Transition Moment Directions Research Articles

Excited states of trans-stilbene and 1,4-diphenylbutadiene. Near and vacuum UV polarization spectroscopy

The UV absorbance spectra of trans-stilbene ((E)-1,2-diphenylethene, DPE) and (E,E’)-1,4-diphenyl-1,3-butadiene (DPB) are investigated by Synchrotron Radiation Linear Dichroism (SRLD) spectroscopy using stretched polyethylene as an anisotropic solvent. The investigation covers the range 58,000–25,000 cm–1 (172–400 nm). The observed polarization data provide information on the transition moment directions of the observed spectral features. The wavenumbers, intensities, and polarization directions of the observed spectral bands are compared with the results of quantum chemical calculations using the semiempirical all-valence-electrons method LCOAO and Time-Dependent Density Functional Theory (TD–DFT) with the functional CAM-B3LYP.

Near and vacuum UV polarization spectroscopy of 1,4-distyrylbenzene

The UV absorbance bands of 1,4-distyrylbenzene (1,4-Bis[(E)-2-phenylethenyl]benzene, DSB) are investigated by Synchrotron Radiation Linear Dichroism (SRLD) spectroscopy using stretched polyethylene as an anisotropic solvent. The observed polarization data provide information on the transition moment directions of the observed spectral features. The investigation covers the range 15,000–58,000 cm−1 (667–172 nm), thereby providing new information on the transitions of DSB in the vacuum UV region. The observed spectrum is characterized by four main band systems centered at 27,600, 41,000, 49,800, and 57,500 cm−1 (362, 244, 201, and 174 nm). In general, the observed bands and their polarization directions are well predicted by the results of quantum chemical calculations using Time-Dependent Density Functional Theory (TD–DFT) with the functional CAM-B3LYP, and with the semiempirical all-valence-electrons method LCOAO.

ECD exciton chirality method today: a modern tool for determining absolute configurations.

The application of the exciton chirality method (ECM) to interpret electronic circular dichroism (ECD) spectra is a well‐established and still popular approach to assign the absolute configuration (AC) of natural products, chiral organic compounds, and organometallic species. The method applies to compounds containing at least two chromophores with electric dipole allowed transitions (e.g., π–π* transitions). The exciton chirality rule correlates the sign of an exciton couplet (two ECD bands with opposite sign and similar intensity) with the overall molecular stereochemistry, including the AC. A correct application of the ECM requires three main prerequisites: (a) the knowledge of the molecular conformation, (b) the knowledge of the directions of the electric transition moments (TDMs), and (c) the assumption that the exciton coupling mechanism must be the major source of the observed ECD signals. All these prerequisites can be easily verified by means of quantum‐mechanical (QM) calculations. In the present review, we shortly introduce the general principles that underpin the use of the ECM for configurational assignments and survey its applications, both classic ones and some reported in the recent literature. Based on these examples, we will stress the advantages of the ECM but also the key requisites for its correct application. Additionally, we will discuss the dependence of the couplet sign on geometrical parameters (angles α,β,γ between TDMs), which can be helpful for discerning the sign of exciton chirality in ambiguous situations. Finally, we will present a molecular orbital (MO) description of the exciton coupling phenomenon.

UV polarisation spectroscopy of 1,4-diethynylbenzene

1,4-diethynylbenzene is investigated by UV linear dichroism polarisation spectroscopy using synchrotron radiation on molecular samples partially aligned in stretched polyethylene. The investigation covers the range from the absorption onset around 32,000 cm–1 (310 nm) to 58,000 cm–1 (170 nm) in the far UV. The polarisation spectra lead to resolution of otherwise overlapping spectral features and to experimental symmetry assignments of the observed molecular states. The observed transition moment directions of the differently polarised components of the weak absorption band between 32,000 and 35,000 cm–1 (310 and 285 nm) support previously suggested vibronic assignments. The observed bands are compared with electronic transitions computed with TD–CAM-B3LYP, CIS and CIS(D). Magnetic Circular Dichroism (MCD) B-terms computed with the semiempirical LCOAO method are also reported. The calculated ordering of electronic states is found to be sensitive to the theoretical model. The absorption in the far UV is predicted to involve the in-plane π and π* components of the C≡C triple bonds and orbitals of mixed valence-Rydberg character.

