Electronic structure of the photoactive yellow protein chromophore: Ab initio study of the low-lying excited singlet states

The excited electronic states of the p-coumaric acid thio-ester chromophore of the Photoactive Yellow Protein (PYP) are characterized in view of identifying the key factors determining the chromophore's isomerisation. These factors include the anionic nature of the chromophore, the presence of sulfur (rather than oxygen or nitrogen) in the ester moiety, and the presence of a hydrogen-bonding environment stabilizing the phenolate moiety. Two twisted stationary S₁ structures are identified, corresponding to a twist around the double bond conjugated with the aromatic ring, and the single bond adjacent to the ring, respectively. The latter structure is accessed directly by relaxation from the Franck–Condon (FC) geometry. These structures are shown to entail a substantial polarization effect (increasing charge separation when moving towards the twisted geometry). Further, an inversion of charge character is observed for the double-bond twisted minimum, which can be accounted for by the vicinity of an S₁–S₀ conical intersection. The S₁–S₀ gap at the minimum geometries depends in a sensitive fashion on the -carbonyl heteroatom. Based upon these observations for the intrinsic properties of the chromophore, we further address the effect of the Arg52 residue, which acts as a counter-ion in the native protein environment.     

Theoretical study of the excited singlet and triplet states of alloxan

The possibility of excited‐state protomeric shifts in the biologically important molecule, alloxan, is investigated. We have focused on the S₁ and T₁ excited states of alloxan and its hydroxy tautomers. Modifications brought in by excitation on the relative stabilities, activation barriers, and optimized geometries, computed at the MNDO, AM1, and PM3 levels of approximation, have been discussed for both excited electronic states. The absorption and fluorescence spectra for the three tautomers are also discussed. Results show significant changes in the geometries on excitation, although the changes are similar for the singlet and triplet excited states. Though the relative stability orders do not change, the 2‐hydroxy tautomer is stabilized, while the 4‐hydroxy tautomer gets destabilized on excitation. The excited states are (n,π*) states, involving the promotion of a nonbonding oxygen lone pair from the CO? CO? CO moiety, which explains why the oxygens of this group become less basic and the 4‐hydroxy tautomer gets destabilized on excitation. However, the activation barriers do not reduce significantly on excitation, and this precludes the possibility of ground‐ or excited‐state proton transfer in the gas phase. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Photochemistry of azidostyrylquinolines: 1. Quantum-chemical study of the structure in the ground and the lower excited singlet states

The structures of isomeric 2-and 4-azidostyrylquinolines and their protonated forms in the ground (S ₀) and the lowest excited singlet (S ₁) states were calculated by the PM3 semiempirical method and the density functional theory (DFT) using the B3LYP/6-31G^* basis set. It was shown that the σ _NN ^* molecular orbital, which is localized on the azide group and is antibonding for the N-N₂ bond, is populated in the S₁ state of these azides in both neutral and protonated forms. Based on this result, it was assumed that the test azides would be photoactive in both forms, i.e., would have a photodissociation quantum yield of φ > 0.1. The calculation of absorption spectra by the TD B3LYP/6-31G^* method showed that the long-wavelength absorption bands of the protonated forms are shifted to visible spectral region, thus suggesting that azidostyrylquinolines in the protonated form will be sensitive to visible light.     

Geometrical relaxation in the excited singlet states of propylene

The consequences of the twist around the double bond in propylene for the properties of its low lying excited singlet states have been investigated by the ab initio large-scale multireference configuration interaction method (MRD-CI). A substantial increase in the dipole moments of the S₁ and S₂ excited states was found for a large interval of the twist angel θ = 50–130°. The variation of the VB covalent VB ionic contributions to the correlated wavefunctions of these two states a function of twisting has been analyzed. The connection with the occurence of an avoided crossing of the two excited singlets near the twist angel θ = 75°, which results in no change in dipole moment directions, is pointed out. The existence of destructive or constructive interference between acceptor and donor substitution has been investigated on the example of the pyramidalization at one of the vinylic C atoms. A competition of opposing effects matrix can invert the dipole moment direction in the excited states. Preliminary investigation of the nonadiabatic coupling elements indicates that the “sudden polarization” effect willnot disappear through vibronic coupling, and that the return of excited molecules to the ground electronic state will not be immediate.     

