Steady-State Linear and Non-linear Optical Spectroscopy of Organic Chromophores and Bio-macromolecules

Abstract

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.

Spectroscopic Properties of Lumiflavin: A Quantum Chemical Study

“…The consideration of low energy, low‐frequency modes is another important factor as demonstrated via sampling of the ground state PES by Marazzi et al . . Vibrational broadening can be also included via the vertical and adiabatic Franck–Condon approaches (VFC and AFC) as demonstrated by Karasulu et al .…”

Charge‐Transfer versus Charge‐Separated Triplet Excited States of [ReI(dmp)(CO)3(His124)(Trp122)]+ in Water and in Modified Pseudomonas aeruginosa Azurin Protein

“…A LANL2DZ basis set, including pseudopotential for the Re atom, was used throughout the calculations. From the GS snapshots, the absorption spectrum was calculated by using TD‐DFT formalism as a convolution of all vertical transitions obtained for each snapshot, following a strategy currently used in our groups …”

“…From the GS snapshots, the absorption spectrum was calculated by using TD-DFT formalism as ac onvolution of all vertical transitions obtained for each snapshot, following a strategy currently used in our groups. [10,[46][47][48][49][50][51] For each of the snapshots obtained from the 3 MLCT and 3 CS dynamics, the lowest triplet state (T 1 )w as calculated at the DFT level and the spin density analyzed to assure the stability of the electronic state. Finally,aQM/MM geometry optimization of every snapshot was performed, calculating again the spin density.A ll QM/MM calculations were carried out by using the Te rachem code, [52] with its interface with the Amber suite to treat the MM environment at the electrostatic embedding level.…”

Recent Advancements in Ln‐Ion‐Based Upconverting Nanomaterials and Their Biological Applications

“…The concept of photon upconversion is developed from anti‐Stokes emission process generated by upconverting luminescent materials. In conventional host luminescent nanomaterials, anti‐Stokes emission is generated through simultaneous two‐photon absorption (STPA) and second harmonic generation (SHG) . These photon absorption processes need an ultrashort pulse laser (e.g., femtosecond pulse laser) with extremely high exciting power‐density (10 6 –10 9 W cm −2 ) to produce large numbers of excitation photons and, the use of such a pulse laser is very expensive .…”

“…These photon absorption processes need an ultrashort pulse laser (e.g., femtosecond pulse laser) with extremely high exciting power‐density (10 6 –10 9 W cm −2 ) to produce large numbers of excitation photons and, the use of such a pulse laser is very expensive . Another drawback is the use of non‐centrosymmetric molecular structure with a weak D–π–A configuration (D: donor, A: acceptor) that results in low two‐photon absorption (TPA) capacity . Many efforts have been made to enhance the TPA capacity by optimizing the atomic or molecular structure, which includes conformation rigidity, strong π‐conjugation, and incorporation of electron donors and acceptor atoms on a π‐conjugated structure .…”