This study explores the structural and electronic factors affecting the absorption spectra of 5-carboxy-tetramethylrhodamine (TAMRA) in water, a widely used fluorophore in imaging and molecular labeling in biophysical studies. Through molecular dynamics (MD) simulations and density functional theory (DFT) calculations, we examine TAMRA UV absorption spectra together with TAMRA-labeled peptides (Arg9, Arg4, Lys9). We found that DFT calculations with different functionals underestimate TAMRA maximum UV absorption peak by ~100 nm, resulting in the maximum at ca. 450 nm instead of the experimental value of ca. 550 nm. However, incorporating MD simulation snapshots of TAMRA in water, the UV maximum peak shifts and is in close agreement with the experimental results due to the rotation of TAMRA N(CH3)2 groups, effectively captured in MD simulations. The method is used to estimate the UV absorption spectra of TAMRA-labeled peptides, matching experimental values.

• Klíčová slova
• UV absorption spectra, fluorescent probes, molecular dynamics simulations, time‐dependent density functional theory,
• MeSH
• fluorescenční barviva chemie   MeSH
• peptidy * chemie   MeSH
• rhodaminy * chemie   MeSH
• simulace molekulární dynamiky * MeSH
• spektrofotometrie ultrafialová MeSH
• teorie funkcionálu hustoty * MeSH
• voda chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• 5-carboxytetramethylrhodamine succinimidyl ester MeSH Prohlížeč
• fluorescenční barviva MeSH
• peptidy * MeSH
• rhodaminy * MeSH
• voda MeSH

In this study, a functionalized graphene oxide-cerium oxide nanocatalysts (FGCe) with varying graphene oxide (GO) contents were prepared using an in-situ reflux method. The prepared nanocatalysts showcased improvement in the crystallinity and BET surface area values with increasing GO contents. The efficacies of prepared catalysts were investigated towards oxidative pyrolysis of alkali lignin in an ethanol-water system. Among various nanocatalyst samples, the best lignin conversion (93 %) and bio-oil yield (86 %) were achieved using 50 mg FGCe nanocatalyst (0.5 wt% GO) at 423 K and 60 min. GC-MS and 1HNMR analyses were used to identify significant lignin conversion products, including 2-pentanone-4-hydroxy-4-methyl, 2-methoxyphenol, nonylcyclopropane, vanillin, apocynin, homovanollic acid, and benzoic acid. Kinetic studies revealed that the activation energy for lignin conversion was 24.36 kJ/mol at 423 K. Mechanistic investigations by density functional theory analysis revealed that the lignin breakdown occurred at oxygen bonds producing aromatic.

• Klíčová slova
• Alkali lignin, Cerium oxide, Density functional theory, Functionalized graphene oxide, Pyrolysis,
• MeSH
• alkálie * chemie   MeSH
• cer * chemie   MeSH
• dusík * chemie   MeSH
• grafit * chemie   MeSH
• katalýza MeSH
• kinetika MeSH
• lignin * chemie   MeSH
• oleje rostlin MeSH
• oxidace-redukce MeSH
• plynová chromatografie s hmotnostně spektrometrickou detekcí MeSH
• polyfenoly MeSH
• pyrolýza * MeSH
• teorie funkcionálu hustoty MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• alkálie * MeSH
• Bio-Oil MeSH Prohlížeč
• cer * MeSH
• ceric oxide MeSH Prohlížeč
• dusík * MeSH
• grafit * MeSH
• graphene oxide MeSH Prohlížeč
• lignin * MeSH
• oleje rostlin MeSH
• polyfenoly MeSH

We use real-time density functional theory on a real-space grid to calculate electronic excitations of bacteriochlorophyll chromophores of the light-harvesting complex 2 (LH2). Comparison with Gaussian basis set calculations allows us to assess the numerical trust range for computing electron dynamics in coupled chromophores with both types of techniques. Tuned range-separated hybrid calculations for one bacteriochlorophyll as well as two coupled ones are used as a reference against which we compare results from the adiabatic time-dependent local density approximation (TDLDA). The tuned range-separated hybrid calculations lead to a qualitatively correct description of the electronic excitations and couplings. They allow us to identify spurious charge-transfer excitations that are obtained with the TDLDA. When we take into account the environment that the LH2 protein complex forms for the bacteriochlorophylls, we find that it substantially shifts the energy of the spurious charge-transfer excitations, restoring a qualitatively correct electronic coupling of the dominant excitations also for TDLDA.

