Minimization of empirical energy functions in proteins including hydrophobic surface area effects

We present analytical expressions to calculate the gradient of the water-accessible surface area of proteins with respect to Cartesian coordinates and dihedral angles. A detailed mathematical analysis leads to corrected equations for the gradient calculation used previously in the ANAREA program. To study the hydrophobic effect of solvent-protein interactions, our expressions have been implemented to further improve the program package FANTOM. We used this version of FANTOM to minimize the ECEPP/2 and the hydrophobic energy of tendamistat. © 1993 John Wiley & Sons, Inc.     

Reciprocal space constraints create real-space anomalies in doped carbon nanotubes

When graphite is doped with electrons, carbon-carbon bonds lengthen and Raman-active phonons soften as antibonding states fill. However, in semiconducting carbon nanotubes, one Raman-active G-band mode increases in frequency at low doping levels. We show how phase constraints on the conduction-band wave function expose a latent bonding character in the conduction band of certain nanotubes. In these tubes, filling the lowest conduction band shortens the axial bonds even as it lengthens the circumferential bonds. The A{1}{LO} phonon, which preferentially stretches the axial bonds, then hardens even as the other phonons soften. Quantum confinement eliminates the angular averaging taken for granted in higher-dimensional systems and develops a new class of states, neither bonding nor antibonding, whose character depends on the angular orientation of the bonds in question.     

Ueber die Bestimmung des Gerbstoffs in Gerbstoffmaterialien

Ohne Zusammenfassung     

"Fast excitation" CID in a quadrupole ion trap mass spectrometer

Collision-induced dissociation (CID) in a quadrupole ion trap mass spectrometer is usually performed by applying a small amplitude excitation voltage at the same secular frequency as the ion of interest. Here we disclose studies examining the use of large amplitude voltage excitations (applied for short periods of time) to cause fragmentation of the ions of interest. This process has been examined using leucine enkephalin as the model compound and the motion of the ions within the ion trap simulated using ITSIM. The resulting fragmentation information obtained is identical with that observed by conventional resonance excitation CID. "Fast excitation" CID deposits (as determined by the intensity ratio of the a(4)/b(4) ion of leucine enkephalin) approximately the same amount of internal energy into an ion as conventional resonance excitation CID where the excitation signal is applied for much longer periods of time. The major difference between the two excitation techniques is the higher rate of excitation (gain in kinetic energy) between successive collisions with helium atoms with "fast excitation" CID as opposed to the conventional resonance excitation CID. With conventional resonance excitation CID ions fragment while the excitation voltage is still being applied whereas for "fast excitation" CID a higher proportion of the ions fragment in the ion cooling time following the excitation pulse. The fragmentation of the (M + 17H)(17+) of horse heart myoglobin is also shown to illustrate the application of "fast excitation" CID to proteins.     

1H-CRAMPS Solid-State NMR and X-Ray Crystal Studies of Inclusion Complexes Formed from 3,3′-bis(9-Hydroxy-9-fluorenyl)-2,2′-binaphthyl Hosts with Acetone

The crystal structures of inclusion compounds of 3,3-bis(9-hydroxy-9-fluorenyl)-2,2-binaphthyl host (1) and its chloro (2) or bromo (3) derivatives substituted in 2,7-positions of the fluorene units with acetone guests (1A–3A) were determined by X-ray studies as well as by ¹H-CRAMPS solid-state NMR. Using this NMR technique allows identification of differently bound guest molecules due to their different chemical shifts caused by the influence of the ring current effects of the host aryl units.     

Reaction of 5,6,7,8-Tetrahydropterin with Iron(III) Acetylacetonate. Detection of Radical Cations by Electrospray Ionization Mass Spectrometry

The experimental conditions developed for the detection of rather stable radical cations in solution by electrospray-ionization mass spectrometry (ESI-MS) of a Fe^II complex of 2-amino-5,6,7,8-tetrahydro-5-methylpteridin-4 (3H)-one ( 1c ) are used to observe the formation of the more unstable radical cations formed from 2-amino-5,6,7,8-tetrahydropteridin-4(3H)-one ( 1a ) and tris(pentane-2,4-dionato)iron(III) ([Fe^III(acac)₃]; 4 ) and to monitor their oxidation to the corresponding p-quinonoid dihydropterin complexes. These results contribute to the understanding of the important role played by 6β-5,6,7,8-tetrahydro-L -biopterin ( 1b ; a homologue of 1a ) together with iron as constituent of some cofactors. The complexes obtained from 1a and iron may be considered, e.g. as a model of the cofactor of the phenylalanine hydroxylase. Moreover, we describe an improved synthesis of 1c .