Charge-transfer transitions in protein circular dichroism calculations

Charge-transfer transitions in proteins play a key role in many biophysical processes, from the behavior of redox proteins to photochemical reactions. We present ab initio calculations on a model dipeptide and more approximate calculations of the electronic excited states of proteins which, taken together, provide the most definitive assignment and characterization of charge-transfer transitions in proteins to date. We have calculated from first principles the electronic circular dichroism (CD) spectra of 31 proteins on the basis of their structures. Compared to previous studies, we achieve more accurate calculated CD spectra between 170 and 190 nm, owing mainly to the importance in alpha-helices of a charge-transfer transition from the lone pair on one peptide group to the pi* orbital on the next peptide group.     

Synchrotron radiation circular dichroism spectroscopy of ribose and deoxyribose sugars, adenosine, AMP and dAMP nucleotides.

Synchrotron radiation circular dichroism (SRCD) spectra of ribose and deoxyribose sugars, adenosine, AMP and dAMP nucleotides and cyclic derivatives were measured in the vacuum ultraviolet region (down to 168 nm for sugars and 175 nm for adenine derivatives) and at different pH values (3, 6-7, 9-10) and temperatures (between 5 and 45 degrees C). The information content in the VUV region is important since the CD bands strongly depend on the chemical structure of the sugar, the presence and orientation of a phosphate group and the protonation state of adenine. On the other hand, single or double deprotonation of the phosphoric acid group has no influence on the spectra. We assign the vacuum ultraviolet (VUV) CD bands of the nucleoside and nucleotides to be due mainly to n-->pi* transitions in the adenine nucleobase based on a comparison with the absorption spectra. The CD bands of the sugars are due to n(O -->sigma*) transitions and are much smaller than the CD signal from the nucleotides in the VUV region. Bands are assigned to both pyranose and open-chain forms.     

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.     

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.     

Synchrotron radiation circular dichroism spectroscopy of proteins and applications in structural and functional genomics

The technique of Synchrotron Radiation Circular Dichroism (SRCD) spectroscopy and its advantages over conventional circular dichroism spectroscopy are described in this tutorial review, as well as recent applications of the technique in structural and functional genomics.Circular dichroism (CD) spectroscopy is a well-established method in biological chemistry and structural biology, but its utility can be limited by the low flux of the light source in the far ultraviolet and vacuum ultraviolet wavelength regions in conventional CD instruments. The development of synchrotron radiation circular dichroism (SRCD), using the intense light of a synchrotron beam, has greatly expanded the utility of the method, especially as a tool for both structural and functional genomics. These applications take advantage of the enhanced features of SRCD relative to conventional CD: the ability to measure lower wavelength data containing more electronic transitions and hence more structural information, the higher signal-to-noise hence requiring smaller samples, the higher intensity enabling measurements in absorbing buffers and in the presence of lipids and detergents, and the ability to do faster measurements enabling high throughput and time-resolved spectroscopy.This article discusses recent developments in SRCD instrumentation, software, sample preparation and methods of analyses, with particular emphasis on their applications to the study of proteins. These advances have led to new applications in structural genomics (SG), including the potential for fold recognition as a means of target selection and the examination of membrane proteins, a class of proteins usually excluded from SG programmes. Other SG uses include detection of macromolecular interactions as a screen for complex formation, and examination of glycoproteins and sugar components. In functional genomics (FG) new applications include screening for ligand binding as a means of identifying function, and examination of structural differences in mutant proteins as a means of gaining insight into function.     

Electronic transition dipole moment directions of reduced anionic flavin in stretched poly(vinyl alcohol) films

The IR and UV/vis linear dichroic spectra of reduced anionic flavin mononucleotide (FMNH-) partially oriented in poly(vinyl alcohol) (PVA) films have been measured to determine the direction of the major electronic transition dipole moments. The IR linear dichroism (LD) was measured in the 1750-1350 cm(-1) region to provide the overall molecular orientation of the FMNH- in the stretched films. Time-dependent density functional theory using the B3LYP functional was used to calculate the normal modes and the transition dipole moments of reduced lumiflavin. The calculated normal modes assisted in IR band assignments and in the determination of the IR transition dipole moment directions which were required for the determination of the orientation parameters for FMNH- in PVA films. The UV/vis LD spectrum was measured over the 200-700 nm region and was resolved into contributions from three pi-->pi* transitions. The directions of the transitions are 90 degrees+/-4 degrees at 440 nm, 79 degrees+/-4 degrees at 350 nm, and 93 degrees+/-4 degrees at 290 nm with counterclockwise rotations with respect to the N5-N10 axis. Comparison of the calculated and experimentally determined transition dipole moments allowed for refined assignment of the transition dipole moment directions. To our knowledge, this is the first experimental evidence that the 350-450 nm absorption arises from two unique transitions. Remarkably, the two lowest energy transition dipole moments for FMNH- are nearly parallel to those obtained in prior studies for both oxidized and semiquinone flavin.     

