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.     

Structure of N-acetylproline amide in liquid water: experimentally measured and numerically simulated infrared and vibrational circular dichroism spectra

A few experimental and theoretical studies on the molecular structure of N-acetylproline amide (AP) in D2O solution have been reported recently. However, there is no consensus of the precise structure of AP in D2O because spectroscopically determined structures and a theoretically simulated one have been found to be different from one another. To determine its aqueous solution structure, IR and vibrational circular dichroism spectra of both L- and D-form AP solutions were measured. Molecular dynamics simulations with two different force fields and density functional theory calculations for the trans and cis rotamers of AP were performed to numerically simulate those spectra. Comparisons between experimentally measured and computationally simulated spectra directly suggest that the AP in water adopts a polyproline II-like conformation and that the force field parameter ff03 in the AMBER 8 suite of programs is more realistic and reliable in predicting molecular structure of AP in water than the ff99 in AMBER 7.     

First-principles calculations of magnetic circular dichroism spectra

An elaborate approach for the prediction of magnetic circular dichroism (MCD) spectra in the framework of highly correlated multiconfigurational ab initio methods is presented. The MCD transitions are computed by the explicit treatment of spin-orbit coupled (SOC) and spin-spin coupled (SSC) N-electron states. These states are obtained from the diagonalization of the SOC and SSC operators along with the spin and orbital Zeeman operators in the basis of a preselected number of roots of the spin-free Hamiltonian. Therefore, zero-field splittings due to the SOC and SSC interactions along with the magnetic field splittings are explicitly accounted for in the ground as well as the excited states. This makes it possible to calculate simultaneously all MCD A, B, and C terms even beyond the linear response limit. The SOC is computed using a multicenter mean-field approximation to the Breit-Pauli Hamiltonian. Two-electron SSC terms are included in the treatment without further approximations. The MCD transition intensities are subjected to numerical orientational averaging in order to treat the most commonly encountered case of randomly oriented molecules. The simulated MCD spectra for the OH, NH, and CH radicals as well as for [Fe(CN)(6)](3-) are in good agreement with the experimental spectra. In the former case, the significant effects of the inert gas matrices in which the experimental spectra were obtained were modeled in a phenomenological way.     

Conformational flexibility of Corey lactone derivatives indicated by absorption and vibrational circular dichroism spectra

Infrared absorption and vibrational circular dichroism (VCD) spectra of four Corey lactone derivatives (diol, benzoate, p-phenylbenzoate, and bisbenzoate) were measured and analyzed on the basis of ab initio computations. The analysis interpreted most of the spectral features as well as the differences among individual compounds. Despite the common rigid lactone residue, conformational behaviors and spectral features of the derivatives were found to be different, because of hydrogen bonding and solvent effects. Recognition of common molecular parts in the spectra of different molecules increases the potential of using VCD for monitoring the purity of intermediates in chiral syntheses. For the derivatives, a conserved spectral component corresponding to the lactone skeleton could be identified on the basis of theoretical analysis but was relatively weak in intensity.     

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.     

Effects of complex formation on vibrational circular dichroism spectra

The determination of absolute configurations of chiral compounds using VCD is performed by comparing measured vibrational circular dichroism (VCD) spectra with calculated spectra. The process is based on two facts: the two enantiomers have rotational strengths of opposite sign, and the absolute configuration of the molecule used in the calculation is known. However, calculations on isolated molecules very often predict VCD intensities of very different magnitude or even different signs compared to the spectra measured in solution. Therefore, we have carefully analyzed what type of changes are induced by complexation of a solvent molecule to a solute. In the theoretical example of benzoyl-benzoic acid (in a particular chiral conformation) hydrogen bonded to the achiral NH3, we distinguish six cases, ranging from no or very small changes in the rotational strengths of solute modes (case A) to changes of sign of rotational strengths (case B), changes in magnitude (case C), nonzero rotational strengths for modes of the achiral solvent ("transfer of chirality", case D), large frequency shifts accompanied by giant enhancements of the IR and VCD intensities of modes involved in hydrogen bonding (case E), and emergence of new peaks (case F). In this work, all of these situations will be discussed and their origin will be elucidated. On the basis of our analysis, we advocate that codes for VCD rotational strength calculation should output for each mode i the angle xi(i) between the electric and magnetic transition dipole moments because only "robust modes" with xi far from 90 degrees should be used for the determination of the absolute configuration.     

