Narrow Results

The solid state structure of dilithium tetraphenylporphyrin bis(etherate) has been determined by X-ray crystallography. The structure shows the lithium atoms are displaced out of the plane of the porphyrin, each coordinated in a square pyramidal fashion to the four nitrogen atoms in addition to a molecule of diethyl ether. The lithium atoms are identical, as required by the crystallographic inversion centre. X-ray data are as follows: (# 2) with a = 10.1908(4) Å, b = 11.6553(4) Å, c = 12.5199(5) Å, α = 111.644(1)°, β = 98.029(1)°, γ = 111.883(1)°, V = 1214.61(9)ų, d_calc = 1.171 g cm^-3 and Z = 1.

Tetra(n-butyl)ammonium nitrite reacts with ‘dichlorophthalocyaninatoruthenium(III) acid’ to yield bis(tetra(n-butyl)ammonium) bisnitrophthalocyaninatoruthenate(II). It crystallizes monoclinic with crystal data: a = 15.114(4) Å, b = 22.34(3) Å, c = 18.206 (11) Å, β = 90.88(5)°; space group P1 21/n 1, Z = 4, and its X-ray crystal structure has been determined. Ru is located in the centre of the slightly distorted phthalocyaninate dianion, and is coordinated to two nitrite ions through their nitrogen (N) atoms in a staggered trans-configuration. The average Ru-N_p (Np pyrrolic N atoms) and Ru-N distance is 1.978(6) and 2.068(5) Å, respectively. The electrochemical and spectroscopic properties (IR, resonance Raman, UV/vis) of the compound are in full agreement with its molecular structure.

The synthesis, characterization and crystal structure of the octanitro-substituted porphyrin 5,10,15,20-tetrakis(3,5-dinitrophenyl)porphyrin, H₂T(3,5-DNP)P, are described. The solid state structure has two porphyrins in the unit cell with eight pyridine solvates and is made up from columnar arrays of the porphyrins. X-ray crystal structure data: monoclinic, space group P1 2₁/n1, a = 14.9996(9) Å, b = 8.2489(5) Å, c = 24.818(2) Å, α = 90 °, β = 104.172(1) °, γ = 90 °, V = 2977.3(3) ų, d_calc = 1.440 g m^-3, Z = 2.

Professor Roger D. Komberg — 2006 Nobel Prize in Chemistry.

In this paper, we present a forecasting scheme for the growth of molecular structures from NMR and X-ray Crystallography experimental techniques released every year by employing an autoregressive (AR) process. The proposed scheme maximises the forecasting accuracy by utilising the optimal AR process order. The optimal model order was derived as the model with the least prediction error. Therefore, the proposed scheme has been efficiently employed to model and predict the annual growth of structures-based NMR and X-ray Crystallography experimental data for the next decade 2019–2028 using the time series of the past 43 years of both experimental datasets. The experimental results showed that the optimal model order to estimate both datasets was $AR(2)$ which belongs to a forecasting accuracy of $98\%$, for both datasets. Indeed, such a high level of accuracy referred to the amount of linearity between the consecutive elements of the original times series. Hence, the forecasting results reveals of an exponential increasing behaviour in the future growth in the annual structures released from both NMR and X-ray Crystallography experiments.

High-throughput computational methods in X-ray protein crystallography are indispensable to meet the goals of structural genomics. In particular, automated interpretation of electron density maps, especially those at mediocre resolution, can significantly speed up the protein structure determination process. TEXTAL^TM is a software application that uses pattern recognition, case-based reasoning and nearest neighbor learning to produce reasonably refined molecular models, even with average quality data. In this work, we discuss a key issue to enable fast and accurate interpretation of typically noisy electron density data: what features should be used to characterize the density patterns, and how relevant are they? We discuss the challenges of constructing features in this domain, and describe SLIDER, an algorithm to determine the weights of these features. SLIDER searches a space of weights using ranking of matching patterns (relative to mismatching ones) as its evaluation function. Exhaustive search being intractable, SLIDER adopts a greedy approach that judiciously restricts the search space only to weight values that cause the ranking of good matches to change. We show that SLIDER contributes significantly in finding the similarity between density patterns, and discuss the sensitivity of feature relevance to the underlying similarity metric.

In the present publication we report on the preparation and spectroscopic features of a penta-coordinate rhodium(III) complex of corrole with bulky ortho-phenyl substituents at the meso positions, Rh(tdcc)(PPh₃)[tdcc = tris(2,6-dichlorophenyl)corrole]. Addition of pyridine to Rh(tdcc)(PPh₃), as well as to the closely related complex of tris(pentafluorophenyl)corrole [Rh(tpfc)(PPh₃)] reported earlier, leads to hexa-coordinated rhodium complexes with pyridine and PPh₃ occupying the axial positions. The structures of these two compounds were investigated by NMR and X-ray crystallography. The catalytic potency of Rh(tdcc)(PPh₃) was found significantly lower than that of Rh(tpfc)(PPh₃), which suggests that excess steric crowding prevents efficient carbene-transfer catalysis.

