Non-planar Conformation Research Articles

Highly nonplanar macrocyclic ring conformation in the crystal structures of Ni(II) and Cu(II) octaphenylporphyrins

Crystal structures of solvated highly nonplanar nickel(II) and copper(II) complexes of 2,3,5,10,12,13,15,20-octaphenylporphyrin are determined by single crystal XRD analysis. The macrocycles in these systems exhibit mainly ruffled and saddled conformations. The average displacement of the pyrrole carbon atom ΔCb from the mean plane of the porphyrin ring is as high as ±0.70 Å. The Hirshfeld surface analysis of both structures reveals mainly H…H (57—59 %) intermolecular short contacts with a smaller contribution from C…H (16—22 %) and H…Cl (11—19 %) interactions. The present work suggests that the nonplanarity of the macrocycle in NiTPP(Ph)4 is largely due to the core Ni(II) ion and less influenced by intermolecular interactions/crystal packing forces, whereas the opposite is true in the case of the nonplanar CuTPP(Ph)4 structure.

The crystal structures of two isomers of 5-(phenyl-iso-thia-zol-yl)-1,3,4-oxa-thia-zol-2-one.

The syntheses and crystal structures of two isomers of phenyl iso-thia-zolyl oxa-thia-zolone, C11H6N2O2S2, are described [systematic names: 5-(3-phenyl-iso-thia-zol-5-yl)-1,3,4-oxa-thia-zol-2-one, (I), and 5-(3-phenyl-iso-thia-zol-4-yl)-1,3,4-oxa-thia-zol-2-one, (II)]. There are two almost planar (r.m.s. deviations = 0.032 and 0.063 Å) mol-ecules of isomer (I) in the asymmetric unit, which form centrosymmetric tetra-mers linked by strong S⋯N [3.072 (2) Å] and S⋯O contacts [3.089 (1) Å]. The tetra-mers are π-stacked parallel to the a-axis direction. The single mol-ecule in the asymmetric unit of isomer (II) is twisted into a non-planar conformation by steric repulsion [dihedral angles between the central iso-thia-zolyl ring and the pendant oxa-thia-zolone and phenyl rings are 13.27 (6) and 61.18 (7)°, respectively], which disrupts the π-conjugation between the heteroaromatic iso-thia-zoloyl ring and the non-aromatic oxa-thia-zolone heterocycle. In the crystal of isomer (II), the strong S⋯O [3.020 (1) Å] and S⋯C contacts [3.299 (2) Å] and the non-planar structure of the mol-ecule lead to a form of π-stacking not observed in isomer (I) or other oxa-thia-zolone derivatives.

Versatile Synthetic Route for β-Functionalized Chlorins and Porphyrins by Varying the Size of Michael Donors: Syntheses, Photophysical, and Electrochemical Redox Properties

One-pot facile synthesis and characterization of novel β-substituted meso-tetraphenylporphyrins and/or chlorins were described. The high regioselective reactivity of active methylene compounds in Michael addition reaction was reported to access β-substituted trans-chlorins. Size-dependent approach was applied for the fine-tuning of product formation from porphyrins to chlorins. Notably, we were able to isolate mono/trisubstituted porphyrin and/or di/tetra-substituted chlorin from one-pot synthesis for the first time in porphyrin chemistry. Single-crystal X-ray diffraction analysis revealed the quasiplanar to moderate nonplanar conformation of chlorins due to trans orientation of β-substituents, whereas porphyrins exhibited higher mean plane deviation from 24-atom core (Δ24) as compared to chlorins. β-Functionalized chlorins exhibited lower protonation constants and much higher deprotonation constants as compared to porphyrins revealing the combined effect of the conformation of macrocyclic core and the electronic nature of β-substituents. Facile synthesis of porphyrins and/or chlorins based on the size of Michael donor employed and in turn resulted in tunable photophysical and electrochemical redox properties are the significant features of the present work.

