Conformation effects on the absorption spectra of macromolecules (original) (raw)
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The Journal of Chemical Physics, 2021
The effect of the shape (habit) of crystalline organic nanoparticles on their absorption spectra is studied by simulations using the discrete dipole approximation, focusing, in particular, on the vibronic structure of the absorption bands in the spectra. Simulations predict a significant effect that, for sufficiently small particles, can be simply rationalized by the depolarization factor. The crystal size and the refractive index of the medium in which the nanoparticles are embedded are also found to have an effect on the absorption spectra. All factors mentioned are found to influence also the spectra of scattered light. These effects, already broadly documented for metallic nanoparticles, are here demonstrated theoretically for the first time for crystalline organic nanoparticles, providing novel insight into the optical response of such particles. The effects are expected to be displayed by all organic nanoparticles, as long as they have a welldefined crystal structure and are large enough for the optical properties to be understandable using a macroscopic dielectric tensor. The effects demonstrated here should be taken into account when rationalizing differences in absorption spectra of a substance in solution and in nanoparticle form, e.g., in deducing the type of intermolecular packing. The effects are much less pronounced for optically isotropic nanoparticles.
Frontiers in Chemistry
Bio-macromolecules as DNA, lipid membranes and (poly)peptides are essential compounds at the core of biological systems. The development of techniques and methodologies for their characterization is therefore necessary and of utmost interest, even though difficulties can be experienced due to their intrinsic complex nature. Among these methods, spectroscopies, relying on optical properties are especially important to determine their macromolecular structures and behaviors, as well as the possible interactions and reactivity with external dyes-often drugs or pollutants-that can (photo)sensitize the bio-macromolecule leading to eventual chemical modifications, thus damages. In this review, we will focus on the theoretical simulation of electronic spectroscopies of bio-macromolecules, considering their secondary structure and including their interaction with different kind of (photo)sensitizers. Namely, absorption, emission and electronic circular dichroism (CD) spectra are calculated and compared with the available experimental data. Non-linear properties will be also taken into account by two-photon absorption, a highly promising technique (i) to enhance absorption in the red and infra-red windows and (ii) to enhance spatial resolution. Methodologically, the implications of using implicit and explicit solvent, coupled to quantum and thermal samplings of the phase space, will be addressed. Especially, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are explored for a comparison with solely QM methods, in order to address the necessity to consider an accurate description of environmental effects on spectroscopic properties of biological systems.
Dynamic light scattering from polymers
Die Makromolekulare Chemie, 1979
Applications of both polarized and depolarized dynamic light scattering to the study of polymers are described. Polarized light scattering is used to study translational diffusion, diffusion virial coefficients, rotational motion of long rod-shaped polymers, longwavelength intramolecular motions, dynamics of pseudogels and gels and density fluctuations in bulk polymers. Depolarized scattering is used to study rotational diffusion of rigid macromolecules, local and long-wavelength intramolecular motions, dynamics in semi-dilute solutions, rotational motion of small molecules in glassy polymers and optical anisotropy fluctuations of bulk polymers.
The Journal of Physical Chemistry B, 2012
Infrared spectroscopy has long provided a means to estimate the secondary structure of proteins and peptides. In particular, the vibrational spectra of the amide I′ band have been widely used for this purpose as the frequency positions of the amide I′ bands are related to the presence of specific secondary structures. Here, we calculate the amide I′ IR spectra of polylysine in aqueous solution in its three secondary structure states, i.e., α-helix, β-sheet, and random coil, by means of a mixed quantum mechanics/molecular dynamics (QM/MD) theoretical−computational methodology based on the perturbed matrix method (PMM). The computed spectra show a good agreement with the experimental ones. Although our calculations confirm the importance of the excitonic coupling in reproducing important spectral features (e.g., the width of the absorption band), the frequency shift due to secondary-structure changes is also well reproduced without the inclusion of the excitonic coupling, pointing to a role played by the local environment. Concerning the β-conformation spectrum, which is characterized by a double-peak amide I′ band due to excitonic coupling, our results indicate that it does not correspond to a generic antiparallel β-sheet (e.g., of the typical size present in native proteins) but is rather representative of extended β-structures, which are common in β-aggregates. Moreover, we also show that the solvent has a crucial role in the shape determination of the β-conformation amide I′ band and in particular in the disappearance of the high-frequency secondary peak in the case of small sheets (e.g., 6-stranded).
Modelling of molecular light scattering
Fluid Phase Equilibria, 2011
The scattering of light originates from the fluctuation in the permittivity that gives rise to a turbidity of the fluid. The turbidity of an otherwise homogeneous fluid is, according to Einstein's theory, proportional to the mean-square fluctuation in the relative permittivity. A general expression for the mean-square fluctuation or variance of a fluctuating property is derived. It shows that the turbidity depends on the second derivatives of an appropriately chosen state function-the choice is dependent on which properties that fluctuate. The paper provides a general derivation and outlines the criteria for the choice of state function. Data for light-scattering are modelled using the Clausius-Mossotti equation and an excess Gibbs energy function. The excess Gibbs energy applied consists of three terms: Flory-Huggins (accounting for the size of the components), Debye-Hückel (accounting for the charges of electrolytes) and Kirkwood (accounting for the dipolar nature of proteins). The present investigation shows that the model parameters determined by light-scattering experiments have a well-defined physical significance and light-scattering data can thus be used in parallel with other data to provide information from which model parameters can be estimated.
The Journal of Physical Chemistry A
A detailed understanding and interpretation of absorption spectra of molecular systems, especially in condensed phases, requires computational models that allow their structural and electronic features to be connected to the observed macroscopic spectra. This work is focused on modeling the electronic absorption spectrum of a fluorescent probe, namely, the 9-(4-((bis(2-((2-(ethylthio)ethyl)thio)ethyl)amino)methyl)phenyl)-6-(pyrrolidin-1-yl)-3H-xanthen-3-one molecule, depicted by a combined classical-quantum chemical approach. Particularly, first classical molecular dynamics (MD) has been used to explore the configurational space, and next, the absorption spectrum has been reconstructed by averaging the results of time-dependent density functional theory (TD-DFT) calculations performed on equispaced molecular conformations extracted from MD to properly sample the configurational space explored at finite temperature. To verify the effect of molecular conformation on the spectral profile, the generated electronic absorption spectra were compared with those obtained considering a single structure corresponding to the optimized one, an approach also referred to as static. This comparison allows one to highlight a sizable though small shift between the maxima of the corresponding reconstructed absorption spectra, highlighting the importance of conformational sampling in the case of this rather flexible molecule. Four different exchange and correlation functionals (PBE, BLYP, PBE0, B3LYP) were considered to compute vertical transition via TD-DFT calculations. From the results obtained in gas and in condensed, here solution, phases, it appears that the magnitude of the shift is actually more affected by the phase in which the system is found than by the functional used. This fact underlines the central importance of conformational mobility, that is flexibility, of this molecule. From a more quantitative point of view, a comparison with available experimental data shows that hybrid functionals, such as PBE0 and B3LYP, enable one to faithfully reproduce the observed absorption maxima.