Two Optimal Value Functions in Parametric Conic Linear Programming

Journal of Optimization Theory and Applications - We consider the conic linear program given by a closed convex cone in an Euclidean space and a matrix, where vector on the right-hand side of the...     

Predicting 19F NMR Chemical Shifts: A Combined Computational and Experimental Study of a Trypanosomal Oxidoreductase–Inhibitor Complex

The absence of fluorine from most biomolecules renders it an excellent probe for NMR spectroscopy to monitor inhibitor–protein interactions. However, predicting the binding mode of a fluorinated ligand from a chemical shift (or vice versa) has been challenging due to the high electron density of the fluorine atom. Nonetheless, reliable ¹⁹F chemical-shift predictions to deduce ligand-binding modes hold great potential for in silico drug design. Herein, we present a systematic QM/MM study to predict the ¹⁹F NMR chemical shifts of a covalently bound fluorinated inhibitor to the essential oxidoreductase tryparedoxin (Tpx) from African trypanosomes, the causative agent of African sleeping sickness. We include many protein–inhibitor conformations as well as monomeric and dimeric inhibitor–protein complexes, thus rendering it the largest computational study on chemical shifts of ¹⁹F nuclei in a biological context to date. Our predicted shifts agree well with those obtained experimentally and pave the way for future work in this area.     

Glycosyl‐Substituted Dicarboxylates as Detergents for the Extraction,Overstabilization, and Crystallization of Membrane Proteins

To tackle the problems associated with membrane protein (MP) instability in detergent solutions, we designed a series of glycosyl‐substituted dicarboxylate detergents (DCODs) in which we optimized the polar head to clamp the membrane domain by including, on one side, two carboxyl groups that form salt bridges with basic residues abundant at the membrane–cytoplasm interface of MPs and, on the other side, a sugar to form hydrogen bonds. Upon extraction, the DCODs 8 b , 8 c , and 9 b preserved the ATPase function of BmrA, an ATP‐binding cassette pump, much more efficiently than reference or recently designed detergents. The DCODs 8 a , 8 b , 8 f , 9 a , and 9 b induced thermal shifts of 20 to 29 °C for BmrA and of 13 to 21 °C for the native version of the G‐protein‐coupled adenosine receptor A_2AR. Compounds 8 f and 8 g improved the diffraction resolution of BmrA crystals from 6 to 4 Å. DCODs are therefore considered to be promising and powerful tools for the structural biology of MPs.     

Decarboxylative cross-couplings of 2-aminopyrimidine-5-carboxylic acids

Decarboxylative CC cross-couplings of 2-aminopyrimidine-5-carboxylic acids under a Pd/Ag-based catalytic system opens a new platform for the introduction of diverse C5 substituents. The reaction methods proceeded efficiently with a wide range of the acids and the coupling partners of aryl iodides, alkenes, bromoalkynes, and azoles. Considering ready availability of 2-aminopyrimidine-5-carboxylic acid from the oxidative dehydrosulfurative CN cross-coupling of the 3,4-dihydropyrimidin-1H-2-thiones, this reaction method unambiguously pave a shortcut to densely substituted 2-aminopyrimidine derivatives with unprecedented diversity.     

Synthesis and photophysical investigation of squaraine rotaxanes by "clicked capping"

Pseudorotaxane complexes of squaraine dyes and tetralactam macrocycles are converted into permanently interlocked rotaxane structures using copper-catalyzed and copper-free cycloaddition reactions with bulky stopper groups. The photophysical properties of the encapsulated squaraine depend on the structure of the macrocycle. In one case, squaraine rotaxanes are produced in near-quantitative yields and with intense near-IR fluorescence. In another case, squaraine fluorescence is greatly diminished upon macrocyclic encapsulation but the signal can be restored by dye displacement with anions.     

Twostep-by-twostep PIRK-type PC methods with continuous output formulas

This paper deals with parallel predictor–corrector (PC) iteration methods based on collocation Runge–Kutta (RK) corrector methods with continuous output formulas for solving nonstiff initial-value problems (IVPs) for systems of first-order differential equations. At n$n$th step, the continuous output formulas are used not only for predicting the stage values in the PC iteration methods but also for calculating the step values at (n+2)$(n+2)$th step. In this case, the integration processes can be proceeded twostep-by-twostep. The resulting twostep-by-twostep (TBT) parallel-iterated RK-type (PIRK-type) methods with continuous output formulas (twostep-by-twostep PIRKC methods or TBTPIRKC methods) give us a faster integration process. Fixed stepsize applications of these TBTPIRKC methods to a few widely-used test problems reveal that the new PC methods are much more efficient when compared with the well-known parallel-iterated RK methods (PIRK methods), parallel-iterated RK-type PC methods with continuous output formulas (PIRKC methods) and sequential explicit RK codes DOPRI5 and DOP853 available from the literature.     

