Unspecified verticality of Franck–Condon transitions, absorption and emission spectra of cyanine dyes, and a classically inspired approximation

A novel near-infrared polymethine dye biosensor for rapid and selective detection of lithocholic acid

Lithocholic acid (LCA), a secondary bile acid, has emerged as a potential early diagnostic biomarker for various liver diseases. In this study, we introduce a novel near-infrared (NIR) polymethine dye-based biosensor, capable of sensitive and selective detection of LCA in phosphate buffer and artificial urine (AU) solutions. The detection mechanism relies on the formation of J-aggregates resulting from the interplay of 3,3-Diethylthiatricarbocyanine iodide (DiSC2(7)) dye molecules and LCA, which induces a distinctive red shift in both absorption and fluorescence spectra. The biosensor demonstrates a detection limit for LCA of 70 μM in PBS solution (pH 7.4), while in AU solution, it responds to an LCA concentration as low as ∼60 μM. Notably, the proposed biosensor exhibits outstanding selectivity for LCA, effectively distinguishing it from common interferents such as uric acid, ascorbic acid, and glucose. This rapid, straightforward, and cost-effective spectrometer-based method underscores its potential for early diagnosis of liver diseases by monitoring LCA concentrations.

Spectroscopic approaches for studies of site-specific DNA base and backbone 'breathing' using exciton-coupled dimer-labeled DNA

DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA 'breathing') play a central role in such processes. Here we review the development and application of novel spectroscopic methods and analyses - both at the ensemble and single-molecule levels - to study structural and dynamic properties of exciton-coupled cyanine and fluorescent nucleobase analogue dimer-labeled DNA constructs at key positions involved in protein-DNA complex assembly and function. The exciton-coupled dimer probes act as 'sensors' of the local conformations adopted by the sugar-phosphate backbones and bases immediately surrounding the dimer probes. These methods can be used to study the mechanisms of protein binding and function at these sites.

Unravelling the Origin of the Vibronic Spectral Signatures in an Excitonically Coupled Indocarbocyanine Cy3 Dimer

The indocarbocyanine Cy3 dye is widely used to probe the dynamics of proteins and DNA. Excitonically coupled Cy3 dimers exhibit very unique spectral signatures that depend on the interchromophoric geometrical orientation induced by the environment, making them powerful tools to infer the dynamics of their surroundings. Understanding the origin of the dimeric spectral signatures is a necessity for an accurate interpretation of the experimental results. In this work, we simulate the vibronic spectrum of an experimentally well-studied Cy3 dimer, and we explain the origin of the experimental signatures present in its linear absorption spectrum. The Franck-Condon harmonic approximations, among other tests, are used to probe the factors contributing to the spectrum. It is found that the first peak in the absorption spectrum originates from the lower energy excitonic state, while the next two peaks are vibrational progressions of the higher energy excitonic state. The polar solvent plays a crucial role in the appearance of the spectrum, being responsible for the localized S1 minimum, which results in an increased intensity of the first peak.

Chemical Transformations Can Occur during DMS Separations: Lessons Learned from Beer's Bittering Compounds

While developing a DMS-based separation method for beer's bittering compounds, we observed that the argentinated forms of humulone tautomers (i.e., [Hum + Ag]⁺) were partially resolvable in a N₂ environment seeded with 1.5 mol % of isopropyl alcohol (IPA). Attempting to improve the separation by introducing resolving gas unexpectedly caused the peaks for the cis-keto and trans-keto tautomers of [Hum + Ag]⁺ to coalesce. To understand why resolution loss occurred, we first confirmed that each of the tautomeric forms (i.e., dienol, cis-keto, and trans-keto) responsible for the three peaks in the [Hum + Ag]⁺ ionogram were assigned to the correct species by employing collision-induced dissociation, UV photodissociation spectroscopy, and hydrogen-deuterium exchange (HDX). The observation of HDX indicated that proton transfer was stimulated by dynamic clustering processes between IPA and [Hum + Ag]⁺ during DMS transit. Because IPA accretion preferentially occurs at Ag⁺, which can form pseudocovalent bonds with a suitable electron donor, solvent clustering also facilitated the formation of exceptionally stable microsolvated ions. The exceptional stability of these microsolvated configurations disproportionately impacted the compensation voltage (CV) required to elute each tautomer when the temperature within the DMS cell was varied. The disparity in CV response caused the peaks for the cis- and trans-keto species to merge when a temperature gradient was induced by the resolving gas. Moreover, simulations showed that microsolvation with IPA mediates dienol to trans-keto tautomerization during DMS transit, which, to the best of our knowledge, is the first observation of keto/enol tautomerization occurring within an ion-mobility device.