• MeSH
• bakteriochlorofyly chemie   MeSH
• Beijerinckiaceae chemie   MeSH
• chemické modely MeSH
• přenos energie MeSH
• světlosběrné proteinové komplexy chemie   MeSH
• teorie funkcionálu hustoty MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• bakteriochlorofyly MeSH
• světlosběrné proteinové komplexy MeSH

AIMS: The aim of the present research was to synthesize glycoluril derivative 2,4-Bis(4- cyanobenzyl)glycoluril through a convergent scheme. BACKGROUND: For this purpose, Sandmeyer reaction procedure was employed for the synthesis of said compound. The structure of the pure compound was confirmed by using different spectroscopic techniques, such as 1HNMR, 13C-NMR and (HR-MS) Mass spectrometry. OBJECTIVE: Convergent synthesis of 2,4-BIS (4-CYANOBENZYL)GLYCOLURIL USING SANDMEYER REACTION and urease inhibition study. METHODS: The structure of the pure compound was confirmed by using different spectroscopic techniques such as 1H-NMR, 13C-NMR and (HR-MS) Mass spectrometry. The electronic properties of the newly synthesized compound and thiourea were determined by using density functional theory. RESULTS: Furthermore, the compound was evaluated against urease enzyme and was found to be potent inhibitors with an IC50 value of 11.5 ± 1.50 μM when compared with standard inhibitor thiourea (IC50 = 21.0 ± 1.90 μM). The compound may serve as a lead compound to synthesize new cyano-based bambusuril in the future with enhanced biological properties. CONCLUSION: We have synthesized a new glycoluril derivative 2,4-Bis(4-cyanobenzyl)glycoluril by the sandmeyer reaction. It has been obtained in the form of light yellowish powder in good yield (96%). Glycoluril based macrocycles have been used in various fields; starting from the 2,4-Bis(4-nitrobenzyl)glycoluril (already reported compound), which has undergone reduction (CH3OH,Pt/C) , diazotization (NaNO2/HCl), cyanation (CuCl/KCN), respectively in order to synthesize the desired new glycoluril derivative. The obtained product will be used as a building block for the synthesis of the cyano based bambusuril marcocycle in the future. The yield of the obtained product has been monitored by using different amounts of cyanating reagent, but the best results are shown by the use of 4 mmol of CuCl/KCN. KCN with CuCl assisted the conversion of diazo group into the cyano group with enhanced yield when used in excess amount. It acts as a catalyst. The solubility characteristic of 2,4-Bis(4-cyanobenzyl)glycoluril has also been determined in different organic solvents. 1H NMR technique proved to be very helpful for the structure determination of our desired product. Benzylic protons give signals at 7.5 ppm and 7.8 ppm, respectively. The downfield peaks confirm the presence of CN group near the benzylic protons. Methine protons show a signal at 5.2 ppm, which ensures the basic skeleton of glycoluril. Ureidyl protons also confirm the synthesis of the heterocyclic 2,4-Bis(4-cyanobenzyl)glycoluril compound. The negative and positive electrostatic potential sites, molecular descriptors, and charge density distribution of frontier molecular orbitals are revealing that 4a with promising sites for electrophilic and nucleophilic attacks would result to enhance the urease inhibition, which is in good agreement with the experimental data.

• Klíčová slova
• (HR-MS) mass spectrometry, 1H NMR, Glycoluril derivative, IC50, bambusuril., density functional theory (DFT), sandmeyer reaction, thiourea, urease enzyme,
• MeSH
• imidazoly MeSH
• inhibitory enzymů * farmakologie   MeSH
• simulace molekulového dockingu MeSH
• teorie funkcionálu hustoty MeSH
• ureasa * metabolismus   MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• glycoluril MeSH Prohlížeč
• imidazoly MeSH
• inhibitory enzymů * MeSH
• ureasa * MeSH

Adsorption of cell-penetrating peptides (CPPs) at cellular membranes is the first and necessary step for their subsequent translocation across cellular membranes into the cytosol. It has been experimentally shown that CPPs rich in arginine (Arg) amino acid penetrate across phospholipid bilayers more effectively than their lysine (Lys) rich counterparts. In this work, we aim to understand the differences in the first translocation step, adsorption of Arg9 and Lys9 peptides at fully hydrated neutral phosphatidylcholine (PC) and phosphatidylethanolamine (PE) lipid bilayers and evaluate in detail the energetics of the process using molecular dynamics (MD) simulations and free energy calculations of adsorption of the single peptide. We show that the adsorption of Arg9 is energetically feasible, with the free energy of adsorption being ∼-5.0 kcal mol-1 at PC and ∼-5.5 kcal mol-1 at PE bilayers. In contrast, adsorption of Lys9 is not observed at PC bilayers, and their adsorption at PE bilayers is very weak, being ∼-0.5 kcal mol-1. We show by energy decomposition and analysis of peptide hydration along the membrane that significantly stronger electrostatic interactions of Arg9 with lipid phosphate groups, together with the greater loss of peptide hydration (and in turn stronger hydrophobic interactions) along the membrane translocation path, are the main driving factors governing the adsorption of Arg-rich peptides at neutral lipid bilayers in contrast to Lys-rich peptides. Finally, we also compare the energetics in lipid/bilayer systems with the density functional theory (DFT) calculations of the corresponding model systems in the continuum water model and reveal the energetic differences in different environments.

