DFT study of core‐modified porphyrin isomers

B3LYP/6‐311+G** calculations were performed systematically on 1,2 (syn) and 1,3 (anti) tautomeric forms of oxa‐ and thia‐ core‐modified porphyrin isomers, which resulted in a total of 86 structures. The structural and energetic variation in all the isomers were analyzed. In corrphycene, hemiporphycene and porphycene the Z forms are more stable compared to the corresponding E forms in both the anti and syn oxa‐ and thiaporphyrin isomers. In contrast, in the syn isomeric forms of [3.0.1.0], [3.1.0.0] and [4.0.0.0] oxaporphyrins and in both syn and anti forms of thiaporphyrin isomers, Z forms are less stable. The HOMO and LUMO values are both negative and varied in a narrow zone, indicating no dramatic effect on the position of heteroatom substitution on the redox properties. The effect of geometric constraints due to the alteration of meso‐bridge length and the hetero atom disposition in the porphyrin core on the relative stabilities of the isomers is analyzed. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Electronic structure and stability of C86 fullerene Isolated‐Pentagon‐Rule isomers

All 19 Isolated‐Pentagon‐Rule isomers of fullerene C₈₆ were investigated by Density Functional Theory (DFT) methods with B3LYP functional at 6‐31G, 6‐31G*, and 6‐31+G* levels. Preliminary distribution of single, double, and delocalized pi‐bonds in molecules of these isomers of fullerene C₈₆ is fulfilled. Obtained results are perfectly supported by DFT quantum–chemical calculations of electronic and geometrical structures of these isomers. The main reason of instability of isomers 1, 3–15, 18, and 19 are phenalenyl‐radical substructures. Thus, there is a possibility to obtain them only as endohedral metallofullerenes or exohedral derivatives. Isomer 2 (C₂) is unstable due to higher local molecular strain. It is shown that empty C₈₆ may be produced and extracted only as isomers 16 (C_s) and 17 (C₂). © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Two isomers of 2,4‐di­benzyl‐8‐azabicyclo­[3.2.1]­octan‐3‐ol

The crystal structures of the title compounds, 2α,4α‐di­benzyl‐3α‐tropanol (2α,4α‐di­benzyl‐8‐methyl‐8‐aza­bi­cyclo­[3.2.1]­octan‐3α‐ol), C₂₂H₂₇NO, (I), and 2α,4α‐di­benzyl‐3β‐tropanol (2α,4α‐di­benzyl‐8‐methyl‐8‐aza­bi­cyclo­[3.2.1]­octan‐3β‐ol), C₂₂H₂₇NO, (II), show that both compounds have a piperidine ring in a chair conformation and a pyrrolidine ring in an envelope conformation. Isomer (I) is asymmetric, the benzyl groups having different orientations, whereas isomer (II) is mirror symmetric, and the N and O atoms, the C atom attached to the hydroxy group, and the methyl C atom attached to the N atom lie on the mirror plane. In the crystal structures of both (I) and (II), the mol­ecules are linked together by intermolecular O—H⋯N hydrogen bonds to form chains that run parallel to the a direction in (I) and parallel to b in (II).     

Identification of position isomers by energy‐resolved mass spectrometry

This study reports an energy‐resolved mass spectrometric (ERMS) strategy for the characterization of position isomers derived from the reaction of hydroxyl radicals (^●OH) with diphenhydramine (DPH) that are usually hard to differentiate by other methods. The isomer analogues formed by ^●OH attack on the side chain of DPH are identified with the help of a specific fragment ion peak (m/z 88) in the collision‐induced dissociation (CID) spectrum of the protonated molecule. In the negative ion mode, the breakdown curves of the deprotonated molecules show an order of stability (supported by density functional theory (DFT) calculations) ortho > meta > para of the positional isomers formed by the hydroxylation of the aromatic ring. The gas phase stability of the deprotonated molecules [M ? H]^? towards the benzylic cleavage depends mainly on the formation of intramolecular hydrogen bonds and of the mesomeric effect of the phenol hydroxyl. The [M ? H]^? molecules of ortho and meta isomers result a peak at m/z 183 with notably different intensities because of the presence/absence of an intramolecular hydrogen bonding between the OH group and C9 protons. The ERMS approach discussed in this report might be an effective replacement for the conventional methods that requires very costly and time‐consuming separation/purification methods along with the use of multi‐spectroscopic methods. Copyright © 2015 John Wiley & Sons, Ltd.     

