Interpretation of synchrotron radiation circular dichroism spectra of anionic, cationic, and zwitterionic dialanine forms

Electronic absorption and synchrotron radiation circular dichroism (SRCD) spectra of the anionic, cationic, and zwitterionic forms of L-alanyl-L-alanine (AA) in aqueous solutions were measured and interpreted by molecular dynamics (MD) and ab initio computations. Time-dependent density functional theory (TD DFT) was applied to predict the electronic excited states. The modeling enabled the assessment of the role of molecular conformation, charge, and interaction with the polar environment in the formation of the spectral shapes. Particularly, inclusion of explicit solvent molecules in the computations appeared to be imperative because of the participation of water orbitals in the amide electronic structure. Implicit dielectric continuum solvent models gave inferior results for clusters, especially at low-energy transitions. Because of the dispersion of transition energies, tens of water/AA clusters had to be averaged in order to obtain reasonable spectral shapes with a more realistic inhomogeneous broadening. The modeling explained most of the observed differences, as the anionic and zwitterionic SRCD spectra were similar and significantly different from the cationic spectrum. The greatest deviation between the experimental and theoretical curves observed for the lowest-energy negative anion signal can be explained by the limited precision of the TD DFT method, but also by the complex dynamics of the amine group. The results also indicate that differences in the experimental spectral shapes do not directly correlate with the peptide main-chain conformation. Future peptide and protein conformational studies based on circular dichroic spectroscopy can be reliable only if such effects of molecular dynamics, solvent structure, and polar solvent-solute interactions are taken into account.     

秋水仙碱立体异构体电子结构及圆二色谱性质的理论研究

采用量子化学密度泛函理论(DFT)在B3LYP/6-311++G二水平上对秋水仙碱四个立体异构体分子几何构型进行了优化,在优化的基础上进行了振动圆二色谱(VCD),紫外-可见光谱(UV-Vis)和电子圆二色谱(ECD)研究.为模拟真实条件,以水为溶剂,计算其对分子电子结构和光谱性质的影响.研究结果表明:秋水仙碱四个立体...     

Ab initio modeling of the electronic circular dichroism induced in porphyrin chromophores

The optical activity in porphyrins can easily be induced by a chiral environment, but it is difficult to determine the underlying mechanisms purely on an experimental basis. Therefore, in this study, magnitudes of the perturbational, dipolar, and direct covalent contributions to the electronic circular dichroism (CD) are evaluated with the aid of quantum chemical computations. Electronic properties of model porphyrin chromophores are analyzed. Time-dependent density functional theory (TD DFT), particularly with the hybrid B3LYP functional, appeared suitable for estimation of the electronic excitation energies and spectral intensities. The transition dipole coupling (TDC) between chirally stacked porphyrins was determined as the most important mechanism contributing to their optical activity. This is in agreement with previous experimental observations, where chiral matrices often induce the stacking and large CD signals. About a 10 times smaller signal could be achieved by a chiral orientation of the phenyl or similar residues covalently attached to the porphyrin core. Also, this prediction is in agreement with known experiments. Perturbation models realized by a chirally arranged porphyrin and a point charge, or by a porphyrin and the methane molecule, provided the smallest CD signals. The electrically neutral methane induced similar CD magnitudes as those of the charge, but spectral shapes were different. For a complex of porphyrin and the alanine cation, a significant influence of the solvent on the resultant CD spectral shape was observed, while for the charge and methane perturbations, a negligible solvent effect was found. Detailed dependence of the induced optical activity on variations of geometrical parameters is discussed. The simulations of the induced porphyrin activity can thus bring important information about the structure and intermolecular interactions in chiral complexes.     

Synthesis and chiroptical properties of cryptophanes having C1-symmetry

New enantiopure cryptophanes 3-7 having C(1)-symmetry have been synthesized. Electronic circular dichroism (ECD) and vibrational circular dichroism (VCD) have been used to investigate their chiroptical properties, and the results are compared to those obtained for cryptophane-A (1) having D(3)-symmetry. The ECD spectra of compounds 3-7 show Cotton effects that differ from those of cryptophane-A. However, our results suggest that a confident determination of the absolute configuration of the monofunctionalized cryptophanes can be made using ECD spectroscopy. Interestingly, we have found that the ECD spectra of cryptophanes, especially the (1)L(b) transition, are very sensitive to the nature of the solvent. These spectral modifications are essentially due to bulk solvent properties rather than the ability of a particular solvent to insert into the cavity of cryptophanes. On the other hand, VCD spectra of the monofunctionalized cryptophanes have not revealed significant spectral modifications with respect to the VCD spectrum of the CHCl(3) at cryptophane-A complex, except for CHCl(3) at 7 and to a smaller extent for CHCl(3) at 6. These spectral modifications, which essentially consist in lower intensities of VCD bands associated with the cryptophane backbone, were perfectly reproduced by ab initio calculations performed at DFT (B3PW91/6-31G*) level. These results clearly demonstrate that VCD measurements associated with DFT calculations allow an easy determination of the absolute configuration of cryptophane-A derivatives.     