Phosphorylation effect on the GSSS peptide conformation in water: infrared, vibrational circular dichroism, and circular dichroism experiments and comparisons with molecular dynamics simulations

The phosphorylation effect on the small peptide conformation in water has not been clearly understood yet, despite the widely acknowledged notion that control of protein activity by phosphorylation works mainly by inducing conformational change. To elucidate the detailed mechanism, we performed infrared (IR) absorption and vibrational and electronic circular dichroism studies of both unphosphorylated and phosphorylated tetrapeptides, GSSS 1 and GSSpS 2. The solution structure of the tetrapeptide is found to be little dependent on the presence of the neutral or negatively charged phosphoryl group, and to be a mixture of extended structures including polyproline II (PII) and beta-sheet conformations. The additional band at 1598 cm(-1) in the amide I IR spectrum of the phosphorylated peptide GSSpS at neutral pD appears to be clear spectroscopic evidence for direct intramolecular hydrogen-bonding interaction between the side chain dianionic phosphoryl group and the backbone amide proton. On the basis of amide I IR band analyses, the authors found that the probability of finding the phosphoryl group strongly H bonded to the backbone proton in GSSpS is about 43% at pD 7.0 and 37 degrees C. Such a H-bonding interaction in GSSpS has the biological standard enthalpy and entropy of -15.1 kJ/mol and -51.2 J/K mol, respectively. Comparisons between the experimentally measured IR and VCD spectra and the numerically simulated ones suggested that the currently available force field parameters need to be properly modified. The results in this paper may shed light on an unknown mechanism of controlling the peptide conformation by phosphorylation.     

氨氯地平圆二色谱的理论解析

采用量子化学密度泛函理论(DFT)和含时密度泛函理论(TD-DFT)在B3LYP/6-311++G**水平上对氨氯地平分子的圆二色谱进行理论研究。计算结果表明:振动圆二色谱(VCD)的803、1113、1190、1238、1348、1509、1514、1736、2972、3022和3091 cm-1处存在吸收峰,产生以上吸收峰的振动均涉及到分子手性中心或者所处的基团与分子手性中心形成相关。研究还发现,甲醇溶液使电子圆二色谱(ECD)的吸收峰红移;甲醇溶液中,S-氨氯地平的ECD谱在207、366 nm处存在正性康登效应,223 nm处存在负性康登效应;以上吸收峰均来源于π-π*电子跃迁。这些结论对于深入理解氨氯地平的手征光学性质具有一定的指导意义。     

Density functional theory calculations and vibrational circular dichroism of aromatic foldamers

Ab initio calculations together with vibrational circular dichroism (VCD) have been used for studying the conformations of a quinoline-derived oligoamide bearing a terminal chiral residue. Three helically folded conformers of the dimer, trimer, and tetramer forms of the oligomer were optimized at the density functional theory (DFT) level using the B3LYP functional and the 6-31G* basis set. For each form, the three conformers differ in their helical handedness and in the conformation of the chiral end group. The calculated structures of the tetramer and also the proportions predicted between them based on their calculated Gibbs free energies differences match remarkably well with experimental data collected on an octamer. Specifically, a R-phenethyl terminal group gives rise to a 91:9 ratio between left handed and right handed helices. The predicted VCD spectrum calculated from the Boltzmann population of the individual conformer reproduces very well the experimental VCD spectrum of the tetramer in CDCl3 solution. The DFT calculations performed for the trimer also allow one to assess the preferred handedness of the helix and the conformation of the chiral end group, but the calculated relative populations differ slightly from experimental data. Finally, this study shows that the dimer fragment is not sufficient to obtain valuable information on the conformation of this aromatic oligoamide foldamer.     

