A New Photocage Derived from Fluorene.

Photolabile protecting groups (PPGs or photocages) are increasingly subject to molecular design to meet requirements such as absorbance in the visible spectral range, high molar absorption coefficients, and high quantum yields of leaving group release. Improvements in these properties for the promising 3-diethylaminobenzyl (DEAMb) photocage, the photoactivity of which is based on the Zimmerman meta effect, are reported. Expansion of the aromatic system with a second aromatic ring resulted in improved spectral properties. A systematic trend relating the electronic (π-donor or acceptor) properties of the new aryl substituent and its position in the DEAMb ring to changes in the spectral properties could be observed. Conclusions from the experimental results were supported by computations obtained by using time-dependent DFT. A second generation of DEAMb-based photocages was designed. A rigid linker was introduced to ensure more efficient conjugation of the aromatic ring π systems by limiting rotational freedom. The resulting fluorenol (9-hydroxyfluorene)-based photocages had superior spectral properties to those of simple biphenyl systems. The best uncaging cross section achieved was 5320 m-1 cm-1 (ϵΦ365 ).

Ultrafast photochemistry of free-base porphyrin: a theoretical investigation of B → Q internal conversion mediated by dark states.

We examine the mechanism of ultrafast internal conversion between the B band (Soret band) and the Q band in porphine (H2P), the prototypical free-base porphyrin, using electronic structure studies and on-the-fly surface-hopping nonadiabatic dynamics. Our study highlights the crucial role of dark states within the N band which are found to mediate B/Q state transfer, necessitating a treatment beyond Gouterman's classic four-orbital model. The sequential B → N → Q pathway dominates largely over the direct B → Q pathway which is found to be energetically unfavorable. Potential energy surface cuts and conical intersections between excited states are determined by TDDFT and validated by CASSCF/CASPT2 and XMCQDPT2 calculations. Both the static analysis and on-the-fly surface-hopping calculations suggest a pathway which involves minor structural deformations via in-plane vibrations. The B → N conversion is a barrierless adiabatic process occurring within ∼20 fs, while the subsequent N → Q conversion occurs via a conical intersection within ∼100 fs, in agreement with time-resolved experiments for porphine and related free base porphyrins. Furthermore, evidence for both sequential and direct transfer to the Qx and Qy states is obtained.

Discovery of polar spirocyclic orally bioavailable urea inhibitors of soluble epoxide hydrolase.

Spirocyclic 1-oxa-9-azaspiro[5.5]undecan-4-amine scaffold was explored as a basis for the design of potential inhibitors of soluble epoxide hydrolase (sEH). Synthesis and testing of the initial SAR-probing library followed by biochemical testing against sEH allowed nominating a racemic lead compound (±)-22. The latter showed remarkable (> 0.5 mM) solubility in aqueous phosphate buffer solution, unusually low (for sEH inhibitors) lipophilicity as confirmed by experimentally determined logD7.4 of 0.99, and an excellent oral bioavailability in mice (as well as other pharmacokinetic characteristics). Individual enantiomer profiling revealed that the inhibitory potency primarily resided with the dextrorotatory eutomer (+)-22 (IC50 4.99 ±â€¯0.18 nM). For the latter, a crystal structure of its complex with a C-terminal domain of sEH was obtained and resolved. These data fully validate (+)-22 as a new non-racemic advanced lead compound for further development as a potential therapeutic agent for use in such areas as cardiovascular disease, inflammation and pain.

Electrocyclic reactions of siloles: a combined experimental and theoretical study.

The reaction of 4-chloro-1,2-dimethyl-4-supersilylsila-1-cyclopentene (2 a) with Li[NiPr2] at -78 °C results in the formation of the formal 1,4-addition product of the silacyclopentadiene derivative 3,4-dimethyl-1-supersilylsila-1,3-cyclopentadiene (4 a) with 2,3-dimethyl-4-supersilylsila-1,3-cyclopentadiene (5 a). In addition the respective adducts of the Diels-Alder reactions of 4 a+4 a and 4 a+5 a were obtained. Compound 4 a, which displays an s-cis-silacyclopentadiene configuration, reacts with cyclohexene to form the racemate of the [4+2] cycloadduct of 4 a and cyclohexene (9). In the reaction between 4 a and 2,3-dimethylbutadiene, however, 4 a acted as silene as well as silacyclopentadiene to yield the [2+4] and [4+2] cycloadducts 10 and 11, respectively. The constitutions of 9, 10, and 11 were confirmed by NMR spectroscopy and their crystal structures were determined. Reaction of 4-chloro-1,2-dimethyl-4-tert-butyl-4-silacyclopent-1-ene (2 c) with KC8 yielded the corresponding disilane (12), which was characterized by X-ray crystal structure analysis (triclinic, P1). DFT calculations are used to unveil the mechanistic scenario underlying the observed reactivity.

