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.

Evidence for the surface-catalyzed suzuki-miyaura reaction over palladium nanoparticles:an operando XAS study

No need to get away: X-ray absorption spectroscopy of catalytically active palladium nanopartlcles during a SuzukiMlyaura cross-coupling reaction revealed that the nanopartlcles were stable under the reaction conditions, and that cross-coupling Involved the direct participation of surface palladium defect sites In the catalytic cycle (see picture). Selective chemical and structural poisons provided further evidence for a heterogeneous active site. © 2010 Wiley-VCH Verlag GmbH & Co. KCaA.

Fundamental Pd0/PdII redox steps in cross-coupling reactions:homogeneous, hybrid homogeneous-heterogeneous to heterogeneous mechanistic pathways for C-C couplings

C–C bond-forming, cross-coupling reactions of organohalides with nucleophilic compounds, catalysed by palladium, are amongst the most important chemical reactions available to the synthetic chemist. The intimate mechanisms of these reactions, involving Pd0/PdII redox steps, have been of great historical interest and continue to be so. The myriad of possible mechanisms is reviewed in this chapter. The interplay of mononuclear Pd species with higher order Pd species, e.g. nanoclusters/nanoparticles are considered as being equally important in cross-coupling reaction mechanisms. A focus is placed on trichotomic behaviour of cross-coupling catalytic manifolds, from homogeneous to hybrid homogeneous–heterogeneous to truly heterogeneous behaviour. For the latter, surface chemistry and metal atom leaching (and various experimental techniques) are broadly discussed. It is now clear that mechanism for general cross‐coupling reactions, that is as presented to undergraduate students studying Chemistry degrees across the world, is undoubtedly more complex than first thought. New opportunities for catalyst design have therefore emerged in the area of Pd nanoparticles and nanocatalysis, with some wonderful applications especially in chemical biology, providing a snapshot of what the future might hold.

Coupling of Heck and hydrogenation reactions in a continuous compact reactor

A continuous multi-step synthesis of 1,2-diphenylethane was performed sequentially in a structured compact reactor. This process involved a Heck C-C coupling reaction followed by the addition of hydrogen to perform reduction of the intermediate obtained in the first step. Both of the reactions were catalysed by microspherical carbon-supported Pd catalysts. Due to the integration of the micro-heat exchanger, the static mixer and the mesoscale packed-bed reaction channel, the compact reactor was proven to be an intensified tool for promoting the reactions. In comparison with the batch reactor, this flow process in the compact reactor was more efficient as: (i) the reaction time was significantly reduced (ca. 7 min versus several hours), (ii) no additional ligands were used and (iii) the reaction was run at lower operational pressure and temperature. Pd leached in the Heck reaction step was shown to be effectively recovered in the following hydrogenation reaction section and the catalytic activity of the system can be mostly retained by reverse flow operation. © 2009 Elsevier Inc. All rights reserved.

Green approach to Palladium Cross-Coupling reactions and development of new methodologies based on highly abundant metals

Transition metal catalyzed cross-coupling reactions represent among the most versatile and useful tools in organic synthesis for the carbon-carbon (C-C) bond formation and have a prominent role in both the academic and pharmaceutical segments. Among them, palladium catalyzed cross-coupling reactions are currently the most versatile. In this thesis, the applications, impact and development of green palladium cross-coupling reactions are discussed. Specifically, we discuss the translation of the Twelve Principles of Green Chemistry and their applications in pharmaceutical organometallic chemistry to stimulate the development of cost-effective and sustainable catalytic processes for the synthesis of active pharmaceutical ingredients (API). The Heck-Cassar-Sonogashira (HCS) and the Suzuki-Miyaura (SM) protocols, using HEP/H2O as green mixture and sulfonated phosphine ligands, allowed to recycle and recover the catalyst, always guaranteeing high yields and fast conversion under mild conditions, with aryl iodides, bromides, triflates and chlorides. No catalyst leakage or metal contamination of the final product were observed during the HCS and SM reactions, respecting the very low limits for metal impurities in medicines established by the International Conference of Harmonization Guidelines Q3D (ICH Q3D). In addition, a deep understanding of the reaction mechanism is very important if the final target is to develop efficient protocols that can be applied at industrial level. Experimental and theoretical studies pointed out the presence of two catalytic cycles depending on the counterion, shedding light on the role of base in catalyst reduction and acetylene coordination in the HCS coupling. Finally, the development of a cross-coupling reaction to form aryldifluoronitriles in the presence of copper is discussed, highlighting the importance of inserting fluorine atoms within biological structures and the use of readily available metals such as copper as an alternative to palladium.