Electronic structures of the ground state and excited singlet states of nucleic acid bases

The self-consistent field (SCF) method is used in the semiempirical approximation (SA) with allowance for singly excited configurations to derive the ground state and singlet excited states for five nucleic acid bases (NAB). Empirical values are used for the nondiagonal elements of the matrix for the two-electron Coulomb integrals. The methyl group in thymine is allowed for via an induction model. Theoretical values are given for the energies of the first four electronic transitions for each base. The locations of these agree well with spectroscopic data. The energies of the first two transitions in adenine are found to be very similar when allowance is made for configuration interaction, so the first absorption band of adenine arises from overlap of two transitions.     

Theoretical study of the singlet electronically excited states of N4

Vertical excitation energies for the lowest eleven singlet states of T_d N₄ were calculated using the TD-DFT method with the B3LYP functional, and at the EOM-CCSD level of theory. The vertical excitation energies for the five lowest-lying excited states were also obtained using the state-averaged CASSCF, CASPT2, CASPT3, and MRCI + Q methods. Our results show that the five lowest-lying states are of valence character. EOM-CCSD/d-aug-cc-pVTZ calculations predict that there are two weakly allowed optical transitions of T₂ symmetry at 10.44 and 10.82 eV. The transition to the third T₂ state, which is predicted to be at 10.89 eV, has an oscillator strength about one order of magnitude higher.     

Low‐lying singlet excited states of isocyanogen

Recent photofragment fluorescence excitation (PHOFEX) spectroscopy experiments have observed the ùA″ singlet excited state of isocyanogen (CNCN) for the first time. The observed spectrum is not completely assigned and significant questions remain about the excited states of this system. To provide insight into the energetically accessible excited states of CNCN, optimized geometries, harmonic vibrational frequencies, and excitation energies for the first three singlet excited states are determined using equation‐of‐motion coupled‐cluster theory with singles and doubles (EOM‐CCSD) and correlation‐consistent basis sets. Additionally, excited state coupled‐cluster methods which approximate the contributions from triples (CC3) are utilized to estimate the effect of higher‐order correlation on the energy of each excited state. For the ùA″ state, our best estimate for T₀ is about 42,200 cm^?1, in agreement with the experimentally estimated upper limit for the zero‐point level of 42,523 cm^?1. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Influence of excited state aromaticity in the lowest excited singlet states of fulvene derivatives

The absorption spectra and excited state dipole moments of four differently substituted fulvenes have been investigated both experimentally and computationally. The results reveal that the excited state dipole moment of fulvenes reverses in the first excited singlet state when compared to the ground state. The oppositely polarized electron density distributions, which dominate the ground state and the first excited singlet state of fulvenes, respectively, reflect the reversed π-electron counting rules for aromaticity in the two states (4n + 2 vs. 4n, respectively). The results show that substituents indeed influence the polarity of fulvenes in the two states, however, cooperative interactions between the substituents and the fulvene moiety are most pronounced in the ground state.     

Two-photon study on the electronic interactions between the first excited singlet states in carotenoid-tetrapyrrole dyads

Electronic interactions between the first excited states (S(1)) of carotenoids (Car) of different conjugation lengths (8-11 double bonds) and phthalocyanines (Pc) in different Car-Pc dyad molecules were investigated by two-photon spectroscopy and compared with Car S(1)-chlorophyll (Chl) interactions in photosynthetic light harvesting complexes (LHCs). The observation of Chl/Pc fluorescence after selective two-photon excitation of the Car S(1) state allowed sensitive monitoring of the flow of energy between Car S(1) and Pc or Chl. It is found that two-photon excitation excites to about 80% to 100% exclusively the carotenoid state Car S(1) and that only a small fraction of direct tetrapyrrole two-photon excitation occurs. Amide-linked Car-Pc dyads in tetrahydrofuran demonstrate a molecular gear shift mechanism in that effective Car S(1) → Pc energy transfer is observed in a dyad with 9 double bonds in the carotenoid, whereas in similar dyads with 11 double bonds in the carotenoid, the Pc fluorescence is strongly quenched by Pc → Car S(1) energy transfer. In phenylamino-linked Car-Pc dyads in toluene extremely large electronic interactions between the Car S(1) state and Pc were observed, particularly in the case of a dyad in which the carotenoid contained 10 double bonds. This observation together with previous findings in the same system provides strong evidence for excitonic Car S(1)-Pc Q(y) interactions. Very similar results were observed with photosynthetic LHC II complexes in the past, supporting an important role of such interactions in photosynthetic down-regulation.     

