UV resonance raman investigation of electronic transitions in alpha-helical and polyproline II-like conformations

UV resonance Raman (UVRR) excitation profiles and Raman depolarization ratios were measured for a 21-residue predominantly alanine peptide, AAAAA(AAARA) 3A (AP), excited between 194 and 218 nm. Excitation within the pi-->pi* electronic transitions of the amide group results in UVRR spectra dominated by amide vibrations. The Raman cross sections and excitation profiles provide information about the nature of the electronic transitions of the alpha-helix and polyproline II (PPII)-like peptide conformations. AP is known to be predominantly alpha-helical at low temperatures and to take on a PPII helix-like conformation at high temperatures. The PPII-like and alpha-helix conformations show distinctly different Raman excitation profiles. The PPII-like conformation cross sections are approximately twice those of the alpha-helix. This is due to hypochromism that results from excitonic interactions between the NV 1 transition of one amide group with higher energy electronic transitions of other amide groups, which decreases the alpha-helical NV 1 (pi-->pi*) oscillator strengths. Excitation profiles of the alpha-helix and PPII-like conformations indicate that the highest signal-to-noise Raman spectra of alpha-helix and PPII-like conformations are obtained at excitation wavelengths of 194 and 198 nm, respectively. We also see evidence of at least two electronic transitions underlying the Raman excitation profiles of both the alpha-helical and the PPII-like conformations. In addition to the well-known approximately 190 nm pi-->pi* transitions, the Raman excitation profiles and Raman depolarization ratio measurements show features between 205-207 nm, which in the alpha-helix likely results from the parallel excitonic component. The PPII-like helix appears to also undergo excitonic splitting of its pi-->pi* transition which leads to a 207 nm feature.     

The electronic structure and spectra of Ru(II) and Ru(III) complexes with imidazole and its derivatives

The calculations of the electronic structure and spectra of [Ru(NH3)5L]2+ (L = imidazole, histidine) and [Ru(NH3)5L]3+ (L = imidazole, N-imidazolate anion, 4-methylimidazole, 4-methyl-1N-imidazolate anion and 1N-bound histidine) complexes are performed in the framework of the CI method in the INDO/CNDO approximation. The MO diagram is obtained. The assignment of all transitions with energies of 4-5 eV is made and the nature of corresponding excited states is discussed. For the Ru(II) complexes, the lower energy observable transition is assigned to d-->pi* type, whereas the higher energy one is assigned to pi-->pi* type. In the spectra of the Ru(III) complexes with charged ligands both transitions are of pi-->d character, while in the case of uncharged ligands, the higher energy transition mostly incorporates pi-->pi* excitations.     

Influence of environment on the electronic structure of Cob(III)alamins: time-resolved absorption studies of the S(1) state spectrum and dynamics

Transient absorption spectroscopy has been used to elucidate the nature of the S1 intermediate state populated following excitation of cob(III)alamin (Cbl(III)) compounds. This state is sensitive both to axial ligation and to solvent polarity. The excited-state lifetime as a function of temperature and solvent environment is used to separate the dynamic and electrostatic influence of the solvent. Two distinct types of excited states are identified, both assigned to pi3d configurations. The spectra of both types of excited states are characterized by a red absorption band (ca. 600 nm) assigned to Co 3d --> 3d or Co 3d --> corrin pi* transitions and by visible absorption bands similar to the corrin pi-->pi* transitions observed for ground state Cbl(III) compounds. The excited state observed following excitation of nonalkyl Cbl(III) compounds has an excited-state spectrum characteristic of Cbl(III) molecules with a weakened bond to the axial ligand (Type I). A similar excited-state spectrum is observed for adenosylcobalamin (AdoCbl) in water and ethylene glycol. The excited-state spectrum of methyl, ethyl, and n-propylcobalamin is characteristic of a Cbl(III) species with a sigma-donating alkyl anion ligand (Type II). This Type II excited-state spectrum is also observed for AdoCbl bound to glutamate mutase. The results are discussed in the context of theoretical calculations of Cbl(III) species reported in the literature and highlight the need for additional calculations exploring the influence of the alkyl ligand on the electronic structure of cobalamins.     