Síntese de poli(1,1'-ferrocenilenovinileno) via acoplamento de McMurry

Com base nas grandes modificações das propriedades de materiais poliméricos resultantes da inclusão de unidades organometálicas, descrevem-se neste trabalho a síntese e a caracterização de um polímero organometálico conjugado com estrutura semelhante à de poli(p-fenilenovinileno) (PPV), o qual apresenta grupos 1,1'-ferrocenileno no lugar de 1,4fenileno em sua cadeia principal. Sintetizado por meio de reação de acoplamento de McMurry de 1,1'-ferrocenodialdeído, o poli(1,1'-ferrocenilenovinileno) (PFV) se apresentou na forma de um sólido de cor laranja, amorfo e insolúvel tanto em solventes polares quanto em apolares. Para caracterização do PFV, empregaram-se os métodos de espectroscopia no infravermelho (FTIR), espectroscopia Raman e análise termogravimétrica (TGA).

Determinação espectrofotométrica do bromidrato de fenoterol em preparações farmacêuticas

Um método espectrofotométrico simples foi desenvolvido para a determinação do bromidrato de fenoterol (BF) em comprimidos, gotas e xarope, como princípio ativo único e associado ao ibuprofeno. O método se baseia na reação de acoplamento oxidativo do BF com o 3-metil-2-benzotiazolinona hidrazona (MBTH), na presença de sulfato cérico, como agente oxidante. A mistura de BF, MBTH e sulfato cérico, em meio ácido, produz um composto colorido (vermelho castanho) com máximo de absorção a 475 nm. A curva de calibração foi linear num intervalo de concentração de 3,0 a 12,0 µg/mL, com coeficiente de correlação linear de 0,9998. Os parâmetros experimentais que afetam o desenvolvimento e a estabilidade do produto colorido foram cuidadosamente estudados e otimizados. O método foi aplicado em amostras comerciais e simuladas, obtendo-se coeficientes de variação entre 0,25 % a 0,82 % e médias de recuperação do padrão que variaram de 98 % a 102 %. O método proposto mostrou-se exato, preciso, linear e não é passível de interferência de excipientes, para as formas farmacêuticas comprimidos e gotas. Não houve interferência do ibuprofeno que consta de uma das formulações analisadas, associado ao BF. Quanto ao xarope, houve interferência do veículo sugerindo reações de seus componentes com o MBTH.

Expanding cyclitol structural diversity by biocatalysis and metalocatalysis. A click chemistry approach

The palladium catalyzed cross-coupling reaction of phenyltrifluoroborate with a chemoenzymatically derived bromoazidoconduritol, combined with 1,3-dipolar cycloaddition, with a variety of alkynes is described. Fourteen new compounds were synthesized in moderate to good yields. The click chemistry reaction can be effected by using sodium ascorbate and CuSO(4) center dot 5H(2)O as catalyst in toluene-H(2)O at room temperature.

Consecutive biocatalysis-palladium catalysis II: Synthesis of conduritol-alkyne conjugates

The palladium-catalyzed cross-coupling reaction of potassium alkynyltrifluoroborates with a chemoenzymatically derived deoxyconduritol is described. Six new compounds were synthesized in moderate to good yields. The alkynyl cross-coupling reaction can be effected using 10 mol% of Pd(PPh(3))(4) as Catalyst in toluene-H(2)O in the presence Of Cs(2)CO(3) as the inorganic base. (C) 2009 Elsevier B.V. All rights reserved.

Synthesis of benzophenones from geminal biaryl ethenes using m-chloroperbenzoic acid

The oxidation of geminal biaryl ethenes 3 and 1,3-enynes 5 using m-chloroperbenzoic acid in dichloromethane at room temperature presents a catalyst-free approach for the synthesis of functionalized benzophenones 4 and ynones 6, respectively. (C) 2009 Elsevier Ltd. All rights reserved.

