Porphyrin/Quinoidal-Bithiophene-Based Macrocycles and Their Dications: Template-Free Synthesis and Global Aromaticity

We report the template-free synthesis and characterization of a new type of porphyrin/quinoidal-bithiophene-based conjugated macrocycle. X-ray crystallographic analysis of the dimer ( 2MC ) revealed a cyclophane-like geometry with large dihedral angles between the porphyrin and the neighboring thiophene rings, and NMR measurements and theoretical calculations confirmed a localized aromatic character of the porphyrin/thiophene rings and quinoidal character of the bithiophene linkers. Restricted rotation of the thiophene rings linked to the porphyrin unit was observed by variable-temperature NMR measurements. The dication ( 2MC²⁺ ) adopts a chair-shaped conformation to facilitate π-electron delocalization around the whole macrocycle. As a result, the molecule is globally aromatic, with a dominant 54 π conjugation pathway. The trimer ( 3MC ) also shows localized aromatic character of porphyrin rings and conformational flexibility, but its dication ( 3MC²⁺ ) is rigid and globally aromatic with a dominant 82 π conjugation pathway.     

Porphyrin/Quinoidal‐Bithiophene‐Based Macrocycles and Their Dications: Template‐Free Synthesis and Global Aromaticity

We report the template‐free synthesis and characterization of a new type of porphyrin/quinoidal‐bithiophene‐based conjugated macrocycle. X‐ray crystallographic analysis of the dimer ( 2MC ) revealed a cyclophane‐like geometry with large dihedral angles between the porphyrin and the neighboring thiophene rings, and NMR measurements and theoretical calculations confirmed a localized aromatic character of the porphyrin/thiophene rings and quinoidal character of the bithiophene linkers. Restricted rotation of the thiophene rings linked to the porphyrin unit was observed by variable‐temperature NMR measurements. The dication ( 2MC²⁺ ) adopts a chair‐shaped conformation to facilitate π‐electron delocalization around the whole macrocycle. As a result, the molecule is globally aromatic, with a dominant 54 π conjugation pathway. The trimer ( 3MC ) also shows localized aromatic character of porphyrin rings and conformational flexibility, but its dication ( 3MC²⁺ ) is rigid and globally aromatic with a dominant 82 π conjugation pathway.     

Highly conjugated multiporphyrins: synthesis, spectroscopic and electrochemical properties

A series of meso-to-meso ethynyl-bridged multiporphyrin arrays have been synthesized using Sonogoshira palladium-catalyzed cross-coupling reactions involving the appropriate ethynylporphyrin and iodoporphyrin precursors. The absorption spectra of these multiporphyrins show splitting of the Soret bands and significant red shifts of the Q bands as compared to the combination of the corresponding components. These conjugated multiporphyrins also show red shifts in their emission spectra as the pi-conjugation is expanded. In the electrochemical measurements, the porphyrins dimer 7 shows two 1 - e- oxidations at E(1/2) = +0.63 and +0.76 V for the first electron abstraction from the two porphyrin rings, indicating electronic communication between the two porphyrin units. The porphyrin trimer 4 exhibits the first and second 1 - e- oxidations at E(1/2) = +0.68 and +0.77 V, respectively, which correspond to the two outer porphyrins. The cyclic voltammogram of pentamer 5 shows two overlapping 1 - e- couples at E(1/2) = +0.56 and +0.66 V, and one 2 - e- couple at E(1/2) = +0.86 V, for the four outer porphyrin units. These results demonstrate that in the porphyrin trimer and pentamer the individual peripheral porphyrin units are electrochemically coupled via a central porphyrin core. The UV-Vis-NIR spectra of the oxidized species of these multiporphyrins exhibit a broad intervalence charge transfer (IVCT) band in the region from 1200 to 3000 nm. The present work shows that a central porphyrin unit appended with ethynyl bridges affords strong electronic interactions between the peripheral porphyrin rings over a distance of about 15 A.     