Electronic structure, spectra, and magnetic circular dichroism of cyclohexa-, cyclohepta-, and cyclooctapyrrole

Three recently obtained expanded porphyrins represent nice examples of compounds for which the electronic and spectral properties can be predicted from symmetry considerations alone. Perimeter-model-based theoretical analysis of the electronic structure of doubly protonated cyclo[6], cyclo[7], and cyclo[8]pyrrole leads to the anticipation of qualitatively the same electronic absorption and magnetic circular dichroism patterns for all three compounds. These predictions are fully confirmed by experiments, as well as DFT and INDO/S calculations. Due to a characteristic pattern of frontier molecular orbitals, a degenerate HOMO and a strongly split LUMO pair, the three cyclopyrroles show comparable absorption intensity in the Q and Soret regions. Magnetic circular dichroism spectra reveal both A and B Faraday terms, of which the signs and magnitudes are in remarkably good agreement with theoretical expectations. The values of the magnetic moments of the two lowest degenerate excited states have also been obtained.     

Ab initio study of the two-photon circular dichroism in chiral natural amino acids

Two-photon circular dichroism spectra calculated within an origin-invariant density functional theory approximation in the absorption region where the lowest electronic excited states appear are presented for all 19 essential amino acids in the gas phase. A comparison of intensities and characteristic features is made with the corresponding two-photon absorption and one-photon circular dichroism spectra for each species. Also, the contributions of the electric dipole, magnetic dipole, and electric quadrupole transitions to the rotational strengths are analyzed in some detail. The remarkable fingerprinting capabilities of the two-photon circular dichroism spectroscopy are highlighted.     

Electronic spectroscopy and computational studies of glutathionylco(III)balamin

We have studied glutathionylcobalamin (GS-Cbl) by optical spectroscopy and with density functional theory (DFT) and time-dependent DFT (TD-DFT) electronic structure methods of truncated geometric models. We examined the geometric structure of the models by comparison of DFT calculations with recent high-resolution experimental X-ray structure data ( Hannibal, L. et al. Inorg. Chem. 2010, 49, 9921) for GS-Cbl, and we examined the TD-DFT excitation simulations by comparison of the models with measured optical spectra. The calculations employed the B3LYP hybrid functional and the nonhybrid BP86 functional in both vacuum and water (conductor polarized continuum model (cpcm)) with the 6-311G(d,p) basis set. The optimized geometric structure calculations for six truncated models were made by varying the chemical structure, solvent model, and the two DFT functionals. All showed similar geometry. Charge decomposition analysis (CDA) and extended charge decomposition analysis (ECDA), especially with BP86 shows the similar charge transfer nature of the Co-S bond in GS-Cbl and the Co-C bond in CH(3)Cbl. Mayer and Wiberg bond orders illustrate the similar covalent nature of the two bonds. Finally, absolute optical spectral simulation calculations were compared with the experimental UV-visible extinction spectrum and the electronic circular dichroism (ECD) differential extinction spectrum. The BP86 method shows more spectral features, and the best fit was found for a GS-Cbl model with 5,6-dimethylbenzimidazole at the BP86/6-311G(d,p) level with a water cpcm solvent model. The excited state transitions were investigated with Martin's natural transition orbitals (NTOs). The BP86 calculations also showed π bonding interactions between Co and the axial S of the GS- ligand in the molecular orbitals (MOs) and NTOs.     