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.     

Environment-controlled interchromophore charge transfer transitions in dipeptides probed by UV Absorption and electronic circular dichroism spectroscopy

Charge transfer (CT) transitions between the C-terminal carboxylate and peptide group have been investigated for alanyl-X and X-alanine dipeptides by far-UV absorption and electronic circular dichroism (ECD) spectroscopy (where X represents different amino acid residues). The spectra used in the present study were obtained by subtracting the spectrum of the cationic species from that of the corresponding zwitterionic peptide spectrum. These spectra displayed three bands, e.g., band I between 44 and 50 kK (kK = 10(3) cm(-1)), band II at 53 kK, and band III above 55 kK, which were, respectively, assigned to a n(COO-) --> pi* CT transition, a pi(COO-) --> pi* CT transition, and a carboxylate pi --> pi* (NV1) transition, respectively By comparison of the intensity, bandwidth, and wavenumber position of band I of some of the investigated dipeptides, we found that positive charges on the N-terminal side chain (for X = K), and to a minor extent also the N-terminal proton, reduce its intensity. This can be understood in terms of attractive Coulomb interactions that stabilize the ground state over the charge transfer state. For alanylphenylalanine, we assigned band I to a n(COO-) --> pi* CT transition into the aromatic side chain, indicating that aromatic side chains interact electronically with the backbone. We also performed ECD measurements at different pH values (pH 1-6) for a selected subset of XA and AX peptides. By subtraction of the pH 1 spectrum from that observed at pH 6, the ECD spectrum of the CT transition was obtained. A titration curve of their spectra reveals a substantial dependence on the protonation state of the aspartic acid side chain of AD, which is absent in DA and AE. This most likely reflects a conformational transition of the C-terminus into a less extended state, though the involvement of a side chain --> peptide CT transition cannot be completely ruled out.     

Novel chiral pyromellitdiimide (1,2,4,5-benzenetetracarboxydiimide) dimers and trimers: exploring their structure,electronic transitions,and exciton coupling

The chiral but highly symmetrical acyclic and cyclic pyromellitic diimide dimers and trimers 2-5 have been obtained and characterized for the first time. The pyromellitdiimide chromophores in these molecules are linked by a rigid diequatorially 1,2-disubstituted cyclohexane skeleton. The structures of the compounds have been determined in detail by molecular modeling and, in the case of cyclic dimer 4 and trimer 5, by means of X-ray diffraction analysis. The electronically excited states of the pyromellitdiimide chromophore (1a) have been studied in these and other model compounds by means of linear dichroism (LD), magnetic circular dichroism (MCD), and circular dichroism (CD) spectroscopy. CD spectra of the rigid cyclic trimer 5 have provided the most detailed information on the excited states of the pyromellitdiimide chromophore. The low-energy tail (340-360 nm) of the absorption envelope can be assigned to out-of-plane polarized n-pi* transitions (I, II). The higher energy bands are due to contributions from up to six pi-pi* transitions, these being polarized either along the long (IV-VI, VIII) or short axis (III, VII). The results of ab initio CIS/cc-pVDZ and semiempirical INDO/S-CI calculations have been compared with the experimental data. CD Cotton effects in the region 200-260 nm, which result from exciton interactions between electric dipole allowed transitions of two pyromellitdiimide chromophores in compounds 2-5, provide reliable and useful information concerning the conformation and absolute configuration of these molecules, which may be extrapolated to other oligoimide systems.     

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.     

Optical absorption of 1H-pyrazolo[3,4-b]quinoline and its derivatives

The results of experimental studies and quantum chemical simulations of the absorption spectra of 1H-pyrazolo[3,4-b]quinoline and its derivatives are presented. The quantum chemical calculations (semi-empirical AM1 and PM3 methods) show similarity in the absorption spectra of 1H-pyrazolo[3,4-b]quinoline and 1,3-dimethyl-1H-pyrazolo[3,4-b]quinoline which are characterized by five strong absorption bands in the spectral range 200-500 nm. A substitution of the methyl groups by at least one phenyl group causes the drastic changes of the absorption spectra mainly within the spectral range 240-370 nm. We attribute these differences to additional molecular double bonding segments C=C of the substituted phenyl groups, i.e. to pi --> pi* transitions. A comparison of measured and the calculated absorption spectra manifests quite satisfactory agreement for all compounds in the part regarding the spectral position of the first oscillator (absorption threshold). At the same time, the measured spectra demonstrate the considerable broadening practically of all absorption bands and even complete damping some of them in the case of phenyl derivatives. The experiments performed with highly and weakly polar organic solvents shows that the solvent effect on the absorption spectra is small. For this reason the discrepancies between the calculated and the measured spectra are attributed to electron-vibronic coupling as well as to rotational dynamics of phenyl rings.     