Multiple interactions in the self-association of porphyrin discotic mesogens

The conformational preferences and the self-associational behaviors of two hemin-derived porphyrin compounds, a tetramethyl ester and a liquid crystalline tetrakis(3,5-didodecyloxyphenyl)ester, have been studied by UV/vis and (1)H NMR spectroscopy in solution. Results indicate that the 3,5-didodecyloxyphenyl units play an important role in both the conformational and the self-associational behaviors of the mesomorphic tetraester. In the monomeric, nonassociated species, the two propionic 3,5-didodecyloxyphenyl esters establish mutual CH/pi interactions that restrict the fluctuative behavior of the chains. In the dimeric, self-associated species, intermolecular CH/pi interactions occur in addition to the pi-pi stacking of the porphyrin cores. The temperature-dependent addition of side CH/pi interactions to the pi-pi stacking of the porphyrin rings accounts for the observed tightening and for the slower dynamics of the dimeric structure. The relationship between the self-associational behavior and the mesomorphism of the hemin-derived porphyrin tetraesters is also discussed.     

Sampling protein conformations and pathways

Protein flexibility and rigidity can be analyzed using constraint theory, which views proteins as 3D networks of constraints involving covalent bonds and also including hydrophobic interactions and hydrogen bonds. This article describes an algorithm, ROCK (Rigidity Optimized Conformational Kinetics), which generates new conformations for these complex networks with many interlocked rings while maintaining the constraints. These new conformations are tracked for the flexible regions of a protein, while leaving the rigid regions undisturbed. An application to HIV protease demonstrates how large the flap motion can be. The algorithm is also used to generate conformational pathways between two distinct protein conformations. As an example, directed trajectories between the closed and the occluded conformations of the protein dihydrofolate reductase are determined.     

Two polymorphs of N‐(2‐methoxyphenyl)‐4‐oxo‐4H‐chromone‐3‐carboxamide

The title compound, C₁₇H₁₃NO₄, crystallizes in two polymorphic forms, each with two molecules in the asymmetric unit and in the monoclinic space group P2₁/c. All of the molecules have intramolecular hydrogen bonds involving the amide group. The amide N atoms act as donors to the carbonyl group of the pyrone and also to the methoxy group of the benzene ring. The carbonyl O atom of the amide group acts as an acceptor of the β and β′ C atoms belonging to the aromatic rings. These intramolecular hydrogen bonds have a profound effect on the molecular conformation. In one polymorph, the molecules in the asymmetric unit are linked to form dimers by weak C—H...O interactions. In the other, the molecules in the asymmetric unit are linked by a single weak C—H...O hydrogen bond. Two of these units are linked to form centrosymmetric tetramers by a second weak C—H...O interaction. Further interactions of this type link the molecules into chains, so forming a three‐dimensional network. These interactions in both polymorphs are supplemented by π–π interactions between the chromone rings and between the chromone and methoxyphenyl rings.     

Hydrogen‐bonded assemblies of 20‐(4‐pyridyl)porphyrin‐54,104,154‐tribenzoic acid with dimethyl sulfoxide and 4‐acetylpyridine in their dimethyl sulfoxide and tetrahydrofuran solvates

Crystals of the title compounds, 20‐(4‐pyridyl)porphyrin‐5⁴,10⁴,15⁴‐tribenzoic acid–dimethyl sulfoxide (2/5), C₄₆H₂₉N₅O₆·2.5C₂H₆OS, (I), and 20‐(4‐pyridyl)porphyrin‐5⁴,10⁴,15⁴‐tribenzoic acid–4‐acetylpyridine–tetrahydrofuran (1/2/10), C₄₆H₂₉N₅O₆·2C₇H₇NO·10C₄H₈O, (II), consist of hydrogen‐bonded supramolecular chains of porphyrin units solvated by molecules of dimethyl sulfoxide [in (I)] and 4‐acetylpyridine [in (II)]. In (I), these chains consist of heterogeneous arrays with alternating porphyrin and dimethyl sulfoxide species, being sustained by COOH...O=S hydrogen bonds. They adopt a zigzag geometry and link on both sides to additional molecules of dimethyl sulfoxide. In (II), the chains consist of homogeneous linear supramolecular arrays of porphyrin units, which are directly connected to one another via COOH...N(pyridyl) hydrogen bonds. As in the previous case, these arrays are solvated on both sides by molecules of the 4‐acetylpyridine ligand via similar COOH(porphyrin)...N(ligand) hydrogen bonds. The two crystal structures contain wide interporphyrin voids, which accommodate disordered/diffused solvent molecules, viz. dimethyl sulfoxide in (I) and tetrahydrofuran in (II).     

