80 research outputs found
Fig. 4. Bogidiella veneris n. sp. from Venus Bay, South Australia. A, B, E, paratype 1 (3.0 mm female); C, D, F, paratype 3 (3.1 mm female). A, gnathopod 1; B, gnathopod 2; C, uropod 1; D, uropod 2; E, uropod 3; F, telson. Scale bar A-F 5 0.1 mm.
No full textFig. 4. Bogidiella veneris n. sp. from Venus Bay, South Australia. A, B, E, paratype 1 (3.0 mm female); C, D, F, paratype 3 (3.1 mm female). A, gnathopod 1; B, gnathopod 2; C, uropod 1; D, uropod 2; E, uropod 3; F, telson. Scale bar A-F 5 0.1 mm
Evolution of the Excitonic State of DNA Stacked Thymines: Intrabase ππ* → S<sub>0</sub> Decay Paths Account for Ultrafast (Subpicosecond) and Longer (>100 ps) Deactivations
No full textMonomer-like
ring puckering decay paths for two stacked quantum
mechanical thymines inside a solvated DNA duplex described at the
molecular mechanics level are mapped using a hybrid CASPT2//CASSCF/MM
protocol that accounts for steric, electronic and electrostatic interactions
within the nucleobases native environment. Asymmetric stacking between
nucleobases open ups different intrabase ππ* decay paths
accounting for distinctive excited state lifetimes, spanning the subps
to subns time window
Evolution of the Excitonic State of DNA Stacked Thymines: Intrabase ππ* → S<sub>0</sub> Decay Paths Account for Ultrafast (Subpicosecond) and Longer (>100 ps) Deactivations
No full textMonomer-like
ring puckering decay paths for two stacked quantum
mechanical thymines inside a solvated DNA duplex described at the
molecular mechanics level are mapped using a hybrid CASPT2//CASSCF/MM
protocol that accounts for steric, electronic and electrostatic interactions
within the nucleobases native environment. Asymmetric stacking between
nucleobases open ups different intrabase ππ* decay paths
accounting for distinctive excited state lifetimes, spanning the subps
to subns time window
The Different Photoisomerization Efficiency of Azobenzene in the Lowest nπ* and ππ* Singlets: The Role of a Phantom State
No full textAzobenzene E⇆Z photoisomerization, following excitation to the bright S(ππ*) state, is investigated by means of ab initio CASSCF optimizations and perturbative CASPT2 corrections. Specifically, by elucidating the S(ππ*) deactivation paths, we explain the mechanism responsible for azobenzene photoisomerization, the lower isomerization quantum yields observed for the S(ππ*) excitation than for the S1(nπ*) excitation in the isolated molecule, and the recovery of the Kasha rule observed in sterically hindered azobenzenes. We find that a doubly excited state is a photoreaction intermediate that plays a very important role in the decay of the bright S(ππ*). We show that this doubly excited state, which is immediately populated by molecules excited to S(ππ*), drives the photoisomerization along the torsion path and also induces a fast internal conversion to the S1(nπ*) at a variety of geometries, thus shaping (all the most important features of) the S(ππ*) decay pathway and photoreactivity. We reach this conclusion by determining the critical structures, the minimum energy paths originating on the bright S(ππ*) state and on other relevant excited states including S1(nπ*), and by characterizing the conical intersection seams that are important in deciding the photochemical outcome. The model is consistent with the most recent time-resolved spectroscopic and photochemical data
Deciphering Low Energy Deactivation Channels in Adenine
No full textThe radiationless decay paths of 9H-adenine in its lowest excited states 1nπ*, 1Lb(1ππ*), and 1La(1ππ*) and in dissociative 1πσ* states have been mapped in vacuo at the CASPT2//CASSCF resolution. The minimum energy path (MEP) of the 1La state, which shows the strongest absorption below 5 eV, is found to decrease monotonically along the puckering coordinate from the vertical excitation to a S0/1La conical intersection (CI). The vertically excited 1nπ* and 1Lb states are found to relax to the respective minima and to require some energy to reach CIs with S0. This picture suggests that 1La alone is responsible of both components of the ultrafast biexponential decay (with τ1 2 1nπ* and 1Lb states do not act as important intermediates in the 1La decay process. We find that the 1La→1πσN9H* internal conversion can be followed by N9−H photocleavage, albeit with tiny quantum yield. The amino N10−H bond photocleavage is hindered by the high barrier encountered along the N10−H bond-breaking path in the 1πσN10H* state
Initial Excited-State Relaxation of the Isolated 11-cis Protonated Schiff Base of Retinal: Evidence for in-Plane Motion from ab Initio Quantum Chemical Simulation of the Resonance Raman Spectrum
No full textThe intensity distribution in the resonance Raman (RR) spectrum of the 11-cis protonated Schiff
base of retinal (PSB11) is modeled for the first time on the basis of ab initio quantum chemical calculations.
