Reaction of Chalcones with Cellular Thiols. The Effect of the 4-Substitution of Chalcones and Protonation State of the Thiols on the Addition Process. Diastereoselective Thiol Addition

Several biological effects of chalcones have been reported to be associated with their thiol reactivity. In vivo, the reactions can result in the formation of small-molecule or protein thiol adducts. Both types of reactions can play a role in the biological effects of this class of compounds. Progress of the reaction of 4-methyl- and 4-methoxychalcone with glutathione and N-acetylcysteine was studied by the HPLC-UV-VIS method. The reactions were conducted under three different pH conditions. HPLC-MS measurements confirmed the structure of the formed adducts. The chalcones reacted with both thiols under all incubation conditions. The initial rate and composition of the equilibrium mixtures depended on the ratio of the deprotonated form of the thiols. In the reaction of 4-methoxychalcone with N-acetylcysteine under strongly basic conditions, transformation of the kinetic adduct into the thermodynamically more stable one was observed. Addition of S-protonated N-acetylcysteine onto the polar double bonds of the chalcones showed different degrees of diastereoselectivity. Both chalcones showed a Michael-type addition reaction with the ionized and non-ionized forms of the investigated thiols. The initial reactivity of the chalcones and the equilibrium composition of the incubates showed a positive correlation with the degree of ionization of the thiols. Conversions showed systematic differences under each set of conditions. The observed differences can hint at the difference in reported biological actions of 4-methyl- and 4-methoxy-substituted chalcones.

Structural, Thermal, and Vibrational Properties of N,N-Dimethylglycine–Chloranilic Acid—A New Co-Crystal Based on an Aliphatic Amino Acid

The new complex of N,N-Dimethylglycine (DMG) with chloranilic acid (CLA) was synthesized and examined for thermal, structural, and dynamical properties. The structure of the reaction product between DMG and CLA was investigated in a deuterated dimethyl sulfoxide (DMSO-d6) solution and in the solid state by Nuclear Magnetic Resonance (NMR) (Cross Polarization Magic Angle Spinning-CPMAS NMR). The formation of the 1:1 complex of CLA and DMG in the DMSO solution was also confirmed by diffusion measurement. X-ray single crystal diffraction results revealed that the N,N-dimethylglycine–chloranilic acid (DMG+–CLA−) complex crystallizes in the centrosymmetric triclinic P-1 space group. The X-ray diffraction and NMR spectroscopy show the presence of the protonated form of N,N-dimethylglycine and the deprotonated form of chloranilic acid molecules. The vibrational properties of the co-crystal were investigated by the use of neutron (INS), infrared (IR), and Raman (RS) spectroscopies, as well as the density functional theory (DFT) with periodic boundary conditions. From the band shape analysis of the N–CH3 bending vibration, we can conclude that the CH3 groups perform fast (τR ≈ 10−11 to 10‒13 s) reorientational motions down to a temperature of 140 K, with activation energy at ca. 6.7 kJmol–1. X-ray diffraction and IR investigations confirm the presence of a strong N+–H···O− hydrogen bond in the studied co-crystal.

Protein Dynamics and Substrate Protonation State Mediate the Catalytic Action of Trans-4-Hydroxy-L-Proline Dehydratase

The enzyme <i>trans</i>-4-Hydroxy-L-proline (Hyp) dehydratase (HypD) is among the most abundant glycyl radical enzymes (GREs) in the healthy human gut microbiome and is considered a promising antibiotic target for the prominent antibiotic-resistant pathogen <i>C</i><i>lostridium difficile.</i> Although an enzymatic mechanism has been proposed, the role of the greater HypD protein environment in mediating radical reactivity is not well understood. To fill this gap in understanding, we investigate HypD across multiple time- and length- scales using electronic structure modeling and classical molecular dynamics. We observe that the Hyp substrate protonation state significantly alters both its enzyme-free reactivity and its dynamics within the enzyme active site. Accurate coupled cluster modeling suggests the deprotonated form of Hyp to be the most reactive protonation state for C5–H_pro-<i>S</i> activation. In the protein environment, hydrophobic interactions modulate the positioning of Cys434 radical to enhance the reactivity of C5–H_pro-<i>S</i> abstraction. Long-time dynamics reveal that changing Hyp protonation states triggers the switching of a Leu643-gated water tunnel, a functional feature that has not yet been observed for members of the GRE superfamily.