This article reviews our recent work in constructing discrete multiporphyrin assemblies and supramolecular arrays through the application of two organising principles - crown ethers and tin(IV)porphyrin phenolates. The role of the crown ethers is illustrated by two examples: (a) the cation-induced control of the reduction potentials within a model 18C6 bearing naphthalene and naphthoquinone chromophores antipodally displaced on the crown ether in the presence of alkali metal cations and (b) in the complexation of dialkylammonium salt within the cavity of a 24C8 bischlorin system. Tin(IV)porphyrin phenolates provide a means of efficiently constructing multiporphyrin assemblies without the use of covalent bond formation. Their potential is illustrated through the formation of discrete trimers, using a “one pot” self-assembly strategy, as well as the generation of supramolecular arrays with sieve like networks.

The nucleophilic attack of a rhodium(I) porphyrin on a chlorotin(IV) corrole yields the heterobinuclear rhodium porphyrin-tin corrole complex where the two metals are bound via a single metal-metal bond. The X-ray structure of the rhodium tetraphenylporphyrin-tin(2,3,7,13,17,18-hexamethyl-8,12-diethylcorrole) complex is reported. The Rh-Sn single bond distance is equal to 2.5069(7) Å and the Rh and Sn atoms are located at 0.076 and 0.793 Å from the porphyrin and the corrole 4N mean planes, respectively.

The X-ray structure, electrochemistry, and optical spectroscopy of the porphycene analog of a benzochlorin, octaethylbenzochloracene (OEBzC) are reported. The OEBzC macrocycle is easier to oxidize and harder to reduce than octaethylporphycene (OEPc). The optical spectra of OEBzC and of the diacid salt are also reported. The optical spectrum for the one-electron oxidation of OEBzC is indicative of π-cation radical formation. In porphyrins, saturation of one pyrrole ring and addition of an exocyclic benzene ring progressively red-shifts the first absorption band. For porphycenes, saturation of one pyrrole ring results in a 35 nm blue shift in the first absorption relative to OEPc. Compared to 2,3-dihydroporphycene (DHPc), the first absorption band in OEBzC is red-shifted 24 nm. These studies further illustrate how the fused exocyclic benzene ring influences the macrocycle conformation, chemical and physical properties of porphycenes.

Several methodologies for the synthesis of corroles that carry minimal-sized electron-withdrawing substituents at the meso-C atoms were investigated; of these the one based on dypyrromethane/aldehyde condensation was fruitful. The new corrole with one C₆F₅ and two CF₃ groups, as well as its cobalt(III) complex, were fully characterized by spectroscopy and X-ray crystallography.

The preparation and spectroscopic properties of a series of metallocorroles with polar head groups CHO and CH=C(CN)(COOH) are reported, as well as the X-ray crystal structure of 5,10,15-tris(pentafluorophenyl)corrolatoaluminium(III)bispyridine (triclinic space group (P-1) with unit cell parameters: a = 9.426(1) Å; b = 13.202(1) Å; c = 19.936(1) Å; α = 74.19(1)°; β = 78.47(1)°; γ = 75.75(1)°; V = 2289.57(8) ų). Amphiphilic aluminium(III) and gallium(III) corroles exhibit electronic absorption (Soret peaks between 410 and 448 nm; Q-bands between 584 and 638 nm) and fluorescence (band maxima between 634 and 706 nm) at lower energies than their hydrophobic analogs.

Corroles that carry either two or three ortho-pyridyl groups at the meso-carbon atoms form stable manganese(III) complexes, from which corresponding water-soluble derivatives are obtained via N-alkylation. These syntheses and the spectroscopic features are disclosed, together with the molecular structure of the manganese(III) corrole that carries three ortho-pyridylium groups. All the manganese(III) corroles may be transformed to stable (nitrido)manganese(V) complexes, whose NMR spectra provide invaluable structural information regarding the identity and number of atropoisomers.