Ab initio study of the one- and two-photon circular dichroism of R-(+)-3-methyl-cyclopentanone

One- and two-photon circular dichroism spectra of R-(+)-3-methyl-cyclopentanone, a system that has been the subject of recent experimental studies of (2+1) resonance-enhanced multiphoton ionization circular dichroism, have been calculated with an origin-invariant density functional theory approximation in the region of the lowest electronic excited states, both for the gas phase and for a selection of solvents. A polarizable continuum model is used in the calculations performed on the solvated system. Two low-lying conformers are analyzed, and a comparison of the intensities and characteristic features is made with the corresponding two-photon absorption for each species, also for the Boltzmann-averaged spectra. The effect of the choice of geometry, basis set, and exchange-correlation functional is carefully analyzed. It is found that a density functional theory approach using the Coulomb attenuating method variant of Becke's three-parameter exchange and the Lee-Yang-Parr correlation functionals with correlation-consistent basis sets of double-zeta quality can reproduce the experimental electronic circular dichroism spectra very well. The features appearing in experiment are characterized in terms of molecular excitations, and the differences in the response of each state in the one- and two-photon processes are highlighted.     

TDDFT Study of the Electronic Structure,Absorption and Emission Spectra of the Light Emitters of the Amazing Firefly Bioluminescence and Solvation Effects on the Spectra

The ground and excited state properties of luciferin (LH₂) and oxyluciferin (OxyLH₂), the bioluminescent chemicals in the firefly, have been characterized using density functional theory (DFT) and time dependent DFT (TDDFT) methods. The effects of solvation on the electronic absorption and emission spectra of luciferin and oxyluciferin were predicted with a self‐consistent isodensity polarized continuum model of the solvent using TDDFT. The S₀→S₁ vertical excitation energies in the gas phase and in water were obtained. Optimizations of the excited state geometries permitted the first predictions of the fluorescence spectra for these biologically important molecules. Shifts in both of the absorption and emission spectra on proceeding from the gas phase to aqueous solution were also predicted.     

Unveiling electronic transitions in three novel chiral azo-compounds using linear and nonlinear circular dichroism: a theoretical-experimental study

Herein, we report on the experimental and theoretically study of the linear absorption, electronic circular dichroism (ECD) spectra, as well as the two-photon absorption circular-linear dichroism measurements of three different chiral azo derivatives in dimethylsulfoxide solution. Using potential energy surfaces and frontier orbital analysis, we established the most stable conformation for each molecule and elucidated their different electronic transitions. Our theoretical calculations allowed us to unambiguously identify the spectral position of such transitions and correlate them with the spectral profiles observed in the two-photon absorption spectra. To further elucidate the characteristics of the main electronic transitions in terms of spectral shape and position, we carried out measurements of the polarization dependent two-photon absorption cross sections and determined the two-photon circular-linear dichroism spectra of these azo dyes.     

The electronic structure and spectra of spin-triplet ground state bis(biuretato)cobalt(III) coordination compounds

The planar coordination compounds of cobalt(III) with bis(biuretato) ligands are highly unusual due to their intermediate spin triplet ground state. Density functional theory (DFT) and time-dependent DFT have been applied in a study of the structure and electronic spectroscopy of this type of coordination compounds. The investigations included prediction and spectroscopic measurements of the absorption and circular dichroism (CD), as well as an experimental study of the magnetic CD. The results obtained by TD-DFT were in excellent agreement with the observed spectral features, both regarding the d-d and the charge transfer regions. There was noted a systematic blue-shift of the TD-DFT results compared to experiment, corresponding to an offset of ca. 0.5 microm(-1) and a scaling factor of 1.25 for the transition energies. The DFT results are rationalized in terms of a qualitative MO analysis.     

Atropisomers of hindered triarylisocyanurates: structure, conformation, stereodynamics, and absolute configuration

The syn and anti diastereoisomers of some 1,3,5-triarylisocyanurate derivatives were isolated and their configuration assigned by NOE experiments and by X-ray diffraction. The kinetics of the syn/anti interconversion were determined, and the experimental activation energies matched satisfactorily the values predicted by DFT computations. Low-temperature NMR spectra were employed to determine the rotation barrier of N-bonded unhindered aryl substituents: these barriers, too, are satisfactorily reproduced by DFT computations. In the case of racemic diastereoisomers, the two expected enantiomers (atropisomers) were isolated by enantioselective HPLC and the absolute configuration established by DFT simulation of the electronic and vibrational circular dichroism spectra.     