Resonance CARS spectra of the lowest excited singlet states of rhodamines

The resonance CARS spectra of the S₁ states of rhodamine 6G, rhodamine B and sulforhodamine were obtained by choosing ω₁ resonant with the S₁ ← S₀ and S₃ ← S₁ transitions simultaneously and by varying the laser beam power density of ω₁ or ω₂. The vibrational frequencies for the S₀ and S₁ states are similar, implying that the structure of the S₁ state is not distorted significantly.     

Time-resolved spectroscopy of the excited singlet states of tirapazamine and desoxytirapazamine

Laser flash photolysis (LFP, 400 nm excitation) of the anti-cancer drug tirapazamine (TPZ) in acetonitrile produces the singlet excited-state S1 with lambda(max) = 544 nm. The lifetime of this state is 130 ps, in good agreement with the reported fluorescence lifetime. The excited state is reduced to the corresponding radical anion by KSCN or KI. The spectrum of the radical anion is in good agreement with previously reported pulse radiolysis studies and time-dependent density functional theory (TD-DFT) calculations. LFP of desoxytirapazamine (dTPZ) also produces the first excited singlet state, S1. The fluorescence quantum yield and lifetime (5.4 ns) of the dTPZ singlet excited state are both much greater than the corresponding values of TPZ. This is explained by DFT calculations that predict that cyclization of TPZ to form an oxaziridine is thermodynamically facile but that cyclization of dTPZ to form an oxadiaziridine is not. Thus, the S1 state of TPZ has a short lifetime and low fluorescence quantum yield due to ready cyclization whereas the cyclization of the S1 state of dTPZ is unimportant and does not limit either the fluorescence quantum yield or the fluorescence lifetime. This conclusion is confirmed by studies of dTPZ', an isomer of dTPZ containing the C=N-O moiety which has a low quantum yield and short fluorescence lifetime similar to that of TPZ.     

The fate of oxygen in the quenching of excited singlet states

Measurement of the efficiency of rubrene-sensitizied photooxidation of 1,3-diphenylisobenzofuran imply that direct formation of singlet oxygen via oxygen quenching of excited rubrene singlets is inefficient. This contrasts with recent publications based upon studies of self-sensitized rubrene photooxidation. The observed inefficiency can be rationalized in terms of the spin-allowed decay of an initially formed ³(T₁ + ¹Δ) complex state to a lower energy ³(T₁ + ³Σ) state prior to complex dissociation.     

Coupled-cluster studies of the lowest excited states of the 11-cis-retinal chromophore

The first few excited states of the 11-cis-retinal (PSB11) chromophore have been studied at the coupled-cluster approximative singles and doubles (CC2) level using triple-zeta quality basis sets augmented with double sets of polarisation functions. The two lowest vertical excitation energies of 2.14 and 3.21 eV are in good agreement with recently reported experimental values of 2.03 and 3.18 eV obtained in molecular beam measurements. Calculations at the time-dependent density functional theory (TDDFT) level using the B3LYP hybrid functional yield vertical excitation energies of 2.34 and 3.10 eV for the two lowest states. Zero-point vibrational energy (ZPVE) corrections of -0.09 and -0.17 eV were deduced from the harmonic vibrational frequencies for the ground and excited states calculated at the density functional theory (DFT) and TDDFT level, respectively, using the B3LYP hybrid functional.     

