Incorporating solvent and ion screening into molecular dynamics using the finite-difference Poisson–Boltzmann method

The finite difference method for solving the Poisson–Boltzmann equation is used to calculate the reaction field acting on a macromolecular solute due to the surrounding water and ions. Comparisons with analytical test cases indicate that the solvation forces can be calculated rapidly and accurately with this method. These forces act to move charged solute atoms towards the solvent where they are better solvated, and to screen interactions between charges. A way of combining such calculations with conventional molecular dynamics force fields is proposed which requires little modification of existing molecular dynamics programs. Simulations on the alanine dipeptide show that solvent forces affect the conformational dynamics by reducing the preference for internal H-bonding forms, increasing the R-alpha helix preference and reducing transition barriers. These solvent effects are similar to previous explicit solvent simulations, but require little more computation than vacuum simulations. The method should scale up with little increase in computational cost to larger molecules such as proteins and nucleic acids.     

Glycoprotein adsorption into bilirubin/cholesterol mixed monolayers at the air-water interface

The adsorption of α₁-acid glycoprotein into bilirubin/cholesterol mixed monolayers with various component molar ratios is investigated using surface pressure-area (π-A) isotherms and (dπ/dA)-A curves. The results showed that the surface area per molecule increased after the adsorption/insertion of glycoprotein molecules into the monolayers. The compressibility of mixed monolayers increased as a result of hydrogen bonding between bilirubin and glycoprotein molecules, while the interactions between bilirubin and cholesterol are weakened. The adsorption of glycoprotein into a monolayer induced changes in molecular surface area depending on the surface pressure and molar fraction of bilirubin. The transmission electron microscopy of mixed monolayers confirmed the insertion of glycoprotein particles of spherical shape with an average diameter of about 80 nm into the monolayer. The text was submitted by the authors in English.     

Photodissociation tandem mass spectrometry at 266 nm of an aliphatic peptide derivatized with phenyl isothiocyanate and 4-sulfophenyl isothiocyanate

Photodissociation (PD) tandem mass spectra have been obtained at 266 nm for the protonated molecules of a tryptic peptide, ASHLGLAR, and of its phenyl isothiocyanate and 4-sulfophenyl isothiocyanate derivatives, generated by matrix-assisted laser desorption/ionization. Derivatization with the aromatic chromophores greatly reduced the intensity of the laser required for efficient PD. Major fragment ions observed in the three spectra are quite similar. General features of the PD tandem mass spectra and their potential utility for analytical purposes are discussed.     

Pairwise decomposition of residue interaction energies using semiempirical quantum mechanical methods in studies of protein-ligand interaction

Pairwise decomposition of the interaction energy between molecules is shown to be a powerful tool that can increase our understanding of macromolecular recognition processes. Herein we calculate the pairwise decomposition of the interaction energy between the protein human carbonic anhydrase II (HCAII) and the fluorine-substituted ligand N-(4-sulfamylbenzoyl)benzylamine (SBB) using semiempirical quantum mechanics based methods. We dissect the interaction between the ligand and the protein by dividing the ligand and the protein into subsystems to understand the structure-activity relationships as a result of fluorine substitution. In particular, the off-diagonal elements of the Fock matrix that is composed of the interaction between the ionic core and the valence electrons and the exchange energy between the subsystems or atoms of interest is examined in detail. Our analysis reveals that the fluorine-substituted benzylamine group of SBB does not directly affect the binding energy. Rather, we find that the strength of the interaction between Thr199 of HCAII and the sulfamylbenzoyl group of SBB affects the binding affinity between the protein and the ligand. These observations underline the importance of the sulfonamide group in binding affinity as shown by previous experiments (Maren, T. H.; Wiley: C. E. J. Med. Chem. 1968, 11, 228-232). Moreover, our calculations qualitatively agree with the structural aspects of these protein-ligand complexes as determined by X-ray crystallography.     

