Using second-order calibration to identify and quantify aromatic sulfonates in water by high-performance liquid chromatography in the presence of coeluting interferences

We used the Generalized Rank Annihilation Method (GRAM), a second-order calibration method, to quantify aromatic sulfonates in water with high-performance liquid chromatography (HPLC) when interferences coeluted with the analytes of interest. With GRAM, we can quantify in only two chromatographic analyses, one for a calibration sample and one for the unknown sample. The calculated concentrations were not statistically different to those obtained when the chromatographic separation of the unknown sample was modified in order to completely separate the analyte from the interferences before univariate calibration. With GRAM, the concentrations are determined much more quickly because a complete resolution is not required.     

Target-templated de novo design of macrocyclic d-/l-peptides: discovery of drug-like inhibitors of PD-1

Peptides are a rapidly growing class of therapeutics with various advantages over traditional small molecules, especially for targeting difficult protein–protein interactions. However, current structure-based methods are largely limited to natural peptides and are not suitable for designing bioactive cyclic topologies that go beyond natural l-amino acids. Here, we report a generalizable framework that exploits the computational power of Rosetta, in terms of large-scale backbone sampling, side-chain composition and energy scoring, to design heterochiral cyclic peptides that bind to a protein surface of interest. To showcase the applicability of our approach, we developed two new inhibitors (PD-i3 and PD-i6) of programmed cell death 1 (PD-1), a key immune checkpoint in oncology. A comprehensive biophysical evaluation was performed to assess their binding to PD-1 as well as their blocking effect on the endogenous PD-1/PD-L1 interaction. Finally, NMR elucidation of their in-solution structures confirmed our de novo design approach.

In silico design of heterochiral cyclic peptides that bind to a specific surface patch on the target protein (PD-1, in this case) and disrupt protein–protein interactions.     

Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets

We have designed four generations of a low molecular weight fragment library for use in NMR-based screening against protein targets. The library initially contained 723 fragments which were selected manually from the Available Chemicals Directory. A series of in silico filters and property calculations were developed to automate the selection process, allowing a larger database of 1.79 M available compounds to be searched for a further 357 compounds that were added to the library. A kinase binding pharmacophore was then derived to select 174 kinase-focused fragments. Finally, an additional 61 fragments were selected to increase the number of different pharmacophores represented within the library. All of the fragments added to the library passed quality checks to ensure they were suitable for the screening protocol, with appropriate solubility, purity, chemical stability, and unambiguous NMR spectrum. The successive generations of libraries have been characterized through analysis of structural properties (molecular weight, lipophilicity, polar surface area, number of rotatable bonds, and hydrogen-bonding potential) and by analyzing their pharmacophoric complexity. These calculations have been used to compare the fragment libraries with a drug-like reference set of compounds and a set of molecules that bind to protein active sites. In addition, an analysis of the overall results of screening the library against the ATP binding site of two protein targets (HSP90 and CDK2) reveals different patterns of fragment binding, demonstrating that the approach can find selective compounds that discriminate between related binding sites.     

Organoruthenaborane Chemistry. X. The SM2-catalysed formation of [ l-(η6-C6Me6)-isocloso-RuB9H9], and some B-phenylamino derivatives. NMR and X-ray diffraction studies

The action of SMe₂ on the ten-vertex nido-ruthenaborane [6-(η⁶-C₆Me₆)RuB₉H_l3] ( 1 ) provides a high-yield route to the unsubstituted isocloso-ruthenaborane [1-(η⁶-C₆Me₆)RuB₉H₉] (2). The benzene analogue [1-(η⁶-C₆Me₆)RuB₉H₉] is prepared similarly. By contrast, reaction of (1) with PhNH₂ gives a variety of B-phenylamino isocloso derivatives, including orange crystals of [1-(η⁶-C₆Me₆)-2-(PhNH)-isocloso-1-RuB 9 H₈] ( 3 ), red-orange [1-(η⁶-C₆Me₆)-2,3-(PhNH)₂-isocloso-1-RuB₉H₇] ( 4 ) and dark-red [1-(η⁶-C₆Me₆)-5,6,7-(PhNH)₃-isocloso-1-RuB₉H₆] ( 5 ). Detailed ¹H and ¹¹B nmr properties of these various compounds are described. The structure of ( 3 ) has been established by a single-crystal X-ray diffraction study of the solvate [1-(η⁶-C₆Me₆)-2-(PhNH)-isocloso-1-RuB₉H₈] · 1/2 CH₂Cl₂; the crystals were monoclinic, space group C2/c, with a = 1895.1(3), b = 1556.6(3), c = 1716.4(3) pm, β = 104.37(1)° and z = 8.     

