Scalable methods for the construction and analysis of virtual combinatorial libraries

One can distinguish between two kinds of virtual combinatorial libraries: viable and accessible . Viable libraries are relatively small in size, are assembled from readily available reagents that have been filtered by the medicinal chemist, and often have a physical counterpart. Conversely, accessible libraries can encompass millions or billions of structures, typically include all possible reagents that are in principle compatible with a particular reaction scheme, and they can never be physically synthesized in their entirety. Although the analysis of viable virtual libraries is relatively straightforward, the handling of large accessible libraries requires methods that scale well with respect to library size. In this work, we present novel, efficient and scalable techniques for the construction, analysis, and in silico screening of massive virtual combinatorial libraries.     

A wide angle and high Mach number parabolic equation

Various parabolic equations for advected acoustic waves have been derived based on the assumptions of small Mach number and narrow propagation angles, which are of limited validity in atmospheric acoustics. A parabolic equation solution that does not require these assumptions is derived in the weak shear limit, which is appropriate for frequencies of about 0.1 Hz and above for atmospheric acoustics. When the variables are scaled appropriately in this limit, terms involving derivatives of the sound speed, density, and wind speed are small but can have significant cumulative effects. To obtain a solution that is valid at large distances from the source, it is necessary to account for linear terms in the first derivatives of these quantities [A. D. Pierce, J. Acoust. Soc. Am. 87, 2292-2299 (1990)]. This approach is used to obtain a scalar wave equation for advected waves. Since this equation contains two depth operators that do not commute with each other, it does not readily factor into outgoing and incoming solutions. An approximate factorization is obtained that is correct to first order in the commutator of the depth operators.     

Molecular structure of alcohol-water mixtures

We use x-ray emission spectroscopy to elucidate the molecular structure of liquid methanol, water, and methanol-water solutions. We find that molecules in the pure liquid methanol predominantly persist as hydrogen-bonded chains and rings with six and/or eight molecules of equal abundance. For water-methanol solutions we find evidence of incomplete mixing at the microscopic level. Our results provide a new explanation for a smaller entropy increase in the solution due to water molecules bridging methanol chains to form rings.     

Experimental determination of the lifetime for the 2p3d(1P0) helium doubly excited state

Two recent theoretical studies [C. Liu, Phys. Rev. A 64, 010501 (2001)]; M. Zitnik, ibid. 65, 032520 (2002)]] predict that the fluorescence lifetimes of helium doubly excited states converging to He+ N=2 should be longer than that of the He+ 2p ion state. This effect is caused by the electric field of the outer electron which, through Stark mixing, gives the inner fluorescing electron some series specific, stabilizing 2s character. We have obtained the first experimental evidence that confirms this effect by measuring the lifetime of the 2p3d(1P0) doubly excited state. This was determined to be 190+/-30 ps compared to 100 ps for the He+ 2p ion state. The measurements were performed using short pulses of synchrotron radiation to form doubly excited states and recording the arrival time of photons from fluorescence.     

Determination of the conformation and stability of simple homopolypeptides using solid-state NMR

15N CPMAS, 13C CPMAS and 1H CRAMPS spectra of several polypeptide samples were compared to determine the useful features of each technique. 13C CPMAS is the most well-established technique and is useful for quick determination of secondary structure. The 15N nucleus is more sensitive to exact hydrogen-bonding parameters, which complicates interpretation of the spectra. However, it is better for resolving end effects and structural types in short oligomers. 1H CRAMPS spectra are similar to 13C CPMAS in the information obtained, but the resolution is not as good. Using 13C CPMAS, the conformation of polyglycine was investigated in detail. Precipitation from solvents such as DCA or TFA resulted in the rippled beta-sheet structure (PG I), while 3(1)-helix (PG II) was formed by precipitation from aqueous solutions of LiBr. Grinding the sample resulted in an increase in the amount of PG I, indicating that this form is more stable in the solid state. These results agree with previous work on poly(L-alanine) showing that the beta-sheet form is more stable in the solid state. Homopolypeptides with larger side chains did not change conformation upon grinding due to the greater difficulty in disrupting van der Waals interactions and inertia of the large side chains.     

Simultaneous analysis of biologically active aminoalkanephosphonic acids

A new approach for simultaneous analysis of biologically active aminoalkanephosphonic acids, namely glyphosate, phosphonoglycine, phosphonosarcosine, phosphonoalanine, phosphono-beta-alanine, phosphonohomoalanine, phosphono-gamma-homoalanine and glufosinate, is presented. This includes a preliminary 31p NMR analysis of these amino acids, their further derivatization to volatile phosphonates (phosphinates) by means of trifluoroacetic acid-trifluoroacetic anhydride-trimethyl orthoacetate reagent and subsequent analysis of derivatization products using MS and/or GC-MS (chemical ionization and/or electron impact ionization).     

Magneto infrared absorption in high electron density GaAs quantum wells

Magneto infrared absorption measurements have been performed in a highly doped GaAs quantum well which has been lifted off and bonded to a silicon substrate, in order to study the resonant polaron interaction. It is found that the pinning of the cyclotron energy occurs at an energy close to that of the transverse optical phonon of GaAs. This unexpected result is explained by a model taking into account the full dielectric constant of the quantum well.