Dynamics of Bacteriorhodopsin in the Dark-Adapted State from Solution Nuclear Magnetic Resonance Spectroscopy

To achieve efficient proton pumping in the light-driven proton pump bacteriorhodopsin (bR), the protein must be tightly coupled to the retinal to rapidly convert retinal isomerization into protein structural rearrangements. Methyl group dynamics of bR embedded in lipid nanodiscs were determined in the dark-adapted state, and were found to be mostly well ordered at the cytosolic side. Methyl groups in the M145A mutant of bR, which displays only 10 % residual proton pumping activity, are less well ordered, suggesting a link between side-chain dynamics on the cytosolic side of the bR cavity and proton pumping activity. In addition, slow conformational exchange, attributed to low frequency motions of aromatic rings, was indirectly observed for residues on the extracellular side of the bR cavity. This may be related to reorganization of the water network. These observations provide a detailed picture of previously undescribed equilibrium dynamics on different time scales for ground-state bR.     

Pseudo-epitaxial C60 films prepared by a hot-wall method

We have used both reflection-geometry and grazing-incidence-geometry X-ray scattering to study thin films of C₆₀ evaporated onto mica substrates via a hot-wall technique. The growth mode yields close-packed C₆₀ planes, which are parallel to the substrate surface and which exhibit out-of-plane correlation lengths of 850 Å. In the film plane the C₆₀ is at best pseudo-epitaxial, with a 0.9° distribution of crystallite orientations, a 450 Å in-plane correlation length, and a 3.7% lattice mismatch, better than obtained by other thin film techniques but far from the accepted definition of single crystal thin film epitaxy.     

Virtual logarithms

The modification of the number field sieve which Joux and Lercier recently used to compute logarithms in a prime field of a record 120 decimal digits makes use of the notion of a virtual logarithm of a prime ideal in a number ring. We provide necessary and sufficient conditions for their method to succeed and give an explicit formula for the virtual logarithm of an ideal.     

The “corset effect” of spin-lattice relaxation in polymer melts confined in nanoporous media

Linear polyethylene oxides with molecular weightsM _w of 1665 and 10170 confined in pores with variable diameters in a solid methacrylate matrix were studied by proton field-cycling nuclear magnetic resonance relaxometry. The pore diameter was varied in the range of 9–57 nm. In all cases, the spin-lattice relaxation time shows a frequency dependence close toT ₁∞ v^3/4 in the range ofv=3·10^?1-2·10¹ MHz as predicted by the tube-reptation model. This protonT ₁ dispersion essentially reproduces that found in a previous deuteron study (R. Kimmich, R.-O. Seitter, U. Beginn, M. Möller, N. Fatkullin: Chem. Phys. Lett. 307, 147, 1999). As a feature particularly characteristic for reptation, this finding suggests that reptation is the dominating chain dynamics mechanism under pore confinement in the corresponding time range. The absolute values of the spin-lattice relaxation times indicate that the diameter of the effective tubes in which reptation occurs is much smaller than the pore diameters on the time scale of spin-lattice relaxation experimens. An estimation leads to a valued ^*～0.5 nm. The impenetrability of the solid pore walls, the uncrossability of polymer chains (“excluded volume”) and the low value of the compressibility in polymer melts create the “corset effect” which reduces the lateral motions of polymer chains to a microscopic scale of only a few tenths of a nanometer.     

Justification of the Shallow-Water Limit for a Rigid-Lid Flow with Bottom Topography

The so-called lake equations arise as the shallow-water limit of the rigid-lid equations—three-dimensional Euler equations with a rigid-lid upper boundary condition—in a horizontally periodic basin with bottom topography. We prove an a priori estimate in the Sobolev space H ^m for m≥ 3 which shows that a solution to the rigid-lid equations can be approximated by a solution of the lake equations for an interval of time which can be estimated in terms of the initial deviation from a columnar configuration and the magnitude of the initial data in H ^m , the gradient of the bottom topography in H ^m+1 , and the aspect ratio of the basin. In particular, any solution to the lake equations remains close to some solution of the rigid-lid equations for an interval of time that can be made arbitrarily large by choosing the aspect ratio of the basin small. Received 10 October 1996 and accepted 15 May 1997     

Consecutive reactions of diethoxydimethylsilane and triethoxymethylsilane with methoxide ions in methanol solution

The consecutive reactions of (CH₃)₂Si(OC₂H₅)₂ and CH₃Si(OC₂H₅)₃ with methoxide ions were investigated in methanol solutions. The reverse transesterification reactions with ethoxide ions could be neglected in both cases since the concentration of ethoxide in methanol solution was assumed to be low due to the fast equilibrium reaction C₂H₅O^? + CH₃OH ? C₂H₅OH + CH₃O^?. The progress of the reactions was followed by monitoring the formation of ethanol with a Fourier-transform infrared spectrometer. All rate constants were determined at 295 K. The reactions between the dialkoxydimethylsilanes and methoxide ions were assumed to consist of two consecutive steps that can be represented by the net reaction; (CH₃)₂Si(OC₂H₅)₂ + 2CH₃O^? → (CH₃)₂Si(OCH₃)₂ + 2C₂H₅O^?. The two consecutive rate constants were established as 1.93 ± 0.12M^?1s^?1 and 1.00 ± 0.12M^?1s^?1, respectively. The consecutive rate constants for the reactions between the trialkoxymethylsilanes and methoxide ions can be written according to the total reaction; CH₃Si(OC₂H₅)₃ + 3CH₃O^? → CH₃Si(OCH₃)₃ + 3C₂H₅O^?. The three rate constants corresponding to each consecutive step were established as 1.12 ± 0.09 M^?1s^?1, 0.82 ± 0.10 M^?1s^?1, and 0.51 ± 0.06 M^?1s^?1, respectively. © 1995 John Wiley & Sons, Inc.     

Direct SCF structure optimization of large molecules on networks of workstations

A program to optimize the structure of large molecules at the Hartree–Fock level of theory running concurrently on a network of workstations is presented. Problems encountered in obtaining nearly optimal speedup and their solutions are discussed. A simple scheduling algorithm is presented that enables up to 99.5% of the code to run in parallel. © 1993 John Wiley & Sons, Inc.