Ordered arrangement of F4TCNQ anions in three-dimensionally oriented P3HT thin films

An ordered arrangement of electron-accepting molecular dopant, 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ), in three-dimensionally (3D) oriented poly(3-hexylthiophene) (P3HT) film was clarified. The 3D oriented P3HT thin films prepared by the friction-transfer technique were doped with F4TCNQ by dipping into an acetonitrile solution. The presence of F4TCNQ anions in the 3D oriented P3HT thin films was investigated by polarized ultraviolet/visible/near-infrared absorption spectroscopy, grazing incidence X-ray diffractometry, polarized Fourier transform infrared spectroscopy (FT-IR), and infrared p-polarized multiple-angle incidence resolution spectroscopy (pMAIRS). The F4TCNQ-doped 3D oriented P3HT films showed anisotropic properties in all characterizations. In particular, the anisotropic molecular vibrations from polarized FT-IR and pMAIRS have clearly revealed orientations of polymeric chains and molecular dopant molecules. Considering the results from several independent techniques indicated that F4TCNQ anions in the 3D oriented P3HT were orderly arranged in a 3D manner with respect to the 3D oriented P3HT such that their molecular long-axis parallel to the P3HT backbone, with in-plane molecular orientation. Additionally, the direction of the optical transition moment of the F4TCNQ anion was found to be parallel to the molecular short-axis.

Determination of dielectric axes and transition moment directions in β-Ga2O3 from the polarization dependence of vibrational spectra

β-Ga2O3 is a promising ultrawide bandgap semiconductor for high power and extreme environment applications. The dominant O—H center in Ga2O3 has been assigned to a Ga(1) vacancy–2H (VGa(1)-2H) complex. An analysis of the polarization dependence of the vibrational absorption of the VGa(1)-2D center in monoclinic β-Ga2O3 provides a unique strategy for the determination of both the orientation of the principal dielectric axes in the near infrared and the direction of the vibrational transition moment of the defect.

Another step toward understanding the binding mode of other derivatives of [Ru(phen)2L] complexes

Linear dichroism (LD), UV-Vis and fluorescence spectroscopy were used to investigate the interaction of the Δ- and Λ-enantiomers of the two complexes of [Ru(phen)2 2-phenylimidazophenanthroline]+2 (referred to as B-complex) and [Ru(phen)2 2-(1-pyrenyl)limidazophenanthroline]+2 (named as P-complex), with ct-DNA. Absorption titration experiments of the enantiomers showed significant hypochromism with red shift indicating a strong perturbation of the DNA on the intra-ligand (IL) and the metal-to-ligand charge transfer (MLCT) transitions of the complexes, and fluorescence titration curves indicate strong binding. LD spectra for the B-enantiomers bound to DNA were qualitatively similar to spectra for the well-studied intercalator [Ru(phen)2dppz]+2, indicating intercalation of the phenyl-imidazophenanthroline part of the complex. However, for Λ-P, the LD-spectrum resembled Δ-B, and Δ-P resembled Λ-B, indicating a mirror image relationship of the transition moment directions relative to the helix axis when going from B to P. For interpretation of the data, and clarifying the nature of the binding mode of the P-complexes, a model was proposed based on the crystal structure previously presented by the Cardin group. The reversed LD is suggested to be due to partial intercalation of the pyrene moiety, pushing the Ru(phen)2-moiety out from the opposite groove and allowing it to rotate anticlockwise around the pyrene-imidazole bond.Communicated by Ramaswamy H. Sarma

For a Correct Application of the CD Exciton Chirality Method: The Case of Laucysteinamide A.

The circular dichroism (CD) exciton chirality method (ECM) is a very popular approach for assigning the absolute configuration (AC) of natural products, thanks to its immediacy and ease of application. The sign of an exciton couplet (two electronic CD bands with opposite sign and similar intensity) can be directly correlated with the molecular stereochemistry, including the AC. However, a correct application of the ECM necessitates several prerequisites: knowledge of the molecular conformation; knowledge of transition moment direction; and preeminence of the exciton coupling mechanism with respect to other sources of CD signals. In recent years, by using quantum-chemical CD calculations, we have demonstrated that some previous applications of ECM were wrong or based on incorrect assumptions. In a recent publication of this journal (Mar. Drugs, 2017, 15(4), 121), the ECM was employed to assign the AC of a marine metabolite, laucysteinamide A. This is a further case of incorrect application of the method, where none of the aforementioned prerequisites is fully met. Using this example, we will discuss the criteria required for a correct application of the ECM.