Substituent effects in porphyrin dimer complexes studied by IR spectroscopy

A series of lanthanide porphyrin dimers have been synthesized and investigated with IR spectroscopic techniques. The spectra of the porphyrin dimers are compared not only with each other but also with those of their component monomer units. The experimental results exhibit that the IR spectra of the porphyrin dimers are closely related to those of their corresponding monomers. A detailed analysis of the IR spectra between the porphyrin dimers and monomers suggest that the dimer molecules can be treated as regular derivatives of metalloporphyrin monomers despite the symmetries of these two systems being different. The dimerization of the porphyrin rings only result in frequency shifts and intensity changes of the IR spectra. These shifts are attributed to the induced π–π interactions between these two macrocycles. The downshifts of the frequencies observed in Ce(OEP)₂ further indicate that the π–π interactions intrinsically decrease the bond strength of the entire molecule. Additionally, only the relative intensities instead of the frequencies of the ethyl vibrations in the region 2800–3000 cm⁻¹ are observed to be sensitive to the types and the positions of the substituent groups. These observations suggest that these ethyl vibrational modes of the OEP moiety can be used as characteristic bands to monitor subtle deformations of the porphyrin rings caused by the substituent groups in the dimer complexes.     

Multiporphyrin arrays on cyclophosphazene scaffolds: synthesis and studies

The stable and robust cyclotriphosphazene and cyclotetraphosphazene rings were used as scaffolds to prepare hexa- and octaporphyrin arrays by treating N(3)P(3)Cl(6) and N(4)P(4)Cl(8), respectively, with 5-(4-hydroxyphenyl)-10,15,20-tri(p-tolyl)porphyrin (N(4) core) or with its thiaporphyrin analogues (N(3)S and N(2)S(2) cores) in THF in the presence of Cs(2)CO(3) under simple reaction conditions. Thiaporphyrins were examined in addition to the normal porphyrin to tune the electronic properties of the resultant arrays. Observation of the molecular ion peaks in the mass spectra confirmed the molecular structures of the arrays. 1D and 2D NMR techniques were employed to characterize the multiporphyrin arrays in detail. The (1)H NMR spectra of the multiporphyrin arrays each show a systematic set of signals, indicating that the porphyrin units are arranged in a symmetrical fashion around the cyclophosphazene rings. All signals in the (1)H NMR spectra were assigned with the aid of COSY and NOESY experiments. The protons of each porphyrin unit are subject to upfield and downfield shifts because of the ring-current effects of neighboring porphyrin units. Optical, electrochemical, and fluorescence studies of the arrays indicated that the porphyrin units retain their independent ground- and excited-state characteristics. Cu(II) and Ni(II) derivatives of hexaporphyrin and octaporphyrin arrays containing N(4) porphyrin units and N(3)S porphyrin units were synthesized, and complete metalation of the arrays was confirmed by their mass spectra and by detailed NMR characterization of the Ni(II) derivatives of hexa- and octaporphyrin arrays containing N(4) porphyrin units. Electrochemical studies indicated that Cu(II) and Ni(II) ions present in the thiaporphyrin units of the arrays can be stabilized in the +1 oxidation state, which is not possible with arrays containing normal porphyrin units.     

Excitation energy transport processes of porphyrin monomer,dimer, cyclic trimer,and hexamer probed by ultrafast fluorescence anisotropy decay

Femtosecond fluorescence anisotropy measurements for a variety of cyclic porphyrin arrays such as Zn(II)porphyrin m-trimer and hexamer are reported along with o-dimer and monomer as reference molecules. In the porphyrin arrays, a pair of porphyrin moieties are joined together via triphenyl linkage to ensure cyclic and rigid structures. Anisotropy decay times of the porphyrin arrays can be well described by the F?rster incoherent excitation hopping process between the porphyrin units. Exciton coupling strengths of 74 and 264 cm(-1) for the m-trimer and hexamer estimated from the observed excitation energy hopping rates are close to those of B800 and B850, respectively, in the LH2 bacterial light-harvesting antenna. Thus, these cyclic porphyrin array systems have proven to be useful in understanding energy migration processes in a relatively weak interaction regime in light of the similarity in overall structures and constituent chromophores to natural light-harvesting arrays.     

