation of force constants: Part VI. Applications of the force relaxation method for geometry optimization

Techniques to improve the computational efficiency of the force relaxation method are discussed. Force constants for fragments in previously computed smaller molecules can be transferred to construct a guess force constant matrix. Additional force constants that may be needed can be computed by a procedure which uses only one additional force calculation per diagonal force constant required. A scaling technique to improve convergence on the optimized geometry is discussed.     

The Vroman effect: a molecular level description of fibrinogen displacement

The molecular level details of the displacement of surface adsorbed fibrinogen from silica substrates were studied by atomic force microscopy, immunochemical assays, fluorescence microscopy, and vibrational sum frequency spectroscopy. The results showed that human plasma fibrinogen (HPF) can be readily displaced from the interface by other plasma proteins near neutral pH because the positively charged alpha C domains on HPF sit between the rest of the macromolecule and the underlying surface. The alpha C domains make weak electrostatic contact with the substrate, which is manifest by a high degree of alignment of Lys and Arg residues. Upon cycling through acidic pH, however, the alpha C domains are irreversibly removed from this position and the rest of the macromolecule is free to engage in stronger hydrogen bonding, van der Waals, and hydrophobic interactions with the surface. This results in a 170-fold decrease in the rate at which HPF can be displaced from the interface by other proteins in human plasma.     

Molecular dynamics simulations of the surface tension of ionic liquids

We report molecular dynamics computer simulations of the surface tension and interfacial thickness of ionic liquid-vapor interfaces modeled with a soft core primitive model potential. We find that the surface tension shows an anomalous oscillatory behavior with interfacial area. This observation is discussed in terms of finite size effects introduced by the periodic boundary conditions employed in computer simulations. Otherwise we show that the thickness of the liquid-vapor interface increases with surface area as predicted by the capillary wave theory. Data on the surface tension of size-asymmetric ionic liquids are reported and compared with experimental data of molten salts. Our data suggest that the surface tensions of size-asymmetric ionic liquids do not follow a corresponding states law.