Rotational Isomerism of an Amide Substituted Squaraine Dye: A Combined Spectroscopic and Computational Study.
Ontology highlight
ABSTRACT:
SUBMITTER: Rosch AT
PROVIDER: S-EPMC8453623 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Lipid lateral diffusion in membrane bilayers is a fundamental process exploited by cells to enable complex protein structural and dynamic reorganizations. For its importance, lipid mobility in both cellular and model bilayers has been extensively investigated in recent years, especially through the application of time-resolved, fluorescence-based, optical microscopy techniques. However, one caveat of fluorescence techniques is the need to use dye-labeled variants of the lipid of interest, thus potentially perturbing the structural and dynamic properties of the native species. Generally, the effect of the dye/tracer molecule is implicitly assumed to be negligible. Nevertheless, in view of the widespread use of optically modified lipids for studying lipid bilayer dynamics, it is highly desirable to well assess this point. Here, fluorescence correlation spectroscopy (FCS) and molecular dynamics (MD) simulations have been combined together to uncover subtle structural and dynamic effects in DOPC planar membranes enriched with a standard Rhodamine-labeled lipid. Our findings support a non-neutral role of the dye-labeled lipids in diffusion experiments, quantitatively estimating a decrease in lipid mobility of up to 20% with respect to the unlabeled species. Moreover, results highlight the existing interplay between dye concentration, lipid lateral diffusion and membrane permeability, thus suggesting possible implications for future optical microscopy studies of biophysical processes occurring at the membrane level.
| S-EPMC6365552 | biostudies-literature
Project description:Dye-decolorizing peroxidase (DyP) of Auricularia auricula-judae has been expressed in Escherichia coli as a representative of a new DyP family, and subjected to mutagenic, spectroscopic, crystallographic and computational studies. The crystal structure of DyP shows a buried haem cofactor, and surface tryptophan and tyrosine residues potentially involved in long-range electron transfer from bulky dyes. Simulations using PELE (Protein Energy Landscape Exploration) software provided several binding-energy optima for the anthraquinone-type RB19 (Reactive Blue 19) near the above aromatic residues and the haem access-channel. Subsequent QM/MM (quantum mechanics/molecular mechanics) calculations showed a higher tendency of Trp-377 than other exposed haem-neighbouring residues to harbour a catalytic protein radical, and identified the electron-transfer pathway. The existence of such a radical in H₂O₂-activated DyP was shown by low-temperature EPR, being identified as a mixed tryptophanyl/tyrosyl radical in multifrequency experiments. The signal was dominated by the Trp-377 neutral radical contribution, which disappeared in the W377S variant, and included a tyrosyl contribution assigned to Tyr-337 after analysing the W377S spectra. Kinetics of substrate oxidation by DyP suggests the existence of high- and low-turnover sites. The high-turnover site for oxidation of RB19 (k(cat) > 200 s⁻¹) and other DyP substrates was assigned to Trp-377 since it was absent from the W377S variant. The low-turnover site/s (RB19 k(cat) ~20 s⁻¹) could correspond to the haem access-channel, since activity was decreased when the haem channel was occluded by the G169L mutation. If a tyrosine residue is also involved, it will be different from Tyr-337 since all activities are largely unaffected in the Y337S variant.
| S-EPMC4357238 | biostudies-literature
Project description:The metallic cyanoacetylides LiC3N, NaC3N, MgC3N and CaC3N have been investigated by combined spectroscopy measurements and theoretical calculations. The theoretical calculations predict for the four species that the linear isomer with formula MCCCN (M= Li, Na, Mg and Ca) is the most stable one. We used the laser ablation molecular beam Fourier transform microwave spectroscopy to synthesize these species by the reaction of metal vapors, produced by laser ablation, and the 3-bromo-2-propynenitrile (BrCCCN). The pure rotational spectra were observed by Fourier transform microwave spectroscopy in the 2-18 GHz frequency region only for LiCCCN and NaCCCN, while no spectral signatures for MgCCCN and CaCCCN could be detected. Finally, we have searched for LiCCCN and NaCCCN species towards the carbon-rich evolved star IRC + 10216 but only upper limits to their abundances have been obtained.
