Symmetry calculation for molecules and transition states

The symmetry of molecules and transition states of elementary reactions is an essential property with important implications for computational chemistry. The automated identification of symmetry by computers is a very useful tool for many applications, but often relies on the availability of three‐dimensional coordinates of the atoms in the molecule and hence becomes less useful when these coordinates are a priori unavailable. This article presents a new algorithm that identifies symmetry of molecules and transition states based on an augmented graph representation of the corresponding structures, in which both topology and the presence of stereocenters are accounted for. The automorphism group order of the graph associated with the molecule or transition state is used as a starting point. A novel concept of label‐stereoisomers, that is, stereoisomers that arise after labeling homomorph substituents in the original molecule so that they become distinguishable, is introduced and used to obtain the symmetry number. The algorithm is characterized by its generic nature and avoids the use of heuristic rules that would limit the applicability. The calculated symmetry numbers are in agreement with expected values for a large and diverse set of structures, ranging from asymmetric, small molecules such as fluorochlorobromomethane to highly symmetric structures found in drug discovery assays. The new algorithm opens up new possibilities for the fast screening of the degree of symmetry of large sets of molecules. © 2014 Wiley Periodicals, Inc.     

The Chemistry of Diet: Medicine,Nutrition, and Staple Foods in Imperial Brazil

Brazilian cuisine is much admired by present-day international chefs. However, in the nineteenth century, local ingredients and recipes were looked down upon by the Portuguese colonists, as well as by visiting European naturalists. This fact, together with medical and chemical views formulated throughout the 1800s, led locally trained doctors to attribute the occurrence of countless diseases that devastated Rio de Janeiro to local staple foods, particularly corn and manioc flour. In the first part of the present article, I review the dietary habits of Brazilians through the eyes of European naturalists who travelled across the country in the early nineteenth century. In the second part, I summarise the ideas formulated by French and German chemists on the components, and consequent nutritional value, of cereals and other sources of flour, and then analyse the appropriation of such ideas—particularly those of Justus Liebig—by Brazilian doctors and their adaptation to local conditions.     

Reactions of a,ß‐unsaturated N‐benzenesulfonyl Imine – N‐[(2E)‐3‐phenyl‐2‐propen‐1‐ylidene]benzenesulfonamide with Methyllithium

α,β‐Unsaturated N‐benzenesulfonyl imine 1 was treated with 1.1 eq methyllithium to afford 1,2‐addition adduct as a sole product. However, when compound 1 was treated with 2 eq MeLi, 1,2‐addition product, benzenesulfonamide derivative 3 and 2H‐1,2‐benzothiazine 1,1‐dioxide derivatives 4 and 5 were isolated.     

Novel and Stereospecific Synthesis of (2S)‐3‐(2,4,5‐Trifluorophenyl)propane‐1,2‐diol from D‐Mannitol

A stereospecific synthesis of (2S)‐3‐(2,4,5‐trifluorophenyl)propane‐1,2‐diol from D ‐mannitol has been developed. The reaction of 2,3‐O‐isopropylidene‐D ‐glyceraldehyde with 2,4,5‐trifluorophenylmagnesium bromide gave [(4R)‐2,2‐dimethyl‐1,3‐dioxolan‐4‐yl](2,4,5‐trifluorophenyl)methanol in 65% yield as a mixture of diastereoisomers (1 : 1). The Ph₃P catalyzed reaction of the latter with C₂Cl₆ followed by reduction with Pd/C‐catalyzed hydrogenation gave (2S)‐3‐(2,4,5‐trifluorophenyl)propane‐1,2‐diol with >99% ee and 65% yield.     

Thin-Layer Chromatographic Quantifcation of trans-Resveratrol in Cosmetic Raw Materials of Botanic Origin

JPC – Journal of Planar Chromatography – Modern TLC - Recently, a growing interest has been observed in preventive and “anti-ageing” medicine, accompanied by a dynamic...     

Luminescent Di‐ and Trinuclear Boron Complexes Based on Aromatic Iminopyrrolyl Spacer Ligands: Synthesis,Characterization, and Application in OLEDs