Circular and linear dichroism of proteins

Circular dichroism (CD) is an important technique in the structural characterisation of proteins, and especially for secondary structure determination. The CD of proteins can be calculated from first principles using the so-called matrix method, with an accuracy which is almost quantitative for helical proteins. Thus, for proteins of unknown structure, CD calculations and experimental data can be used in conjunction to aid structure analysis. Linear dichroism (LD) can be calculated using analogous methodology and has been used to establish the relative orientations of subunits in proteins and protein orientation in an environment such as a membrane. However, simple analysis of LD data is not possible, due to overlapping transitions. So coupling the calculations and experiment is an important strategy. In this paper, the use of LD for the determination of protein orientation and how these data can be interpreted with the aid of calculations, are discussed. We review methods for the calculation of CD spectra, focusing on semiempirical and ab initio parameter sets used in the matrix method. Lastly, a new web interface for online CD and LD calculation is presented.     

Luminescent alkynylplatinum(II) complexes of 2,6-bis(N-alkylbenzimidazol-2'-yl)pyridine-type ligands with ready tunability of the nature of the emissive states by solvent and electronic property modulation

A new class of luminescent alkynylplatinum(II) complexes of tridentate bis(N-alkylbenzimidazol-2'-yl)pyridines (bzimpy), [Pt(R,R'-bzimpy)(C[triple chemical bond]C-R')]X (X=PF(6), OTf), and one of their chloro precursor complexes, [Pt(R,R'-bzimpy)Cl]PF(6), have been synthesized and characterized; one of the alkynyl complexes has also been structurally characterized by X-ray crystallography. Electrochemical studies showed that the oxidation wave is alkynyl ligand-based in nature with some mixing of the metal center-based contribution, whereas the two quasi-reversible reduction couples are mainly bzimpy-based reductions. The electronic absorption and luminescence properties of the complexes have also been investigated. In solution, the high-energy and intense absorption bands are assigned as the pi-pi* intraligand (IL) transitions of the bzimpy and alkynyl ligands, whereas the low-energy and moderately intense absorptions are assigned to an admixture of metal-to-ligand charge-transfer (MLCT) (dpi(Pt)-->pi*(R,R'-bzimpy)) and ligand-to-ligand charge-transfer (LLCT) (pi(C[triple chemical bond]C-R')-->pi*(R,R'-bzimpy)) transitions. Upon variation of the electronic effects of the arylalkynyl ligands, vibronic-structured or structureless emission bands, originating from triplet metal-perturbed intraligand (IL) or an admixture of triplet metal-to-ligand charge-transfer (MLCT) and ligand-to-ligand charge-transfer (LLCT) excited states respectively, were observed in solution. Interestingly, two of the complexes showed a dual luminescence that was sensitive to the polarity of the solvents. Upon cooling from 298 K to 155 K, drastic color, UV/Vis, and luminescence changes were observed in a butyronitrile solution of 1, and were ascribed to the formation of aggregate species through PtPt and pi-pi stacking interactions. DFT and time-dependent DFT (TD-DFT) calculations have been performed to verify and elucidate the results of the electrochemical and photophysical properties.     

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.     

Ab initio calculation of the vibrational and electronic spectra of trans- and cis-azobenzene

We report accurate geometries and harmonic force fields for trans- and cis-azobenzene determined by second-order M?ller-Plesset perturbation theory. For the trans isomer, the planar structure with C(2h) symmetry, found in a recent gas electron diffraction experiment, is verified. The calculated vibrational spectra are compared with experimental data and density functional calculations. Important vibrational frequencies are localized and discussed. For both isomers, we report UV spectra calculated using the second-order approximate coupled-cluster singles-and-doubles model CC2 with accurate basis sets. Vertical excitation energies and oscillator strengths have been determined for the lowest singlet n(pi)* and (pi)(pi)* transitions. The results are compared with the available experimental data and second-order polarization propagator (SOPPA) and density functional (DFT) calculations. For both isomers, the CC2 results for the excitation energies into the S(1) and S(2) states agree within 0.1 eV with experimental gas-phase measurements.     

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.     