Giant porphyrin wheels with large electronic coupling as models of light-harvesting photosynthetic antenna

Starting from a 1,3-phenylene-linked diporphyrin zinc(II) complex 2ZA, repeated stepwise Ag(I)-promoted coupling reactions provided linear oligomers 4ZA, 6ZA, 8ZA, and 12ZA. The intramolecular cyclization reaction of 12ZA under dilute conditions (1x10(-6) M) gave porphyrin ring C12ZA with a diameter of approximately 35 A in 60% yield. This synthetic strategy has been applied to a 1,3-phenylene-linked tetraporphyrin 4ZB to provide 8ZB, 12ZB, 16ZB, 24ZB, and 32ZB. The intramolecular coupling reaction of 24ZB gave a larger 24-mer porphyrin ring C24ZB with a diameter of approximately 70 A in 34% yield. These two large porphyrin rings were characterized by means of 1H NMR spectroscopy, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectroscopy, UV-visible spectroscopy, gel permeation chromatography (GPC) analysis, and scanning tunneling microscopy (STM) techniques. The STM images of C12ZA reveal largely circular structures, whereas those of C24ZB exhibit mostly ellipsoidal shapes, indicating more conformational flexibility of C24ZB. Similar to the case of C12ZA, the efficient excitation energy transfer along the ring has been confirmed for C24ZB by using the time-correlated single-photon counting (TCSPC) and picosecond transient absorption anisotropy (TAA) measurements, and occurs with a rate of (35 ps)(-1) for energy hops between neighboring tetraporphyrin subunits. Collectively, the present work provides an important step for the construction of large cyclic-arranged porphyrin arrays with ample electronic interactions as a model of light-harvesting antenna.     

Electron delocalization in various triply linked zinc(II) porphyrin arrays: role of antiaromatic junctions between aromatic porphyrins

A series of meso-meso, β-β, β-β triply linked linear, radial and square-type zinc(II) porphyrin arrays consist of the constituent porphyrin units and naphthalene junctions. To understand the unique nature of triply linked porphyrin arrays, numerous research activities have been focused on the electronic structures of the constituent porphyrin units. In this study, however, we have paid attention to the role of the naphthalene junction in the electronic delocalization of various triply linked porphyrin arrays. On the basis of our study, we have unveiled that unique π-conjugation behaviors in triply linked porphyrin arrays are induced by their intrinsic molecular orbital interactions and subsequently by antiaromatic junctions. Furthermore, the structural deformation by triple linkages gives rise to a deteriorative effect on the electronic delocalization between inner and outer porphyrin units. Finally, we propose a different type of electron delocalization in linear multichromophoric systems by alternating aromatic and antiaromatic units.     

SnIV Porphyrin Scaffolds for Axially Bonded Multiporphyrin Arrays: Synthesis and Structure Elucidation by NMR Studies

A simple, one‐step, supramolecular strategy was adopted to synthesize Sn^IV‐porphyrin‐based axially bonded triads and higher oligomers by using meso‐pyridyl Sn^IV porphyrin, meso‐hydroxyphenyl‐21,23‐dithiaporphyrin, and Ru^II porphyrin as building blocks and employing complementary and non‐interfering Sn^IV?O and Ru^II ??? N interactions. The multiporphyrin arrays are stable and robust and were purified by column chromatography. ¹H, ¹H–¹H COSY and NOESY NMR spectroscopic studies were used to unequivocally deduce the molecular structures of Sn^IV‐porphyrin‐based triads and higher oligomers. Absorption and electrochemical studies indicated weak interaction among the different porphyrin units in triads and higher oligomers, in support of the supramolecular nature of the arrays. Steady‐state fluorescence studies on triads indicated the possibility of energy transfer in the singlet state from the basal Sn^IV porphyrin to the axial 21,23‐dithiaporphyrin. However, the higher oligomers were weakly fluorescent due to the presence of heavy Ru^II porphyrin unit(s), which quench the fluorescence of the Sn^IV porphyrin and 21,23‐dithiaporphyrin units.     