Nitrated isomers of 2‐(trichloromethyl)quinoline

In the closely related quinoline compounds 8‐nitro‐2‐(trichloromethyl)quinoline, (I), 6‐nitro‐2‐(trichloromethyl)quinoline, (II), and 5‐nitro‐2‐(trichloromethyl)quinoline, (III), all C₁₀H₅Cl₃N₂O₂, which are of both reactivity and pharmacological interest, and for which the biological activity and cytotoxicity appear to be based on the positions of the CCl₃ and nitro substituents, the nitro group is only coplanar with its aromatic substrate in (II). The deviation of the nitro group from coplanarity is concluded to be a function of both its position with respect to the trichloromethyl group and the intermolecular contacts in which it participates. The discrepancies between the crystal structures and the molecular shapes predicted by ab initio calculations are also explained in these terms. The quinoline ring is not rigorously planar in any of the structures, which may be explained by stress produced by the CCl₃ substituent.     

Deep‐blue light‐emitting polyfluorenes containing spiro[fluorene‐9,9′‐thioxanthene‐S,S‐dioxide] isomers

Blue light‐emitting polyfluorenes, PPF‐FSOs and PPF‐SOFs were synthesized via introducing spiro[fluorene‐9,9′‐thioxanthene‐S,S‐dioxide] isomers (2,7‐diyl and 2′,7′‐diyl) (FSO/SOF) into the poly[9,9‐bis(4‐(2‐ethylhexyloxy) phenyl)fluorene‐2,7‐diyl] (PPF) backbone, respectively. With the increasing contents of FSO and SOF moieties, the absorption and PL spectra of PPF‐FSOs show slight red shift, while that of PPF‐SOFs exhibit blue shift, respectively. The HOMO and LUMO levels reduce gradually with increasing SOF unit in PPF‐SOFs. The polymers emit blue light peaked around 430–445 nm and show an excellent spectral stability with the variation in current densities. The distinctly narrowing EL spectra were observed with the incorporation of isomers in the polymers. The full width at half maximum reduced by 15 nm for PPF‐SOFs, resulting in a blue shift with the CIE coordinates from (0.16, 0.11) to (0.16, 0.08). With a device configuration of ITO/PEDOT:PSS/EML/CsF/Al, a maximum luminance efficiency (LE_max) of 2.00 cd A^?1, a maximum external quantum efficiency (EQE_max) of 3.76% with the CIE coordinates of (0.16, 0.08) for PPF‐SOF15 and a LE_max of 1.68 cd A^?1, a EQE_max of 2.38% with CIE (0.16, 0.12) for PPF‐FSO10 were obtained, respectively. The result reveals that spiro[fluorene‐9,9′‐thioxanthene‐S,S‐dioxide] isomers are promising blocks for deep‐blue light‐emitting polymers. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55 , 2332–2341     

Quantum topology phase diagrams for the cis‐ and trans‐isomers of the cyclic contryphan‐Sm peptide

Within the quantum theory of atoms in molecules (QTAIM) framework we present a quantum topology phase diagram (QTPD) using the Poincaré–Hopf relation of a total of 17 all new QTAIM topologies of the cis‐ and trans‐isomers of the cyclic contryphan‐Sm peptide. The resultant QTPD consists of separate regions for the cis‐ and trans‐isomers that only overlap for topologies associated with the lowest energy minima of the cis‐ and trans‐isomers. We determine the QTAIM topologies of 29 “missing” isomers. A new, contracted formulation of the QTPD is presented, this contracted formulation includes the interamino acid bond critical points (BCPs) that link together the amino acid units, the disulphide bridge “pivot” BCP and side chain bonding interactions. The seven interamino acid BCPs linking the amino acid units coincide with the so‐called peptide backbone, the conventional qualitative approach to reduce the complexity of the peptide. We expand the interpretation of ellipticity to include the associated eigenvectors and find that higher values of the ellipticity ? are associated with a greater preference to conserve folding states. We quantify previous qualitative findings that suggested the disulfide bond is central to the folding behavior of the cyclic contryphan‐Sm peptide and why the cis‐isomer is the major form of the cyclic contryphan‐Sm peptide. © 2014 Wiley Periodicals, Inc.     