Unusual reactivity of tris(pyrazolyl)borate zirconium benzyl complexes

The synthesis and reactivity of [Tp*Zr(CH2Ph)2][B(C6F5)4] (2, Tp* = HB(3,5-Me2pz)3, pz = pyrazolyl) have been explored to probe the possible role of Tp'MR2+ species in group 4 metal Tp'MCl3/MAO olefin polymerization catalysts (Tp' = generic tris(pyrazolyl)borate). The reaction of Tp*Zr(CH2Ph)3 (1) with [Ph3C][B(C6F5)4] in CD2Cl2 at -60 degrees C yields 2. 2 rearranges rapidly to [{(PhCH2)(H)B(mu-Me2pz)2}Zr(eta2-Me2pz)(CH2Ph)][B(C6F5)4] (3) at 0 degrees C. Both 2 and 3 are highly active for ethylene polymerization and alkyne insertion. Reaction of 2 with excess 2-butyne yields the double insertion product [Tp*Zr(CH2Ph)(CMe=CMeCMe=CMeCH2Ph)][B(C6F5)4] (4). Reaction of 3 with excess 2-butyne yields [{(PhCH2)(H)B(mu-Me2pz)2}Zr(Cp*)(eta2-Me2pz)][B(C6F5)4] (6, Cp* = C5Me5) via three successive 2-butyne insertions, intramolecular insertion, chain walking, and beta-Cp* elimination.     

Mass-analyzed threshold ionization study of vinyl bromide cation in the first excited electronic state using vacuum-ultraviolet radiation generated by four-wave mixing in Hg

The vibrational spectrum of the vinyl bromide cation in the first excited electronic state A 2A' was obtained by one-photon mass-analyzed threshold ionization (MATI) spectroscopy. The use of an improved vacuum-ultraviolet radiation source based on four-wave sum frequency mixing in Hg resulted in excellent sensitivity for MATI signals. From the MATI spectrum, the ionization energy to the A 2A' state of the cation was determined to be 10.9150+/-0.0006 eV. Nearly complete vibrational assignments for the MATI peaks were possible by utilizing the vibrational frequencies and Franck-Condon factors calculated at the density-functional theory (DFT) and time-dependent DFT/B3LYP levels with the 6-311+G(df,p) basis set.     

Factors affecting the catalytic epoxidation of olefins by iron porphyrin complexes and H2O2 in protic solvents

The catalytic epoxidation of cyclohexene by iron(III) porphyrin complexes and H2O2 has been investigated in alcohol solvents to understand factors affecting the catalyst activity in protic solvents. The yields of cyclohexene oxide and the Fe(III/II) reduction potentials of iron porphyrin complexes were significantly affected by the protic solvents, and there was a close correlation between the product yields and the reduction potentials of the iron porphyrin catalysts. The role of alcohol solvents was proposed to control the electronic nature of iron porphyrin complexes that determines the catalyst activity in the epoxidation of olefins by H2O2. We have also demonstrated that an electron-deficient iron porphyrin complex can catalyze the epoxidation of olefins by H2O2 under conditions of limiting substrate with high conversion efficiency in a solvent mixture of CH3OH and CH2Cl2.     

Use of N-N bond stereodynamics in ring-closing metathesis to form medium-sized rings and macrocycles

A unique strategy based on double ring-closing metathesis for the formation of a 14-membered macrocyclic enamide has been developed. This strategy hinges upon the well-known stereodynamic and conformational behavior of N-substituted diacylhydrazines, which promotes an effective ring-closing metathesis of hydrazine-derived dienes and enynes to form 8- to 14-membered rings.     

Chiral separation of homocysteine by derivatization with 4-aminosulfonyl-7-fluoro-2,1,3-benzoxadiazole followed by capillary electrophoresis using gamma-cyclodextrin

Homocysteine was derivatized with 4-aminosulfonyl-7-fluoro-2,1,3-benzoxadiazole (ABD-F) to form an inclusion complex with cyclodextrin and to facilitate UV detection. ABD-homocysteine showed interaction with beta- and gamma-cyclodextrin in capillary electrophoresis at pH 2.25 as indicated by the decreased migration time. However, chiral separation of D,L-ABD-homocysteine was observed using gamma-CD only. Optimal separation was obtained at pH 2.25, 50 mM gamma-CD concentration, and 20 kV applied voltage. L-ABD-Homocysteine migrated faster than the D-isomer as demonstrated by a spiking experiment using dithiothreitol-reduced L-homocystine.