DFT study of vibrational circular dichroism spectra of D-lactic acid-water complexes

This paper presents a discussion of the interaction energies, conformations, vibrational absorption (VA, harmonic and anharmonic) and vibrational circular dichroism (VCD) spectra for conformers of monomeric chiral d(-)-lactic acid and their complexes with water at the DFT(B3LYP)/aug-cc-pVDZ and DFT(B3LYP)/aug-cc-pVTZ levels. A detailed analysis has been performed principally for the two most stable complexes with water, differing by lactic acid conformation. The VCD spectra were found to be sensitive to conformational changes of both free and complexed molecules, and to be especially useful for discriminating between different chiral forms of intermolecular hydrogen bonding complexes. In particular, we show that the VCD modes of an achiral water molecule after complex formation acquire significant rotational strengths whose signs change in line with the geometry of the complex. Using the theoretical prediction, we demonstrate that the VCD technique can be used as a powerful tool for structural investigation of intermolecular interactions of chiral molecules and can yield information complementary to data obtained through other molecular spectroscopy methods.     

Vibrational-electronic interaction in the infrared circular dichroism spectra of transition-metal complexes

The circular dichroism spectra of the quasi-tetrahedral complexes of transition-metal ions with (?)-spartein, [M(l-sp)Cl₂], over the C-H stretching vibration range, show an optical activity which is weak in the Zn(II) case, but enhanced in the Co(II) and Ni(II) analogues through the coupling of the sharp vibrational transition with underlying broad d-d electronic excitation.     

Near-IR absorption and fluorescence spectra and AFM observation of the light-harvesting 1 complex on a mica substrate refolded from the subunit light-harvesting 1 complexes of photosynthetic bacteria Rhodospirillum rubrum

The subunit light-harvesting 1 (LH 1) complexes isolated from photosynthetic bacteria Rhodospirillum rubrum using n-octyl-beta-glucoside were reassociated and adsorbed on a mica substrate using spin-coat methods with the aim of using this LH complex in a nanodevice. The near-IR absorption and fluorescence spectra of the LH 1 complexes indicated that the LH 1 complex on the mica was stable, and efficient energy transfer from a carotenoid to a bacteriochlorophyll a was observed. Atomic force microscopy of the reassociated LH 1 complexes, under air, showed the expected ringlike structure. The outer and inner diameters of the ringlike structure of the LH 1 complex were approximately 30 and 8 nm, respectively, and the ringlike structure protruded by 0.2-0.6 nm.     

Magnetic circular dichroism studies 23. 1. Magnetic circular dichroism spectra of indole alkaloids

The magnetic circular dichroism spectra of a number of indole alkaloids show two B-terms of opposite sign in the 250–330 nm wavelength region associated with the ¹L_b and ¹L_a electronic transitions, the long wavelength, ¹L^b, band being of positive sign, whereas both bands strongly overlap in absorption. Various substituents in different positions of the indole ring cause a red shift of both bands and a broadening of the long wavelength B-term. The sign pattern, howver, remains unchanged in all examples thus far investigated. Dihydroindole and oxindole, on the other hand, exhibit MCD. bands with the opposite sign sequence as compared to the indole chromophore. This observation allows identification of the indole chromophore in alkaloids from the sign pattern of the MCD. bands.     

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...     

Electronic circular dichroism spectra from the complex polarization propagator

The complex linear polarization propagator approach has been applied to the calculation of electronic circular dichroism spectra of 3R-chloro-1-butyne, 3R-methylcyclopentanone, 3S-methylcyclohexanone, 4R-1,1-dimethyl-[3]-(1,2)ferrocenophan-2-on, S-3,3,3',3'-tetramethyl-1,1'-spirobi[3H,2,1]-benzoxaselenole, and the fullerene C84. Using time-dependent Kohn-Sham density functional theory, it is shown that a direct and efficient evaluation of the circular dichroism spectrum can be achieved. The approach allows for the determination of the circular dichroism at an arbitrary wavelength thereby, in a common formulation and implementation, covering the visible, ultraviolet, and x-ray regions of the spectrum. In contrast to traditional methods, the entire manifold of excited states is taken into account in the calculation of the circular dichroism at a given wavelength.     