Reaction between H₂TFcP (TFcP^2- is a dianion of 5,10,15,20-tetraferrocenylporphyrin) with tin(II) chloride results in formation of the trans-Cl₂SnTFcP complex, which was characterized by UV-vis, MCD, ¹H and ¹³C NMR, and APCI MS methods. X-ray single crystal analysis was used to determine the structure of the target compound. Crystallography reveals a very unusual α,α,β,β-conformation of the ferrocene groups and largely planar structure of the porphyrin macrocycle. Density functional theory calculations predict that the HOMO in trans-Cl₂SnTFcP is predominantly ferrocene centered, while LUMO is primarily localized over the porphyrin core. Redox properties of the trans-Cl₂SnTFcP complex were investigated using electrochemical (CV and DPV), spectroelectrochemical, and chemical oxidation approaches. Electrochemical experiments conducted in low-polarity solvent using non-coordinating electrolyte reveal the sequential oxidation of ferrocene substituents along with porphyrin-based single-electron oxidation and reduction processes. The first ferrocene oxidation process is separated by 130 mV from the next three ferrocene based oxidations, which are more closely spaced. Mixed-valence [trans-Cl₂SnTFcP]⁺ was generated in situ by spectroelectrochemical and chemical oxidation approaches and characterized by UV-vis-NIR spectroscopy.

Sterically bulky substituents at the β-carbons of the pyrrole rings of porphyrins are sufficient to cause large out-of-plane porphyrin distortions even in the absence of substituent groups at the meso carbons. It is well established that substituents at the meso-positions only or at both the β-pyrrole and the meso-positions are sufficiently bulky to result in large non-planar distortions of the macrocycle. However, no systematic studies of the effects of bulky β-pyrrole substituents alone have been reported. Herein, molecular simulations and X-ray crystallography of nickel(II) 2,3,7,8,12,13,17,18-octa(isopropyl)porphyrin reveal that large out-of-plane distortions (>1.5 Å) are induced by the steric repulsion of the β-isopropyl groups but fail to lead to a single strongly energetically favored conformer. The molecular simulations indicate that multiple conformers differing in the orientation of the isopropyl groups and the macrocycle conformation coexist in solution and this is confirmed by resonance Raman spectroscopy. Large downshifts in the structure-sensitive lines result from the non-planar distortion, and line broadenings result from structural heterogeneity. The heterogeneity originates from tradeoffs between energy contributions from steric repulsion and macrocycle distortion. Simulations for 5-nitro-2,3,7,8,12,13,17,18-octa(isopropyl)porphyrin suggest two possible orientations of the nitro group with respect to the macrocycle mean plane — one nearly vertical (as in the crystal structure) and another that is nearly parallel. INDO/S semiempirical calculations indicate an orbital of the NO₂ group resides between the porphyrin frontier orbitals with significant mixing of the nitro and porphyrin orbitals.KEYWORDS: porphyrin, non-planar, resonance Raman, X-ray crystallography, crystal structure, isopropyl, nitro, conformer, molecular mechanics, molecular simulations, density functional theory, steric crowding, conformational heterogeneity.

Tuberculosis is a deadly disease caused by Mycobacterium tuberculosis. Like most bacterial pathogens, iron acquisition, regulation, and storage are critical for its survival. Due to the poor solubility of iron under physiological conditions, both eukaryotes and prokaryotes possess ferritins, large protein complexes that store iron and keep it bioavailable. Mtb encodes for two ferritin homologs: a heme-containing bacterioferritin (Mtb-BfrA) and a non-heme eukaryotic-like ferritin (Mtb-BfrB). A conserved feature of bacterioferritins is the presence of a heme group at the interface between two subunits of each dimer that is related by a non-crystallographic two-fold axis. The structure of a selenomethionine derivative of Mtb-BfrA was previously reported (PDB ID: 2WTL); however, a proposed heme degradation product was modeled into the heme-binding site, as electron density for intact heme was not observed. Here, the purification and structure determination of recombinant Mtb-BfrA is reported. As-isolated Mtb-BfrA from Escherichia coli is not fully heme loaded. However, the absorption spectrum features suggest binding of intact heme. In an attempt to fully complement Mtb-BfrA with heme, two different methodologies are described. Electronic spectroscopy and structure determination were used to confirm varying amounts of intact bis-methionine coordinated heme to Mtb-BfrA. We also report that increased heme incorporation only slightly increases Mtb-BfrA ferroxidase activity. Finally, the cognate partner of Mtb-BfrA is proposed to be a putative encoded gene which is located approximately 300 bps upstream of Mycobacterium tuberculosisbfrA, homologous to the cognate partner of Pseudomonas aeruginosa bacterioferritin, a 7 kDa ferrodoxin Bfd.