The electronic absorption spectra of some acyl azides molecular orbital treatment

The electronic absorption spectra of benzoyl azide and its derivatives: p-methyl, p-methoxy, p-chloro and p-nitrobenzoyl azide were investigated in different solvents. The observed spectra differ basically from the electronic spectra of aryl azides or alkyl azides. Four intense pi-pi* transitions were observed in the accessible UV region of the spectrum of each of the studied compounds. The contribution of charge transfer configurations to the observed transitions is rather weak. Shift of band maximum with solvent polarity is minute. On the other hand, band intensity is highly dependent on the solvent used. The observed transitions are delocalized rather than localized ones as in the case with aryl and alkyl azides. The attachment of the CO group to the azide group in acyl azides has a significant effect on the electronic structure of the molecule. The arrangements as well as energies of the molecular orbitals are different in acyl azides from those in aryl azides. The first electronic transition in phenyl azide is at 276 nm, whereas that of bezoyle azide is at 251 nm. Ab initio molecular orbital calculations using both RHF/6-311G* and B3LYP/6-31+G* levels were carried out on the ground states of the studied compounds. The wave functions of the excited states were calculated using the CIS and the AM1-CI procedures.     

On the performance of quantum chemical methods to predict solvatochromic effects: the case of acrolein in aqueous solution

The performance of the Hartree-Fock method and the three density functionals B3LYP, PBE0, and CAM-B3LYP is compared to results based on the coupled cluster singles and doubles model in predictions of the solvatochromic effects on the vertical n-->pi* and pi-->pi* electronic excitation energies of acrolein. All electronic structure methods employed the same solvent model, which is based on the combined quantum mechanics/molecular mechanics approach together with a dynamical averaging scheme. In addition to the predicted solvatochromic effects, we have also performed spectroscopic UV measurements of acrolein in vapor phase and aqueous solution. The gas-to-aqueous solution shift of the n-->pi* excitation energy is well reproduced by using all density functional methods considered. However, the B3LYP and PBE0 functionals completely fail to describe the pi-->pi* electronic transition in solution, whereas the recent CAM-B3LYP functional performs well also in this case. The pi-->pi* excitation energy of acrolein in water solution is found to be very dependent on intermolecular induction and nonelectrostatic interactions. The computed excitation energies of acrolein in vacuum and solution compare well to experimental data.     

A new pathway for the rapid decay of electronically excited adenine

Combined density functional and multireference configuration interaction methods have been used to calculate the electronic spectrum of 9H-adenine, the most stable tautomer of 6-aminopurine. In addition, constrained minimum energy paths on excited potential energy hypersurfaces have been determined along several relaxation coordinates. The minimum of the first (1)[n-->pi*] state has been located at an energy of 4.54 eV for a nuclear arrangement in which the amino group is pyramidal whereas the ring system remains planar. Close by, another minimum on the S(1) potential energy hypersurface has been detected in which the C(2) center is deflected out of the molecular plane and the electronic character of S(1) corresponds to a nearly equal mixture of (1)[pi-->pi*] and (1)[n-->pi*] configurations. The adiabatic excitation energy of this minimum amounts to 4.47 eV. Vertical and adiabatic excitation energies of the lowest n-->pi* and pi-->pi* transitions as well as transition moments and their directions are in very good agreement with experimental data and lend confidence to the present quantum chemical treatment. On the S(1) potential energy hypersurface, an energetically favorable path from the singlet n-->pi* minimum toward a conical intersection with the electronic ground state has been identified. Close to the conical intersection, the six-membered ring of adenine is strongly puckered and the electronic structure of the S(1) state corresponds to a pi-->pi* excitation. The energetic accessibility of this relaxation path at about 0.1 eV above the singlet n-->pi* minimum is presumably responsible for the ultrafast decay of 9H-adenine after photoexcitation and explains why sharp vibronic peaks can only be observed in a rather narrow wavelength range above the origin. The detected mechanism should be equally applicable to adenosine and 9-methyladenine because it involves primarily geometry changes in the six-membered ring whereas the nuclear arrangement of the five-membered ring (including the N(9) center) is largely preserved.     

