Non‐Bonded Interactions Drive the Sub‐Picosecond Bilin Photoisomerization in the Pfr State of Phytochrome Cph1

Phytochromes are protein‐based photoreceptors harboring a bilin‐based photoswitch in the active site. The timescale of photosignaling via C₁₅=C₁₆ E‐to‐Z photoisomerization has been ambiguous in the far‐red‐absorbing P_fr state. Here we present a unified view of the structural events in phytochrome Cph1 post excitation with femtosecond precision, obtained via stimulated Raman and polarization‐resolved transient IR spectroscopy. We demonstrate that photoproduct formation occurs within 700 fs, determined by a two‐step partitioning process initiated by a planarization on the electronic excited state with a 300 fs time scale. The ultrafast isomerization timescale for P_fr‐to‐P_r conversion highlights the active role of the nonbonding methyl–methyl clash initiating the reaction in the excited state. We envision that our results will motivate the synthesis of new artificial photoswitches with precisely tuned non‐bonded interactions for ultrafast response.     

Influence of Heterogeneity on the Ultrafast Photoisomerization Dynamics of Pfr in Cph1 Phytochrome

Photoisomerization of a protein‐bound chromophore is the basis of light sensing and signaling in many photoreceptors. Phytochrome photoreceptors can be photoconverted reversibly between the Pr and Pfr states through photoisomerization of the methine bridge between rings C and D. Ground‐state heterogeneity of the chromophore has been reported for both Pr and Pfr. Here, we report ultrafast visible (Vis) pump–probe and femtosecond polarization‐resolved Vis pump–infrared (IR) probe studies of the Pfr photoreaction in native and ¹³C/¹⁵N‐labeled Cph1 phytochrome with unlabeled PCB chromophore, demonstrating different S₀ substates, Pfr‐I and Pfr‐II, with distinct IR absorptions, orientations and dynamics of the carbonyl vibration of ring D. We derived time constants of 0.24 ps, 0.7 ps and 6 ps, describing the complete initial photoreaction. We identified an isomerizing pathway with 0.7 ps for Pfr‐I, and silent dynamics with 6 ps for Pfr‐II. We discuss different origins of the Pfr substates, and favor different facial orientations of ring D. The model provides a quantum yield for Pfr‐I of 38%, in line with ~35% ring D rotation in the electronic excited state. We tentatively assign the silent form Pfr‐II to a dark‐adapted state that can convert to Pfr‐I upon light absorption.     

Synthesis of Analogues of the Antitumor （1→6）-Branched （1→3）-Glucohexaose

β-D-Glcp-(1→）3-[β-D-Glcp-(1→6)-]α-D-Manp-(1→3)-β-D-Glcp-(1→3)-[β-D-Glcp(1→6)-]D-Glcp(18)and β-D-Glcp(1→3)-[β-D-Glcp(1→6)-]α-D-Manp-(1→3)-β-D-Glcp(1→3)-[β-D-Glcp(1→6)-]β-D-Glcp-D-(1→3)-Glcp-1→OM3(29)were synthesized as the analogues of the immunomodulator β-D-Glcp-(1→3)-[β-D-Glcp(1→6)-]α-D-Glcp(1→3)-β-D-Glcp(1→63)-[β-D-Glcp(1→6)-]D-Glcp through coupling of trisaccharide donors 9 with trisaccharide acceptor 16 and tetrasaccharide acceptor 27 followed by deprotection,respectively.     