• MeSH
• fosfatidylcholiny chemie   MeSH
• fosfolipidy MeSH
• lipidové dvojvrstvy chemie   MeSH
• penetrační peptidy * chemie   MeSH
• polylysin * MeSH
• simulace molekulární dynamiky MeSH
• teorie funkcionálu hustoty MeSH
• termodynamika MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• fosfatidylcholiny MeSH
• fosfolipidy MeSH
• lipidové dvojvrstvy MeSH
• penetrační peptidy * MeSH
• polyarginine MeSH Prohlížeč
• polylysin * MeSH

An increasing number of products containing synthetic cannabinoids pose a growing crisis to public health worldwide. Recently, a rising number of cases of serious adverse health effects, intoxications, and death cases associated with synthetic cannabinoids were reported. The current study represents the comprehensive structural analysis of three new synthetic cannabinoids (AB-, ADB- and AMB-FUBINACA) in solution investigated by electronic and vibrational circular dichroism together with the conventional methods of infrared and ultraviolet absorption spectroscopy, all supported by the density functional theory (DFT) calculations. The best level of theory to reproduce the experimental wavenumbers and wavelengths was found to be the B3PW91 method with a 6-311++G(d,p) basis set including the implicit solvent effect simulation. Very good agreement between the experimental and simulated spectra allowed us to determine the absolute configuration and a detailed interpretation of the IR absorption, VCD, ECD and UV spectra of AB-, ADB- and AMB-FUBINACA. In addition, the HOMO and LUMO electronic transitions were calculated.

• Klíčová slova
• Chiroptical spectroscopy, DFT calculation, Drugs, Synthetic cannabinoids, Vibrational spectroscopy,
• MeSH
• cirkulární dichroismus MeSH
• kanabinoidy * MeSH
• teorie funkcionálu hustoty MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• kanabinoidy * MeSH

It has been recognized that the C-H⋯O structural motif can be present in destabilizing as well as highly stabilizing intermolecular environments. Thus, it should be of interest to describe the strength of the C-H⋯O hydrogen bond for constant structural factors so that this intrinsic strength can be quantified and compared to other types of interactions. This description is provided here for C2h-symmetric dimers of acrylic acid by means of the calculations that employ the coupled-cluster theory with singles, doubles, and perturbative triples [CCSD(T)] together with an extrapolation to the complete basis set (CBS) limit. Dimers featuring the C-H⋯O and O-H⋯O hydrogens bonds are carefully investigated in a wide range of intermolecular separations by the CCSD(T)/CBS approach, and also by the symmetry-adapted perturbation theory (SAPT) method, which is based on the density-functional theory (DFT) treatment of monomers. While the nature of these two types of hydrogen bonding is very similar according to the SAPT-DFT/CBS calculations and on the basis of a comparison of the intermolecular potential curves, the intrinsic strength of the C-H⋯O interaction is found to be about a quarter of its O-H⋯O counterpart that is less than one might anticipate.

• Klíčová slova
• CCSD(T), DFT, SAPT, hydrogen bonding, noncovalent interactions,
• MeSH
• polymery * MeSH
• teorie funkcionálu hustoty MeSH
• vodíková vazba MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• polymery * MeSH

There has been a growing interest in quantitative predictions of the intermolecular binding energy of large complexes. One of the most important quantum chemical techniques capable of such predictions is the domain-based local pair natural orbital (DLPNO) scheme for the coupled cluster theory with singles, doubles, and iterative triples [CCSD(T)], whose results are extrapolated to the complete basis set (CBS) limit. Here, the DLPNO-based focal-point method is devised with the aim of obtaining CBS-extrapolated values that are very close to their canonical CCSD(T)/CBS counterparts, and thus may serve for routinely checking a performance of less expensive computational methods, for example, those based on the density-functional theory (DFT). The efficacy of this method is demonstrated for several sets of noncovalent complexes with varying amounts of the electrostatics, induction, and dispersion contributions to binding (as revealed by accurate DFT-based symmetry-adapted perturbation theory (SAPT) calculations). It is shown that when applied to dimeric models of poly(3-hydroxybutyrate) chains in its two polymorphic forms, the DLPNO-CCSD(T) and DFT-SAPT computational schemes agree to within about 2 kJ/mol of an absolute value of the interaction energy. These computational schemes thus should be useful for a reliable description of factors leading to the enthalpic stabilization of extended systems.