To adequately represent the structure of PSB11, 4-cis-γ,η-dimethyl-C9H9 NH2+ is chosen as a model. The RR
spectra of the model PSB11 and of several isotopomers are compared with the experimental spectra of PSB11
in solution. An excellent agreement is obtained in the structurally sensitive fingerprint region of the spectra
(1100−1300 cm-1), where most of the observed details are quantitatively reproduced by the simulations. The
900−1100-cm-1 region of the RR spectrum of PSB11, which contains the signatures of the S0,S1 potential
energy changes due to the protein environment, is also well reproduced. On the basis of the simulations, it is
concluded that the activity observed at ca. 970 cm-1 in the spectrum of PSB11 in solution is due to in-plane
modes, while a superposition of in-plane and out-of-plane motions is responsible for the increased RR activity
in rhodopsin. The present analysis of RR activities along with the computed relaxation path structure provides
support for the interpretation of the initial relaxation of photoexcited PSB11 in solution in terms of initial
in-plane motion out of the Franck−Condon region followed by slow out-of-plane (i.e., cis → trans torsional)
evolution along a flat energy plateau. Furthermore, the quality of the simulated spectra suggests that the quantum
chemical method used in this work can be employed quantitatively to assist in the characterization of
photoreaction intermediates in the visual cycle
Computational Clues for a New Mechanism in the Glycosylase Activity of the Human DNA Repair Protein hOGG1. A Generalized Paradigm for Purine-Repairing Systems?
No full textA theoretical density functional theory (DFT, B3LYP) investigation has been carried out on the catalytic
cycle responsible for the glycosylase activity of the human DNA repair protein hOGG1: enzyme activation,
cleavage of the glycosidic bond, and expulsion of the damaged base. An unprecedented large quantum
mechanics (QM) model system has been used, which includes a complete oxoG molecule, the deoxyribose
ring bonded to the phosphate groups, and most of the surrounding residues that simulate the protein binding
pocket. It has been found that Asp268 does not play any role in Lys249 activation and that the oxoG basis
acts as a coenzyme, triggering nucleophile activation by Lys249 deprotonation. An SN2 nucleophilic attack
by Lys249 on the anomeric carbon then follows. This is the rate-determining step of the process with an
activation barrier of 16.7 kcal mol-1 in good agreement with the experimental value of 17.1 kcal mol-1. The
expelled oxoG plays again as an enzyme cofactor at the end of the process by activating (via proton transfer)
ribose ring opening and Schiff base formation. This study suggests a recurring catalytic strategy in the enzymatic
cleavage of purine nucleoside where the activation of the leaving group by protonation of the nucleoside
base (via an enzymatic general acid) triggers the cleavage of the glycosidic bond
Computational Evidence for the Catalytic Mechanism of Human Glutathione S-Transferase A3-3: A QM/MM Investigation
No full textA Quantum Mechanics/Molecular Mechanics (QM/MM) computational
investigation
of the catalytic mechanism of the human glutathione transferase A3-3
(hGSTA3-3) has been carried out. The results demonstrate that the
isomerization reaction is concerted, but highly asynchronous: in the
first reaction phase the glutathione (GSH) negative sulfur (thiolate)
acts as a base and deprotonates carbon C4 of the substrate Δ5-androstene-3,17-dione (Δ5-AD); in the second
reaction phase the hydroxyl proton of the tyrosine fragment Y9 is
transferred to C6 affording the Δ4-androstene-3,17-dione
product (Δ4-AD). The initial state of the enzyme
is subsequently restored by transferring a proton from the GSH sulfur
to the tyrosine negative oxygen. There is no evidence for a “genuine”
stepwise mechanism involving the formation of a real dienolate intermediate
as suggested in previous papers. Furthermore, our computations have
evidenced that, when we consider the whole process (including the
restoring of the enzyme), GSH behaves as a base/acid catalyst (as
hypothesized by some authors), but it requires the participation of
the tyrosine Y9 acting as a proton shuttle. A “fingerprint
analysis” has been used to rank the electrostatic effects on
the catalysis of the various residues surrounding the active site.