Calculations on the electronic excited states of ureas and oligoureas

We report CASPT2 calculations on the electronic excited states of several ureas. For monoureas, we find an electric dipole forbidden n --> pi* transition between 180 and 210 nm, dependent on the geometry and substituents of the urea. We find two intense pinb --> pi* transitions between 150 and 210 nm, which account for the absorptions seen in the experimental spectra. The n' --> pi* and pib --> pi* transitions are at wavelengths below 125 nm, which is below the lower limit of the experimental spectra. Parameter sets modeling the charge densities of the electronic transitions have been derived and permit calculations on larger oligoureas, using the exciton matrix method. For glycouril, a urea dimer, both the CASPT2 method and the matrix method yield similar results. Calculations of the electronic circular dichroism spectrum of an oligourea containing eight urea groups indicate that the experimental spectrum cannot be reproduced without the inclusion of electronic excitations involving the side chains. These calculations are one of the first attempts to understand the relationship between the structure and excited states of this class of macromolecule.     

Synthesis, characterization, crystal structure and DFT studies on 1-acetyl-3-(2,4-dichloro-5-fluoro-phenyl)-5-phenyl-pyrazoline

The title compound, 1-acetyl-3-(2,4-dichloro-5-fluoro-phenyl)-5-phenyl-pyrazoline, has been synthesized and characterized by elemental analysis, IR, UV-vis and X-ray single crystal diffraction. Density functional (DFT) calculations have been carried out for the title compound by using B3LYP method at 6-31G* basis set. The calculated results show that the predicted geometry can well reproduce the structural parameters. Predicted vibrational frequencies have been assigned and compared with experimental IR spectra and they are supported each other. The theoretical electronic absorption spectra have been calculated by using TD-DFT method. Molecular orbital coefficients analyses suggest that the above electronic transitions are mainly assigned to n-->pi* and pi-->pi* electronic transitions. On the basis of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations between C(p,m)(0),S(m)(0),H(m)(0) and temperatures.     

Electronic absorption spectra of benzoquinone and its hydroxy substituents and effect of solvents on their spectra

The electronic absorption spectra of 1,4-benzoquinone (BQ) and its 2,5-dihydroxy and tetrahydroxy derivatives have been studied in detail. The interpretation of the electronic bands is made on the basis of PPP and CNDO calculations. It is found that the pi --> pi* transitions are well predicted by the PPP method. The predictions of the CNDO method are however superior both in their accuracy as well as ability to predict the n --> pi* transitions. The effect of solvents on the electronic absorption bands have also been investigated in detail. Linear correlations are found between the solvent's dielectric constant and wavelength of the absorption bands. The solvent shifts are explained on the basis of the polarities of the solute and solvent molecules as well as due to hydrogen bonding.     

Absorption and fluorescence spectra of uracil in the gas phase and in aqueous solution: a TD-DFT quantum mechanical study

Here we present the first computations of fluorescence spectra in aqueous solution at an accurate quantum mechanical level. From a methodological point of view, our study shows that by only taking into account both bulk effects and explicit solvent molecules it is possible to reproduce solvent effects on the energy and the intensities of the electronic spectra, especially for what concerns pi/pi* transition. The computed absorption and fluorescence spectra are in a good agreement with the available experimental results. The energy ordering between the lowest energy n-pi* and the pi/pi* transitions in uracil strongly depends on the nature of the embedding medium. The geometry of the first solvation shell is remarkably sensitive to the specific electronic state, suggesting that solvent degrees of freedom can act as S1/S2 coupling modes.     

Ab initio n-electron valence state perturbation theory study of the adiabatic transitions in carbonyl molecules: formaldehyde, acetaldehyde, and acetone

