Finite-bandwidth effects on the causal prediction of ultrasonic attenuation of the power-law form

Kramers-Kronig (K-K) relations exist as a consequence of causality, placing nonlocal constraints on the relationship between dispersion and absorption. The finite-bandwidth method of applying these relations is examined where the K-K integrals are restricted to the spectrum of the experimental data. These finite-bandwidth K-K relations are known to work with resonant-type data and here are applied to dispersion data consistent with a power-law attenuation coefficient (exponent from 1 to 2). Bandwidth-restricted forms of the zero and once-subtracted K-K relations are used to determine the attenuation coefficient from phase velocity. Analytically, it is shown that these transforms produce the proper power-law form of the attenuation coefficient as a stand-alone term summed with artifacts that are dependent on the integration limits. Calculations are performed to demonstrate how these finite-bandwidth artifacts affect the K-K predictions under a variety of conditions. The predictions are studied in a local context as a function of subtraction frequency, bandwidth, and power-law exponent. The K-K predictions of the power-law exponent within various decades of the spectrum are also examined. In general, the agreement between finite-bandwidth K-K predictions and exact values grows as the power-law exponent approaches 1 and with increasing bandwidth.     

Processing MALDI Mass Spectra to Improve Mass Spectral Direct Tissue Analysis

Profiling and imaging biological specimens using MALDI mass spectrometry has significant potential to contribute to our understanding and diagnosis of disease. The technique is efficient and high-throughput providing a wealth of data about the biological state of the sample from a very simple and direct experiment. However, in order for these techniques to be put to use for clinical purposes, the approaches used to process and analyze the data must improve. This study examines some of the existing tools to baseline subtract, normalize, align, and remove spectral noise for MALDI data, comparing the advantages of each. A preferred workflow is presented that can be easily implemented for data in ASCII format. The advantages of using such an approach are discussed for both molecular profiling and imaging mass spectrometry.     

EPR and magnetic properties of heteronuclear Mn(n)Mg(6-)(n)(O(2)CNEt(2))(12): impact of structural distortions on Mn(II) in weak ligand fields

The reaction between Mn(6)L(12) and Mg(6)L(12) (L = N,N-diethylcarbamate) results in isolation of heteronuclear complexes Mn(n)Mg(6)(-)(n)L(12). A series was prepared with different doping factors n by varying the Mn/Mg ratio in the crystallization solutions. Single-crystal X-ray diffraction shows that MnMg(5)L(12) is isostructural with Mn(6)L(12) and Mg(6)L(12). Magnetic susceptibility data on the series Mn(n)Mg(6)(-)(n)L(12) (n = 1-6) are consistent with antiferromagnetic Mn.Mn interactions. At low n, the magnetic data demonstrate the formation of magnetically isolated Mn(2+) centers. This was confirmed by measurement of the EPR spectrum at a doping factor n = 0.06 in solution, as a powder, and as single crystals. These show hyperfine interactions consistent with isolated Mn(2+). The EPR spectrum of Mn(0.06)Mg(5.94)L(12) exhibits a dominant signal at g(eff) = 4, and a wide series of less intense signals spanning 200-6000 G in the X-band regime. This unusual behavior in a weak-field Mn(2+) complex is attributed to the substantial distortions from cubic ligand field geometry in this system. The g(eff) = 4 signals are attributed to a C(2)-symmetric hexacoordinate Mn(2+) ion with D > 0.3 cm(-)(1) and E/D = 0.33. The wide series is assigned to an axial C(4)(v) pentacoordinate Mn(2+) site with D = 0.05 cm(-)(1). Comparison of the g(eff) = 4 signals to the g = 4.1 signals exhibited by the tetramanganese complex in photosystem II belies the fact that they almost certainly arise from different spin systems. In addition, the similarity of the spectrum of Mn(n)Mg(6)(-)(n)L(12) to mononuclear Mn(4+) complexes suggests that considerable care must be exercised in the use of EPR as a fingerprint for the manganese oxidation state, particularly in manganese proteins where molecular composition may not be precisely established.     

An efficient methodology to study cyclodextrin clusters: application to α-CD hydrated monomer, dimer, trimer and tetramer

The hydrated α-cyclodextrin (α-CD) clusters resulting from the following process: nα-CD + n(H₂O)₆ → α-CD_n · 6nH₂O, with n = 1, 2, 3, 4, have been investigated using semiempirical (PM3), ab initio Hartree-Fock and Density Functional Theory (BLYP functional) levels of theory. The largest structure containing 576 atoms and 5,760 contracted basis functions (6-31G(d,p) basis set) poses as a considerable hard task for quantum chemical calculations. As the number of basis function increases rapidly with the cluster size, an alternative procedure to make the calculations feasible is certainly welcome, in order to perform BLYP calculations with an adequate basis set. Through the aid of a computer program that we developed, it became of practical use the selection of atom by atom basis sets, using the common chemical sense, enabling quantum mechanical calculations to be performed for very large molecular interacting systems (inclusion complexes), at an affordable computational cost. In this article we show how an appropriate selection of basis functions, leaving the CH_n groups with a minimal basis set and the oxygen atoms (and OH groups) with a better quality basis set, lower considerably the computational cost with no significant loss in the calculated interaction energies. A regular pattern is observed for α-CD hydrated monomer, dimer, trimer and tetramer, therefore adding support to the use of this procedure when studying larger hydrogen bonded clusters where electron correlation effects are important. We show that the procedure reported here enables DFT calculations for hydrated cyclodextrin using basis set up to the 6-311++G(3df,3pd) triple zeta quality .     