A presence of bulky 2,6-di-iso-propylphenoxy groups in bis-tert-butylisocyano adduct of 2(3),9(10),16(17),23(24)-tetrachloro-3(2),10(9),17(16),24(23)-tetra(2,6-di-iso-propylphenoxy)-phthalocyaninato iron(II) complex allows separation of two individual positional isomers and a mixture of the remaining two isomers using conventional chromatography. X-ray structures of “$D_{2h}$” and “$C_{4h}$” isomers were confimed by X-ray crystallography. Density functional theory (DFT) and time-dependent DFT (TDDFT) calculations of each individual positional isomer allowed insight into their electronic structures and vertical excitation energies, which were correlated with the experimental UV-vis and MCD spectra.

A reaction between 5,10,15,20-tetra(4-hydroxyphenyl)porphyrin and 1-bromopyrene resulted in the formation of 5,10,15,20-tetra[4-(4-(pyrenyl-1)butoxy)phenyl]porphyrin (1), while cross-condensation between 4-(4-(pyrenyl-1)butoxy)benzaldehyde, ferrocenecaboxaldehyde, and pyrrole resulted in the formation of 5-ferrocenyl-10,15,20-tri[4-(4-(pyrenyl-1)butoxy)phenyl]porphyrin (2), 5,10-diferrocenyl-15,20-di[4-(4-(pyrenyl-1)butoxy)phenyl]porphyrin (3), and 5,15-diferrocenyl-10,20-di[4-(4-(pyrenyl-1)butoxy)phenyl]porphyrin (4). All pyrene-containing porphyrins were characterized by ¹H NMR, UV-vis, MCD, and high-resolution ESI methods, while their electronic structures and the nature of the excited states were elucidated using density functional theory (DFT) and time-dependent DFT (TDDFT) calculations. The molecular structure of 1 and its fluorescence quenching upon the addition of C${}_{60}$ fullerene was also investigated using X-ray crystallography and steady-state fluorescence approaches.

The reaction of tetra($p$-tolyl)porphyrinato titanium (IV) oxide (2) with 4,7-diethyl-5,6-dimercaptobenzo[1,2,3] trithiole (3a) produced the corresponding titanium (IV) complex, tetra($p$-tolyl)porphyrinato titanium (IV) trithiolobenzenedithiolate (4a), fused with a trithiole ring. Related compounds 4b and 4c were prepared by a similar reaction of 2 with 5,8-diethyl-6,7-dimercaptobenzo[1,4]dithiin (3b) and 3,6-diethyl-4,5-dimercapto-1,2-bis(2-cyanoethylthio)benzene (3c). The structure of 4b was determined by X-ray crystallography. Compound 4c was further treated with cesium hydroxide to produce the corresponding dithiolate anion 4c2S, which was deposited on the gold electrode. The electrochemical property of the gold electrode was determined by cyclic voltammetry. The structure of simplified model compound 4b$\prime$ was optimized using the DFT method with the Gaussian 09 program. The optimized structure was utilized to calculate the NMR chemical shifts, the HOMO and LUMO energy levels, and the electronic transition in the absorption spectrum.

The syntheses of indium, gallium and aluminum porphyrin dimers with a single hydroxo-bridge, $\{$[M(Porph)]₂(OH)${\}}^{+}$, are described. Emphasis is given to indium and gallium derivatives. The X-ray structures for $\{$ [Ga(OEP)]₂(OH)$\}$ ClO₄ and $\{$ [In(OEP)]₂(OH)$\}$ ClO₄ (two forms) are presented. The dimeric molecules can be synthesized by the acid-treatment of the corresponding hydroxo-ligated monomeric complexes [M(OEP)(OH)] and [M(TPP)(OH)]. The nature of the starting material (the hydroxo-ligated monomer) was first suggested by IR spectroscopy and further proved by proton-deuterium exchange followed by ¹H NMR spectroscopy. The structure of a monomeric indium hydroxide complex, [In(OEP)(OH)], is also presented. The synthesis of the dimer for all metals can be monitored by UV-vis spectroscopy, which clearly demonstrates that a blue-shift of the Soret band accompanies formation of the dimer from the monomer. A strong $\pi$–$\pi$interaction between the two porphyrin rings of these $\mu$-hydroxo-bridged dimers is confirmed both by solution state studies (¹H NMR and UV-vis spectroscopy) and the X-ray structures of $\{$ [M(OEP)]₂(OH)$\}$ ClO₄ (M = In, Ga). In addition, exposure of methylene chloride solutions of these bridged complexes to white light afforded the corresponding chloro derivatives, [M(Porph)Cl]. The stereochemistry of a range of $\mu$-hydroxo dimers is discussed and DFT simulations at the HSEH1PBE/SDD level of theory provide suitable structural models and further electronic structure insights on selected [Ga(Porph)(OH)] and $\{$ [Ga(Porph)]₂(OH)$\}$${}^{+}$ derivatives.