Modeling the Electronic Absorption Spectra of the Indocarbocyanine Cy3

Accurate modeling of optical spectra requires careful treatment of the molecular structures and vibronic, environmental, and thermal contributions. The accuracy of the computational methods used to simulate absorption spectra is limited by their ability to account for all the factors that affect the spectral shapes and energetics. The ensemble-based approaches are widely used to model the absorption spectra of molecules in the condensed-phase, and their performance is system dependent. The Franck–Condon approach is suitable for simulating high resolution spectra of rigid systems, and its accuracy is limited mainly by the harmonic approximation. In this work, the absorption spectrum of the widely used cyanine Cy3 is simulated using the ensemble approach via classical and quantum sampling, as well as, the Franck–Condon approach. The factors limiting the ensemble approaches, including the sampling and force field effects, are tested, while the vertical and adiabatic harmonic approximations of the Franck–Condon approach are also systematically examined. Our results show that all the vertical methods, including the ensemble approach, are not suitable to model the absorption spectrum of Cy3, and recommend the adiabatic methods as suitable approaches for the modeling of spectra with strong vibronic contributions. We find that the thermal effects, the low frequency modes, and the simultaneous vibrational excitations have prominent contributions to the Cy3 spectrum. The inclusion of the solvent stabilizes the energetics significantly, while its negligible effect on the spectral shapes aligns well with the experimental observations.

Acriflavine in aqueous solution: excitation and hydration

Using TD-DFT/DFT, the ground and excited states of the acriflavine dye were studied in an aqueous medium. The mutual influence of photoexcitation and strong hydrogen bonds with the solvent was studied by comparing the purely implicit and combined modeling of the aqueous environment of the dye. The excitation of acriflavine was calculated considering the vibronic coupling. The effect of photoexcitation on dye vibrations was analyzed. The spatial structure of the acriflavine H-dimer was obtained and its absorption was estimated.

Coumarin 343 in aqueous solution: theoretical analysis of absorption

Vibronic coupling and hydration were taken into account when describing the absorption of coumarin C343 (both neutral and anionic forms) in an aqueous media. It was shown that the B3LYP functional with the 6-31 +  + G(d,p) basis set and the IEFPCM solvent continuum model give theoretical vibronic absorption spectra, which are coincide with the experimental ones. Of the structural differences between C343⁰ and C343^-, there is a different twisting of the carboxyl group additionally changing due to excitation. Upon excitation, a significant shift in the electron density occurs from the C10 atom to the C4 atom only. Thus, a charge transfer on the scale of the entire molecule does not occur. Different hydration complexes with strongly bound water molecules have been analyzed.

Excitation of rhodamine 800 in aqueous media: a theoretical investigation

The main goal of this work was to obtain a calculated absorption spectrum of rhodamine 800 in an aqueous solution, which most accurately reproduces the experimental one. To achieve this result, I used the hybrid functionals supported by Gaussian 16 software package. In this case, the basis set (6-31++G(d,p)) and the solvent model (IEFPCM) were not varied. The B3PW91 functional gave the best agreement with the experimental absorption spectrum of the dye in an aqueous medium. B3P86, B971, B972, B98, X3LYP, APF, HSE06, and N12SX functionals also give good absorption energy coincidence. The B3PW91/6-31++G(d,p)/IEFPCM theory level chosen in this way made it possible to calculate the various characteristics of rhodamine 800 in the ground and excited states. An important result of this work was the establishment of the vibronic nature of the short-wavelength smaller maximum of the absorption spectrum. The influence of the strong H-bond of the exocyclic nitrogen atom with the water molecule on the dye excitation was analyzed.

UVPD Spectroscopy of Differential Mobility-Selected Prototropic Isomers of Rivaroxaban

Two ion populations of protonated Rivaroxaban, [C₁₉H₁₈ClN₃O₅S + H]⁺, are separated under pure N₂ conditions using differential mobility spectrometry prior to characterization in a hybrid triple quadrupole linear ion trap mass spectrometer. These populations are attributed to bare protonated Rivaroxaban and to a proton-bound Rivaroxaban-ammonia complex, which dissociates prior to mass-selecting the parent ion. Ultraviolet photodissociation (UVPD) and collision-induced dissociation (CID) studies indicate that both protonated Rivaroxaban ion populations are comprised of the computed global minimum prototropic isomer. Two ion populations are also observed when the collision environment is modified with 1.5% (v/v) acetonitrile. In this case, the protonated Rivaroxaban ion populations are produced by the dissociation of the ammonium complex and by the dissociation of a proton-bound Rivaroxaban-acetonitrile complex prior to mass selection. Again, both populations exhibit a similar CID behavior; however, UVPD spectra indicate that the two ion populations are associated with different prototropic isomers. The experimentally acquired spectra are compared with computed spectra and are assigned to two prototropic isomers that exhibit proton sharing between distal oxygen centers.

Abbreviations for dyes, stains and fluorescent probes used in biology and medicine in the 21st century. A bright future or the last gasp?

I summarize here the history of the use of abbreviations, mostly in subject areas related to dyes, stains and fluorescent probes used in biology and medicine. The dozen most popular abbreviations in these fields are identified and their salient characteristics noted. The pros and cons of each abbreviation are discussed with relevant citations. Certain abbreviations that are not in the list, e.g., AZAN and LN, are mentioned because they have an unusual origin; while others, i.e., INEPT and INADEQUATE are presented because they are bizarre. A related topic is abbreviations used for citations, which require further efforts to decipher. In the past, brevity helped conserve materials, such as ink and paper, and promoted more rapid publishing. I suggest that the use of many abbreviations in the current era of electronic publishing may not be necessary.