Light‐Induced Electron Transfer over Distances of 5, 10, and 15 Å within Water‐Filled Yoctowells

A small series of variable‐depth yoctowell cavities with ′functional′ walls on aminated silica particles and gold electrodes has been established. The dimensions of the gaps formed were 2.2 nm in diameter with varying ′functional′ depths of 5, 10, and 15 Å, depending on the length of bolaphiles applied and the position of the positive rim; these gaps were prepared through a Michael addition of the incorporated ene‐amide groups. Using this construct and electrostatic interactions between the positive rim and anionic quinones as a means of immobilization, a porphyrin–quinone dyad system has been prepared. The distance between the donor and acceptor was changed systematically in aqueous solution, whilst maintaining a similar environment in each case. Upon photoexcitation of the porphyrin, efficient electron transfer occurs between the porphyrin and quinone units in a distance‐dependent manner on the nanosecond timescale.     

From Single Molecule to Crystal: Mapping Out the Conformations of Tartaric Acids and Their Derivatives

Stereoisomers of one of the most important organic compounds, tartaric acid, optically active and meso as well as the ester or amide derivatives, can show diverse structures related to the rotation around the three carbon–carbon bonds. This study determines the controlling factors for conformational changes of these molecules in vacuo, in solution, and in the crystalline state using DFT calculations, spectroscopic measurements, and X‐ray diffraction. All structural variations can be logically accounted for by the possibility of formation and breaking of hydrogen bonds between the hydroxy or amide donors and oxygen acceptors, among these the hydrogen bonds that close five‐membered rings being the most stable. These findings are useful in designing molecular and crystal structures of highly polar, polyfunctional, chiral compounds.     

Amitriptylinium picrate: conformational disorder

In the structure of the title salt [systematic name: 3‐(10,11‐dihydro‐5H‐dibenzo[a,d][7]annulen‐5‐ylidene)‐N,N‐dimethylpropan‐1‐aminium 2,4,6‐trinitrophenolate] of a tricyclic antidepressant, C₂₀H₂₄N⁺·C₆H₂N₃O₇⁻, the dimethylaminopropyl subunit possesses a classical static conformational disorder. The central cycloheptadiene ring adopts a bent conformation that is intermediate between boat and chair forms, leading to a butterfly shape for the hetero‐tricyclic moiety. In a complementary fashion, donors from amitriptyline and acceptors from picrate form intermolecular C—H...O hydrogen bonds and N—H...O salt bridges. These hydrogen bonds cluster amitriptyline and picrate ions into a closed R₄⁴(36) hetero‐tetramer, whereas intermolecular C—H...π interactions between amitriptyline ions cluster them into homo‐dimers. Significant π–π stacking interactions are also observed between aromatic rings of amitriptyline and picrate, and these, combined with the C—H...π interactions, associate molecules into linear arrays along the [11] direction.     

Electrical conduction through linear porphyrin arrays

Electrical conduction measurements were made on two extreme types of directly linked porphyrin arrays by using nanoelectrodes. One type is the directly linked Zn(II)porphyrin arrays, consisting of 48 Zn(II)porphyrin moieties (Z48), and the other type is the completely flat, tape-shaped Zn(II)porphyrin arrays, consisting of eight Zn(II)porphyrin units (T8). The I-V curve for Z48 exhibits the diode-like behavior and the hysteresis depending on the voltage sweep direction presumably due to the conformational heterogeneity arising from the dihedral angle distribution in Z48. On the other hand, the I-V curve for T8 is nearly symmetric without any hysteresis, leading to the higher conductivity and the smaller band gap. These results illustrate that the stronger pi-electron conjugation in T8, as compared with that of Z48, results in better electrical conduction.     

Investigation of aromatic-backbone amide interactions in the model peptide acetyl-Phe-Gly-Gly-N-methyl amide using molecular dynamics simulations and protein database search.

