Supramolecular hydrogen‐bonding patterns in the organic–inorganic hybrid compound bis(4‐amino‐5‐chloro‐2,6‐dimethylpyrimidinium) tetrathiocyanatozinc(II)–4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine–water (1/2/2)

Zinc thiocyanate complexes have been found to be biologically active compounds. Zinc is also an essential element for the normal function of most organisms and is the main constituent in a number of metalloenzyme proteins. Pyrimidine and aminopyrimidine derivatives are biologically very important as they are components of nucleic acids. Thiocyanate ions can bridge metal ions by employing both their N and S atoms for coordination. They can play an important role in assembling different coordination structures and yield an interesting variety of one‐, two‐ and three‐dimensional polymeric metal–thiocyanate supramolecular frameworks. The structure of a new zinc thiocyanate–aminopyrimidine organic–inorganic compound, (C₆H₉ClN₃)₂[Zn(NCS)₄]·2C₆H₈ClN₃·2H₂O, is reported. The asymmetric unit consist of half a tetrathiocyanatozinc(II) dianion, an uncoordinated 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidinium cation, a 4‐amino‐5‐chloro‐2,6‐dimethylpyrimidine molecule and a water molecule. The Zn^II atom adopts a distorted tetrahedral coordination geometry and is coordinated by four N atoms from the thiocyanate anions. The Zn^II atom is located on a special position (twofold axis of symmetry). The pyrimidinium cation and the pyrimidine molecule are not coordinated to the Zn^II atom, but are hydrogen bonded to the uncoordinated water molecules and the metal‐coordinated thiocyanate ligands. The pyrimidine molecules and pyrimidinium cations also form base‐pair‐like structures with an R₂²(8) ring motif via N—H…N hydrogen bonds. The crystal structure is further stabilized by intermolecular N—H…O, O—H…S, N—H…S and O—H…N hydrogen bonds, by intramolecular N—H…Cl and C—H…Cl hydrogen bonds, and also by π–π stacking interactions.     

Effects of substituents on synthetic analogs of chlorophylls. Part 1: Synthesis, vibrational properties and excited-state decay characteristics

Understanding the effects of substituents on the spectra of chlorins is essential for a wide variety of applications. Recent developments in synthetic methodology have made possible systematic studies of the properties of the chlorin macrocycle as a function of diverse types and patterns of substituents. In this paper, the spectral, vibrational and excited-state decay characteristics are examined for a set of synthetic chlorins. The chlorins bear substituents at the 5,10,15 (meso) positions or the 3,13 (beta) positions (plus 10-mesityl in a series of compounds) and include 24 zinc chlorins, 18 free base (Fb) analogs and one Fb or zinc oxophorbine. The oxophorbine contains the keto-bearing isocyclic ring present in the natural photosynthetic pigments (e.g. chlorophyll a). The substituents cause no significant perturbation to the structure of the chlorin macrocycle, as evidenced by the vibrational properties investigated using resonance Raman spectroscopy. In contrast, the fluorescence properties are significantly altered due to the electronic effects of substituents. For example, the fluorescence wavelength maximum, quantum yield and lifetime for a zinc chlorin bearing 3,13-diacetyl and 10-mesityl groups (662 nm, 0.28, 6.0 ns) differ substantially from those of the parent unsubstituted chlorin (602 nm, 0.062, 1.7 ns). Each of these properties of the lowest singlet excited state can be progressively stepped between these two extremes by incorporating different substituents. These perturbations are associated with significant changes in the rate constants of the decay pathways of the lowest excited singlet state. In this regard, the zinc chlorins with the red-most fluorescence also have the greatest radiative decay rate constant and are expected to have the fastest nonradiative internal conversion to the ground state. Nonetheless, these complexes have the longest singlet excited-state lifetime. The Fb chlorins bearing the same substituents exhibit similar fluorescence properties. Such combinations of factors render the chlorins suitable for a range of applications that require tunable coverage of the solar spectrum, long-lived excited states and red-region fluorescence.     