On the lower excited electronic states of biacetyl

An ab initio SCF and CI study has been carried out for the ground and electronically excited states of biacetyl (CH₃COCOCH₃). The second absorption band in the 4.40 eV region has been assigned to a ¹A_g → ¹B_g nπ^* transition The character of the lower-lying states has been analyzed in terms of the CI wavefunctions.     

On the lower excited electronic states of glyoxal

The polarization of both nπ* absorption bands of glyoxal has been measured in a glass matrix of 2-methyltetrahydrofuran by the photoselection method. The second absorption band in the 30 000 cm^?1 region has been assigned to a ¹A_g → ¹B_g nπ* transition. Its intensity is mainly induced by interaction with the solvent. An absorption band at about 43 000 cm^?1 has been ascribed to a charge transfer transition in complexes of glyoxal and 2-MTHF.     

Picosecond study of electronically excited singlet states of nucliec acid components,Chem. Phys. Letters 83(1981)276.

Time-resolved fluorescence spectroscopy in the nanosecond and picosecond regimes is used to investigate the dynamics of excimer formation in α-perylene crystals Relaxation into the totally relaxed excimer state occurs by thermal activation of the partially relaxed excimer state. The potential barrier height is 310 ± 30 cm^?1.     

Fluorescence-dip IR spectra of jet-cooled benzoic acid dimer in its ground and first excited singlet states

The IR spectra of three isotopomers of the benzoic acid dimer have been recorded under jet-cooled conditions using the double resonance method of fluorescence-dip IR spectroscopy. In so doing, the spectra are assuredly due exclusively to dimers in the ground-state zero-point level at a rotational temperature of 3-5 K. Even under these conditions, the three isotopomers have remarkably broad spectra, extending from 2600 to almost 3150 cm-1. The spectra show extensive substructure consisting of some 15-20 transitions where only a single OH stretch fundamental should appear in the harmonic limit. The comparison of the undeuterated d0-d0 dimer with the ring-deuterated d5-d5 dimer tests the effect of mixing with the C-H stretches and overtones of the C-H bends. The mixed OH/OD ring-deuterated d6-d5 dimer shifts the frequency and changes the form of the OH stretch normal mode. The analogous OH stretch IR spectrum of the d0-d0 dimer out of the S1 excited-state zero-point level has also been recorded. In this case, much of the closely-spaced substructure is not apparent. What remains is a set of three bands separated from one another by about 180 cm-1. Preliminary results of model calculations of the anharmonic coupling, responsible for the broadening and substructure, are presented. These calculations indicate that it is OH stretch-OH bend coupling, rather than coupling with the intermolecular stretch, that is responsible for much of the observed structure and breadth.     

Theoretical study of photoinduced singlet and triplet excited states of 4-dimethylaminobenzonitrile and its derivatives

Singlet and triplet low-lying states of the 4-dimethylaminobenzonitrile and its derivatives have been studied by the density functional theory and ab initio methodologies. Calculations reveal that the existence of the methyl groups in the phenyl ring and the amino twisting significantly modify properties of their excited states. A twisted singlet intramolecular charge-transfer state can be accessed through decay of the second planar singlet excited state with charge-transfer character along the amino twisting coordinate or by an intramolecular charge-transfer reaction involved with a locally first excited singlet state. Plausible charge-transfer triplet states and intersystem crossing processes among singlet and triplet states have been explored by spin-orbit coupling calculations. The intersystem crossing process was predicted to be the dominant deactivation channel of the photoexcited 4-dimethylaminobenzonitrile.     

Spectrometric evidence ford-orbital participation in the lowest excited singlet states of naphthalenethiols

Tellurium can be determined polarographically in the range 10^?5–10^?8M by means of the Te⁰_ads→Te^2- reduction in 1M perchloric acid as supporting electrolyte. Pulse polarography, a.c. polarography and linear sweep cyclic voltammetry can be used to determine tellurium in the p.p.b. range. Copper(II), arsenic(III) and selenium(IV) interfere, but the interferences can be overcome by a standard addition method.