Synthesis of β-（ 1→6）-Branched （ 1→3）-Glucononaoside with Alter-nate β- and α-Bonds in the Backbone

Lauryl glycoside of β-D-Glcp-(1→3)-[β-D-Glcp-(1→6)-]α-D-Glcp-(1→3)-β-D-Glcp-(1→3)-[β-D-Glcp-(1→6)-]α-D-Glcp-(1→3)-β-D-Glcp-(1→3)-[β-D-Glcp-(1→6)-]β-D-Glcp was synthesized through 3 3 3 strategy. 3-O-Allyl-2,4,6-tri-O-benzoyl-β-D-glucopyranosyl-(1→3)- -[2, 3, 4, 6-tetra-O-benzoyl-β-D-glucopyranosyl-(1→6)-] 1,2-O-isopropylidene-α-D-glucofuranose was used as the key intermediate which was converted to the corresponding trisaccharide donor and acceptor readily.     

Heck Reaction as Key Step in the Synthesis of Hydrogenated 2‐benzazepin‐1‐ones

Two strategies were pursued for the synthesis of 2‐benzazepin‐1‐ones 16 and 17 with an N/O‐acetal or enamide in 3‐position. Establishment of the propionaldehyde substructure first and subsequently the amide moiety via a four step sequence failed to provide amides 11 . However the Pd‐catalyzed Heck reaction of 2‐iodobenzamides 13 with allyl alcohol and subsequent reaction of the products 14 / 15 with acid led to 2‐benzazepin‐1‐ones in a two‐step sequence. Depending on the size of the N‐substituent the 3‐methoxy derivative 16a or the dihydro‐2‐benzazepine 17b was formed.     

NMR analysis of a series of 1,2‐bis(1‐R‐5‐oxo‐2,3‐dihydro‐1H‐pyrrol‐4‐ylidene)ethanes and X‐ray crystal structure analysis of the R = mesityl compound

Four tetramethyl 4,4′‐(ethane‐1,2‐diylidene)bis[1‐R‐5‐oxo‐4,5‐dihydro‐1H‐pyrrole‐2,3‐dicarboxylate] compounds, denoted class (1), are a series of conjugated buta‐1,3‐dienes substituted with a heterocyclic group. The compounds can be used as dyes and pigments due to their long‐range conjugated systems. Four structures were studied using ¹H NMR, ¹³C NMR and mass spectroscopy, viz. with R = 2,4,6‐trimethylphenyl, (1a), R = cyclohexyl, (1b), R = tert‐butyl, (1c), and R = isopropyl, (1d). A detailed discussion is presented regarding the characteristics of the three‐dimensional structures based on NMR analysis and the X‐ray crystal structure of (1a), namely tetramethyl 4,4′‐(ethane‐1,2‐diylidene)bis[5‐oxo‐1‐(2,4,6‐trimethylphenyl)‐4,5‐dihydro‐1H‐pyrrole‐2,3‐dicarboxylate], C₃₆H₃₆N₂O₁₀. The conjugation plane and stability were also studied via quantum chemical calculations.     

PO → Si intramolecular coordination in the derivatives of 1,4‐phosphasilacyclohexane 1‐oxides

The chair and boat conformers for a series of derivatives of 1,4‐phosphasilacyclohexane 1‐oxides have been calculated at the B3LYP/6‐311+G** level of theory in the gas phase and taking into account the effect of solvent polarity using the IEF‐PCM model. The stability of the boat conformers containing pentacoordinate silicon due to formation of the P?O→Si intramolecular coordination bond depends on the environment of the phosphorus atom and polarity of the solvent, and the strength of the transannular bond depends also on the nature of the substituents at the silicon atom. The highly polar boat conformers are strongly stabilized in the DMSO solution. NBO analysis showed the importance of the σ(C? Si) → σ*(H₃C? N) hyperconjugative interaction in the two H₃C? N? C? Si fragments of the ring favoring the formation of the pentacoordinate silicon atom. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Structural Variability of R2C Adducts of 3a,6a‐Diaza‐1,4‐diphosphapentalene: Tuning the N→P Bonding