Effect of ionic surfactants on drainage and equilibrium thickness of emulsion films

This paper presents new theoretical and experimental results that quantify the role of surfactant adsorption and the related interfacial tension changes and interfacial forces in the emulsion film drainage and equilibrium. The experimental results were obtained with plane-parallel microscopic films from aqueous sodium dodecyl sulphate solutions formed between two toluene droplets using an improved micro-interferometric technique. The comparison between the theory and the experimental data show that the emulsion film drainage and equilibrium are controlled by the DLVO interfacial forces. The effect of interfacial viscosity and interfacial tension gradient (the Marangoni number) on the film drainage is also significant.     

A concise synthesis of chilenine via a sequential reaction process

A new short synthesis of chilenine has been achieved in two steps. The precursor amide was readily prepared by the condensation of the corresponding amine and acid. Treatment of the amide with oxalyl chloride in the presence of AlCl₃ at room temperature afforded the desired product chilenine through sequential Friedel-Crafts acylation, amide cyclization to imide, and intramolecular Friedel-Crafts type reaction. The synthesis suggests a new potential of oxalyl chloride for a two-carbon synthon.     

Fullerene C60-perylene-3,4:9,10-bis(dicarboximide) light-harvesting dyads: spacer-length and bay-substituent effects on intramolecular singlet and triplet energy transfer

Novel covalent fullerene C(60)-perylene-3,4:9,10-bis(dicarboximide) (C(60)-PDI) dyads (1-4) were synthesized and characterized. Their electrochemical and photophysical properties were investigated. Electrochemical studies show that the reduction potential of PDI can be tuned relative to C(60) by molecular engineering through altering the substituents on the PDI bay region. It was demonstrated using steady-state and time-resolved spectroscopy that a quantitative, photoinduced energy transfer takes place from the PDI moiety, acting as a light-harvesting antenna, to the C(60) unit, playing the role of energy acceptor. The bay-substitution (tetrachloro [1 and 2] or tetra-tert-butylphenoxy [3 and 4]) of the PDI antenna and the linkage length (C(2) [1 and 3] or C(5) [2 and 4]) to the C(60) acceptor are important parameters in the kinetics of energy transfer. Femtosecond transient absorption spectroscopy indicates singlet-singlet energy-transfer times (from the PDI to the C(60) unit) of 0.4 and 5 ps (1), 4.5 and 27 ps (2), 0.8 and 12 ps (3), and 7 and 50 ps (4), these values being ascribed to two different conformers for each C(60)-PDI system. Subsequent triplet-triplet energy-transfer times (from the C(60) unit to the PDI) are slower and in the order of 0.8 ns (1), 6.2 ns (2), 2.7 ns (3), and 9 ns (4). Nanosecond transient absorption spectroscopy of final PDI triplet states show a marked influence of the bay substitution (tetrachloro- or tetra-tert-butylphenoxy), and triplet-state lifetimes (10-20 micros) and the PDI triplet quantum yields (0.75-0.52) were estimated. The spectroscopy showed no substantial solvent effect upon comparing toluene (non-polar) to benzonitrile (polar), indicating that no electron transfer is occurring in these systems.     

Convergent assembly of highly potent analogues of bryostatin 1 via pyran annulation: bryostatin look-alikes that mimic phorbol ester function

Highly potent bryostatin analogues which contain the complete bryostatin core structure have been synthesized using a pyran annulation approach as a key strategic element. The A ring pyran was assembled using a pyran annulation reaction between a C1-C8 hydroxy allylsilane and an aldehyde comprising C9-C13. This pyran was transformed to a new hydroxy allylsilane and then coupled with a preformed C ring aldehyde subunit in a second pyran annulation, with concomitant formation of the B ring. This tricyclic intermediate was elaborated to bryostatin analogues which displayed nanomolar to subnanomolar affinity for PKC, but displayed properties indistinguishable from a phorbol ester in a proliferation/attachment assay.