New bis‐ and tris(iminopyrrole)‐functionalized linear (1,2‐(HNC₄H₃‐C(H)?N)₂‐C₆H₄ ( 2 ), 1,3‐(HNC₄H₃‐C(H)?N)₂‐C₆H₄ ( 3 ), 1,4‐(HNC₄H₃‐C(H)?N)₂‐C₆H₄ ( 4 ), 4,4′‐(HNC₄H₃‐C(H)?N)₂‐(C₆H₄‐C₆H₄) ( 5 ), 1,5‐(HNC₄H₃C‐(H)?N)₂‐C₁₀H₆ ( 6 ), 2,6‐(HNC₄H₃C‐(H)?N)₂‐C₁₀H₆ ( 7 ), 2,6‐(HNC₄H₃C‐(H)?N)₂‐C₁₄H₈ ( 8 )) and star‐shaped (1,3,5‐(HNC₄H₃‐C(H)?N‐1,4‐C₆H₄)₃‐C₆H₃ ( 9 )) π‐conjugated molecules were synthesized by the condensation reactions of 2‐formylpyrrole ( 1 ) with several aromatic di‐ and triamines. The corresponding linear diboron chelate complexes (Ph₂B[1,3‐bis(iminopyrrolyl)‐phenyl]BPh₂ ( 10 ), Ph₂B[1,4‐bis(iminopyrrolyl)‐phenyl]BPh₂ ( 11 ), Ph₂B[4,4′‐bis(iminopyrrolyl)‐biphenyl]BPh₂ ( 12 ), Ph₂B[1,5‐bis(iminopyrrolyl)‐naphthyl]BPh₂ ( 13 ), Ph₂B[2,6‐bis(iminopyrrolyl)‐naphthyl]BPh₂ ( 14 ), Ph₂B[2,6‐bis(iminopyrrolyl)‐anthracenyl]BPh₂ ( 15 )) and the star‐shaped triboron complex ([4′,4′′,4′′′‐tris(iminopyrrolyl)‐1,3,5‐triphenylbenzene](BPh₂)₃ ( 16 )) were obtained in moderate to good yields, by the treatment of 3 – 9 with B(C₆H₅)₃. The ligand precursors are non‐emissive, whereas most of their boron complexes are highly fluorescent; their emission color depends on the π‐conjugation length. The photophysical properties of the luminescent polyboron compounds were measured, showing good solution fluorescence quantum yields ranging from 0.15 to 0.69. DFT and time‐dependent DFT calculations confirmed that molecules 10 and 16 are blue emitters, because only one of the iminopyrrolyl groups becomes planar in the singlet excited state, whereas the second (and third) keeps the same geometry. Compound 13 , in which planarity is not achieved in any of the groups, is poorly emissive. In the other examples ( 11 , 12 , 14 , and 15 ), the LUMO is stabilized, narrowing the gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital (HOMO–LUMO), and the two iminopyrrolyl groups become planar, extending the size of the π‐system, to afford green to yellow emissions. Organic light‐emitting diodes (OLEDs) were fabricated by using the new polyboron complexes and their luminance was found to be in the order of 2400 cd m^?2, for single layer devices, increasing to 4400 cd m^?2 when a hole‐transporting layer is used.     

BODIPY: A Highly Versatile Platform for the Design of Bimodal Imaging Probes

In molecular imaging, multimodal imaging agents can provide complementary information, for improving the accuracy of disease diagnosis or enhancing patient management. In particular, optical/nuclear imaging may find important preclinical and clinical applications. To simplify the preparation of dual‐labeled imaging agents, we prepared versatile monomolecular multimodal imaging probe (MOMIP) platforms containing both a fluorescent dye (BODIPY) and a metal chelator (polyazamacrocycle). One of the MOMIP was conjugated to a cyclopeptide (i.e., octreotide) and radiolabeled with ¹¹¹In. In vitro and in vivo studies of the resulting bioconjugate were conducted, highlighting the potential of these BODIPY‐based bimodal probes. This work also confirmed that the biovector and/or the bimodal probes must be chosen carefully, due to the impact of the MOMIP on the overall properties of the resulting imaging agent.     

Dioxygen Binding in the Active Site of Histone Demethylase JMJD2A and the Role of the Protein Environment

JMJD2A catalyses the demethylation of di‐ and trimethylated lysine residues in histone tails and is a target for the development of new anticancer medicines. Mechanistic details of demethylation are yet to be elucidated and are important for the understanding of epigenetic processes. We have evaluated the initial step of histone demethylation by JMJD2A and demonstrate the dramatic effect of the protein environment upon oxygen binding using quantum mechanics/molecular mechanics (QM/MM) calculations. The changes in electronic structure have been studied for possible spin states and different conformations of O₂, using a combination of quantum and classical simulations. O₂ binding to this histone demethylase is computed to occur preferentially as an end‐on superoxo radical bound to a high‐spin ferric centre, yielding an overall quintet ground state. The favourability of binding is strongly influenced by the surrounding protein: we have quantified this effect using an energy decomposition scheme into electrostatic and dispersion contributions. His182 and the methylated lysine assist while Glu184 and the oxoglutarate cofactor are deleterious for O₂ binding. Charge separation in the superoxo‐intermediate benefits from the electrostatic stabilization provided by the surrounding residues, stabilizing the binding process significantly. This work demonstrates the importance of the extended protein environment in oxygen binding, and the role of energy decomposition in understanding the physical origin of binding/recognition.