3a,6a‐Diaza‐1,4‐diphosphapentalene (DDP) reacts with hexachlorocyclopentadiene to form a stable adduct (ClC)₄C=DDP ( 4 ). The phosphorus atom involved into coordination has a pyramidal arrangement but retains partial double bonding with carbon [1.752(3) Å]. At the same time, the P–N bond remains covalent [1.824(3) Å]. The adduct 4 is better described as a zwitterionic compound with strongly delocalized positive and negative charges. A similar zwitterionic adduct DDP=C(CN)₂ was prepared by the reactions of dichloro‐DDP ( 7 ) with malononitrile in the presence of Et₃N. DFT calculations showed that related structures are formed in the case of the substituents (ClC)₄C=, (HC)₄C=, (NC)₂C=, and (MeCO)₂C=, possessing electron‐delocalizing properties. Compounds with other R₂C groups (R = Ph, Me, C₆F₅, Cl), possessing electronegative properties as well, but insufficient e‐delocalization, demonstrate the noncovalent P–N bonding and a little shorter R₂C–P bond lengths (ca. 1.70 Å).     

N → C2 → C3 migration of the dichlorophosphino group in the synthesis of phosphorylated NH‐pyrroles

A successive N → C₂ → C₃ migration of the dichlorophosphino group has been found to occur in phosphorylation of unsubstituted pyrrole with phosphorus trichloride. As a result of this migration, a number of hitherto unknown C‐phosphorylated N‐unsubstituted pyrroles have been obtained. © 2008 Wiley Periodicals, Inc. Heteroatom Chem 19:671–676, 2008; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20495     

Two‐Step Spin Transition in a 1D FeII 1,2,4‐Triazole Chain Compound

A thermochromic 1D spin crossover coordination (SCO) polymer [Fe(βAlatrz)₃](BF₄)₂ ? 2 H₂O ( 1? 2 H₂O), whose precursor βAlatrz, (1,2,4‐triazol‐4‐yl‐propionate) has been tailored from a β‐amino acid ester is investigated in detail by a set of superconducting quantum interference device (SQUID), ⁵⁷Fe Mössbauer, differential scanning calorimetry, infrared, and Raman measurements. An hysteretic abrupt two‐step spin crossover (T_1/2^↓=230 K and T_1/2^↑=235 K, and T_1/2^↓=172 K and T_1/2^↑=188 K, respectively) is registered for the first time for a 1,2,4‐triazole‐based Fe^II 1D coordination polymer. The two‐step SCO configuration is observed in a 1:2 ratio of low‐spin/high‐spin in the intermediate phase for a 1D chain. The origin of the stepwise transition was attributed to a distribution of chains of different lengths in 1? 2 H₂O after First Order Reversal Curves (FORC) analyses. A detailed DFT analysis allowed us to propose the normal mode assignment of the Raman peaks in the low‐spin and high‐spin states of 1? 2 H₂O. Vibrational spectra of 1? 2 H₂O reveal that the BF₄^? anions and water molecules play no significant role on the vibrational properties of the [Fe(βAlatrz)₃]²⁺ polymeric chains, although non‐coordinated water molecules have a dramatic influence on the emergence of a step in the spin transition curve. The dehydrated material [Fe(βAlatrz)₃](BF₄)₂ ( 1 ) reveals indeed a significantly different magnetic behavior with a one‐step SCO which was also investigated.     

Hydrogen‐bonded sheets of R22(10) and R44(24) rings in 1‐deoxy‐1‐morpholino‐d‐fructopyranose

In the title compound, C₁₀H₁₉NO₆, both rings adopt almost perfect chair conformations and their mutual orientation is influenced by an intramolecular O—H...N hydrogen bond. The molecules are linked by three independent O—H...O hydrogen bonds into sheets containing equal numbers of R₂²(10) and R₄⁴(24) rings.     