Selected deoxyoctanucleotides and their daunomycin complexes: Infrared absorption and vibrational circular dichroism spectra

The infrared absorption (IR) and vibrational circular dichroism (VCD) spectra are reported for six self-complementary deoxyoctanucleotides complexed with the anthracycline drug daunomycin. The oligomers included d(CGCGCGCG)·d(CGCGCGCG), d(CGCATGCG)·d(CGCATGCG) and d(CGCTAGCG)·d(CGCTAGCG), which possess a 5′CGC triplet, and d(CGATATCG)·d(CGATATCG), d(CGTATACG)·d(CGTATACG) and d(CGAATTCG) ·d(CGAATTCG), which have either 5′CGA or 5′CGT triplets. The latter three triplets were said to be favorable intercalation sites for this drug, while the former three were considered to be non-preferred. Changes in the VCD spectra upon drug binding indicate a perturbation of the structure at the base step involving cytosine (Cy) and guanine (Gu), which appears to comprise the daunomycin intercalation site. The VCD spectra also show distinct changes as the drug binds with base sequences that contain 5′CGC triplets compared to those with either 5′CGA or 5′CGT triplets. These differences are attributed to specific binding interactions of the DNA components with the functional groups of the aglycone chromophore and its amino sugar moiety.     

Calculation of the circular dichroism spectra of carbon monoxy- and deoxy myoglobin: interpretation of a time-resolved circular dichroism experiment

A calculation of the circular dichroism (CD) spectra of carbon monoxy- and deoxy myoglobin is carried out in relation with a time-resolved CD experiment. The calculation is based on the polarizability theory and the parameters are adjusted to fit the experimental absorption and CD spectra. By performing the calculation for intermediate configurations of the protein, we are able to propose an explanation of the CD structure observed on a sub-100 ps time scale. The role of the proximal histidine is, in particular, clearly demonstrated in the first step of the myoglobin relaxation from its liganded to it deliganded form.     

Bile pigment complexes with cyclodextrins: electronic and vibrational circular dichroism study

Chiral recognition of bilirubin IX-α, biliverdin IX-α, and bilirubin ditaurate dianions by cyclodextrins was studied using a combination of vibrational and electronic circular dichroism. Biliverdin forms inclusion complexes with β-cyclodextrin and β-methylcyclodextrin. Bilirubin bonds to both cyclodextrins by means of hydrogen bonds and only shallow inclusions that are restricted by the presence of COO⁻ in the pigment structure. Bilirubin ditaurate complexes are realized by a weak inclusion of the whole molecule, or some part of it, into the cyclodextrin cavity and stabilization of the conformation by hydrogen bonds. Bilirubin and bilirubin ditaurate can be recognized by cyclodextrin and methylcyclodextrin in the form of opposite conformers. Spectroscopic characteristics of the different conformations of the bile pigments were obtained for the first time by vibrational circular dichroism techniques.     

Density functional calculations on electronic circular dichroism spectra of chiral transition metal complexes

Time-dependent density functional theory (TD-DFT) has for the first time been applied to the computation of circular dichroism (CD) spectra of transition metal complexes, and a detailed comparison with experimental spectra has been made. Absorption spectra are also reported. Various Co(III) complexes as well as [Rh(en)(3)](3+) are studied in this work. The resulting simulated CD spectra are generally in good agreement with experimental spectra after corrections for systematic errors in a few of the lowest excitation energies are applied. This allows for an interpretation and assignment of the spectra for the whole experimentally accessible energy range (UV/vis). Solvent effects on the excitations are estimated via inclusion of a continuum solvent model. This significantly improves the computed excitation energies for charge-transfer bands for complexes of charge +3, but has only a small effect on those for neutral or singly charged complexes. The energies of the weak d-to-d transitions of the Co complexes are systematically overestimated due to deficiencies of the density functionals. These errors are much smaller for the 4d metal complex. Taking these systematic errors and the effect of a solvent into consideration, TD-DFT computations are demonstrated to be a reliable tool in order to assist with the assignment and interpretation of CD spectra of chiral transition metal complexes.     