Charge transfer in the Cl-CO cluster induced by core ionization

Ab initio calculations of core-ionization spectra of the anion-molecule Cl-CO cluster are performed. Particular attention is paid to the investigation of charge-transfer screening processes accompanying core ionization of the CO molecule in the cluster. The charge-transfer processes are very efficient and favored by the presence of a low-lying unoccupied pi* orbital in CO capable of accepting an electron from Cl-. The O1s(-1) and C1s(-1) core-ionization spectra are calculated and compared. Both reveal a breakdown of the quasiparticle picture of core ionization caused by the charge-transfer processes. Remarkable differences between these two spectra are found which manifest themselves in distinct intensity distributions in the prominent low-energy spectral bands. The underlying reason for these differences is elucidated and linked with the preference of the pi* orbital to localize mainly on carbon. Core-ionization spectra of anion-molecule clusters are very sensitive to the type of the molecule involved as the comparative analysis of the O1s(-1) core-ionization spectra of the Cl-CO and Cl-H(2)O clusters show.     

Electrochemical and spectroscopic characterization of the novel charge-transfer ground state in diimine complexes of ytterbocene

The novel charge-transfer ground state found in alpha,alpha'-diimine adducts of ytterbocene (C(5)Me(5))(2)Yb(L) [L = 2,2'-bipyridine (bpy) and 1,10-phenanthroline (phen)] in which an electron is spontaneously transferred from the f(14) metal center into the lowest unoccupied (pi*) molecular orbital (LUMO) of the diimine ligand to give an f(13)-L(*)(-) ground-state electronic configuration has been characterized by cyclic voltammetry, UV-vis-near-IR electronic absorption, and resonance Raman spectroscopies. The voltammetric data demonstrate that the diimine ligand LUMO is stabilized and the metal f orbital is destabilized by approximately 1.0 V each upon complexation for both bpy and phen adducts. The separation between the ligand-based oxidation wave (L(0/-)) and the metal-based reduction wave (Yb(3+/2+)) in the ytterbocene adducts is 0.79 V for both bpy and phen complexes. The UV-vis-near-IR absorption spectroscopic data for both the neutral adducts and the one-electron-oxidized complexes are consistent with those reported recently, but previously unreported bands in the near-IR have been recorded and assigned to ligand (pi*)-to-metal (f orbital) charge-transfer (LMCT) transitions. These optical electronic excited states are the converse of the ground-state charge-transfer process (e.g., f(13)-L(*-) <--> f(14)-L(0)). These new bands occur at approximately 5000 cm(-1) in both adducts, consistent with predictions from electrochemical data, and the spacings of the resolved vibronic bands in these transitions are consistent with the removal of an electron from the ligand pi* orbital. The unusually large intensity observed in the f --> f intraconfiguration transitions for the neutral phenanthroline adduct is discussed in terms of an intensity-borrowing mechanism involving the low-energy LMCT states. Raman vibrational data clearly reveal resonance enhancement for excitation into the low-lying pi* --> pi* ligand-localized excited states, and comparison of the vibrational energies with those reported for alkali-metal-reduced diimine ligands confirms that the ligands in the adducts are reduced radical anions. Differences in the resonance enhancement pattern for the modes in the bipyridine adduct with excitation into different pi* --> pi* levels illustrate the different nodal structures that exist in the various low-lying pi* orbitals.     

Circular dichroism, optical rotation and absolute configuration of 2-cyclohexenone-cis-diol type phenol metabolites: redefining the role of substituents and 2-cyclohexenone conformation in electronic circular dichroism spectra

The absolute configurations of 2-cyclohexenone cis-diol metabolites resulting from the biotransformation of the corresponding phenols have been determined by comparison of their experimental and calculated circular dichroism spectra (TDDFT at the PCM/B2LYP/Aug-cc-pVTZ level), optical rotations (calculated at the PCM/B3LYP/Aug-cc-pVTZ level) and by stereochemical correlation. It is found that circular dichroism spectra and optical rotations of 2-cyclohexenone derivatives are strongly dependent on the ring conformation (M or P sofa S(5) or half-chair), enone non-planarity and the nature and positions of the hydroxy and alkyl substituents. The effect of non-planarity of the enone chromophore, including the distortion of the C=C bond, is determined for the model structures by TDDFT calculations at the PCM/B2LYP/6-311++G(2d,2p) level. Non-planarity of the C=C bond in the enone chromophore is commonly encountered in 2-cyclohexenone derivatives and it is a source of significant rotatory strength contribution to the electronic circular dichroism spectra. It is shown that the two lowest-energy transitions in acrolein and 2-cyclohexenone and its derivatives are n(C=O)-π(C=O)* and π(C=C)-π(C=O)*, as expected, while the shorter-wavelength (below 200 nm) transitions are of more complex nature. In 2-cyclohexenone and its alkyl derivatives it is predominantly a mixture of π(C=C)-π(C=C)* and π(C=C)-σ* transitions, whereas the presence of hydroxy substituent results in a dominant contribution due to the n(OH)-π(C=O)* transition. A generalized model for correlation of the CD spectra of 2-cyclohexenones with their structures is presented.