This analysis highlights the role played by the arginine residue R15
in stabilizing the initial complex in agreement with previous suggestions
based on crystal structures
On the Mechanism of the cis−trans Isomerization in the Lowest Electronic States of Azobenzene: S<sub>0</sub>, S<sub>1</sub>, and T<sub>1</sub>
No full textIn this paper, we identify the most efficient decay and isomerization route of the S1, T1, and S0
states of azobenzene. By use of quantum chemical methods, we have searched for the transition states
(TS) on the S1 potential energy surface and for the S0/S1 conical intersections (CIs) that are closer to the
minimum energy path on the S1. We found only one TS, at 60° of CNNC torsion from the E isomer, which
requires an activation energy of only 2 kcal/mol. The lowest energy CIs, lying also 2 kcal/mol above the S1
minimum, were found on the torsion pathway for CNNC angles in the range 95−90°. The lowest CI along
the inversion path was found ca. 25 kcal/mol higher than the S1 minimum and was characterized by a
highly asymmetric molecular structure with one NNC angle of 174°. These results indicate that the S1
state decay involves mainly the torsion route and that the inversion mechanism may play a role only if the
molecule is excited with an excess energy of at least 25 kcal/mol with respect to the S1 minimum of the E
isomer. We have calculated the spin−orbit couplings between S0 and T1 at several geometries along the
CNNC torsion coordinate. These spin−orbit couplings were about 20−30 cm-1 for all the geometries
considered. Since the potential energy curves of S0 and T1 cross in the region of twisted CNNC angle,
these couplings are large enough to ensure that the T1 lifetime is very short (∼10 ps) and that thermal
isomerization can proceed via the nonadiabatic torsion route involving the S0−T1−S0 crossing with
preexponential factor and activation energy in agreement with the values obtained from kinetic measures
Solvent Effects on the Vibrational Activity and Photodynamics of the Green Fluorescent Protein Chromophore: A Quantum-Chemical Study
No full textVibrational activities in the Raman and resonance Raman spectra of the cationic, neutral, and
anionic forms of 4‘-hydroxybenzylidene-2,3-dimethyl-imidazolinone, a model compound for the green
fluorescent protein chromophore, have been obtained from quantum-chemical calculations in vacuo and
with the inclusion of solvent effects through the polarizable continuum model. It is found that inclusion of
solvent effects improves slightly the agreement with experimental data for the cationic and neutral forms,
whose spectra are qualitatively well-described already by calculations in vacuo. In contrast, inclusion of
solvent effects is crucial to reproduce correctly the activities of the anionic form. The structural effects of
solvation are remarkable both in the ground and in the lowest excited state of the anionic chromophore
and influence not only the vibrational activity but also the photodynamics of the lowest excited state.
CASPT2//CASSCF photoreaction paths, computed by including solvent effects at the CASSCF level, indicate
a facile torsional deformation around both exocyclic CC bonds. Rotation around the exocyclic CC double
bond is shown to lead to a favored radiationless decay channel, more efficient than that in gas phase, and
which explains the ultrafast fluorescence decay and ground-state recovery observed in solution. Conversely,
rotation around the exocyclic CC single bond accounts for the bottleneck observed in the ground-state
recovery cycle. It is also speculated that the ultrafast radiationless decay channel would be hampered in
protein for unfavorable electrostatic interactions and steric reasons
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