The application of the recently developed second-order n-electron valence state perturbation theory (NEVPT2) to small carbonyl molecules (formaldehyde, acetaldehyde, and acetone) is presented. The adiabatic transition energies are computed for the singlet and triplet n-->pi(*), pi-->pi(*), and sigma-->pi(*) states performing a full geometry optimization of the relevant states at the single state CASSCF level and taking into account the zero point energy correction in the harmonic approximation. The agreement with the known experimental values and with previously published high level calculations confirms that NEVPT2 is an efficient tool to be used for the interpretation of molecular electronic spectra. Moreover, different insight into the nature of the excited states has been obtained. Some of the transitions presented here have never been theoretically computed previously [(3)(pi-->pi(*)) and (3)(sigma-->pi(*)) adiabatic transitions in acetaldehyde and acetone] or have been studied only using moderate level (single reference based) ab initio methods (all adiabatic transitions in acetaldehyde). In the present work a consistent disagreement between NEVPT2 and experiment has been found for the (3)(pi-->pi(*)) adiabatic transition in all molecules: this result is attributed to the low intensity of the transition to the first vibrational levels of the excited state. The n-->pi(*) singlet and triplet vertical transition energies are also reported for all the molecules.     

Absorption spectrum and solvatochromism of the [Ru(4,4'-COOH-2,2'-bpy)2(NCS)2] molecular dye by time dependent density functional theory

We present a combined Density Functional/Time Dependent Density Functional study of the molecular structure, electronic states, and optical absorption spectrum of [Ru(4,4'-COOH-2,2'-bpy)(2)(NCS)(2)], a widely used charge-transfer sensitizer in nanocrystalline TiO(2) solar cells. Calculations have been performed both for the complex in vacuo and in ethanol and water solvents, using a continuum model to account for solute-solvent interactions. Inclusion of the solvent leads to important changes of the energies and composition of the molecular orbitals of the complex; as a consequence, whereas the computed spectrum for the Ru-complex in vacuo deviates from the experimental one in both energy and shape, the spectra calculated in the presence of the solvent are in good agreement with the experiment. The first two absorption bands are found to originate from mixed ruthenium-NCS to bipyridine-pi* transitions rather than to pure metal-to-ligand-charge-transfer (MLCT) transitions, whereas the third band arises from intraligand pi --> pi* transitions. The experimentally observed blue-shift of the spectrum in water with respect to ethanol is well reproduced by our calculations and appears to be related to a decreased dipole moment in the excited state.     

Photochemical electron transfer reactions of tirapazamine

The absorption and fluorescence spectra of 3-aminobenzo-1,2,4-triazine di-N-oxide (tirapazamine) have been recorded and exhibit a dependence on solvent that correlates with the Dimroth ET30 parameter. Time-dependent density functional theory calculations reveal that the transition of tirapazamine in the visible region is pi-->pi* in nature. The fluorescence lifetime is 98+/-2 ps in water. The fluorescence quantum yield is approximately 0.002 in water. The fluorescence of tirapazamine is efficiently quenched by electron donors via an electron-transfer process. Linear Stern-Volmer fluorescence quenching plots are observed with sodium azide, potassium thiocyanate, guanosine monophosphate and tryptophan (Trp) methyl ester hydrochloride. Guanosine monophosphate, tyrosine (Tyr) methyl ester hydrochloride and Trp methyl ester hydrochloride appear to quench the fluorescence at a rate greater than diffusion control implying that these substrates complex with tirapazamine in its ground state. This complexation was detected by absorption spectroscopy.     

Spectral shifts of the n → π* and π → π* transitions of uracil based on a modified form of solvent reorganization energy

According to our recent studies on the nonequilibrium solvation, the solvent reorganization energy is found to be the cost of maintaining the residual polarization P', which equilibrates with the extra electric field E(ex). On the basis of this solvent reorganization energy and the well-established equilibrium solvation energy, a novel and reasonable expression for the spectral shift of the electronic absorption spectra is proposed in this work. Furthermore, the two lowest transitions of uracil in aqueous solution are investigated as test cases with the TDDFT/6-311++G** method. The obtained spectral shift is 0.48 eV for n → π* transition and -0.14 eV for π → π* transition, agreeing well with available experimental results. The contributions to the shift are discussed and the electrostatic plus polarization components are found to be crucial for the electronic absorption spectra of uracil in aqueous solution.     

Conformational energetics and excited state level ordering in 11-cis retinal.