A Structural Model of Nitro‐Porphyrin Dyes Based on Spectroscopy and Density Functional Theory

Nitro-porphyrins are an important class of commercial dyes with a range of potential applications. The nitro group is known to dramatically affect the photophysics of the porphyrin, but there are few systematic investigations of the contributing factors. To address this deficiency, we present spectroscopic studies of a series of nitro-porphyrins, accompanied by density functional theory calculations to elucidate their structures. In particular, we explore how the positions of the substituents affect the energy levels and nuclear geometry. As expected, nitro groups on the meso-phenyl rings cause small changes to the orbital energies by induction, while those at the β-pyrrole positions more strongly conjugate into the aromatic system. In addition, however, we find evidence that β-pyrrole nitro groups distort the porphyrin, creating two non-planar conformations with distinct properties. This unexpected result helps explain the anomalous photophysics of nitro-porphyrins reported throughout the literature, including inhomogeneous line broadening and biexponential fluorescence decay. © 2017 Wiley Periodicals, Inc.

Two-Photon Spectroscopy of a Series of Platinum Acetylides: Conformation-Induced Ground-State Symmetry Breaking.

With the goal of elucidating electronic and conformational effects on structure-spectroscopic property relationships in platinum acetylides, we synthesized a series of nominally centrosymmetric chromophores trans-Pt(PBu3)2(C≡C-Phenyl-X)2, where X = diphenylamino (DPA), NH2, OCH3, t-Bu, CH3, H, F, benzothiazole (BTH), CF3, CN, and NO2. We collected one- and two-photon absorption spectra and also performed density functional theory (DFT) and time-dependent (TD) DFT calculations on the ground- and excited-state properties of these compounds. The DFT calculations revealed facile rotation between the two ligands, suggesting that the compounds exhibit nonplanar ground-state conformations in solution. TDDFT calculation of the S1 state energy and transition dipole moment for a nonplanar conformation gave good agreement with experiment. Two-photon absorption spectra obtained from these compounds allowed estimation of the change of permanent electric dipole moment upon vertical excitation from ground state to S1 state. The values are small Δμ < 1.0 D for neutral substituents such as CH3, H, and F but increase sharply to Δμ ≈ 11 D for electron-accepting NO2. When in a nonplanar conformation, the corresponding calculated Δμ values showed good agreement with the experimental data indicating that the two-photon spectra result from nonplanar ground-state conformations. Previously studied related chromophores having extended conjugation ( Rebane, A.; Drobizhev, M.; Makarov, N. S.; Wicks, G.; Wnuk, P.; Stepanenko, Y.; Haley, J. E.; Krein, D. M.; Fore, J. L.; Burke, A. R.; Slagle, J. E.; McLean, D. G.; Cooper, T. M. J. Phys. Chem. A 2014 , 118 , 3749 - 3759 ) show similar dependence of Δμ on the substituents, which allows us to conclude that the excited-state properties of these floppy chromophores are a function of the electronic properties of the substituents, ligand size, and nonplanar molecular conformation.

Conformational Landscapes of Metal(II) Porphyrinato, Chlorinato, and Morpholinochlorinato Complexes.

The macrocycle conformation of [meso-tetraarylporphyrinato]metal complexes is metal-dependent. Furthermore, hydroporphyrins and some of their analogues are known to be more conformationally flexible than the parent porphyrins, but the extent to which this is reflected in their metal-dependent conformations was much less studied. meso-Tetraarylmorpholinochlorins are intrinsically nonplanar chlorin analogues in which the five-membered pyrroline moiety was replaced by a six-membered morpholine moiety. The metal complexes (M = Ni2+, Cu2+, Zn2+, Pd2+, Ag2+) of meso-aryl-2,3-dimethoxychlorins and meso-arylmorpholinochlorins were prepared. Their conformations were determined using X-ray crystal structure diffractometry and compared against those of their free bases, as well as against the conformations of the corresponding metalloporphyrins. Out-of-plane displacement plots visualized and quantified the conformational changes upon stepwise conversion of a pyrrole moiety to a dimethoxypyrroline moiety and to a dialkoxymorpholine moiety, respectively. The generally nonplanar macrocycle conformations were found to be central-metal-dependent, with the smaller ions showing more nonplanar conformations and with the metallomorpholinochlorins generally showing a much larger conformational range than the corresponding metallochlorins, which, in turn, were more nonplanar than the corresponding porphyrins. This attests to the larger conformational flexibility of the morpholinochlorin macrocycle compared to that of a chlorin or even a porphyrin macrocycle. The degree of nonplanarity affects the electronic structure of the metal complexes, as can also be seen in a comparison of their UV-vis spectra. We thus further define the conformational and electronic effects governing pyrrole-modified porphyrins.