| S-EPMC6739221 | biostudies-literature
Project description:We present a computational study on tetrapnictide dianions Pn 4 2- (Pn = P, As, Sb, Bi), using density functional theory (DFT), coupled-cluster [DLPNO-CCSD(T)] and complete active space self-consistent field (CASSCF) methods. Environmental effects such as solvation and coordination of counterions are included. The calculations reveal that out of three isomers (square-planar, butterfly and capped-triangle), the square planar isomers are generally the most stable. The counterion (Li+ and Mg2+) used in the calculations have a substantial effect on the relative stabilities. The square planar isomers show considerable biradical character. Calculated reactions toward alkenes indicate that this unusual electronic structure has significant implications on the reactivity of the Pn 4 2- dianions.
| S-EPMC7590082 | biostudies-literature
Project description:The structural dependence of the photo-physical properties of substituted 2,3-distyryl (23DSI) indoles were studied using several spectroscopic techniques including steady-state UV-VIS spectroscopy, steady-state fluorescence spectroscopy, steady-state excitation spectroscopy, time correlated single photon counting (TCSPC) spectroscopy, and time-resolved fluorescence upconversion spectroscopy (TRFLS). Each of 23DSI derivatives investigated showed distinct fluorescence emission and UV-VIS spectra, indicating strong structural dependence of the emission and the excitation. The UV-VIS spectra of the 23DSI derivatives showed three main identical absorption bands with minor deviations in the absorbance caused by substituent groups on the distyryl rings. The time-resolved fluorescence up-conversion studies indicated that the fluorescence undergoes a mono-exponential decay whereas the calculated fluorescence lifetime showed relatively short fluorescence lifetimes of approximately 1 ns. All of the 23DSI derivatives showed two-photon absorption upon direct excitation of 1.6 W laser pulses at 800 nm. These studies suggest that the substituents, attached to distyryl core, are capable of boosting or hindering fluorescence intensities by distorting the ?-conjugation of the 23DSI molecule. Our studies showed that 23DSI (p-F) has the highest fluorescence emission quantum yield. Theoretical calculations for the ground state of 23DSI derivatives confirmed differences in electron densities in 23DSI derivatives in the presence of different substituent attachments. The excellent fluorescence emission, high fluorescence quantum yield and two-photon absorption properties of these 23DSI molecules make them attractive candidates for potential applications in the fields of biological imaging, biomedicine, fluorescent probes, and photodynamic inactivation (PDI). B. subtilis samples, treated with micro molar solutions of 23DSI (p-OCH3) and 23DSI (p-CH3), showed very effective photodynamic inactivation (PDI) upon irradiation with white light.
| S-EPMC6643299 | biostudies-literature
Project description:Metal-ligand cooperation is an important aspect in earth-abundant metal catalysis. Utilizing ligands as electron reservoirs to supplement the redox chemistry of the metal has resulted in many new exciting discoveries. Here, we demonstrate that iron bipyridine-diimine (BDI) complexes exhibit an extensive electron-transfer series that spans a total of five oxidation states, ranging from the trication [Fe(BDI)]3+ to the monoanion [Fe(BDI]-1. Structural characterization by X-ray crystallography revealed the multifaceted redox noninnocence of the BDI ligand, while spectroscopic (e.g., 57Fe Mössbauer and EPR spectroscopy) and computational studies were employed to elucidate the electronic structure of the isolated complexes, which are further discussed in this report.
| S-EPMC8653161 | biostudies-literature
Project description:For all the amides detected in the interstellar medium (ISM), the corresponding nitriles or isonitriles have also been detected in the ISM, some of which have relatively high abundances. Among the abundant nitriles for which the corresponding amide has not yet been detected is cyanoacetylene (HCCCN), whose amide counterpart is propiolamide (HCCC(O)NH2). With the aim of supporting searches for this amide in the ISM, we provide a complete rotational study of propiolamide from 6 GHz to 440 GHz. Time-domain Fourier transform microwave (FTMW) spectroscopy under supersonic expansion conditions between 6 GHz and 18 GHz was used to accurately measure and analyze ground-state rotational transitions with resolved hyperfine structure arising from nuclear quadrupole coupling interactions of the 14N nucleus. We combined this technique with the frequency-domain room-temperature millimeter wave and submillimeter wave spectroscopies from 75 GHz to 440 GHz in order to record and assign the rotational spectra in the ground state and in the low-lying excited vibrational states. We used the ReMoCA spectral line survey performed with the Atacama Large Millimeter/submillimeter Array toward the star-forming region Sgr B2(N) to search for propiolamide. We identified and measured more than 5500 distinct frequency lines of propiolamide in the laboratory. These lines were fitted using an effective semi-rigid rotor Hamiltonian with nuclear quadrupole coupling interactions taken into consideration. We obtained accurate sets of spectroscopic parameters for the ground state and the three low-lying excited vibrational states. We report the nondetection of propiolamide toward the hot cores Sgr B2(N1S) and Sgr B2(N2). We find that propiolamide is at least 50 and 13 times less abundant than acetamide in Sgr B2(N1S) and Sgr B2(N2), respectively, indicating that the abundance difference between both amides is more pronounced by at least a factor of 8 and 2, respectively, than for their corresponding nitriles. Although propiolamide has yet to be included in astrochemical modeling networks, the observed upper limit to the ratio of propiolamide to acetamide seems consistent with the ratios of related species as determined from past simulations. The comprehensive spectroscopic data presented in this paper will aid future astronomical searches.
