A gradient descent algorithm for minimizing amino acid coupling reactions when synthesizing cyclic-peptide libraries

Combinatorial chemistry has become an invaluable tool in medicinal chemistry for the identification of new drug leads. For example, libraries of predetermined sequences and head-to-tail cyclized peptides are routinely synthesized in our laboratory using the IRORI approach. Such libraries are used as molecular toolkits that enable the development of pharmacophores that define activity and specificity at receptor targets. These libraries can be quite large and difficult to handle, due to physical and chemical constraints imposed by their size. Therefore, smaller sub-libraries are often targeted for synthesis. The number of coupling reactions required can be greatly reduced if the peptides having common amino acids are grouped into the same sub-library (batching). This paper describes a schedule optimizer to minimize the number of coupling reactions by rotating and aligning sequences while simultaneously batching. The gradient descent method thereby reduces the number of coupling reactions required for synthesizing cyclic peptide libraries. We show that the algorithm results in a 75% reduction in the number of coupling reactions for a typical cyclic peptide library.     

Synthesis, crystal structures, and photophysical properties of homodinuclear lanthanide xanthene-9-carboxylates

Three new homodinuclear lanthanide(III) complexes of xanthene-9-carboxylic acid, [Ln2(XA)6(DMSO)2(H2O)2](Ln = Eu (1), Tb (2) and Gd (3); HXA = xanthene-9-carboxylic acid; DMSO = dimethylsulfoxide), have been synthesized, of which 1 and 2 were structurally characterized by single-crystal X-ray diffraction. These compounds crystallize in the monoclinic space group P21/n with a =17.849(4) A, b = 9.6537(19) A, c = 23.127(5) A, beta = 109.06(3) degrees , and V = 3766.5(13) A3 for 1 and a =17.809(4) A, b = 9.6548(19) A, c = 23.075(5) A, beta = 108.97(3) degrees , and V = 3752.1(13) A3 for 2. The crystal structures of 1 and 2 consist of homodinuclear species that are bridged by two oxygen atoms from two carboxylate ligands. The two lanthanide ions are related by a center of inversion. Each lanthanide ion is coordinated by eight oxygen atoms in an overall distorted square-prismatic geometry. Six of the oxygen atoms are furnished by the carboxylate moieties, and the remaining two oxygen atoms are provided by water and DMSO molecules. The photophysical properties of these complexes in the solid state at room temperature have been investigated. The quantum yields were found to be 0.06 +/- 0.01 and 7.30 +/- 0.73% for 1 and 2, respectively.     

Ionic-liquid matrices for quantitative analysis by MALDI-TOF mass spectrometry

Ionic liquid matrices (ILMs) were tested as MALDI matrices for quantification of oligodeoxynucleotides (ODNs), peptides, and small proteins. Good calibrations with high linearity and reproducibility were achieved over a broad concentration range for all the tested ILMs in spite of their different physical states. However, the standard deviation is higher for ILMs that are solid with visible crystals. The experimental results indicate various ILMs have different sensitivity owing to changes in their cation components. More importantly, we found that the slopes of the calibration curves correlate with the inverse of the peptide molecular weights, presenting an opportunity to predict a priori, the relative sensitivities (slopes of calibration plots) for various analytes that have similar hydrophobicites.     

Enhancing the ion-transport selectivity of multilayer polyelectrolyte membranes

Alternating adsorption of polycations and polyanions on permeable supports provides a convenient and versatile method for preparing composite membranes with selective, ultrathin polyelectrolyte skins. Control over charge and composition in the polyelectrolyte skin allows highly selective separation of ions according to charge, size, or hydration energy.     

Source level reduction and sonar beam aiming in landing big brown bats (Eptesicus fuscus)

Reduction of echolocation call source levels in bats has previously been studied using set-ups with one microphone. By using a 16 microphone array, sound pressure level (SPL) variations, possibly caused by the scanning movements of the bat, can be excluded and the sonar beam aiming can be studied. During the last two meters of approach flights to a landing platform in a large flight room, five big brown bats aimed sonar beams at the landing site and reduced the source level on average by 7 dB per halving of distance. Considerable variation was found among the five individuals in the amount of source level reduction ranging from 4 to 9 dB per halving of distance. These results are discussed with respect to automatic gain control and intensity compensation and the combination of the two effects. It is argued that the two effects together do not lead to a stable echo level at the cochlea. This excludes a tightly coupled closed loop feed back control system as an explanation for the observed reduction of signal SPL in landing big brown bats.     

Modular Design of Domain Assembly in Porous Coordination Polymer Crystals via Reactivity-Directed Crystallization Process

The mesoscale design of domain assembly is crucial for controlling the bulk properties of solids. Herein, we propose a modular design of domain assembly in porous coordination polymer crystals via exquisite control of the kinetics of the crystal formation process. Employing precursors of comparable chemical reactivity affords the preparation of homogeneous solid-solution type crystals. Employing precursors of distinct chemical reactivity affords the preparation of heterogeneous phase separated crystals. We have utilized this reactivity-directed crystallization process for the facile synthesis of mesoscale architecture which are either solid-solution or phase-separated type crystals. This approach can be also adapted to ternary phase-separated type crystals from one-pot reaction. Phase-separated type frameworks possess unique gas adsorption properties that are not observed in single-phasic compounds. The results shed light on the importance of crystal formation kinetics for control of mesoscale domains in order to create porous solids with unique cooperative functionality.     

Analysis of rare earth sulfides, selenides and tellurides

The rare earth content of sulfides, selenides and tellurides is determined by titration with EDTA using Xylenol Orange as indicator. Sulfur is measured by titration of sulfate with lead nitrate solution after removal of rare earths on a cation exchanger. Selenium metal is precipitated from hydrochloric-sulfurous acid solution. Metallic tellurium is deposited from strongly acidic solutions containing sulfurous acid and hydrazine sulfate. An evaluation of the accuracy and precision of these methods is made.