Synthesis, structures, and properties of 2,5-dianthrylthiophene derivatives

The title thiophene derivatives bearing two 9-, 1-, or 2-anthryl groups were synthesized by cyclization of the corresponding 1,3-diynes with sodium sulfide or by Suzuki–Miyaura coupling. X-ray analysis and DFT calculations revealed that the molecules adopt nonplanar conformations depending on the steric demand of the anthryl groups. The dihedral angles between the arene units are an important contributor to the photophysical properties in the electronic spectra as well as the electrochemical data.

Internal Dynamics of the 3-Pyrroline-N-Oxide Ring in Spin-Labeled Proteins.

Site-directed spin labeling is a versatile tool to study structure as well as dynamics of proteins using EPR spectroscopy. Methanethiosulfonate (MTS) spin labels tethered through a disulfide linkage to an engineered cysteine residue were used in a large number of studies to extract structural as well as dynamic information on the protein from the rotational dynamics of the nitroxide moiety. The ring itself was always considered to be a rigid body. In this contribution, we present a combination of high-resolution X-ray crystallography and EPR spectroscopy of spin-labeled protein single crystals demonstrating that the nitroxide ring inverts fast at ambient temperature while exhibiting nonplanar conformations at low temperature. We have used quantum chemical calculations to explore the potential energy that determines the ring dynamics as well as the impact of the geometry on the magnetic parameters probed by EPR spectroscopy.

The role of molecular structure on impact resistance and bending strength of photocured urethane-dimethacrylate polymer networks

The objective of this study was to investigate the influence of molecular structure on impact resistance (an) and bending strength (σ) of photocured urethane-dimethacrylate polymer networks. Urethane-dimethacrylate (UDMA) monomers were synthesized through reaction of oligoethylene glycol monomethacrylate (OEGMMA) with diisocyanate (DI). OEGMMA varied within the length of the oligooxyethylene chain, which consisted of one to four oxyethylene units. DI varied in chemical character: aliphatic, cycloaliphatic or aromatic. The molecular structure of UDMA polymers was characterized by X-ray powder diffraction, which allowed the calculation of the d-spacing (d) and dimensions of microgel agglomerates (D). The measurements of the polymerization shrinkage were used for the determination of the degree of conversion (DC), whereas the concentration of double bonds was used as a measure of the crosslink density (q). It was found that all structural parameters depend on the UDMA chemical structure. The increasing length of the oligooxyethylene chains caused the decrease in d and q, in contrast to the increase in D and DC. The DI chemical character caused the increase in the DC and q accordingly: symmetrical cycloaliphatic or aromatic < asymmetrical cycloaliphatic and aromatic < substituted aliphatic < linear aliphatic. The compact packing and high DC in polymers derived from aliphatic DIs gave rise to the decrease in d and the increase in D. The non-planar conformation of cycloaliphatic DIs emerged in high d as well as D. The planar conformation of aromatic DIs resulted in the decrease in d as well as D. The study indicated that mechanical behavior of UDMA polymer networks can be explained in terms of the structural parameters. DC and q appeared to be the main factors determining both mechanical properties of poly(UDMA)s. The an was also shown to be affected by d. Particularly high linear correlations were found on a semi-logarithmic scale for the DC and d with an. an increased as the DC increased, whereas d decreased.

Geometrical distortion leads to Griffith strength reduction in graphene membranes

Geometrical distortion plays an important role in modulating the mechanical responses of low-dimensional materials. Upon a structural transition from planar to non-planar conformations, the elastic energy stored in a membrane will be redistributed in between the stretching and bending modes of deformation. In this work, we present a molecular simulation based study that demonstrates remarkable reduction in the Griffith strength of graphene with the presence of out-of-plane distortion. The reduction is much more significant in mode II crack where the wrinkles are delocalized compared to the results for mode I crack where localized buckles are activated. Atomistic stress analysis and theoretical models based on the linear elastic fracture mechanics explain this strength reduction as a consequence of the out-of-plane distortion that releases in-plane elastic deformation, and predict the mechanical resistance of crack-containing graphene membranes. These findings are important for using graphene, and in general two-dimensional materials, as structural or functional membrane components where the non-planar distortion in unavoidable.