Comparison of the Electronic and Vibrational Optical Activity of a Europium(III) Complex

The geometry and the electronic structure of chiral lanthanide(III) complexes are traditionally probed by electronic methods, such as circularly polarised luminescence (CPL) and electronic circular dichroism (ECD) spectroscopy. The vibrational phenomena are much weaker. In the present study, however, significant enhancements of vibrational circular dichroism (VCD) and Raman optical activity (ROA) spectral intensities were observed during the formation of a chiral bipyridine–Eu^III complex. The ten‐fold enhancement of the vibrational absorption and VCD intensities was explained by a charge‐transfer process and the dominant effect of the nitrate ion on the spectra. A much larger enhancement of the ROA and Raman intensities and a hundred‐fold increase of the circular intensity difference (CID) ratio were explained by the resonance of the λ=532 nm laser light with the ⁷F₀ → ⁵D₀ transitions. This phenomenon is combined with a chirality transfer, and mixing of the Raman and luminescence effects involving low‐energy ⁷F states of europium. The results thus indicate that the vibrational optical activity (VOA) may be a very sensitive tool for chirality detection and probing of the electronic structure of Eu^III and other coordination compounds.     

Definitive assignments of the visible-near-IR bands of porphyrin-naphthalocyanine rare-earth sandwich double- and triple-decker compounds by magnetic circular dichroism spectroscopy

A series of heteroleptic rare-earth sandwich complexes [M(Nc)(OEP)] (M = La, Nd, Eu, Dy, and Lu; Nc = 2,3-naphthalocyaninate; OEP = octaethylporphyrinate) have been investigated by electronic absorption and magnetic circular dichroism (MCD) spectroscopy. The electronic absorption spectra of the neutral forms showed two characteristic transitions (bands I and II) in the near-IR region, both of which were systematically shifted depending on the size of their central metal. In the MCD spectra, a relatively intense Faraday A term and a significantly weak Faraday B term have been observed corresponding to bands II and I, respectively. The spectral features were successfully interpreted using a simple MO model by considering the relevant interactions of Gouterman's four orbitals of the constituent chromophores. The model succeeded in assigning the MCD spectra of the related compounds, the oxidized and reduced forms of the dimer ([M(Nc)(OEP)]+ and [M(Nc)(OEP)]-), and neutral forms of the triple-decker compounds (M2(Nc)(OEP)2, M = Nd, Eu). DFT calculations of the dimers supported the validity of this model.     

Vibrational spectral simulation for peptides of mixed secondary structure: method comparisons with the Trpzip model hairpin

Infrared absorption and vibrational circular dichroism (IR and VCD) spectra of model fragments of TrpZip-style beta-hairpin structures are simulated using density functional theory (DFT) methods to estimate the influence of fragment size, end effects, conformational irregularities, peptide side chains, and solvent. Different fragmentation schemes, computing the strands and turn segments separately, were tested by varying the sizes of each and their respective overlaps. For suitably overlapping fragments, atomic property tensors were found to be reliably transferable, as tested by their ability to generate simulated spectra in good agreement with results from ab initio DFT computations for the entire peptide. This fragment approach significantly reduces computational times and opens up a wider range of systems that can be studied with a DFT-based approach as compared to previous methods based on uniform repeating sequences. However, vacuum calculations do not adequately represent the frequency dispersion of solvated molecules, and thus, some alternate strategies for solvation correction are explored for improving the simulation accuracy. Unlike for regular periodic secondary structure, the solvent significantly impacts the spectral shapes of hairpins, due to the different degrees of hydration of individual amide groups, which can be exposed to or shielded from water due to external vs internal hydrogen bonding. This is amplified by the shielding of selected amides from the solvent due to bulky side chains. The peptide plus solvent was structurally modeled with molecular dynamics methods, and then an electrostatic field-based parametrization correction was added to the force field and intensity tensors to compensate for the solvent dipolar field. The effect of the shielding and subsequent reordering of modes has a larger impact on VCD than IR band shapes.     

DNA oligonucleotide-cis-platin binding: Ab initio interpretation of the vibrational spectra

The cis-platin binding to the d(CCTGGTCC)*d(GGACCAGG) model DNA octamer was monitored with infrared absorption (IR) and vibrational circular dichroism (VCD) spectroscopies. The spectra were modeled with the aid of density functional computations and a Cartesian coordinate-based transfer of molecular property tensors from smaller DNA fragments. Because of the fragmentation, the tensors could be calculated with a higher precision. Environmental effects, such as the presence of the solvent or the cis-platin ligand, could be included in the modeling. The solvent was modeled by an explicit inclusion of hydrogen-bound water molecules, positions of which were estimated from a molecular dynamics simulation, or by the polarized continuum COSMO model. The B3LYP and BPW91 functionals used for the calculations of the spectral parameters were combined with the relativistic LANL2DZ platinum pseudo-potentials. The simulations reproduced the main IR and VCD DNA spectral features and explained most of the changes observed experimentally upon metal binding. The results confirmed that the influence of the ligand on DNA vibrational properties is quite complex; it originates in the geometry deformation and normal mode coupling pattern changes of the platinated octamer, as well as in local perturbations of the electronic structure and force field of the GC base pairs to which the platinum is bound. Many of the local effects could be accounted for by a point charge used in place of the metal in the GC complex.     