Weakly polar interactions between the side-chain aromatic rings and hydrogens of backbone amides (Ar-HN) are found in unique conformational regions. To characterize these conformational regions and to elucidate factors that determine the conformation of the Ar-HN interactions, four 4-ns molecular dynamics simulations were performed using four different low-energy conformations obtained from simulated annealing and one extended conformation of the model tripeptide Ac-Phe-Gly-Gly-NH-CH(3) as starting structures. The Ar(i)-HN(i+1) interactions were 4 times more frequent than were Ar(i)-HN(i+2) interactions. Half of the conformations with Ar(i)-HN(i+2) interactions also contained an Ar(i)-HN(i+1) interaction. The solvent access surface area of the Phe side chain and of the amide groups of Phe1, Gly2, and Gly3 involved in Ar-HN interactions was significantly smaller than in residues not involved in such interactions. The number of hydrogen bonds between the solvent and Phe1, Gly2, and Gly3 amide groups was also lower in conformations with Ar-HN interactions. For each trajectory, structures that contained Ar(i)-HN(i), Ar(i)-HN(i+1), and Ar(i)-HN(i+2) interactions were clustered on the basis of similarity of selected torsion angles. Attraction energies between the aromatic ring and the backbone amide in representative conformations of the clusters ranged from -1.98 to -9.24 kJ mol(-1) when an Ar-HN interaction was present. The most representative conformations from the largest clusters matched well with the conformations from the Protein Data Bank of Phe-Gly-Gly protein fragments containing Ar-HN interactions.     

Off-lattice Monte Carlo method with constraints: Long-time dynamics of a protein model without nonbonded interactions

A method is proposed to perform computer simulations of protein dynamics in the long-time regime. The method is based upon a Monte Carlo technique. The only molecular degrees of freedom considered are bond rotations. All other degrees of freedom including the amide plane torsions are kept rigid. These constraints approximately account for all interactions related to chemical bonding. An individual Monte Carlo step adopts the Go and Scheraga algorithm where local conformational changes in a small window of the protein backbone are performed. By using correlated rotations, the conformation of residues outside the window remains invariant. To test the reliability of the method, the nonbonded interactions are turned off in the present application. Exact statistical averages are compared with values obtained from data of computer simulation involving 2 × 10⁶ scans of the window along the protein backbone. Time is related to the number of scans of the window along the protein backbone. End-to-end distance autocorrelation functions decay to 1/e of its initial value in about 10³–10⁴ scans of the window algorithm. Time decay follows a stretched exponential Kohlrausch decay law. © 1993 John Wiley & Sons, Inc.     

Conformational and docking studies of acyl homoserine lactones as a robust method to investigate bioactive conformations

A method aiming at investigating possible bioactive conformations of acyl homoserine lactone (AHL) quorum sensing (QS) modulators is established. The method relies on the exhaustive conformational analysis of AHLs by varying torsion angles around the amide group then on the selection of the closest conformation to those known from co-crystallized XRD data of AHL-receptor complexes. These latter are then docked as rigid ligand within the receptor binding site, leading to interactions with binding site residues which are highly consistent as compared with the data arising from XRD studies. The method is first validated using AHLs for which XRD data of their complexes with their cognate receptor are available, then extended to examples for which the binding mode is still unknown.Three compounds were used to validate the method: hexanoyl homoserine lactone (HHL) as an example of autoinducer, 3-oxo-butanoyl homoserine lactone (OBHL), as a representative model of 3-oxo-AHLs, and 4-(4-chlorophenoxy)butanoyl homoserine lactone (CPOBHL) as an example of a QS inhibitor. The conformational analysis of these three compounds to their cognate protein (TraR, SdiA, LasR and CviR) provides the data which enable the next rigid docking step. Further rigid docking of the closest conformations compared to the known bioactive ones within the binding sites allows to recover the expected binding mode with high precision (atomic RMSD < 2 Å). This “conformational analysis/torsion angle filter/rigid ligand docking” method was then used for investigating three non-natural AHL-type QS inhibitors without known co-crystallized XRD structures, namely was 2-hexenoyl homoserine lactone (HenHL), 3-oxo-4-phenylbutanoyl homoserine lactone (OPBHL) and 3-(4-bromophenyl)propanoyl homoserine lactone (BPPHL). Results provide insights into their possible binding mode by identifying specific interactions with some key residues within the receptor binding site, allowing discussion of their biological activity.