Effects of substituents on synthetic analogs of chlorophylls. Part 2: Redox properties, optical spectra and electronic structure

The optical absorption spectra and redox properties are presented for 24 synthetic zinc chlorins and 18 free base analogs bearing a variety of 3,13 (beta) and 5,10,15 (meso) substituents. Results are also given for a zinc and free base oxophorbine, which contain the keto-bearing isocyclic ring present in the natural photosynthetic pigments such as chlorophyll a. Density functional theory calculations were carried out to probe the effects of the types and positions of substituents on the characteristics (energies, electron distributions) of the frontier molecular orbitals. A general finding is that the 3,13 positions are more sensitive to the effects of auxochromes than the 5,10,15 positions. The auxochromes investigated (acetyl>ethynyl>vinyl>aryl) cause a significant redshift and intensification of the Qy band upon placement at the 3,13 positions, whereas groups at the 5,10,15 positions result in much smaller redshifts that are accompanied by a decrease in relative Qy intensity. In addition, the substituent-induced shifts in first oxidation and reduction potentials faithfully track the energies of the highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO), respectively. The calculations show that the LUMO is shifted more by substituents than the HOMO, which derives from the differences in the electron densities of the two orbitals at the substituent sites. The trends in the substituent-induced effects on the wavelengths and relative intensities of the major features (By, Bx, Qx, Qy) in the near-UV to near-IR absorption bands are well accounted for using Gouterman's four-orbital model, which incorporates the effects of the substituents on the HOMO-1 and LUMO+1 in addition to the HOMO and LUMO. Collectively, the results and analysis presented herein and in the companion paper provide insights into the effects of substituents on the optical absorption, redox and other photophysical properties of the chlorins. These insights form a framework that underpins the rational design of chlorins for applications encompassing photomedicine and solar-energy conversion.     

Two complementary routes to 7-substituted chlorins. Partial mimics of chlorophyll B

Chlorophyll a and chlorophyll b exhibit distinct spectra yet differ only in the nature of a single substituent (7-methyl versus 7-formyl, respectively). Two complementary approaches have been developed for the synthesis of 7-substituted chlorins. The first approach is a de novo route wherein 2,9-dibromo-5-p-tolyldipyrromethane (Eastern half) and 9-formyl-2,3,4,5-tetrahydro-1,3,3-trimethyldipyrrin (Western half) undergo acid-catalyzed condensation followed by metal-mediated oxidative cyclization. The resulting zinc chlorin is sterically uncongested and bears (1) a geminal dimethyl group in the reduced, pyrroline ring, (2) a bromo substituent at the 7-position, and (3) a p-tolyl group at the 10-position. The second approach entails regioselective 7-bromination of a 10,15-diarylchlorin that lacks a substituent at the 5-position. In an extension of this latter approach, a 5,15-diarylchlorin that lacks a substituent at the 10-position undergoes regioselective bromination at the 8-position. The introduction of a TIPS-ethynyl, acetyl, or formyl group at the 7-position was achieved using Pd-catalyzed reactions with the corresponding 7-bromochlorin. In the 10-p-tolyl-substituted zinc chlorins, the series of substituents (7-TIPS-ethynyl, 7-acetyl, 7-formyl) progressively causes (1) a bathochromic shift in the absorption maximum of the B band (405 to 426 nm) and (2) a hypsochromic shift in the position of the Qy band (605 to 598 nm). The trends mirror those for chlorophyll b versus chlorophyll a but are of lesser magnitude. Taken together, the facile access to chlorins that bear auxochromes at the 7-position enables wavelength tunability and provides the foundation for fundamental spectroscopic studies.     