Semiempirical molecular orbital theory and semiclassical solvent effect theory are used to analyze the conformational and electronic properties of the 12-s-cis and 12-s-trans conformers of 11-cis retinal. The goal is to examine the influence of solvent environment on the equilibrium geometries of these conformers as well as to provide a perspective on the electronic transitions that contribute to the four band systems that are observed in the 200-500 nm region of the optical spectrum. We conclude that the 12-s-cis isomer is more stable in vacuum, but that the 12-s-trans conformer is preferentially stabilized in both polar and nonpolar solvent environment due to dispersive as well as electrostatic interactions. This observation is in substantial agreement with previous literature results. In contrast, our analysis of the excited state manifold indicates that the spectral features observed in the absorption spectrum are associated with a complex set of overlapping transitions. A total of 18 pi*<--pi transitions contribute to the four bands, and in some cases, conformation changes the relative contribution of the individual transitions that define the overall band shape. This study provides the first definitive assignments for all four band systems.     

The guanine tautomer puzzle: quantum chemical investigation of ground and excited states

Combined density functional and multireference configuration interaction methods have been employed to explore the ground and low-lying electronically excited states of the most important tautomeric and rotameric forms of guanine with the purpose of resolving the conflicting assignments of IR-UV bands found in the literature. The calculations predict sharp 1(pi-->pi*) origin transitions for the RN1 rotamer of the 7H-amino-hydroxy species and the RN7 rotamer of the 9H-amino-hydroxy species. The other 9H-amino-hydroxy rotamer, RN1, undergoes ultrafast nonradiative decay and is thus missing in the UV spectra. Because of its very small Franck-Condon factor and the presence of a conical intersection close by, it appears questionable, whether the 1(pi-->pi*) origin transition of 9H-amino-oxo-guanine can be observed experimentally. Vibrational overlap is more favorable for the 1(pi-->pi*) origin transition of the 7H- amino-oxo form, but also this tautomer is predicted to undergo ultrafast nonradiative decay of the 1(pi-->pi*) population. The good agreement of calculated IR frequencies of the amino-oxo species with recent IR spectra in He droplets and their mismatch with peaks observed in IR-UV spectra indicate that none of the bands stem from 7H- or 9H-amino-oxo guanine. Instead, our results suggest that these bands originate from 7H-imino-oxo guanine tautomers. In the excited-state dynamics of the biologically relevant 9H-amino-oxo tautomer, a diffuse charge transfer state is predicted to play a significant role.     

Site-dependent spectral shifts in core-to-pi* excitations of pyridine clusters

Site- and element-selective core-to-pi* excitation in free pyridine clusters is investigated. The experimental results indicate the occurrence of site- and size-dependent spectral shifts in the C 1s and N 1s --> pi* excitation regime. Specifically, we observe in the C 1s regime a substantial and site-dependent redshift of the low energy slopes of the C 1s --> pi* band by 90 meV in clusters relative to the bare molecule, whereas the high energy slopes of this band remain almost unchanged. In contrast, a size-dependent blueshift of the same order of magnitude is found for the entire N 1s --> pi* band. This is distinctly different from previous results on van der Waals clusters, where exclusively redshifts in 1s --> pi* transitions are observed. The experimental results are compared to ab initio calculations, which serve to simulate the 1s --> pi*( v = 0) transitions. These results clearly indicate that the spectral shifts are primarily a result of electrostatic interactions between the molecular moieties and that an antiparallel orientation of molecular units preferably dominates in variable-size pyridine clusters.     

Application of density functional theory for studies of excited states and phosphorescence of platinum(II) acetylides

The electronic states of different conformations of platinum acetylides Pt(PH3)2(C[triple bond]C-Ph)2 and Pt(PH3)2(C[triple bond]C-PhC[triple bond]C-Ph)2 (PE1 and PE2) were calculated with density functional theory (DFT) using effective core potential basis sets. Time dependent DFT calculations of UV absorption spectra showed strong dependence of the intense absorption band maxima on mutual orientation of the phenyl rings with respect to the P-Pt-P axis. Geometry optimization of the first excited triplet state (T1) indicates broken symmetry structure with the excitation being localized in one ligand. This splits the two substitution ligands into a nondistorted aromatic ring with the C[triple bond]C-Ph bonds for one side and into a quinoid structure with a cumulenic C=C=C link on the other side. Quadratic response (QR) calculations of spin-orbit coupling and phosphorescence radiative lifetime (tauR) indicated a good agreement with experimental tauR values reported for solid PE1 and PE2 and PE2 capped with dendrimers in tetrahydrofuran solutions. The QR calculations reproduced an increase of tauR upon prolongation of pi chain of ligands and concommittant redshift of the phosphorescence. Moreover, it is shown how the phosphorescence borrows intensity from sigma-->pi* transitions localized at the C[triple bond]C-Pt-P fragments and that there is no intensity borrowing from delocalized pi-->pi* transitions.     