Time shift correction in second-order liquid chromatographic data with iterative target transformation factor analysis

When the generalized rank annihilation method (GRAM) is applied to liquid chromatographic data with diode-array detection, an important problem is the time shift of the peak of the analyte in the test sample. This problem leads to erroneous predictions. This time shift can be corrected if a time window is selected so that the chromatographic profile of the analyte in the test sample is trilinear with the peak of the analyte in the calibration sample. In this paper we present a new method to determine when this condition is met. This method is based on the curve resolution with iterative target transformation factor analysis (ITTFA). The calibration and test matrices are independently decomposed into profiles and spectra, and aligned before GRAM is applied. Here we study two situations: first, when the calibration matrix has one analyte and second, when it has two analytes. When the calibration matrix has two analytes, we selectively determine the time window for the analyte to be quantified. There were considerably fewer prediction errors after correction.     

Synthesis and structure of Pt(II) phosphonato-phosphine complexes and of a P,O-stabilized metal-metal-bonded Pt2Ag2 complex

As part of our interest in the design and reactivity of P,O ligands, and because the insertion chemistry of small molecules into a metal alkyl bond is very dependent on the ancillary ligands, the behavior of Pt-methyl complexes containing the beta-phosphonato-phosphine ligand rac-Ph2PCH(Ph)P(O)(OEt)2 (abbreviated PPO in the following) toward CO insertion has been explored. New, mononuclear Pt(II) complexes containing one or two PPO ligands, [PtClMe(kappa2-PPO)] (1), [Pt{C(O)Me}Cl(kappa2-PPO)] (2), [PtMe(CO)(kappa2-PPO)]OTf (3 x OTf), [PtMe(OTf)(kappa2-PPO)] (4), trans-[PtClMe(kappa1-PPO)2] (5), [PtMe(kappa2-PPO)(kappa1-PPO)]BF4 (6 x BF4), [PtMe(kappa2-PPO)(kappa1-PPO)]OTf (6 x OTf), and [Pt{C(O)Me}(kappa2-PPO)(kappa1-PPO)]BF4 (7 x BF4) have been prepared and characterized. Hemilability of the ligands is observed in the cations 6 and 7 in which the terminally bound and chelating PPO ligands exchange their role on the NMR time-scale. The acetyl complexes 2 and 7 are stable in solution, but the former deinserts CO upon chloride abstraction. We also demonstrate the ability of PPO to behave as an assembling ligand and to stabilize a heterometallic Pt-Ag metal complex, [PtMe(kappa2-PPO){mu-(eta1-P;eta1-O)PPO)}Ag(OTf)(Pt-Ag)]OTf (8 x OTf), which was obtained by reaction of 5 with AgOTf to generate more reactive, cationic complexes. Whereas the first equivalent of AgOTf abstracted the chloride ligand, the second equivalent added to the cationic complex with formation of a Pt-Ag bond (2.819(1) A). The complexes 1, 2, 4, 5 x CH2Cl2, and (8 x OTf)2 have been structurally characterized by single-crystal X-ray diffraction. The latter has a dimeric nature in the solid state, with two silver-bound triflates acting as bridging ligands between two Pt-Ag moieties. In addition to the Ag-Pt bond, the Ag+ cation is stabilized by a dative O -->Ag interaction involving one of the PPO ligands.     

Amberlite XAD-2 functionalized with 2-aminothiophenol as a new sorbent for on-line preconcentration of cadmium and copper

A new functionalized resin has been applied in an on-line preconcentration system for copper and cadmium determination. Amberlite XAD-2 was functionalized by coupling it to 2-aminothiophenol (AT-XAD) by means of an NN spacer. This resin was packed in a minicolumn and used as sorbent in the on-line system. Metal ions were sorbed in the minicolumn, from which it could be eluted directly to the nebulizer-burner system of the flame atomic absorption spectrometer (FAAS). Elution of Cd(II) and Cu(II) from minicolumn can be made with 0.50 mol l⁻¹ HCl or HNO₃. The enrichment factors obtained were 28 (Cd) and 14 (Cu), for 60 s preconcentration time, and 74 (Cd) and 35 (Cu), if used 180 s preconcentration time. The proposed procedure allowed the determination of cadmium and copper with detection limits of 0.14 and 0.54 μg l⁻¹, respectively, when used preconcentration periods of 180 s. The effects of foreign ions on the adsorption of these metal ions are reported. The validation of the procedure was carried out by analysis of certified reference material. This procedure was applied to cadmium and copper determination in natural, drink and tap water samples.     

Density functional theory study of vibrational spectra, and assignment of fundamental vibrational modes of succinimide and N-bromosuccinimide

This work deals with the vibrational spectroscopy of succinimide and N-bromosuccinimide. The mid and far FTIR and FT-Raman spectra were measured in the condensed state. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT) using standard B3LYP/6-31G(*) and B3LYP/6-311+G(**) methods and basis set combinations. The vibrational spectra were interpreted, with the aid of normal coordinate analysis based on a scaled quantum mechanical force field. The infrared and Raman spectra were also predicted from the calculated intensities. Comparison of simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. Unambiguous vibrational assignment of all the fundamentals were made using the total energy distribution (TED).