MOVIPAC: Vibrational spectroscopy with a robust meta‐program for massively parallel standard and inverse calculations

We present the software package MO VI PAC for calculations of vibrational spectra, namely infrared, Raman, and Raman Optical Activity (ROA) spectra, in a massively parallelized fashion. MO VI PAC unites the latest versions of the programs SNF and AKIRA alongside with a range of helpful add‐ons to analyze and interpret the data obtained in the calculations. With its efficient parallelization and meta‐program design, MO VI PAC focuses in particular on the calculation of vibrational spectra of very large molecules containing on the order of a hundred atoms. For this purpose, it also offers different subsystem approaches such as Mode‐ and Intensity‐Tracking to selectively calculate specific features of the full spectrum. Furthermore, an approximation to the entire spectrum can be obtained using the Cartesian Tensor Transfer Method. We illustrate these capabilities using the example of a large π‐helix consisting of 20 (S)‐alanine residues. In particular, we investigate the ROA spectrum of this structure and compare it to the spectra of α‐ and 3₁₀‐helical analogs. © 2012 Wiley Periodicals, Inc.     

DANGLE: A Bayesian inferential method for predicting protein backbone dihedral angles and secondary structure

This paper introduces DANGLE, a new algorithm that employs Bayesian inference to estimate the likelihood of all possible values of the backbone dihedral angles ? and ψ for each residue in a query protein, based on observed chemical shifts and the conformational preferences of each amino acid type. The method provides robust estimates of ? and ψ within realistic boundary ranges, an indication of the degeneracy in the relationship between shift measurements and conformation at each site, and faithful secondary structure state assignments. When a simple degeneracy-based filtering procedure is applied, DANGLE offers an ideal compromise between accuracy and coverage when compared with other shift-based dihedral angle prediction methods. In addition, per residue analysis of shift/structure degeneracy has potential to be a useful new approach for studying the properties of unfolded proteins, with sufficient sensitivity to identify regions of residual structure in the acid denatured state of apomyoglobin.     

Synthesis,Complexes and Metal Extraction Ability of R1R2NC(X)NHP(Y)(0Ph)2

Abstract

The new 1,1-disubstituted 3-diphenoxy(thio)phosphoryl-(thio)ureas, R¹R²NC(X)NHP(0Ph)₂, HA, with X,Y = O,S, were synthesized by addition of secondary mines to the corresponding P-iso(thio)cyanates. This reaction is reversible if X,Y = S. (PhO)₂P(Y)Cl reacts with H₂NC(X)NR₂ in the presence of an HCl acceptor only if X,Y a 0. Side reactions are observed. Phosphorylated derivatives of biuret were isolated from such a reaction mixture.     

A Direct Assembly Approach to the Synthesis of N,N′-Bridged Calix[4]pyrroles: The Synthesis of a 1,5-Diazacyclononatriene Locked in a Saddle Conformation

Ring closure of 1,2-bis(1-pyrrolylmethyl)benzene in the acid-catalysed condensation with acetone yields the 1,5-diazacyclononatriene [ O -C₆H₄(CH₂NC₄H₃-2)₂C(CH₃)₂] as the sole identifiable product. The twisted or saddle conformation of the 1,5-diazacyclononatriene, which was confirmed by X-ray crystal structure determination, is conformationally rigid in solution. The conformation of the 1,5-diazacyclononatriene prevents the formation of the target N,N′-bridged calix[4]pyrrole by further acid-catalysed condensation with acetone, the reaction affording unidentified oligomers/polymers instead. The acid-catalysed condensation of 1,3- and 1,4-bis(1-pyrrolylmethyl)benzene with acetone also yields unidentified oligomers/polymers.     

Mixed electrolytes in hydrophobic interaction chromatography†

An essential part of the modulation of protein‐binding capacity in hydrophobic interaction chromatography is the buffer‐salt system. Besides using “single” electrolytes, multicomponent electrolyte mixtures may be used as an additional tool. Both the protein solubility and the binding capacity depend on the position of a salt in the so‐called Hofmeister series. Specific interactions are observed for an individual protein‐salt combination. For salt mixtures, selectivity, recovery, and binding capacity do not behave like for the single salts that are positioned in between the two mixed components in the Hofmeister series, as the continuous correlation would suggest. Thus, finding strategies for mixed salts could potentially lead to improved capacities in hydrophobic interaction chromatography. Mixtures of ammonium sulfate, sodium citrate, sodium sulfate, sodium chloride, sodium acetate, and glycine were used to investigate the binding capacities for lysozyme and a monoclonal antibody on various hydrophobic resins. Resin capacity for two investigated proteins increases when mixtures consisting of a chaotropic and a kosmotropic salt are applied. It seems to be related to the rather basic isoelectric points of the proteins.     

Synthesis of Benzopyran Derivatives,XIV: New Procedure for the Preparation of 2,2-Dimethyl-2H-chromenes

2,2-Dimethyl-4-methoxychromans (1–12) have been converted into 2,2-dimethyl-2H-chromenes (13–24) in acidic media.