Synthesis,Characterization, and Electronic Structures of Porphyrins Fused with Polycyclic Aromatic Ring Systems

A series of porphyrins fused with acenaphthylene, phenanthroline, and benzofluoranthene polycyclic aromatic rings were prepared by means of a 3+1 porphyrin synthesis approach and subsequent retro‐Diels–Alder reaction of bicyclo[2.2.2]octadiene‐fused precursors. Analysis of the magnetic circular dichroism spectra and the results of time‐dependent DFT calculations are used to identify the reasons for the trends observed in the wavelengths and relative intensities of the Q bands of the products. Michl's perimeter model is used as a conceptual framework to explain the changes in the relative energies of the frontier π‐molecular orbitals.     

Simulations of structure and vibrational spectra of deoxyoctanucleotides

Combined molecular dynamics and ab initio computations were applied for analysis of infrared absorption and vibrational circular dichroism spectra of deoxyoctanucleotides. Unlike for previous idealized models, molecular geometries of these shorter DNA fragments in solutions were obtained as dynamic averages from simulations in a periodic water box. Vibrational spectra for the whole octamers including hydrogen-bonded solvent molecules were simulated on the basis of density-functional calculations on small fragments and subsequent transfer of molecular property tensors. Explicit and continuum solvent models were compared. Apparently, the DNA segments retain an approximate B-conformation in the aqueous solutions, but the terminal base pairs significantly deviate from the planar arrangement and the vibrational circular dichroism spectrum for (CG)(2) nucleotide indicates a larger average helical twist. Sodium counterions moved freely around the molecule during the simulation and do not influence spectral intensities. Simulated absorption spectra faithfully reproduced the experimental signal of principal functional groups, while only qualitative agreement was obtained for the dependence on the basis sequence.     

Density functional calculation of the electronic absorption spectrum of Cu+ and Ag+ aqua ions

The UV absorption of aqueous Cu+ and Ag+ has been studied using Time Dependent Density Functional Theory (TDDFT) response techniques. The TDDFT electronic spectrum was computed from finite temperature dynamical trajectories in solution generated using the Density Functional Theory (DFT) based Ab Initio Molecular Dynamics (AIMD) method. The absorption of the two ions is shown to arise from similar excitation mechanisms, namely transitions from d orbitals localized on the metal center to a rather delocalized state originating from hybridization of the metal s orbital to the conduction band edge of the solvent. The ions differ in the way the spectral profile builds up as a consequence of solvent thermal motion. The Cu+ absorption is widely modulated, both in transition energies and intensities by fluctuations in the coordination environment which is characterized by the formation of strong coordination bonds to two water molecules in an approximately linear geometry. Though, on average, absorption intensities are typical of symmetry forbidden transitions of metal ions in the solid state, occasionally very short (<100 fs) bursts in intensity are observed, associated with anomalous Cu-H interactions. Absorption by the Ag+ complex is in comparison relatively stable in time, and can be interpreted in terms of the energy splitting of the metal 4d manifold in an average crystal field corresponding to a fourfold coordination in a distorted tetrahedral arrangement. Whereas the spectral profile of the Ag+ aqua ion is in good agreement with experiment, the overall position of the band is underestimated by 2 eV in the BLYP approximation to DFT. The discrepancy with experiment is reduced to 1.3 eV when a hybrid functional (PBE0) is used. The remaining inaccuracy of TDDFT in this situation is related to the delocalized character of the target state in d-->s transitions.     

Vibrational circular dichroism spectroscopy of chiral pheromones: frontalin (1,5-dimethyl-6,8-dioxabicyclo[3.2.1]octane)

Ab initio density functional theory (DFT) is used to predict the vibrational absorption and circular dichroism spectra of the insect pheromone 1,5-dimethyl-6,8-dioxabicyclo[3.2.1]octane: frontalin. Excellent agreement with experimental spectra is obtained for the structure in which the six-membered ring is in a chair conformation and the seven-membered ring is in a boat conformation. Vibrational circular dichroism (VCD) intensities, predicted on the basis of the previously determined absolute configuration, are in excellent agreement with experiment. We conclude that VCD spectroscopy, in combination with ab initio DFT, is now an efficient tool for determining the absolute configuration and/or conformation of chiral organic molecules, including pheromones.