Protein Dynamics and Substrate Protonation State Mediate the Catalytic Action of Trans-4-Hydroxy-L-Proline Dehydratase

The enzyme <i>trans</i>-4-Hydroxy-L-proline (Hyp) dehydratase (HypD) is among the most abundant glycyl radical enzymes (GREs) in the healthy human gut microbiome and is considered a promising antibiotic target for the prominent antibiotic-resistant pathogen <i>C</i><i>lostridium difficile.</i> Although an enzymatic mechanism has been proposed, the role of the greater HypD protein environment in mediating radical reactivity is not well understood. To fill this gap in understanding, we investigate HypD across multiple time- and length- scales using electronic structure modeling and classical molecular dynamics. We observe that the Hyp substrate protonation state significantly alters both its enzyme-free reactivity and its dynamics within the enzyme active site. Accurate coupled cluster modeling suggests the deprotonated form of Hyp to be the most reactive protonation state for C5–H_pro-<i>S</i> activation. In the protein environment, hydrophobic interactions modulate the positioning of Cys434 radical to enhance the reactivity of C5–H_pro-<i>S</i> abstraction. Long-time dynamics reveal that changing Hyp protonation states triggers the switching of a Leu643-gated water tunnel, a functional feature that has not yet been observed for members of the GRE superfamily.

Extraction-Chromogenic System for Cobalt Based on 5-Methyl-4-(2-thiazolylazo) Resorcinol and Benzalkonium Chloride

The interaction between CoII and 5-methyl-4-(2-thiazolylazo)-resorcinol (MTAR) was studied in a water-chloroform system, in the presence or absence of benzalkonium chloride (BZC) as a cationic ion-association reagent. The optimum pH, concentration of the reagents and extraction time for the extraction of Co were found. In the presence of BZC, the extracted ion-associate could be represented by the formula (BZ+)[CoIII(MTAR2–)2], where MTAR is in its deprotonated form. The following extraction-spectrophotometric characteristics were determined: absorption maximum, molar absorptivity, Sandell’s sensitivity, limit of detection, limit of quantification, constant of extraction, distribution ratio and fraction extracted. In the absence of BZC, the extraction is incomplete and occurs in a narrow pH range. The extracted chelate contains one deprotonated and one monoprotonated ligand: [CoIII(MTAR2–)(HMTAR–)].

Copper(II) and Zinc(II) Complexes Derived from N,N’-Bis(4-bromosalicylidene)propane-1,3-diamine: Syntheses, Crystal Structures and Antimicrobial Activity

A mononuclear copper(II) complex, [CuL] (1), and a phenolato-bridged trinuclear zinc(II) complex, [Zn3Cl2L2(DMF)2] (2), where L is the deprotonated form of N,N’-bis(4-bromosalicylidene)propane-1,3-diamine (H2L), have been prepared and characterized by elemental analyses, IR and UV-Vis spectroscopy, and single crystal X-ray diffraction. The Cu atom in complex 1 is in square planar coordination, while the terminal and central Zn atoms in complex 2 are in square pyramidal and octahedral coordination, respectively. The antibacterial activities of the complexes have been tested on the bacteria Staphylococcus aureus and Escherichia coli, and the yeast Candida parapsilosis.

Exploring the Ability of Luminescent Metal Assemblies to Bind and Sense Anionic or Ionizable Analytes A Ru(phen)2bipy-Based Dizinc Complex for Bisphenol A (BPA) Recognition

The synthesis of a new RuII complex, in which the metal is coordinated by two 1,10-phenanthroline ligands and a 2,2′-bipyridyl unit linked, via methylene bridges in its 4 and 4′ positions, to two 1,4,7,10-tetraazacyclododecane (cyclen) macrocycles ([Ru(phen)2L]2+) is reported. Protonation and ZnII binding by [Ru(phen)2L]2+ have been analyzed by potentiometric titration, evidencing the formation of mixed hetero-binuclear and hetero-trinuclear ZnII/RuII complexes. These complexes were tested as bis-phenol A (BPA) binders. Only the dizinc complex with [Ru(phen)2L]2+ is able to bind BPA in aqueous solution, affording a remarkably stable {Zn2[Ru(phen)2L]BPA(H−2)}4+ adduct at neutral pH, in which BPA is bound in its doubly deprotonated form to the two ZnII ions. BPA binding was found to quench the luminescence emission of the RuII(phen)2bipy core. Although the quenching effect is modest, this study demonstrates that appropriately designed dizinc complexes can be used for binding and optical sensing of BPA in water.