Nucleophilic Addition of Potassium Alkynyltrifluoroborates to D-Glucal Mediated by BF(3)center dot OEt(2): Highly Stereoselective Synthesis of alpha-C-glycosides

A convenient, mild and highly stereoselective method for C-glycosidation (alkynylation) of D-glucal with various potassium alkynyltrifluoroborates, mediated by BF(3)center dot OEt(2) and involving oxonium intermediates, preferentially provides the alpha-acetylene glycoside products with good yields.

Spectrophotometric determination of fenoterol hydrobromide in pharmaceutical preparations

A simple spectrophotometric method has been developed,for the determination of fenoterol hydrobromide (FH) in tablets, drops and syrup, as the only active principle and associated with ibuprofen. The method is based on the oxidative coupling reaction of the FH with 3-methyl-2-benzothiazolinone hydrazone (MBTH) and ceric sulphate as oxidant reagent. The mixture of the drug, MBTH and ceric sulfate, in acid medium, produces a red brown color compound, with absorption maximum at 475 nm. The calibration curve was linear over a concentration range from 3.0 to 12.0 mu g/mL, with correlation coefficient of 0.9998. The different experimental parameters affecting the development and stability of the color compound were carefully studied and optimized. The method was applied successfully to assay FH in dosage forms and simulated samples. The coefficient of variation was from 0.25 % to 0.82 % and average recoveries of the standard from 98 % to 102 %. The excipients (tablets and drops) did not interfere in the analysis and the results showed that method can be used for determination of the FH isolated or associated with ibuprofen with precision, accuracy and specificity. In case of syrup, the interference in the analysis suggests a possible reaction between vehicle components with MBTH.

Synthesis of unnatural cyclitols via a combined enzymatic-palladium catalysis approach

The Suzuki-Miyaura cross-coupling reaction of a hydroxylated vinyl bromide obtained by a chemoenzymatic approach with a diverse range of potassium organotrifluoroborates has been accomplished catalyzed by Pd(PPh(3))(4) in satisfactory yields. A variety of functional groups are tolerated in the nucleophilic partner. (C) 2008 Elsevier B.V. All rights reserved.

Synthesis of 2-Aryl- and 2,5-Diarylfurans and Thiophenes by Suzuki-Miyaura Reactions Using Potassium Trifluoroborate Salts and Heteroaryltellurides

The Suzuki-Miyaura cross-coupling reaction of 2-(butyltellanyl) or 2,5-bis-(butyltellanyl)furans and thiophenes with potassium aryltrifluoroborate salts catalyzed by palladium afforded 2-aryl- or 2,5-diaryl-furans and thiophenes in moderate to good yields.

Crystal and molecular structures of dichloro((Z)-2-chloro-2-phenylvinyl)(organo)tellurium(IV) for organo = n-butyl and phenyl

In each of the title compounds, R[Ph(Cl)C=(H)C]TeCl(2), R = nBu (1) and Ph (2), the primary geometry about the Te(IV) atom is a pseudo-trigonal-bipyramidal arrangement, with two Cl atoms in apical positions, and the lone pair of electrons and C atoms in the equatorial plane. As the Te(IV) is involved in two, an intra- and an inter-molecular, Te center dot center dot center dot Cl interactions the coordination geometry might be considered as a Psi-pentagonal bipyramid in each case. In addition, in (2) there is a hint of a Te center dot center dot center dot pi interaction (Te center dot center dot center dot C = 3.911(3) A). The key feature in the crystal structure of both compounds is the formation of supramolecular chains mediated by Te center dot center dot center dot Cl contacts. (1): C(12)H(15)Cl(3)Te, triclinic, P (1) over bar, a = 5.9471 (11), b = 10.7826(22), c = 11.7983(19) angstrom, alpha = 75.416(12), beta = 78.868(13), gamma = 80.902(14)degrees, V = 713.6(2) angstrom(3), Z = 2, R(1) = 0.021; (2): C14HIIC13Te, orthorhombic, Pcab, a=7.7189(10), b=17.415(2), c=21.568(3)angstrom, V = 2899.3(6) angstrom(3), Z = 8, R(1) = 0.027.