Enhancing and optimizing electronic transport in biphenyl derivative single-molecule junctions attached to carbon nanotubes electrodes

Abstract We investigate, by means of ab initio calculations based on non-equilibrium Green's function method coupled to density function theory, electronic transport in molecular junctions composed of biphenyl (BP) and biphenyl within (-2H+) defect (BP2D) molecules attached to metallic (9,0) carbon nanotubes. We demonstrate that the BP2D junction exhibits unprecedented electronic transport properties, and that its conductance can be up to three orders of magnitude higher than biphenyl single-molecule junctions. These findings are explained in terms of the non-planar molecular conformation of BP2D, and of the stronger electronic coupling between the BP2D molecule and the organic electrodes, which confers high stability to the junction. Our results suggest that BP2D attached to carbon nanotubes can be explored as an efficient and highly stable platform in single-molecule electronics with extraordinary transport properties.

Synthesis and structure of 4-methyl-1-N-(p-tolyl)imidazole as organic corrosion inhibitor

ABSTRACTHeterocyclic organic compounds containing nitrogen, sulfur or oxygen atoms are often used to protect metals from corrosion acting as organic corrosion inhibitors. Their inhibiting role is based on excellent ligand abilities and formation of stabile metal complex. Two requirements are essential for using selected class of organic inhibitors: (a) ligand capacity in the conditions of corrosion such as atmospheric conditions, acid or neutral corrosion, etc., and (b) nontoxicity, i.e., environmentally friendly inhibitors. Imidazole derivatives are capable to fulfil both requirements and they are, from that point of view, very promising and profound class of ligands. Synthesis and X-ray diffraction molecular and crystal structure of 4-methyl-1-N-(p-tolyl)imidazole has been reported, since it exhibits the most prominent corrosion inhibiting role. The synthesis, starting from 4-methylimidazole and 4-bromotoluene, is based on Ullmann-type coupling reaction by applying modifications of N-arylation by arylhalogenides and Cu2O as an efficient catalyst.The molecular and crystal structure of prepared N-substituted imidazole derivative reveals non-planar molecular conformation and the supramolecular assembling of the molecules via C-H···N intermolecular hydrogen bonds between Csp2-H proton donor groups and basic imidazole nitrogen atom. The molecules are related by a 21 screw axis parallel to [0 1 0] in the form of infinite C(4) zig-zag 1D chains via C-H···N intermolecular hydrogen bonds. Such alignment produces additional weak stacking interaction between imidazole and phenyl ring of related chains.

Spectral-Luminescent Properties of meso-Tetraarylporphyrins Revisited: The Role of Aryl Type, Substitution Pattern and Macrocycle Core Protonation

Both the ground (S0) and the lowest singlet excited states (S1) for a series of 5,10,15,20-tetraarylporphyrins consisting of two symmetrically and four asymmetrically substituted derivatives (A4, AB3, trans-A2B2, cis-A2B2, A3B and B4, where A=phenyl and B=mesityl) are studied by absorption and fluorescence spectroscopies. The rotational degree of freedom of the aryl rings is found to play a crucial role in the discrimination between the radiative and radiationless decays of the S1 states. This feature is dramatically enhanced upon going from the free base molecules to their mono and diprotonated forms because of the nonplanar macrocycle conformation of the latters. The progressive A to B replacement of the aryl substituents leads to additive spectral changes over the whole series in the free base form. For both mono- and diprotonated species such a gradual additive pattern is broken by a “spectral jump” from the trans to the cis derivative, which is proposed to be a signature of the transition between two macrocycle conformations with different flexibility.

On-Surface Synthesis and Characterization of Honeycombene Oligophenylene Macrocycles.