The E and Z isomers of 3‐(benzoxazol‐2‐yl)­prop‐2‐enoic acid

The carboxyl­ic acid group and the double bond are coplanar in (E)‐3‐(benzoxazol‐2‐yl)­prop‐2‐enoic acid, C₁₀H₇NO₃, whereas in isomeric (Z)‐3‐(benzoxazol‐2‐yl)­prop‐2‐enoic acid, also C₁₀H₇NO₃, they are almost orthogonal. In both isomers, a strong O—H⋯N hydrogen bond, with the carboxyl­ic acid group as a donor and the pyridine‐like N atom as an acceptor, and weak C—H⋯O interactions contribute to the observed supramolecular structures, which are completed by π–π stacking interactions between oxazole and benzenoid rings.     

Intramolecular hydrogen bond in 3‐imino‐propenylamine isomers: AIM and NBO studies

The molecular structure and intramolecular hydrogen bond energy of 18 conformers of 3‐imino‐propenyl‐amine were investigated at MP2 and B3LYP levels of theory using the standard 6‐311++G** basis set. The atom in molecules or AIM theory of Bader, which is based on the topological properties of the electron density (ρ), was used additionally and the natural bond orbital (NBO) analysis was also carried out. Furthermore calculations for all possible conformations of 3‐imino‐propenyl‐amin in water solution were also carried out at B3LYP/6‐311++G** and MP2/6‐311++G** levels of theory. The calculated geometrical parameters and conformational analyses in gas phase and water solution show that the imine–amine conformers of this compound are more stable than the other conformers. B3LYP method predicts the IMA‐1 as global minimum. This stability is mainly due to the formation of a strong N? H···N intramolecular hydrogen bond, which is assisted by π‐electrons resonance, and this π‐electrons are established by NH2 functional group. Hydrogen bond energies for all conformers of 3‐imino‐propenyl‐amine were obtained from the related rotamers methods. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Site‐specific separation and detection of phosphopeptide isomers with pH‐mediated stacking capillary electrophoresis‐electrospray ionization‐tandem mass spectrometry

This study reported a pH‐mediated stacking CE coupled with ESI MS/MS method to determine the phosphorylation sites of three synthetic phosphopeptides containing structural isomers. These phosphopeptides mimic the phosphopeptides (amino acid residues 12–25) derived from the trypsin‐digested products of human lamin A/C protein. The LODs were determined to be 118, 132 and 1240 fmol for SGAQASS¹⁹TpPL²²SPTR, SGAQASS¹⁹TPL²²SpPTR, and SGAQASS¹⁹TpPL²²SpPTR, respectively. The established method was employed to analyze the phosphorylation sites of the trypsin‐digested products of glutathione S‐transferase‐lamin A/C (1–57) fusion protein that had been phosphorylated in vitro by cyclin‐dependent kinase 1. The results indicated that this method is feasible to specifically determine the phosphorylation site from phosphopeptide isomers in the trypsin‐digested products of a kinase‐catalyzed phosphoprotein, which should benefit the investigation of protein kinase‐mediated cellular signal transduction.     

Ring opening of pyridines: the pseudo‐cis and pseudo‐trans isomers of tetra‐n‐butylammonium 4‐nitro‐5‐oxo‐2‐pentenenitrilate

The reaction of 2‐chloro‐5‐nitropyridine with two equivalents of base produces the title carbanion as an intermediate in a ring‐opening/ring‐closing reaction. The crystal structures of the tetra‐n‐butylammonium salts of the intermediates, C₁₆H₃₆N⁺·C₅H₃N₂O₃⁻, revealed that pseudo‐cis and pseudo‐trans isomers are possible. One crystal structure displayed a mixture of the two isomers with approximately 90% pseudo‐cis geometry and confirms the structure predicted by the S_N(ANRORC) mechanism. The pseudo‐cis intermediate undergoes a slow isomerization over a period of months to the pseudo‐trans isomer, which does not have the appropriate geometry for the subsequent ring‐closing reaction. The structure of the pure pseudo‐trans isomer is also reported. In both isomers, the negative charge is highly delocalized, but relatively small differences in C—C bond distances indicate a system of conjugated double bonds with the nitro group bearing the negative charge. The packing of the two unit cells is very similar and largely determined by the interactions between the planar carbanion and the bulky tetrahedral cation.     