| S-EPMC7611197 | biostudies-literature
Project description:Cyanoacetamide is a -CN bearing molecule that is also an amide derivative target molecule in the interstellar medium. The aim of our investigation is to analyze the feasibility of a plausible formation process of protonated cyanoacetamide under interstellar conditions and to provide direct experimental frequencies of the ground vibrational state of the neutral form in the microwave region in order to enable its eventual identification in the interstellar medium. We used high-level theoretical computations to study the formation process of protonated cyanoacetamide. Furthermore, we employed a high-resolution laser-ablation molecular beam Fourier transform spectroscopic technique to measure the frequencies of the neutral form. We report the first rotational characterization of cyanoacetamide, and a precise set of the relevant rotational spectroscopic constants have been determined as a first step to identifying the molecule in the interstellar medium. We fully explored the potential energy surface to study a gas-phase reaction on the formation process of protonated cyanoacetamide. We found that an exothermic process with no net activation barrier is initiated by the high-energy isomer of protonated hydroxylamine, which leads to protonated cyanoacetamide.
| S-EPMC7116755 | biostudies-literature
Project description:Centers for Disease Control and Prevention (CDC) warns the use of one-way valves or vents in face masks for potential threat of spreading COVID-19 through expelled respiratory droplets. Here, we have developed a nanoceutical cotton fabric duly sensitized with non-toxic zinc oxide nanomaterial for potential use as a membrane filter in the one-way valve for the ease of breathing without the threat of COVID-19 spreading. A detailed computational study revealed that zinc oxide nanoflowers (ZnO NFs) with almost two-dimensional petals trap SARS-CoV-2 spike proteins, responsible to attach to ACE-2 receptors in human lung epithelial cells. The study also confirmed significant denaturation of the spike proteins on the ZnO surface, revealing removal of the virus upon efficient trapping. Following the computational study, we have synthesized ZnO NF on a cotton matrix using a hydrothermal-assisted strategy. Electron-microscopic, steady-state, and picosecond-resolved spectroscopic studies confirm attachment of ZnO NF to the cotton (i.e., cellulose) matrix at the atomic level to develop the nanoceutical fabric. A detailed antimicrobial assay using Pseudomonas aeruginosa bacteria (model SARS-CoV-2 mimic) reveals excellent antimicrobial efficiency of the developed nanoceutical fabric. To our understanding, the nanoceutical fabric used in the one-way valve of a face mask would be the choice to assure breathing comfort along with source control of COVID-19 infection. The developed nanosensitized cloth can also be used as an antibacterial/anti CoV-2 washable dress material in general.
| S-EPMC8231689 | biostudies-literature
Project description:In this paper, substituted anilines are industrially obtained by direct hydrogenation of nitroaromatic compounds with molecular H2 using metals as catalysts. Previous theoretical studies proposed that the mechanism of the reaction depends on the nature of the metal used as a catalyst, and that rationally designed bimetallic materials might show improved catalytic performance. Herein, we present IR spectroscopic studies of nitrobenzene interactions with monometallic Ni/SiO2, Cu/SiO2 and Pd/SiO2, and with bimetallic CuNi/SiO2 and CuPd/SiO2 catalysts, both in the absence and presence of H2, combined with density functional theory (DFT) calculations on selected bimetallic NiCu(111) and PdCu(111) models. The results obtained experimentally confirm that the reaction mechanism on non-noble metals such as Ni proceeds through N-O bond dissociation, generating nitrosobenzene intermediates, while, on noble metals, such as Pd, H-attack is necessary to activate the NO bond. Moreover, a bimetallic CuPd/SiO2 catalyst with a Pd enriched surface is prepared that exhibits an enhanced H2 dissociation ability and a particular reactivity at the boundary between the two metals.
| S-EPMC8398056 | biostudies-literature