• Klíčová slova
• CCSD(T), DFT-SAPT, DLPNO, intermolecular binding, noncovalent interactions,
• MeSH
• analýza nákladů a výnosů MeSH
• kvantová teorie * MeSH
• statická elektřina MeSH
• teorie funkcionálu hustoty MeSH
• termodynamika MeSH
• Publikační typ
• časopisecké články MeSH

Vibrational circular dichroism (VCD) spectroscopy appears as a useful method for characterizing optically active substances in the solid state. This is particularly important for active pharmaceutical ingredients. However, measurement and interpretation of the spectra bring about many difficulties. To assess the experimental and computational methodologies, we explore an anti-inflammatory drug, naproxen. Infrared (IR) and VCD spectra of the pure compound and its cocrystals with alanine and proline were recorded, and the data were interpreted by quantum chemical simulations based on a cluster model and density functional theory. Although unpolarized IR spectroscopy can already distinguish pure ingredients from cocrystals or a mixture, the VCD technique is much more sensitive. For example, the naproxen carboxyl group strongly interacts with the zwitterionic alanine in the cocrystal via two strong hydrogen bonds, which results in a rather rigid structure crystallizing in the chiral P212121 Sohncke group and its VCD is relatively strong. In contrast, the d-proline and (S)-naproxen cocrystal (P21 group) involves a single hydrogen bond between the subunits, which together with a limited motion of the proline ring gives a weaker signal. Solid-state VCD spectroscopy thus appears useful for exploring composite crystal structures and interactions within them, including studies of pharmaceutical compounds.

• Klíčová slova
• alanine, cocrystals, density functional theory, naproxen, proline, solid state, spectra modeling, vibrational circular dichroism,
• MeSH
• cirkulární dichroismus * metody   MeSH
• krystalizace * MeSH
• molekulární konformace MeSH
• molekulární modely MeSH
• naproxen * chemie   MeSH
• prolin chemie   MeSH
• stereoizomerie MeSH
• teorie funkcionálu hustoty MeSH
• vibrace MeSH
• vodíková vazba MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• naproxen * MeSH
• prolin MeSH

Oxidative stress can lead to various derivatives of the tyrosine residue in peptides and proteins. A typical product is 3-nitro-L-tyrosine residue (Nit), which can affect protein behavior during neurodegenerative processes, such as those associated with Alzheimer's and Parkinson's diseases. Surface enhanced Raman spectroscopy (SERS) is a technique with potential for detecting peptides and their metabolic products at very low concentrations. To explore the applicability to Nit, we use SERS to monitor tyrosine nitration in Met-Enkephalin, rev-Prion protein, and α-synuclein models. Useful nitration indicators were the intensity ratio of two tyrosine marker bands at 825 and 870 cm-1 and a bending vibration of the nitro group. During the SERS measurement, a conversion of nitrotyrosine to azobenzene containing peptides was observed. The interpretation of the spectra has been based on density functional theory (DFT) simulations. The CAM-B3LYP and ωB97XD functionals were found to be most suitable for modeling the measured data. The secondary structure of the α-synuclein models was monitored by electronic and vibrational circular dichroism (ECD and VCD) spectroscopies and modeled by molecular dynamics (MD) simulations. The results suggest that the nitration in these peptides has a limited effect on the secondary structure, but may trigger their aggregation.

• Klíčová slova
• Density functional theory (DFT), Electronic circular dichroism (ECD), Nitration, Oxidative stress, Surface-enhanced Raman spectroscopy (SERS), Vibrational circular dichroism (VCD),
• MeSH
• azosloučeniny chemie   MeSH
• cirkulární dichroismus MeSH
• peptidy chemická syntéza   chemie   MeSH
• Ramanova spektroskopie metody   MeSH
• sekundární struktura proteinů MeSH
• simulace molekulární dynamiky MeSH
• teorie funkcionálu hustoty MeSH
• tyrosin analogy a deriváty   analýza   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• 3-nitrotyrosine MeSH Prohlížeč
• azobenzene MeSH Prohlížeč
• azosloučeniny MeSH
• peptidy MeSH
• tyrosin MeSH