High purity anatase TiO(2) nanocrystals: near room-temperature synthesis, grain growth kinetics, and surface hydration chemistry

High purity, spherical anatase nanocrystals were prepared by a modified sol-gel method. Mixing of anhydrous TiCl(4) with ethanol at about 0 degrees C yielded a yellowish sol that was transformed into phase-pure anatase of 7.7 nm in size after baking at 87 degrees C for 3 days. This synthesis route eliminates the presence of fine seeds of the nanoscale brookite phase that frequently occurs in low-temperature formation reactions and also significantly retards the phase transformation to rutile at high temperatures. Heating the as-is 7.7 nm anatase for 2 h at temperatures up to 600 degrees C leads to an increase in grain size of the anatase nanoparticles to 32 nm. By varying the calcination time from 2 to 48 h at 300 degrees C, the particle size could be controlled between 12 and 15.3 nm. The grain growth kinetics of anatase nanoparticles was found to follow the equation, D(2) - D(0)(2) = k(0)t(m)e((-)(E)(a)/(RT)) with a time exponent m = 0.286(+/-9) and an activation energy of E(a) = 32 +/- 2 kJ x mol(-)(1). Thermogravimetric analysis in combination with infrared and X-ray photoemission spectroscopies has shown the anatase nanocrystals at different sizes to be composed of an interior anatase lattice with surfaces that are hydrogen-bonded to a wide set of energetically nonequivalent groups. With a decrease in particle size, the anatase lattice volume contracts, while the surface hydration increases. The removal of the surface hydration layers causes coarsening of the nanoparticles.     

Anomalous magnetic susceptibilities of the alkaline earth hexammines

The magnetic susceptibility of the metallic compounds Ca(NH₃)₆, Sr(NH₃)₆ and Ba(NH₃)₆ has been measured by the Faraday method in the range 2–200 K. The susceptibility of Ca(NH₃)₆ is strongly dependent on temperature and exhibits a broad minimum near 120 K and a peak near 10 K. In contrast to Ca(NH₃)₆, the susceptibilities of Sr(NH₃)₆ and Ba(NH₃)₆ are diamagnetic and decrease rapidly as the temperature is lowered. At low temperatures Ba(NH₃)₆ has the largest mass susceptibility of any nonsuperconducting metal.     

Responsive hydrogels from the intramolecular folding and self-assembly of a designed peptide

A general peptide design is presented that links the pH-dependent intramolecular folding of beta-hairpin peptides to their propensity to self-assemble, affording hydrogels rich in beta-sheet. Chemical responsiveness has been specifically engineered into the material by linking intramolecular folding to changes in solution pH, and mechanical responsiveness, by linking hydrogelation to self-assembly. Circular dichroic and infrared spectroscopies show that at low pH individual peptides are unstructured, affording a low-viscosity aqueous solution. Under basic conditions, intramolecular folding takes place, affording amphiphilic beta-hairpins that intermolecularly self-assemble. Rheology shows that the resulting hydrogel is rigid but is shear-thinning. However, quick mechanical strength recovery after cessation of shear is observed due to the inherent self-assembled nature of the scaffold. Characterization of the gelation process, from the molecular level up through the macroscopic properties of the material, suggests that by linking the intramolecular folding of small designed peptides to their ability to self-assemble, responsive materials can be prepared. Cryo-transmission electron and laser scanning confocal microscopies reveal a water-filled porous scaffold on both the nano- and microscale. The environmental responsiveness, morphology, and peptidic nature make this hydrogel a possible material candidate for biomedical and engineering technology.     

Spectral Properties of Interval Exchange Maps

 In [7], Nogueira and Rudolph proved that for irreducible permutations not of rotation class almost every (a.e.) interval exchange transformation (i.e.t.) is topological weak mixing. It is conjectured that the claim holds if topological weak mixing is replaced by weak mixing. Here we study the behaviour of eigenfunctions of i.e.t. Our analysis gives alternative proofs of results due to Katok and Stepin [4] and Veech [10]: for certain permutations a.e. i.e.t. is weak mixing and for irreducible permutations a.e. i.e.t. is totally ergodic. (Received 1 February 2001)     

Lead optimization mapper: automating free energy calculations for lead optimization

Alchemical free energy calculations hold increasing promise as an aid to drug discovery efforts. However, applications of these techniques in discovery projects have been relatively few, partly because of the difficulty of planning and setting up calculations. Here, we introduce lead optimization mapper, LOMAP, an automated algorithm to plan efficient relative free energy calculations between potential ligands within a substantial library of perhaps hundreds of compounds. In this approach, ligands are first grouped by structural similarity primarily based on the size of a (loosely defined) maximal common substructure, and then calculations are planned within and between sets of structurally related compounds. An emphasis is placed on ensuring that relative free energies can be obtained between any pair of compounds without combining the results of too many different relative free energy calculations (to avoid accumulation of error) and by providing some redundancy to allow for the possibility of error and consistency checking and provide some insight into when results can be expected to be unreliable. The algorithm is discussed in detail and a Python implementation, based on both Schrödinger’s and OpenEye’s APIs, has been made available freely under the BSD license.