Magnetic circular dichroism spectra of triphenylene and coronene

The absorption spectra of triphenylene (I) and coronene (II) are assigned by using the MCD spectra and the results of the SCF screened potential π-MO CI calculations. The calculated Faraday A/D values for the ¹E and ¹E_1u excited states of I and II are in excellent agreement with the experimental values, in contrast to the calculated Faraday B value for the ¹E_1u state of II.     

The circular dichroism in the visible region of the 1:1 copper(II):l-arginine species

Contrary to an earlier report, the 1:1 complex of copper(II) with l-argininate manifests obvious circular dichroism in the visible region.     

Quantum chemical study on the circular dichroism spectra and specific rotation of donor-acceptor cyclophanes

The structures of donor,acceptor-substituted cyclophanes were optimized by DFT and MP2 methods and compared with the X-ray crystallographic structures. The electronic circular dichroism (CD) spectra of these chiral cyclophanes were simulated by time dependent density functional theory (TD-DFT) with several functionals including different amounts of "exact" Hartree-Fock exchange. The experimental oscillator and rotatory strengths were best reproduced by the BH-LYP/TZV2P method. The specific rotation and vibrational circular dichroism (VCD) spectra were also calculated at the BH-LYP/aug-cc-pVDZ and B3-LYP/6-31G(d) levels, respectively, and compared with the experimental data. Better performance was obtained with the ECD, rather than the specific rotation or the VCD spectral calculations in view of the computation time and accuracy for the determination of absolute configuration (AC). The exciton coupling model can be applied only for the cyclophanes without CT-character. However, the split pattern found in the experiment does not appear to originate from a simple two-transition coupling, indicating that this method should be applied with caution to the AC determination. This conclusion was supported by the TD-DFT investigations of the transition moments and the roles of excited-state electronic configuration associated with these split bands. Cyclophanes with donor-acceptor interactions showed Cotton effects at the CT band and couplets at the 1La and 1Lb bands. Although the degree of charge transfer between the rings is very small, as revealed by a Mulliken-Hash analysis, the split Cotton effects are due to a large separation in energy of the donor and acceptor orbitals. The effect of the distance and angle between the donor and acceptor moieties in model (intermolecular) CT complexes on the calculated CD spectra was also studied and compared with those obtained for various paracyclophanes.     

Magnetic circular dichroism spectra of benzo[a]pyrene

Magnetic circular dichroism (MCD) and absorption spectra of benzo[a]pyrene have been measured. The absorption spectra have been assigned by comparing the experimental results with the signs of Faraday B terms and transition energies computed by using the Pariser—Parr—Pople SCF-π-MO CI method.     

The absorption and circular dichroism spectra of chiral olefins

Absorption and CD spectra over the quartz and vacuum UV region down to 165 nm are reported for a range of chiral alkenes in the vapour phase and in solution from +70° to ?185°C. A major couplet of oppositely-signed CD bands with comparable band areas, near 48 and 55 kK, is observed in a number of dissymmetric olefins and in some cases a weaker Rydberg CD absorption is found at lower frequency. The Rydberg CD band is characterised by its sharp vibronic structure in the vapour phase and by large blue-shifts produced on passing to the condensed phase and by a reduction in temperature. The olefin couplet of major CD bands with opposite sign is assigned to a near-complete mixing of the electric-dipole π_x→π_x^* and the magnetic-dipole π_x→π_y^* excitations, producing a pair of isotiopic absorption bands with the same polarisation and comparable dipole strengths associated with the CD couplet. Three mixing mechanisms are discussed; sterically-induced π-bond torsion, a first-order static field model, and a second-order dynamic-coupling model dependent, respectively, upon the effective charge and upon the mean polarisability of dissymmetrically-located substituent. The latter two models give the octant rule previously proposed empirically connecting the sign of the rotational strength of the lower- and higher-frequency member of the olefin CD couplet with the position of the substituent in the chromophore coordinate frame.     