Employing Theories Far beyond Their Limits - Linear Dichroism Theory.

Using linear polarized light, it is possible in case of ordered structures, such as stretched polymers or single crystals, to determine the orientation of the transition moments of electronic and vibrational transitions. This not only helps to resolve overlapping bands, but also assigning the symmetry species of the transitions and to elucidate the structure. To perform spectral evaluation quantitatively, a sometimes "Linear Dichroism Theory" called approach is very often used. This approach links the relative orientation of the transition moment and polarization direction to the quantity absorbance. This linkage is highly questionable for several reasons. First of all, absorbance is a quantity that is by its definition not compatible with Maxwell's equations. Furthermore, absorbance seems not to be the quantity which is generally compatible with linear dichroism theory. In addition, linear dichroism theory disregards that it is not only the angle between transition moment and polarization direction, but also the angle between sample surface and transition moment, that influences band shape and intensity. Accordingly, the often invoked "magic angle" has never existed and the orientation distribution influences spectra to a much higher degree than if linear dichroism theory would hold strictly. A last point that is completely ignored by linear dichroism theory is the fact that partially oriented or randomly-oriented samples usually consist of ordered domains. It is their size relative to the wavelength of light that can also greatly influence a spectrum. All these findings can help to elucidate orientation to a much higher degree by optical methods than currently thought possible by the users of linear dichroism theory. Hence, it is the goal of this contribution to point out these shortcomings of linear dichroism theory to its users to stimulate efforts to overcome the long-lasting stagnation of this important field.

Symmetry and diffusivity of the interstitial hydrogen shallow-donor center in In2O3

Uniaxial-stress experiments performed for the 3306 cm−1 vibrational line assigned to the interstitial-hydrogen, shallow-donor center in In2O3 reveal its symmetry and transition-moment direction. The defect alignment that can be produced by a [001] stress applied at 165 K is due to a process that is also a hydrogen-diffusion jump, providing a microscopic determination of the diffusion constant for H in In2O3 and its mechanism. Our experimental results strongly complement the theoretical predictions for the structure and diffusion of the interstitial hydrogen donor center in In2O3.

Electronic states of Myricetin. UV–Vis polarization spectroscopy and quantum chemical calculations

Myricetin (3,3′,4′,5,5′,7′-hexahydroxyflavone) was investigated by linear dichroism spectroscopy on molecular samples partially aligned in stretched poly(vinyl alcohol) (PVA). At least five electronic transitions in the range 40,000–20,000cm−1 were characterized with respect to their wavenumbers, relative intensities, and transition moment directions. The observed bands were assigned to electronic transitions predicted with TD-B3LYP/6-31+G(d,p).

Study of aryl triazoles for absolute configuration determination

A variety of chiral mono- and di-1,4-disubstituted 1,2,3-triazoles were synthesized by CuAAC ‘click chemistry’ as model compounds and their spectroscopic properties characterized. The UV and CD studies of these compounds showed that 4-substituted aryl triazoles give rise to moderate exciton CD curves, under either homo- or hetero-coupling. The direction of the electric transition moment of the non-symmetric chromophores was determined by conformational analysis and supported by NMR data. The signs of the Cotton effects of the CD spectra were in complete agreement with the determined directions of the electric transition moments of the chromophores. Therefore, 4-substituted aryl triazoles can be used for the determination of the absolute configuration of organic compounds. In addition, the 4-(4-bromophenyl)-1,2,3-triazole allows for red-shifted chromophores to be obtained via Suzuki reactions, thus avoiding overlap with the substrate absorptions.

UV transition moments of tyrosine.