Melanopsin and the Non‐visual Photochemistry in the Inner Retina of Vertebrates

Melanopsin (Opn4), a member of the G‐protein‐coupled receptor family, is a vitamin A‐based opsin in the vertebrate retina that has been shown to be involved in the synchronization of circadian rhythms, pupillary light reflexes, melatonin suppression and other light‐regulated tasks. In nonmammalian vertebrates there are two Opn4 genes, Opn4m and Opn4x, the mammalian and Xenopus orthologs respectively. Opn4x is only expressed in nonmammalian vertebrates including reptiles, fish and birds, while Opn4m is found in a subset of retinal ganglion cells (RGCs), the intrinsically photosensitive (ip) RGCs of the inner retina of both mammals and nonmammalian vertebrates. All opsins described utilize retinaldehyde as chromophore, photoisomerized from 11‐cis‐ to all‐trans‐retinal upon light exposure. Visual retinal photoreceptor cones and rods, responsible for day and night vision respectively, recycle retinoids through a process called the visual cycle that involves the retinal pigment epithelium or glial Müller cells. Although Opn4 has been characterized as a bistable photopigment, little is known about the mechanism/s involved in its chromophore regeneration. In this review, we will attempt to shed light on the visual cycle taking place in the inner retina and discuss the state of the art in the nonvisual photochemistry of vertebrates.     

Conformational analysis of the disaccharide methyl α‐d‐mannopyranosyl‐(1→3)‐2‐O‐acetyl‐β‐d‐mannopyranoside monohydrate

The crystal structure of methyl α‐d ‐mannopyranosyl‐(1→3)‐2‐O‐acetyl‐β‐d ‐mannopyranoside monohydrate, C₁₅H₂₆O₁₂·H₂O, ( II ), has been determined and the structural parameters for its constituent α‐d ‐mannopyranosyl residue compared with those for methyl α‐d ‐mannopyranoside. Mono‐O‐acetylation appears to promote the crystallization of ( II ), inferred from the difficulty in crystallizing methyl α‐d ‐mannopyranosyl‐(1→3)‐β‐d ‐mannopyranoside despite repeated attempts. The conformational properties of the O‐acetyl side chain in ( II ) are similar to those observed in recent studies of peracetylated mannose‐containing oligosaccharides, having a preferred geometry in which the C2—H2 bond eclipses the C=O bond of the acetyl group. The C2—O2 bond in ( II ) elongates by ～0.02 Å upon O‐acetylation. The phi (?) and psi (ψ) torsion angles that dictate the conformation of the internal O‐glycosidic linkage in ( II ) are similar to those determined recently in aqueous solution by NMR spectroscopy for unacetylated ( II ) using the statistical program MA′AT, with a greater disparity found for ψ (Δ = ～16°) than for ? (Δ = ～6°).     

Photochemistry of 1‐Cyclopropyl‐6‐fluoro‐1,4‐dihydro‐4‐oxo‐7‐ (piperazin‐1‐yl)quinoline‐3‐carboxylic Acid (=Ciprofloxacin) in Aqueous Solutions

The 1‐cyclopropyl‐6‐fluoro‐1,4‐dihydro‐4‐oxo‐7‐(piperazin‐1‐yl)quinoline‐3‐carboxylic acid (=ciprofloxacin; 1 ) undergoes low‐efficiency (Φ=0.07) substitution of the 6‐fluoro by an OH group on irradiation in H₂O via the ππ* triplet (detected by flash photolysis, λ_max 610 nm, τ 1.5 μs). Decarboxylation is a minor process (≤5%). The addition of sodium sulfite or phosphate changes the course of the reaction under neutral conditions. Reductive defluorination is the main process in the first case, while defluorination is accompanied by degradation of the piperazine moiety in the presence of phosphate. In both cases, the initial step is electron‐transfer quenching of the triplet (k_q=2.3⋅10⁸M ⁻¹ s⁻¹ and 2.2⋅10⁷M ⁻¹ s⁻¹, respectively). Oxoquinoline derivative 1 is much more photostable under acidic conditions, and in this case the F‐atom is conserved, and the piperazine group is stepwise degraded (Φ=0.001).