Normalization and noise-reduction algorithm for fringe patterns

This paper presents a fringe pattern normalization and noise-reduction algorithm. Locally the background noise is suppressed, the modulation normalized and the noise smoothed. An expression to calculate the cosine-only term is formulated. It is related to the directional derivatives of the intensity fringes. Two-dimensional Fourier series are used to calculate the parameters needed for the algorithm. Experimental work is presented using diffraction and ESPI images. The programming is relatively simple and involves mainly local convolutions. The processing time using a 2 GHz computer to normalize an image of 256 × 256 pixels is approximately one second.     

Homogeneous hydrogenation of ketones to alcohols with ruthenium complex catalysts

A number of ruthenium triphenylphosphine complexes catalyse the reduction of ketones to their corresponding alcohols in the presence of water. The most convenient catalyst precursors are carbonyl containing complexes which do not promote decarbonylation of the substrate. The hydrogenation of acetone with hydridochlorocarbonyltris(triphenylphosphine)ruthenium is first order with respect to the substrate concentration, the catalyst concentration, the hydrogen pressure and the water concentration. Turnover numbers up to 15,000 have been achieved with this catalyst. Other ketones are also reduced by RuHCl(CO)(PPh₃)₃ and the rate of the reaction is dependent on the nature of the substrate.     

Synthesis of novel 2,5-dihydro-1,5,2-diazaphosphinines from primary enamine phosphonates and from alkyl phosphonates

A simple method for the preparation of phosphorus-containing pyrimidine analogues such as 2,5-dihydro-2-ethoxy-1,5,2-diazaphosphinine 2-oxides 9, 12-15 and adducts 3, 10 is described. Dihydrophosphinines 9, 12-15 are prepared from primary enamine phosphonates and nitriles or from phosphonates and nitriles in the presence of base, while highly stable hydrogen-bonded amine-dihydro-diazaphosphinine adducts 3, 10 are obtained by the addition of amine to dihydrophosphinines 9 or by reaction of alkylphosphonates with nitriles in the presence of LDA.     

The use of solid-phase supported 1-N-piperazine-4-N-carboxaldehyde in Vilsmeier reactions

A Vilsmeier salt supported on solid phase was prepared using piperazine bound to Merrifield resin. Piperazine was selected because it contains two secondary amines: one of the amines is protected upon binding to the resin, and the second was formylated to give resin-1-N-piperazine-4-N-carboxaldehyde (9). Activation of the formamide with either bis(trichloromethyl)carbonate (BTC) or POCl(3) afforded the Vilsmeier salt 10. Several olefins were used to test the supported Vilsmeier reagent. The in-solution activation with BTC and POCl(3) of various secondary amides was also evaluated: dimethylformamide (1), N-methyformanilide (4), 4-formylmorpholine (5), and 1,4-dicarboxylpiperazine (6), which showed that amides with one additional heteroatom increase the yields in the Vilsmeier salt formation.     

Regioselective synthesis of 4- and 5-oxazole-phosphine oxides and -phosphonates from 2H-azirines and acyl chlorides

A simple and efficient regioselective synthesis of 4-oxazole-phosphine oxides 11 and -phosphonates 12 from 2H-azirine-phosphine oxides 1 and -phosphonates 6 is described. The key step for the synthesis of oxazoles 11 is a base-mediated ring closure of vinylogous α-aminophosphorus compounds derived from phosphine oxides 4 and from phosphonates 8. These derivatives 4 and 8 are obtained by reaction of functionalized azirines 1 and 6 with acyl chlorides 2 and subsequent acid-catalyzed ring opening of N-acylaziridine-phosphine oxides 3 and -phosphonates 7. Regioselective thermal ring cleavage of N-acylaziridine-phosphine oxides 3 leads α-chloro-β-(N-acylamido)-phosphine oxides 13 and their treatment with bases gives 5-oxazole-phosphine oxides 16.     

Asymmetric synthesis of 2H-azirines derived from phosphine oxides using solid-supported amines. Ring opening of azirines with carboxylic acids

A simple and efficient asymmetric synthesis of 2H-azirine-2-phosphine oxides 3 is described. The key step is a solid-phase bound achiral or chiral amine-mediated Neber reaction of beta-ketoxime tosylates derived from phosphine oxides 1. Reaction of 2H-azirines 3 and 11 with carboxylic acids 4 gives phosphorylated ketamides 5 and 12. Ring closure of ketamides 5 and 12 with triphenylphosphine and hexachloroethane in the presence of triethylamine leads to the formation of phosphorylated oxazoles 8 and 13.     

Synthesis of pyrazine-phosphonates and -phosphine oxides from 2H-azirines or oximes

[reaction: see text] Tetrasubstituted pyrazines containing two phosphonate groups 2 in positions 2 and 5 and trisubstituted pyrazines containing a phosphonate 5 or a phosphine oxide group 7 in position 2 are obtained by thermal treatment of 2H-azirine-2-phosphonates 1 and -phosphine oxides 6. These pyrazines can also be prepared from beta-ketoxime tosylates 9 and 10 or from oxime derived from phosphine oxide 11.     

PepFun: Open Source Protocols for Peptide-Related Computational Analysis

Peptide research has increased during the last years due to their applications as biomarkers, therapeutic alternatives or as antigenic sub-units in vaccines. The implementation of computational resources have facilitated the identification of novel sequences, the prediction of properties, and the modelling of structures. However, there is still a lack of open source protocols that enable their straightforward analysis. Here, we present PepFun, a compilation of bioinformatics and cheminformatics functionalities that are easy to implement and customize for studying peptides at different levels: sequence, structure and their interactions with proteins. PepFun enables calculating multiple characteristics for massive sets of peptide sequences, and obtaining different structural observables derived from protein-peptide complexes. In addition, random or guided library design of peptide sequences can be customized for screening campaigns. The package has been created under the python language based on built-in functions and methods available in the open source projects BioPython and RDKit. We present two tutorials where we tested peptide binders of the MHC class II and the Granzyme B protease.