To assist polarized-light spectroscopy for protein-structure analysis, the UV spectrum of p-cresol, the chromophore of tyrosine, was studied with respect to transition moment directions and perturbation by solvent environment. From linear dichroism (LD) spectra of p-cresol aligned in stretched matrices of poly(vinyl alcohol) and polyethylene, the lowest π-π* transition (Lb) is found to have pure polarization over its entire absorption (250-300 nm) with a transition moment perpendicular to the symmetry axis (C1-C4), both in polar and nonpolar environments. For the second transition (La), polarized parallel with the symmetry axis, a certain admixture of intensity with orthogonal polarization is noticed, depending on the environment. While the Lb spectrum in cyclohexane shows a pronounced vibrational structure, it is blurred in methanol, which can be modeled as due to many microscopic polar environments. With the use of quantum mechanical (QM) calculations, the transition moments and solvent effects were analyzed with the B3LYP and ωB97X-D functionals in cyclohexane, water, and methanol using a combination of implicit and explicit solvent models. The blurred Lb band is explained by solvent hydrogen bonds, where both accepting and donating a hydrogen causes energy shifts. The inhomogeneous solvent-shift sensitivity in combination with robust polarization can be exploited for analyzing tyrosine orientation distributions in protein complexes using LD spectroscopy.

Vibrational Cross-Angles in Condensed Molecules: A Structural Tool

The fluctuations of three-dimensional molecular conformations of a molecule in different environments play critical roles in many important chemical and biological processes. X-ray diffraction (XRD) techniques and nuclear magnetic resonance (NMR) methods are routinely applied to monitor the molecular conformations in condensed phases. However, some special requirements of the methods have prevented them from exploring many molecular phenomena at the current stage. Here, we introduce another method to resolve molecular conformations based on an ultrafast MIR/T-Hz multiple-dimensional vibrational spectroscopic technique. The model molecule (4'-methyl-2'-nitroacetanilide, MNA) is prepared in two of its crystalline forms and liquid samples. Two polarized ultrafast infrared pulses are then used to determine the cross-angles of vibrational transition moment directions by exciting one vibrational band and detecting the induced response on another vibrational band of the molecule. The vibrational cross-angles are then converted into molecular conformations with the aid of calculations. The molecular conformations determined by the method are supported by X-ray diffraction and molecular dynamics simulation results. The experimental results suggest that thermodynamic interactions with solvent molecules are not altering the molecular conformations of MNA in the solutions to control their ultimate conformations in the crystals.

Terahertz Spectroscopy in Polymer Research: Assignment of Intermolecular Vibrational Modes and Structural Characterization of Poly(3-Hydroxybutyrate)

This paper reviews our recent spectroscopic study on poly(3-hydroxybutyrate) (PHB) for the terahertz (THz) frequency region. Clear differences are observed between the absorption spectra of crystalline and amorphous PHB, indicating that the higher order conformation of PHB determines the THz spectra. The THz polarization spectra are measured for a stretched PHB sample and the directions of the vibrational transition moments are determined. The spectra are found to have temperature dependences owing to which the peaks at lower frequencies shift with temperature, suggesting a large anharmonicity of the vibrational potential. To investigate low frequency vibrational modes more thoroughly, low-frequency Raman spectra are also measured for crystalline PHB. The observed vibrational modes in both THz and Raman spectra were successfully assigned by a quantum mechanical simulation of spectra with the Cartesian coordinate tensor transfer (CCT) method, which can provide realistic spectra of the PHB by considering the intermolecular interactions among polymer chains. The potential of CCT for the assignment of THz spectra is demonstrated. On the basis of these results, the structural change in PHB is studied. The isothermal crystallization of PHB is monitored with the help of THz absorption spectra. The observed spectra clearly show the crystal growth, and the crystallization rate is estimated by Avrami's model. Next, the isothermal crystallization spectra are analyzed using two-dimensional correlation spectroscopy (2DCOS). By using the synchronous and asynchronous data plots, the correlation between the absorption peaks and the temporal order of the changes in spectral intensity is determined.

Transition moment directions and selected spectroscopic properties of Ivabradine

Based on the Kawski–Gryczynski method the value of angle β=38° between absorption and fluorescence transition moments of Ivabradine was determined. Such a high value of β is responsible for low emission anisotropy of Ivabradine in a rigid polyvinyl alcohol matrix and in anhydrous glycerol despite the elongated shape of the fluorophore. Selected steady-state and time-resolved spectroscopic results support the analysis.