Evidence for Quantum Chemical Effects in Receptor-Ligand Binding Between Integrin and Collagen Fragments - A Computational Investigation With an Impact on Tissue Repair, Neurooncolgy and Glycobiology.

The collagen-integrin interactions are mediated by the doubly charged Mg2+ cation. In nature this cation seems to have the optimal binding strength to stabilize this complex. It is essential that the binding is not too weak so that the complex becomes unstable, however, it is also of importance that the ligand-receptor binding is still labile enough so that the ligand can separate from the receptor in a suited environment. In the case of crystal growing for experimentally useful integrin-collagen fragment complexes it turned out that Co2+ cations are ideal mediators to form stable complexes for such experiments. Although, one can argue that Co2+ is in this context an artificial cation, however, it is now of special interest to test the impact of this cation in cell-culture experiments focusing on integrin-ligand interactions. In order to examine, in particular, the role cobalt ions we have studied a Co2+ based model system using quantum chemical calculations. Thereby, we have shown that hybrid and long-range corrected functional, which are approximations provide already a sufficient level of accuracy. It is of interest to study a potential impact of cations on the binding of collagen-fragments including collagens from various species because different integrins have numerous biological functions (e.g. Integrin - NCAM (Neural cell adhesion molecule) interactions) and are triggered by intact and degraded collagen fragments. Since integrin-carbohydrate interactions play a key role when bio-medical problems such as tumor cell adhesion and virus-host cell infections have to be addressed on a sub-molecular level it is essential to understand the interactions with heavy-metal ions also at the sub-atomic level. Our findings open new routes, especially, in the fields of tissue repair and neuro-oncology for example for cell-culture experiments with different ions. Since Co2+ ions seem to bind stronger to integrin than Mg2+ ions it should be feasible to exchange these cations in suited tumor tissues although different cations are present in other metalloproteins which are active in such tissues. Various staining methods can be applied to document the interactions of integrins with carbohydrate chains and other target structures. Thereby, it is possible to study a potential impact of these interactions on biological functions. It was therefore necessary to figure out first which histological-glycobiological experimental settings of tumor cells are suited for our purpose. Since the interactions of several metalloproteins (integrin, ADAM12) with polysialic acid and the HNK-1 epitope play a crucial role in tumor tissues selected staining methods are proper tools to obtain essential information about the impact of the metal ions under study.

Ultrafast carbon monoxide photolysis and heme spin-crossover in myoglobin via nonadiabatic quantum dynamics.

Light absorption of myoglobin triggers diatomic ligand photolysis and a spin crossover transition of iron(II) that initiate protein conformational change. The photolysis and spin crossover reactions happen concurrently on a femtosecond timescale. The microscopic origin of these reactions remains controversial. Here, we apply quantum wavepacket dynamics to elucidate the ultrafast photochemical mechanism for a heme-carbon monoxide (heme-CO) complex. We observe coherent oscillations of the Fe-CO bond distance with a period of 42 fs and an amplitude of ∼1 Å. These nuclear motions induce pronounced geometric reorganization, which makes the CO dissociation irreversible. The reaction is initially dominated by symmetry breaking vibrations inducing an electron transfer from porphyrin to iron. Subsequently, the wavepacket relaxes to the triplet manifold in ∼75 fs and to the quintet manifold in ∼430 fs. Our results highlight the central role of nuclear vibrations at the origin of the ultrafast photodynamics of organometallic complexes.

Sensitized Two-Photon Activation of Coumarin Photocages.

Here we report the design of a new coumarin-based photolabile protecting group with enhanced two-photon absorption. Two-photon excited fluorescence (TPEF), color-tuned ultrafast transient absorption spectroscopy and infrared (IR) measurements are employed to photochemically characterize the newly designed ATTO 390-DEACM-cargo triad. Increased two-photon cross-section values of the novel cage in comparison to the widely used protecting group DEACM ([7-(diethylamino)coumarin-4-yl]methyl) are extracted from TPEF experiments. Femtosecond pump-probe experiments reveal a fast intramolecular charge transfer, a finding that is confirmed by quantum chemical calculations. Uncaging of glutamate is monitored in IR measurements by photodecarboxylation of the carbamate linker between the photolabile protecting group and the glutamate, showing the full functionality of the novel two-photon activatable photocage.

Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation.

The hemoprotein myoglobin is a model system for the study of protein dynamics. We used time-resolved serial femtosecond crystallography at an x-ray free-electron laser to resolve the ultrafast structural changes in the carbonmonoxy myoglobin complex upon photolysis of the Fe-CO bond. Structural changes appear throughout the protein within 500 femtoseconds, with the C, F, and H helices moving away from the heme cofactor and the E and A helices moving toward it. These collective movements are predicted by hybrid quantum mechanics/molecular mechanics simulations. Together with the observed oscillations of residues contacting the heme, our calculations support the prediction that an immediate collective response of the protein occurs upon ligand dissociation, as a result of heme vibrational modes coupling to global modes of the protein.