Complex polarization propagator calculations of magnetic circular dichroism spectra

It is demonstrated that the employment of the nonlinear complex polarization propagator enables the calculation of the complete magnetic circular dichroism spectra of closed-shell molecules, including at the same time both the so-called Faraday A and B terms. In this approach, the differential absorption of right and left circularly polarized light in the presence of a static magnetic field is determined from the real part of the magnetic field-perturbed electric dipole polarizability. The introduction of the finite lifetimes of the electronically excited states into the theory results in response functions that are well behaved in the entire spectral region, i.e., the divergencies that are found in conventional response theory approaches at the transition energies of the system are not present. The applicability of the approach is demonstrated by calculations of the ultraviolet magnetic circular dichroism spectra of para-benzoquinone, tetrachloro-para-benzoquinone, and cyclopropane. The present results are obtained with the complex polarization propagator approach in conjunction with Kohn-Sham density functional theory and the standard adiabatic density functionals B3LYP, CAM-B3LYP, and BHLYP.     

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.     

Reliability of computed signs and intensities for vibrational circular dichroism spectra

We present in detail a novel measure that improves the reliability of the assignment procedure for vibrational circular dichroism (VCD) spectra extending the useful robustness concept introduced by Nicu and Baerends. This measure enables spectroscopists to single out bands with unreliable VCD intensities that can be disregarded during analysis and determination of absolute configuration. The previously proposed robustness criterion is shown to be gauge dependent and less reliable than the one proposed here.     

Signatures of counter-ion association and hydrogen bonding in vibrational circular dichroism spectra

We study the effect of counter-ion complexation on the example of Cl(-) ions interacting with the [Co(en)(3)](3+) complex. The H-bonding of the N-H groups of the ethylenediamine (en) ligands with the Cl(-) ions may lead to giant enhancement of the VCD intensity for the N-H stretches, but may also lead to VCD sign changes in the finger print region of N-H wagging, twisting and scissoring motions. Such sign changes should not be mistaken for signatures of the presence of the other enantiomer. We elucidate the mechanism for the sign changes and give a recommendation on how to deal with this problem. We also show that the experimental spectrum is only in good accord with the calculations if complexation of 5 Cl(-) ions (two axial, three equatorial) is assumed, but not with two (axial) or three (equatorial) Cl(-) ions, thus showing the potential of VCD to be used as an experimental probe for complexation.     

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.     

Magnetic circular dichroism and absorption spectra of phosphinidene in noble-gas matrices

Electronic magnetic circular dichroism and absorption spectra are reported for the A 3pi(i) <-- X 3sigma- transitions of phosphinidene (PH) isolated in Ar, Kr, and Xe matrices at cryogenic temperatures (approximately 1.4-20 K) and over a range of magnetic field strengths (0-5 T). The results are analyzed by the method of moments, and parameters are extracted by fitting the experimental data to a model in which the A 3pi(i) term is split by spin-orbit (SO) coupling interactions, while the X 3sigma- term is split by spin-spin and higher-order SO coupling. The analysis indicates that, unlike the equivalent imidogen (NH) systems, ground-state PH radicals isolated in noble-gas matrices do not behave as free rotors. Trends in excited-state SO coupling constants are attributed to the external heavy-atom effect and guest-host orbital mixing. It is tentatively concluded that librational amplitudes of the guest radical decrease in the order Ar > Xe > Kr, probably as a consequence of competition between stronger guest-host interactions and larger matrix sites in heavier hosts.     

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.     

A combined theoretical and experimental study of the structure and vibrational absorption, vibrational circular dichroism, Raman and Raman optical activity spectra of the L-histidine zwitterion

A combined theoretical and experimental study of the vibrational absorption (VA)/IR, vibrational circular dichroism (VCD), Raman and Raman optical activity (ROA) spectra of l-histidine in aqueous solution has been undertaken to answer the questions (i) what are the species present and (ii) which conformers of the species are present under various experimental conditions. The VA spectra of l-histidine have been measured in aqueous solution and the spectral bands which can be used to identify both species (cation, zwitterion, anion) and conformer of the species have been identified and subsequently used to identify the species (zwitterion) and conformer (gauche minus minus, gauche minus plus for the side chain dihedral angles) present in solution at pH 7.6. The VCD spectral intensities have been used subsequently in combination with further theoretical studies to confirm the conclusions that have been arrived at by only analyzing the VA/IR spectra. Finally a comparison of measured Raman and ROA spectra of l-histidine with Raman and ROA spectral simulations for the conformers and species derived from the combined VA/IR and VCD experimental and theoretical work is presented as a validation of the conclusions arrived at from VA/IR and VCD spectroscopy. The combination of VA/IR and VCD with Raman and ROA is clearly superior and both sets of experiments should be performed.     

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.