We report the on-surface formation and characterization of [30]-honeycombene, a cyclotriacontaphenylene, which consists of 30 phenyl rings (C180H120) and has a diameter of 4.0 nm. This shape-persistent, conjugated, and unsubstituted hexagonal hydrocarbon macrocycle was obtained by solvent-free synthesis on a silver (111) single-crystal surface, making solubility-enhancing alkyl side groups unnecessary. Side products include strained macrocycles with square, pentagonal, and heptagonal shape. The molecules were characterized by scanning tunneling microscopy and density functional theory (DFT) calculations. On the Ag(111) surface, the macrocycles act as molecular quantum corrals and lead to the confinement of surface-state electrons inside the central cavity. The energy of the confined surface state correlates with the size of the macrocycle and is well described by a particle-in-the-box model. Tunneling spectroscopy suggests conjugation within the planar rings and reveals influences of self-assembly on the electronic structure. While the adsorbed molecules appear to be approximately planar, the free molecules have nonplanar conformation, according to DFT.

Facile Conversion of Ni(II) Cyclopropylchlorins into Novel β-Substituted Porphyrins through Acid-Catalyzed Ring-Opening Reaction.

The conversion of cyclopropylchlorins into porphyrins represents a key step in the synthetic manipulation of macrocycles with tunable physical and chemical properties. Herein, we report a facile method for the synthesis of novel β-substituted porphyrins from cyclopropylchlorins. A series of Ni(II) cyclopropylchlorins was converted into the corresponding Ni(II) and free base porphyrins using TFA and H2SO4 under mild reaction conditions in good yields (75-86%). The new chlorins and porphyrins were characterized by various spectroscopic techniques and the single-crystal X-ray diffraction method. The reaction proceeds very fast (<5 min.) with complete conversion of chlorin into porphyrin with distinct color change. Facile conversion, shorter reaction time scale, and good yield (75-86%) without any side products are the significant features of this new protocol. These porphyrinoids exhibited red-shifted electronic spectral features with varying degrees nonplanar conformation, tunable redox properties, and porphyrin core basicity.

Two-electron Oxidation of a Twisted Non Anti-aromatic 40π Expanded Isophlorin

Expanded isophlorins are typical examples for stable anti-aromatic systems. Paratropic ring current effects are observed in their NMR spectra mainly due to their planar conformation. Herein we report the synthesis of the first twisted 40 π expanded isophlorin and also its two-electron oxidation to a 38 π dication. It sustains the twisted conformation for the 4n π and (4n + 2) π electrons. Due to the non-planar conformation, they do not display ring current effects in their respective1H NMR spectrum. NICS calculations reveal the non-(anti)aromatic features for the neutral 40 π and the 38 π dication species.

Quercetin Influence on Thermal Denaturation of Bovine Serum Albumin.

The effect of quercetin (QUER) binding on bovine serum albumin (BSA) thermal denaturation was systematically investigated by means of differential scanning calorimetry (DSC). Additional information concerning thermodynamic and structural binding parameters was provided by isothermal titration calorimetry (ITC) and molecular docking. The most relevant effect of QUER is manifested in the modification of the two-step thermal fingerprint of protein denaturation. Higher QUER concentrations result in a single-step denaturation thermogram, ascribed to the interplay between specific and nonspecific binding and enhancement of the solvent unfolding action. Analysis of ITC data indicate sequential binding of two molecules of QUER occurring spontaneously at different binding sites of BSA involving hydrophobic, electrostatic and hydrogen binding forces. Identification of QUER binding sites was possible through corroboration of DSC runs in the presence of site markers and molecular docking. Modeling of ligand-protein interaction confirmed the experimental data. On one hand, a neutral form of QUER binds in a nonplanar conformation to Sudlow's site I, a large hydrophobic cavity of subdomain IIA of BSA and decreases its thermal stability. On the other hand, a second molecule of QUER, the anionic form, is bound in planar conformation to Sudlow's site II, situated in the subdomain IIIA of the folded protein, and increases the thermal stability of the corresponding structural domain of the protein.