Versatile site-specific conjugation of small molecules to siRNA using click chemistry

We have previously demonstrated that conjugation of small molecule ligands to small interfering RNAs (siRNAs) and anti-microRNAs results in functional siRNAs and antagomirs in vivo. Here we report on the development of an efficient chemical strategy to make oligoribonucleotide-ligand conjugates using the copper-catalyzed azide-alkyne cycloaddition (CuAAC) or click reaction. Three click reaction approaches were evaluated for their feasibility and suitability for high-throughput synthesis: the CuAAC reaction at the monomer level prior to oligonucleotide synthesis, the solution-phase postsynthetic "click conjugation", and the "click conjugation" on an immobilized and completely protected alkyne-oligonucleotide scaffold. Nucleosides bearing 5'-alkyne moieties were used for conjugation to the 5'-end of the oligonucleotide. Previously described 2'- and 3'-O-propargylated nucleosides were prepared to introduce the alkyne moiety to the 3' and 5' termini and to the internal positions of the scaffold. Azido-functionalized ligands bearing lipophilic long chain alkyls, cholesterol, oligoamine, and carbohydrate were utilized to study the effect of physicochemical characteristics of the incoming azide on click conjugation to the alkyne-oligonucleotide scaffold in solution and on immobilized solid support. We found that microwave-assisted click conjugation of azido-functionalized ligands to a fully protected solid-support bound alkyne-oligonucleotide prior to deprotection was the most efficient "click conjugation" strategy for site-specific, high-throughput oligonucleotide conjugate synthesis tested. The siRNA conjugates synthesized using this approach effectively silenced expression of a luciferase gene in a stably transformed HeLa cell line.     

Effects of substituents on synthetic analogs of chlorophylls. Part 3: The distinctive impact of auxochromes at the 7- versus 3-positions

Assessing the effects of substituents on the spectra of chlorophylls is essential for gaining a deep understanding of photosynthetic processes. Chlorophyll a and b differ solely in the nature of the 7-substituent (methyl versus formyl), whereas chlorophyll a and d differ solely in the 3-substituent (vinyl versus formyl), yet have distinct long-wavelength absorption maxima: 665 (a) 646 (b) and 692 nm (d). Herein, the spectra, singlet excited-state decay characteristics, and results from DFT calculations are examined for synthetic chlorins and 13(1)-oxophorbines that contain ethynyl, acetyl, formyl and other groups at the 3-, 7- and/or 13-positions. Substituent effects on the absorption spectra are well accounted for using Gouterman's four-orbital model. Key findings are that (1) the dramatic difference in auxochromic effects of a given substituent at the 7- versus 3- or 13-positions primarily derives from relative effects on the LUMO+1 and LUMO; (2) formyl at the 7- or 8-position effectively "porphyrinizes" the chlorin and (3) the substituent effect increases in the order of vinyl < ethynyl < acetyl < formyl. Thus, the spectral properties are governed by an intricate interplay of electronic effects of substituents at particular sites on the four frontier MOs of the chlorin macrocycle.     

Synthesis and Crystal Structure of a New Schiff Base 4-[(2-hydroxy-benzylidene)-amino]-<Emphasis Type="Italic">N</Emphasis>-(5-methyl-isoxazol-3-yl)-benzenesulfonamide

Abstract  The structure of the title compound (C₁₇H₁₅N₃O₄S)₂ the schiff base, bis(N-(5-methyl-3-isoxazolyl)-4-[(2-hydroxy benzylidene)-amino]) benzene sulfonamide was elucidated by H¹, C¹³ NMR, UV–VIS and IR spectroscopic techniques. The X-ray structure was determined in order to establish the conformation of the molecule. The compound crystallizes in the triclinic space group P-1, with a = 11.419(1), b = 11.426(0), c = 13.316(1) ?, α = 71.94(2), β = 89.79(1), γ = 89.14(2)° and Z = 4. Two benzene rings and azomethine group are practically coplanar, as a result of intramolecular hydrogen bonds involving the hydroxy O atom and azomethine N atom. The component species further interact via N–H···N and C–H···O hydrogen bonds and π–π stacking interactions. Index Abstract  The title compound (C₁₇H₁₅N₃O₄S)₂, Schiff base, bis(N-(5-methyl-3-isoxazolyl)-4-[(2-hydroxy benzylidene)-amino]) benzene sulfonamide was synthesized by the condensation of 4-amino-N-(5-methyl-3-isoxazolyl) benzene sulfonamide (SMZ) and 2-hydroxy benzaldehyde (SA). Its structure was confirmed by single crystal X-ray diffraction analysis. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Cyclic chlorophosphites as scaffolds for the one-pot synthesis of α-aminophosphonates under solvent-free conditions