A structural systematic study of three isomers of difluoro‐N‐(4‐pyridyl)benzamide

The isomers 2,3‐, (I), 2,4‐, (II), and 2,5‐difluoro‐N‐(4‐pyridyl)benzamide, (III), all with formula C₁₂H₈F₂N₂O, all exhibit intramolecular C—H...O=C and N—H...F contacts [both with S(6) motifs]. In (I), intermolecular N—H...O=C interactions form one‐dimensional chains along [010] [N...O = 3.0181 (16) Å], with weaker C—H...N interactions linking the chains into sheets parallel to the [001] plane, further linked into pairs via C—H...F contacts about inversion centres; a three‐dimensional herring‐bone network forms via C—H...π(py) (py is pyridyl) interactions. In (II), weak aromatic C—H...N(py) interactions form one‐dimensional zigzag chains along [001]; no other interactions with H...N/O/F < 2.50 Å are present, apart from long N/C—H...O=C and C—H...F contacts. In (III), N—H...N(py) interactions form one‐dimensional zigzag chains [as C(6) chains] along [010] augmented by a myriad of weak C—H...π(arene) and O=C...O=C interactions and C—H...O/N/F contacts. Compound (III) is isomorphous with the parent N‐(4‐pyridyl)benzamide [Noveron, Lah, Del Sesto, Arif, Miller & Stang (2002). J. Am. Chem. Soc. 124 , 6613–6625] and the three 2/3/4‐fluoro‐N‐(4‐pyridyl)benzamides [Donnelly, Gallagher & Lough (2008). Acta Cryst. C 64 , o335–o340]. The study expands our series of fluoro(pyridyl)benzamides and augments our understanding of the competition between strong hydrogen‐bond formation and weaker influences on crystal packing.     

A structural systematic study of four isomers of difluoro‐N‐(3‐pyridyl)benzamide

The four isomers 2,4‐, (I), 2,5‐, (II), 3,4‐, (III), and 3,5‐difluoro‐N‐(3‐pyridyl)benzamide, (IV), all with formula C₁₂H₈F₂N₂O, display molecular similarity, with interplanar angles between the C₆/C₅N rings ranging from 2.94 (11)° in (IV) to 4.48 (18)° in (I), although the amide group is twisted from either plane by 18.0 (2)–27.3 (3)°. Compounds (I) and (II) are isostructural but are not isomorphous. Intermolecular N—H...O=C interactions form one‐dimensional C(4) chains along [010]. The only other significant interaction is C—H...F. The pyridyl (py) N atom does not participate in hydrogen bonding; the closest H...N_py contact is 2.71 Å in (I) and 2.69 Å in (II). Packing of pairs of one‐dimensional chains in a herring‐bone fashion occurs viaπ‐stacking interactions. Compounds (III) and (IV) are essentially isomorphous (their a and b unit‐cell lengths differ by 9%, due mainly to 3,4‐F₂ and 3,5‐F₂ substitution patterns in the arene ring) and are quasi‐isostructural. In (III), benzene rotational disorder is present, with the meta F atom occupying both 3‐ and 5‐F positions with site occupancies of 0.809 (4) and 0.191 (4), respectively. The N—H...N_py intermolecular interactions dominate as C(5) chains in tandem with C—H...N_py interactions. C—H...O=C interactions form R₂²(8) rings about inversion centres, and there are π–π stacks about inversion centres, all combining to form a three‐dimensional network. By contrast, (IV) has no strong hydrogen bonds; the N—H...N_py interaction is 0.3 Å longer than in (III). The carbonyl O atom participates only in weak interactions and is surrounded in a square‐pyramidal contact geometry with two intramolecular and three intermolecular C—H...O=C interactions. Compounds (III) and (IV) are interesting examples of two isomers with similar unit‐cell parameters and gross packing but which display quite different intermolecular interactions at the primary level due to subtle packing differences at the atom/group/ring level arising from differences in the peripheral ring‐substitution patterns.     

p‐Decyl­phenyl isocyanide and p‐decyl­benzo­nitrile: isomorphous iso­nitrile/nitrile isomers

p‐Decyl­phenyl isocyanide, p‐C₁₀H₂₁–C₆H₄–NC or C₁₇H₂₅N, and p‐decyl­benzo­nitrile, p‐C₁₀H₂₁–C₆H₄–CN or C₁₇H₂₅N, are isomorphous. The mol­ecules lie in mirror planes, with the C₆ rings perpendicular to the mirror. The packing of both mol­ecules includes an aliphatic region, with close to ideal packing of the C₁₀H₂₁ chains, and an aromatic region, with phenyl ring–CN interactions. In addition, the CN ends of the mol­ecules are also involved in a CN⋯NC dipolar interaction.     