Testing a new analytical approach for determination of vibrational transition moment directions in low symmetry planar molecules: 1-D- and 2-D-naphthalene

A new analytical approach for improving the precision in determination of vibrational transition moment directions of low symmetry molecules (lacking orthogonal axes) is discussed in this paper. The target molecules are partially uniaxially oriented in nematic liquid crystalline solvent and are studied by IR absorption spectroscopy using polarized light. The fundamental problem addressed is that IR linear dichroism measurements of low symmetry molecules alone cannot provide sufficient information on molecular orientation and transition moment directions. It is shown that computational prediction of these quantities can supply relevant complementary data, helping to reveal the hidden information content and achieve a more meaningful and more precise interpretation of the measured dichroic ratios.The combined experimental and theoretical/computational method proposed by us recently for determination of the average orientation of molecules with Cs symmetry has now been replaced by a more precise analytical approach. The new method introduced and discussed in full detail here uses a mathematically evaluated angle between two vibrational transition moment vectors as a reference. The discussion also deals with error analysis and estimation of uncertainties of the orientational parameters. The proposed procedure has been tested in an analysis of the infrared linear dichroism (IR–LD) spectra of 1-D- and 2-D-naphthalene complemented with DFT calculations using the scaled quantum mechanical force field (SQM FF) method.

Average Orientation of a Molecular Rotor Embedded in a Langmuir–Blodgett Monolayer

A molecular rotor in which a naphthalene rotator is attached through a silicon atom to three fatty acid chains has been synthesized, and Langmuir-Blodgett techniques were used to deposit on silica surfaces monolayers of its calcium salt, both neat and diluted with stearic acid salts. The monolayer films have been characterized by ellipsometry and Fourier transform infrared (FT-IR) grazing-incidence attenuated total internal reflection (GATR) spectroscopy on Si-SiO(2) and by UV-vis absorption spectroscopy on SiO(2). The measurements were combined with calculations of the electronic (INDO/S) and vibrational (DFT) transition moment directions to deduce the average orientation of the rotor molecules, including the naphthalene ring, relative to the surface. In both neat and mixed films, the naphthalene ring is found to preferentially tilt toward the surface, enough that its rotation is most likely hindered. A comparable picture was obtained from molecular mechanics calculations on a mixed film of the naphthalene rotor and stearic acid.

Electronic and Vibrational Transition Moment Directions in 7-Dimethylamino-3-methyl-N-methyl-d3-4-phenylethynylcarbostyril

We report the synthesis and photophysical characterization of 7-dimethylamino-3-methyl-N-methyl-d(3)-4-phenylethynylcarbostyril, a chromophore of interest as a rotator in surface-mounted molecular rotors. Measurement of UV-vis absorption and fluorescence spectra, steady state fluorescence and excitation anisotropy, and linear dichroism in the IR and UV-vis permitted a determination of absolute vibrational and electronic transition moment directions in this previously unreported chromophore. The first singlet-singlet absorption and fluorescence are polarized perpendicular to the axle of the rotator. Density functional theory calculations of electronic excitation and vibrational frequencies gave results in very good agreement with those observed. Calculated IR transition moment directions showed rather poor agreement with experiment.

Correlation between Structure and Shape of the Polarized Infrared Absorption Spectra of 4-Chloro-2′-hydroxy-4′-alkyloxyazobenzenes

Polarized infrared spectra of liquid crystalline 4-chloro-2'-hydroxy-4'-alkyloxyazobenzenes (CHAB) with C(5), C(6), and C(7) alkyl chains measured at 25 °C were compared, with particular attention being paid to the influence of chain length on formation of ordered boundary layers. The effect of chain elongation is discussed on the basis of calculations of the optimized geometry of dimeric species, which reflects the role of association in ordered phases. The impact of the varying intermolecular interactions on the spectra of C(5), C(6), and C(7) derivatives measured as a function of the polarization angle is analyzed by principal component analysis (PCA). The polarization-angle-dependent results are contrasted with the transition moment directions obtained from the density functional theory (DFT) calculations. The continuum spread down to 500 cm(-1) and a pseudoband at ca. 600 cm(-1) ascribed to the Fermi resonance between ν(OH) and γ(OH) modes is an additional phenomenon whose features also depend on alkyl chain length.