Basics of Orientation Measurements in Infrared and
            <scp>R</scp>
            aman Spectroscopy

Ikeda, Richard M.; Chase, Bruce; Everall, Neil

doi:10.1002/9780470027325.s0501m.pub2

Cited by 3 publications

(4 citation statements)

References 7 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Thus, components of the TMs perpendicular to the film are probed, which are not accessible in polarization-dependent IR measurements at normal incidence (ϑ = 0°). 41 For sample CB, one finds a preferred alignment of a (TM of ν s (CO), Figure 2b, Figure 4) perpendicular to the sample plane (S zz = 0.10 ± 0.01), whereas b (TM of ν as (CO)) is oriented mainly parallel to it (S zz = −0.33 ± 0.01). This already indicates that the NDI unit is tilted with respect to the substrate.…”

Section: ■ Materials and Methodsmentioning

confidence: 91%

See 1 more Smart Citation

Infrared Transition Moment Orientational Analysis on the Structural Organization of the Distinct Molecular Subunits in Thin Layers of a High Mobility n-Type Copolymer

et al. 2015

View full text Add to dashboard Cite

The IR-based method of infrared transition moment orientational analysis (IR-TMOA) is employed to unravel molecular order in thin layers of the semiconducting polymer poly[N,N'-bis(2-octyldodecyl)-1,4,5,8-naphthalenediimide-2,6-diyl]-alt-5,5'-(2,2'-bithiophene) (P(NDI2OD-T2)). Structure-specific vibrational bands are analyzed in dependence on polarization and inclination of the sample with respect to the optical axis. By that the molecular order parameter tensor for the respective molecular moieties with regard to the sample coordinate system is deduced. Making use of the specificity of the IR spectral range, we are able to determine separately the orientation of atomistic planes defined through the naphthalenediimide (NDI) and bithiophene (T2) units relative to the substrate, and hence, relative to each other. A pronounced solvent effect is observed: While chlorobenzene causes the T2 planes to align preferentially parallel to the substrate at an angle of 29°, using a 1:1 chloronaphthalene:xylene mixture results in a reorientation of the T2 units from a face on into an edge on arrangement. In contrast the NDI unit remains unaffected. Additionally, for both solvents evidence is observed for the aggregation of chains in accord with recently published results obtained by UV-vis absorption spectroscopy.

show abstract

Section: ■ Materials and Methodsmentioning

confidence: 91%

“…41 In the framework of the this model the TM a exhibits an angle of 39°relative to the substrate (Θ = 51°), while b features an angle of 19°to it (Θ = 71°). The resulting normal vector of the NDI plane is tilted 45°away from the substrate normal, which is tantamount to the inclination of the NDI plane out of the film.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

Infrared Transition Moment Orientational Analysis on the Structural Organization of the Distinct Molecular Subunits in Thin Layers of a High Mobility n-Type Copolymer

et al. 2015

View full text Add to dashboard Cite

show abstract

“…79,84 Once the angle between the carbonyl group and the PART is known, the orientation order parameters for the CO bonds, ⟨P 2 ⟩ CO and ⟨P 4 ⟩ CO , can be calculated from the experimentally determined ⟨P 2 ⟩ and ⟨P 4 ⟩ values using the Legendre addition theorem. 90 Figure 6B shows the most probable orientation distribution function of CO groups in the disordered parts of an insulin fibril ( Figure 6B, red curve) calculated based on ⟨P 2 ⟩ CO and ⟨P 4 ⟩ CO . The function shows a binormal distribution for the C O group orientation with maxima at approximately 10°and 90°.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

Structural Organization of Insulin Fibrils Based on Polarized Raman Spectroscopy: Evaluation of Existing Models

Sereda

Sawaya²,

Lednev

2015

J. Am. Chem. Soc.

View full text Add to dashboard Cite

Many different proteins undergo misfolding and self-assemble into amyloid fibrils, resulting in a range of neurodegenerative diseases. The limitations of conventional methods of structural biology for fibril characterization have led to the use of polarized Raman spectroscopy for obtaining quantitative structural information regarding the organization of amyloid fibrils. Herein, we report the orientation of selected chemical groups and secondary structure elements in aligned insulin fibrils, including β-sheets, which possess a high level of orientation in the cross-β core, and α-helices in the disordered portions of the fibrils. Strong orientation of disulfide bonds in amyloid fibrils was also revealed, indicating their association with the fibril core. The determined orientation of chemical groups provides strong constraints for modeling the overall structure of amyloid fibrils, including the core and disordered parts. The developed methodology allows for the validation of structural models proposed in the literature for amyloid fibrils. Specifically, the polarized Raman data obtained herein strongly agreed with two insulin fibril models (Jiménez et al., Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 9196-9201 and Ivanova et al., Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 18990-18995) yet revealed significant qualitative and quantitative differences. This work demonstrates the great potential of polarized Raman spectroscopy for structural characterization of anisotropic biological species.

show abstract

“…As a consequence, the interfacial interaction between organics and clay minerals remains inaccessible by these techniques. Vibrational spectroscopies are some of the few molecular-level probes that are inherently orientation sensitive and provide an alternative method for probing the organization of both clay particles and organic molecules in the same preparation [17]. Moreover, Fourier transform infrared (FTIR) spectroscopy allows the study of dynamic processes on a 10 -14 -10 -12 s time scale, which is attainable for molecular dynamic simulations.…”

Section: Introductionmentioning

confidence: 99%

Orientation measurements of clay minerals by polarized attenuated total reflection infrared spectroscopy

Grégoire

Dazas

Hubert

et al. 2020

Journal of Colloid and Interface Science

View full text Add to dashboard Cite

The orientation and organization of molecular guests within the interlayer of clay minerals control the reactivity and performance of tailored organo-clay materials. Such a detailed investigation of hybrid structure on the molecular scale is usually provided by computational methods with limited experimental validation. In this study, polarized attenuated total reflection infrared spectroscopy was used to extract quantitative orientation measurements of montmorillonite particles. The validity of the evanescent electric field amplitude calculations necessary to derive the order parameter was critically evaluated to propose a methodology for determining the orientation of the normal to the clay layer relative to a reference axis, enabling comparison with the results obtained from X-ray scattering experiments and molecular dynamic simulations. Subsequently, the orientation of the interlayer water dipole and surface hydroxyls with respect to the normal of the clay layer was experimentally determined, showing good agreement with molecular simulations. This methodology may provide quantitative insights into the molecular-level description of interfacial processes between organic molecules and clay minerals.

show abstract

Basics of Orientation Measurements in Infrared and R aman Spectroscopy

Abstract: The sections in this article are Introduction Polarized IR Spectroscopy Experimental Determinations Tilted Film Method Thick Samples Polarized R aman Spectroscopy … Show more

Cited by 3 publications

References 7 publications

Infrared Transition Moment Orientational Analysis on the Structural Organization of the Distinct Molecular Subunits in Thin Layers of a High Mobility n-Type Copolymer

Infrared Transition Moment Orientational Analysis on the Structural Organization of the Distinct Molecular Subunits in Thin Layers of a High Mobility n-Type Copolymer

Structural Organization of Insulin Fibrils Based on Polarized Raman Spectroscopy: Evaluation of Existing Models

Orientation measurements of clay minerals by polarized attenuated total reflection infrared spectroscopy

Contact Info

Product

Resources

About