Electronic Absorption Spectra of Some 2-Thiouracil Derivatives

Abstract

The electronic absorption spectra of 2-thiouracil and some of its derivatives were investigated using polar and nonpolar solvents. The present analysis is facilitated via computer deconvolution of the observed spectra and molecular orbital (MO) computations. Comparison between the experimentally observed and theoretically computed spectra in addition to a quantitative assignment of all transitions observed were undertaken. The computed dipole moments are used to indicate the polarity of the excited state and hence predict its solvent dependence. The spectra are, in general, very well predicted and assigned using INDO/S computational results. The spectrum of the trifluoro derivative is much more complicated and the corresponding states show much more solvent dependence than those observed for other thiouracil studied.     

Syntheses and electronic spectroscopy of [PtL(L')][ClO4] complexes (HL = 6-phenyl-2,2'-bipyridine; L' = pyridine, 4-aminopyridine, 2-aminopyridine, and 2,6-diaminopyridine)

Four cyclometalated Pt(II) complexes, [PtL(L')][ClO4] [HL = 6-phenyl-2,2'-bipyridine; L' = pyridine (1), 4-aminopyridine (2), 2-aminopyridine (3), 2,6-diaminopyridine (4)], were designed and synthesized to probe intramolecular N...Pt interactions. The crystal structures of the compounds show that the pyridine ligands are almost perpendicular to the planes of the molecules. In addition, the pendant NH2 groups of the 2-aminopyridine and 2,6-diaminopyridine ligands are close to the metal centers in complexes 3 and 4, with the Pt-N(H2) distances (3.065(3)-3.107(3) A) significantly shorter than the sum of the van der Waals radii of Pt and N. These compounds were also studied by electronic spectroscopy. All the complexes display intense intraligand pi-->pi* transitions at 200-340 nm (epsilon = 10(4)-10(3) M-1 cm-1) and moderately intense (epsilon approximately 10(3) M-1 cm-1) metal (Pt)-to-ligand (pi*) charge-transfer (MLCT) transitions. For 1 and 2, the MLCT transitions occur at approximately 390 nm, but the MLCT transition of 4 is exceptionally low in energy (492 nm). The low-temperature emission spectra of the complexes in frozen EMD glass indicate that 3 pi pi* is the emissive excited state for 1 and 2 but the emission of 3 is from a 3MLCT excited state. On the basis of the spectroscopic results, the order of energy of the MLCT excited states is established as 1 approximately 2 > 3 > 4. It is proposed that the red shifts of the MLCT transitions in 3 and 4 are due to increased electron-donating abilities of the ancillary pyridine ligands and intramolecular interactions between the orbitals of amine nitrogen lone pairs. Crystal data for the complexes are as follows. 1: triclinic P1, Z = 2, a = 8.7917(2) A, b = 10.6398(3) A, c = 11.9592(3) A, alpha = 107.130(1) degrees, beta = 92.522(1) degrees, gamma = 111.509(1) degrees. 2.CH3CN: triclinic P1, Z = 2, a = 7.0122(4) A, b = 12.9653(8) A, c = 14.0283(9) A, alpha = 107.3100(10) degrees, beta = 102.7640(10) degrees, gamma = 91.6320(10) degrees. 3.CH3CN: triclinic P1, Z = 2, a = 7.6459(1) A, b = 10.8433(1) A, c = 14.8722(2) A, alpha = 99.383(1) degrees, beta = 93.494(1) degrees, gamma = 101.385(1) degrees. 4.CH3CN: triclinic P1, Z = 2, a = 7.862(2) A, b = 10.977(3) A, c = 14.816(5) A, alpha = 99.34(2) degrees, beta = 92.64(2) degrees, gamma = 104.11(2) degrees.