Synthesis, characterization, and structure-property investigation of conformationally rigid regioisomers of poly(p-phenylene ethynylene)s

A series of rigid poly(p-phenylene ethynylene)s (PPE1–PPE4) with biphenyl- (M1–M3) and phenyl- (M4) side groups is prepared from appropriately functionalized monomers. Herein, the solution and solid state absorption studies show the polymers have adopted twisted and rigid conformations, as supported by deep HOMO energy levels (−5.76 to −5.81 eV). The absorption maxima of PPE1–PPE3 are shifted to shorter wavelength (λmax = 375–381 nm) as compared to linear poly(p-phenylene ethynylene)s (446 nm), implying a nonplanar conformation. The self-assembly of polymers into fibers is examined using scanning electron microscopy. The fibers are not observed in PPE4 with short phenyl side group, suggesting the important role of the interplay between rigidity, position, and size of the side chains toward the formation of fibers. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 3652–3662

Crystal structures of unsymmetrically mixed β-pyrrole substituted nickel(II)-meso-tetraphenylporphyrins

Crystal structures of solvated unsymmetrically substituted meso-tetraphenylporphyrins, 2,3,12,13,17-pentachloro-5,7,8,10,15,18,20-hepta-phenylporphyrin, H2TPP(Ph)3(Cl)5, 1 and its nickel(II), NiTPP(Ph)3(Cl)5, 2 were determined by single crystal XRD analysis. In addition, a new unsymmetrically substituted porphyrin, 2,3,12,13,17-pentacyano-5,7,8,10,15,18,20-heptaphenyl-porphinato nickel(II) complex, NiTPP(Ph)3(CN)5, 3 complex was synthesized and its solvated structure was examined by crystallography. These porphyrins exhibited dramatic nonplanar conformation of the macrocycle as evidenced from the average displacement of the β-pyrrole carbon (±ΔC β) from the mean plane of the porphyrin ring and the trend in nonplanarity varies in the order: 2 (1.189(5) Å) > 1 (1.036(6) Å) > 3 (0.895(6) Å). The normal-coordinate structural decomposition analysis of these structures revealed mainly saddle distortion of the macrocycle combined with small degree of ruffled or domed distortions. The Hirshfeld surface analysis of structures 1-3 revealed solvate dependent intermolecular contacts with varying degree of H …H (43–49%), C …H (17–19%), H …Cl (25–30%) and N …H (∼19%) contact contributions. Crystal structures of solvated 2,3,12,13,17-penta(chloro or cyano)-5,7,8,10,15,18,20-heptaphenylporphyrin H2TPP(Ph)3(Cl)5, and their Ni(II) complexes, NiTPP(Ph)3(Cl)5 and NiTPP(Ph)3(CN)5 were determined by single crystal XRD. They revealed nonplanar conformation of the macrocycle (ΔCb > ± 0.9 Å). The structures were examined by normal-coordinate structural decomposition and Hirshfeld surface analyses.

The interaction and binding of flavonoids to human serum albumin modify its conformation, stability and resistance against aggregation and oxidative injuries

BackgroundInteractions of ligands with proteins imply changes in the properties of the macromolecules that may deeply modify their biological activities and conformations and allow them to acquire new and, sometimes, unexpected abilities. The flavonoid phloretin has several pharmacological properties that are starting to be elucidated, one of which is the well-known inhibition of glucose transport. MethodsThe interactions of phloretin to human serum albumin have been investigated by fluorescence, UV–visible, FTIR spectroscopy, native electrophoresis, protein ligand docking studies, fluorescence and scanning electron microscopy. ResultsSpectroscopic investigations suggest that the flavonoid binds to human serum albumin inducing a decrease in α-helix structures as shown by deconvolution of FTIR Amide I′ band. Fluorescence and displacement studies highlight modifications of environment around Trp214 with the primary binding site located in the Sudlow's site I. In the hydrophobic cavity of subdomain IIA, molecular modeling studies suggest that phloretin is in non-planar conformation and hydrogen-bonded with Ser202 and Ser454. These changes make HSA able to withstand protein degradation due to HCLO and fibrillation. General significanceOur work aims to open new perspectives as far as the binding of flavonoids to HSA are concern and shows as the properties of both compounds can be remarkable modified after the complex formation, resulting, for instance, in a protein structure much more resistant to oxidation and fibrillation.This article is part of a Special Issue entitled “Science for Life” Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.