Living anionic polymerization of (E)‐1,3‐pentadiene and (Z)‐1,3‐pentadiene isomers

The anionic polymerization of (E)‐1,3‐pentadiene (EP) and (Z)‐1,3‐pentadiene (ZP) together with mixture of the E/Z isomers are investigated, respectively. The kinetic analysis shows that the activation energy for EP (86.17 kJ/mol) is much higher than that for ZP (59.03 kJ/mol). GPC shows that it is the EP rather than the ZP isomer that undergoes anionic living polymerization affording quantitative products of the polymers with well‐controlled molecular weights and narrow molecular weight distributions (1.05 ≤? ≤ 1.09). In addition, THF as polar additive has proved its validity to reduce the molecular weight distribution of poly(ZP) from 1.38 to as low as 1.19. The microstructure and sequence distributions of polypentadiene are characterized by ¹H NMR and quantitative ¹³C NMR. Finally, the distinctive reaction activity of two isomers can be elucidated by two different mechanisms which involve the presence of four forms of zwitterions for EP and the typical [1,5]‐sigmatropic hydrogen‐shift phenomenon for ZP. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 2291–2301     

Regiospecific synthesis of 5‐(1H‐indol‐2‐yl)‐1‐ and 2‐methyl‐6,7‐dihydro‐2H‐indazole isomers

A regiospecific approach to each N‐methyl‐5‐(1H‐indol‐2‐yl)‐6,7‐dihydro‐2H‐indazole isomer is reported. The 1‐methyl isomer 1 was prepared from 5‐bromo‐1‐methyl‐6,7‐dihydro‐1H‐indazole 3 and indole‐2‐boronate 5 by palladium catalyzed Suzuki coupling. The 2‐methyl regioisomer 2 was synthesized via addition of lithium (1‐carboxylato‐1H‐indole‐2‐yl)lithium 6 with 2‐methyl‐2,4,6,7‐tetrahydro‐indazol‐5‐one 8 followed by acid catalyzed dehydration.     

L‐Valine assisted distinction between the stereo‐isomers of D‐hexoses by positive ion ESI tandem mass spectrometry

The binary mixtures of 7 hexoses and 20 amino acids were investigated by electrospray ionization ion trap mass spectrometry (ESI‐ITMS). The adduct ions of the amino acid and the hexose were detected for 12 amino acids but not for the other 8 amino acids which are basic acidic amino acids and amides. The ions of amino acid–hexose complexes were further investigated by tandem mass spectrometry (MS/MS), and some of them just split easily into two parts whereas the others gave rich fragmentation, such as the complex ions of isoleucine, phenylalanie, tyrosine, and valine. We found that hexoses could be complexed by two molecules of valine but only by one molecule of the other amino acids. Among seven kinds of valine–hexose complexes coordinated by potassium ion, the MS² spectra of the ion at m/z 453 yielded unambiguous differentiation. And the fragmentation ions are sensitive to the stereochemical differences at the carbon‐4 of hexoses in the complexes, as proved by the MS². Copyright © 2010 John Wiley & Sons, Ltd.     

Synthesis and mutagenic potency of structural isomers of 2‐amino‐1‐methyl‐6‐phenylimidazo[4,5‐b]pyridine

Synthesis of 2‐amino‐1‐methyl‐6‐phenylimidazo[4,5‐b]pyridine (PhIP), three structural isomers, and two desphenyl PhIP congeners has been carried out. Mutagenic potency was evaluated using S. typhimurium strain TA98 in the Ames test. Mutagenic potency increased in relation to structural features in these heterocyclic amines that allow extended resonance between the phenyl and imidazo[4,5‐b]pyridine N²‐amino substituents. By contrast, PhIP isomers, whose substitution disallows involvement of the phenyl group in their aminoimidazo resonance hybrids, and desphenyl congeners were from 86‐ to 234‐fold less mutagenic than PhIP.     

Hydro­gen‐bonding patterns in two structural isomers of 3,6‐bis(2‐chloro­phenyl)‐1,4‐di­hydro‐1,2,4,5‐tetrazine

Two structural isomers, 3,6‐bis(2‐chloro­phenyl)‐1,4‐di­hydro‐1,2,4,5‐tetrazine, (I), and 3,5‐bis(2‐chloro­phenyl)‐4‐amino‐1H‐1,2,4‐triazole, (II), both C₁₄H₁₀Cl₂N₄, form chain‐like structures in the solid state, stabilized by N—H⋯N and N—H⋯Cl hydrogen bonds. A contribution from weak interactions to the strong hydrogen‐bond network is observed in both structures. The secondary graph sets for intermolecular hydrogen bonds [(11) for (I) and (12) for (II)] indicate the similarity between the networks.