Interpreting DNA vibrational circular dichroism spectra using a coupling model from two-dimensional infrared spectroscopy

Two-dimensional infrared spectroscopy was recently used to measure the vibrational couplings between carbonyl bonds located on DNA nucleobases (Krummel, A. T.; Mukherjee, P.; Zanni, M. T. J. Phys. Chem. B 2003, 107, 9165 and Krummel, A. T.; Zanni, M. T. J. Phys. Chem. B 2006, 110, 13991). Here, we extend the coupling model derived from these 2D IR experiments to simulate the vibrational absorption and vibrational circular dichroism (VCD) spectra of three double-stranded DNA oligomers: poly(dG)-poly(dC), poly(dG-dC), and dGGCC. Using this model, we determine that the VCD spectrum of A-form poly(dG)-poly(dC) is dominated by interactions between stacked bases, whereas the coupling between base pairs and stacked bases carries equal importance in the VCD spectrum of B-form poly(dG-dC). We also simulate the absorption and VCD spectra of dGGCC, which is a combination of A- and B-form configurations. These simulations give insight into the structural interpretation of VCD and absorption spectroscopies that have long been used to monitor DNA secondary structure and kinetics.     

Magnetic circular dichroism and absorption spectra of methylidyne in a krypton matrix

Electronic absorption and magnetic circular dichroism spectra are reported for the A(2)Δ, B(2)Σ(-), and C(2)Σ(+) ← X(2)Π transitions of methylidyne radicals isolated in a Kr matrix at cryogenic temperatures. The results are interpreted in the framework of a model in which the X(2)Π term is split by combination of spin-orbit and crystal-field interactions with the atoms of the host matrix. Analysis of the zeroth moments of the spectra yields an empirical spin-orbit coupling constant A(Π) = 11 ± 2 cm(-1) and orbital reduction factor κ = 0.26 ± 0.05, corresponding to a crystal-field splitting of V(Π) = 43 ± 10 cm(-1) for the X(2)Π term. For the A(2)Δ excited-state term, analysis of the first MCD moments gives a spin-orbit coupling constant of A(Δ) = 4.4 ± 0.9 cm(-1).     

Vibronic structure of the circular dichroism and absorption spectra of bianthryls

It will be shown that factors of virtually no influence on the vibronic structure of the absorption spectra in biaryls may profoundly change the correspoding vibronic structure in the CD spectra. This is illustrated by the theoretical analysis of the experimental vibronic absorption and CD spectra of some bianthryl derivatives.     

Charge-transfer transitions in the vacuum-ultraviolet of protein circular dichroism spectra

Circular dichroism (CD) is widely used in the structural characterization and secondary structure determination of proteins. The vacuum UV region (below 190 nm), where charge-transfer transitions have an influence on the CD spectra, can be accessed using synchrotron radiation circular dichroism (SRCD) spectroscopy. Recently, charge-transfer transitions in a conformationally diverse set of dipeptides have been characterized ab initio using complete active space self-consistent field calculations, and the relevant charge distributions have been parametrized for use in the matrix method for calculations of protein CD. Here, we present calculations of the vacuum UV CD spectra of 71 proteins, for which experimental SRCD spectra and X-ray crystal structures are available. The theoretical spectra are calculated considering charge-transfer and side chain transitions. This significantly improves the agreement with experiment, raising the Spearman correlation coefficient between the calculated and the experimental intensity at 175 nm from 0.12 to 0.79. The influence of the conformation on charge-transfer transitions is analyzed in detail, showing that the n --> pi* charge-transfer transitions are most important in alpha-helical proteins, whereas in beta strand proteins the pi --> pi* charge-transfer transition along the chain in the amino- to carboxy-end direction is most dominant.