New α-aminophosphonates of the type (OCH₂CMe₂CH₂O)P(O)CH(NHCO₂R)(R′) [6a-i, 7a-e, and 8a-c] have been synthesized in high yields by a three-component reaction using (OCH₂CMe₂CH₂O)PCl (3), benzamide (or urethane or benzyl carbamate), and an aldehyde without using any catalyst under solvent-free conditions. This route can be readily adapted for bis-aminophosphonates as well as optically active binaphthoxy α-aminophosphonates; it also tolerates the phenolic -OH group as shown by the synthesis of hydroxy functionalized aminophosphonates. Partial hydrolysis of compounds 7a-d leads to products in which the phosphorinane ring is cleaved first. Compounds (OCH₂CMe₂CH₂O)P(O)CH[NHC(O)Ph](9-anthryl) (6f) and optically pure (R,S)-(−)-(C₂₀H₁₂O₂)P(O)CH(NHCO₂Et)(Ph) (14a) were characterized by X-ray crystallography.     

Supramolecular interactions in salts/cocrystals involving pyrimidine derivatives of sulfonate/carboxylic acid

The crystal structures of three compounds involving aminopyrimidine derivatives are reported, namely, 5-fluorocytosinium sulfanilate–5-fluorocytosine–4-azaniumylbenzene-1-sulfonate (1/1/1), C₄H₅FN₃O⁺·C₆H₆NO₃S⁻·C₄H₄FN₃O·C₆H₇NO₃S, I , 5-fluorocytosine–indole-3-propionic acid (1/1), C₄H₄FN₃O·C₁₁H₁₁NO₂, II , and 2,4,6-triaminopyrimidinium 3-nitrobenzoate, C₄H₈N₅⁺·C₇H₄NO₄⁻, III , which have been synthesized and characterized by single-crystal X-ray diffraction. In I , there are two 5-fluorocytosine (5FC) molecules (5FC-A and 5FC-B) in the asymmetric unit, with one of the protons disordered between them. 5FC-A and 5FC-B are linked by triple hydrogen bonds, generating two fused rings [two R₂²(8) ring motifs]. The 5FC-A molecules form a self-complementary base pair [R₂²(8) ring motif] via a pair of N—H…O hydrogen bonds and the 5FC-B molecules form a similar complementary base pair [R₂²(8) ring motif]. The combination of these two types of pairing generates a supramolecular ribbon. The 5FC molecules are further hydrogen bonded to the sulfanilate anions and sulfanilic acid molecules via N—H…O hydrogen bonds, generating R₄⁴(22) and R⁶₆(36) ring motifs. In cocrystal II , two types of base pairs (homosynthons) are observed via a pair of N—H…O/N—H…N hydrogen bonds, generating R₂²(8) ring motifs. The first type of base pair is formed by the interaction of an N—H group and the carbonyl O atom of 5FC molecules through a couple of N—H…O hydrogen bonds. Another type of base pair is formed via the amino group and a pyrimidine ring N atom of the 5FC molecules through a pair of N—H…N hydrogen bonds. The base pairs (via N—H…N hydrogen bonds) are further bridged by the carboxyl OH group of indole-3-propionic acid and the O atom of 5FC through O—H…O hydrogen bonds on either side of the R₂²(8) motif. This leads to a DDAA array. In salt III , one of the N atoms of the pyrimidine ring is protonated and interacts with the carboxylate group of the anion through N—H…O hydrogen bonds, leading to the primary ring motif R₂²(8). Furthermore, the 2,4,6-triaminopyrimidinium (TAP) cations form base pairs [R₂²(8) homosynthon] via N—H…N hydrogen bonds. A carboxylate O atom of the 3-nitrobenzoate anion bridges two of the amino groups on either side of the paired TAP cations to form another ring [R₃²(8)]. This leads to the generation of a quadruple DADA array. The crystal structures are further stabilized by π–π stacking ( I and III ), C—H…π ( I and II ), C—F…π ( I ) and C—O…π ( II ) interactions.