Molecular Properties of Bare and Microhydrated Vitamin B5–Calcium Complexes

Pantothenic acid, also called vitamin B5, is an essential nutrient involved in several metabolic pathways. It shows a characteristic preference for interacting with Ca(II) ions, which are abundant in the extracellular media and act as secondary mediators in the activation of numerous biological functions. The bare deprotonated form of pantothenic acid, [panto-H]−, its complex with Ca(II) ion, [Ca(panto-H)]+, and singly charged micro-hydrated calcium pantothenate [Ca(panto-H)(H2O)]+ adduct have been obtained in the gas phase by electrospray ionization and assayed by mass spectrometry and IR multiple photon dissociation spectroscopy in the fingerprint spectral range. Quantum chemical calculations at the B3LYP(-D3) and MP2 levels of theory were performed to simulate geometries, thermochemical data, and linear absorption spectra of low-lying isomers, allowing us to assign the experimental absorptions to particular structural motifs. Pantothenate was found to exist in the gas phase as a single isomeric form showing deprotonation on the carboxylic moiety. On the contrary, free and monohydrated calcium complexes of deprotonated pantothenic acid both present at least two isomers participating in the gas-phase population, sharing the deprotonation of pantothenate on the carboxylic group and either a fourfold or fivefold coordination with calcium, thus justifying the strong affinity of pantothenate for the metal.

Reactions of Pentaphenylantimony and Penta-Para-Tolylanimony with Calixarene [4-t-BuC6H2OH(S-2)]4

Pentaphenylantimony and penta-para-tolylantimony react with calixarene [4-t-BuC6H2OH(S-2)]4 (СArH) by way of arene elimination and formation of the [Ph4Sb]+[СAr]- × TolH (1), [p-Tol4Sb]+[CAr]- × H2O (2) ionic products with a yield up to 96%. The compound has been identified by IR spectroscopy and X-ray diffraction analysis. According to the X-ray diffraction data, compounds 1 and 2 are ionic complexes with solvate molecules of toluene (1) and water (2). The cation has a tetrahedral coordination of the antimony atom with aryl ligands at the polyhedron vertices; the anion is represented by the deprotonated form of p-tert-butylthiacalix[4]arene. The three tert-butyl groups, the phenyl ring and solvated toluene in the structure of compound 1, and two tert-butyl fragments in the structure of compound 2 are disordered over two positions. The tetrahedral coordination of antimony atoms in the cations of compounds 1 and 2 is slightly distorted. The CSbC angles deviate from the theoretical value and vary within 106.0(4)−117.7(4)° (1), 105.75(15)−112.84(15)° (2). The average Sb–C bond lengths are 2.101(3) and 2.106(4) Å in structures 1 and 2, respectively. The [СAr]- anion is in the cone conformation, the upper rim of which is represented by the tert-butyl groups in the para-position, while the lower one is represented by hydroxy groups, one of which is deprotonated. The СAr–O– bond length (1.318(4) (1) and 1.326(4) (2) Å) is less than the average value of the СAr–OH bond lengths (1.338(4) (1) and 1.343(4) (2) Å), which indicates increasing multiplicity of the bond and localization of a negative charge on the oxygen atom. Intramolecular hydrogen bonds with the neiboring O atom are observed. The H∙∙∙O distances are 2.16, 1.69, 1.77 Å in 1 and 1.92, 1.79, 1.76 Å in 2. Dihedral angles between opposite phenoxide rings are 60.64° and 87.07° (1) and 83.85° and 80.42° (2), which indicates somewhat less symmetric anion in structure 1 than in structure 2. The formation of the crystal spatial structure is due to the formation of hydrogen bonds between ions with participation of oxygen and sulfur atoms, as well as СН∙∙∙π–interactions, while the ions form chains in the crystal of compound 1, and layers in the crystal of compound 2. Complete tables of atom coordinates, bond lengths and valence angles are deposited at the Cambridge Crystallographic Data Center (No. 1850118 (1); No. 2013220 (2); [email protected] or http://www.ccdc.cam.ac.uk/data_request/cif).

One Order of Magnitude Increase of Triplet State Lifetime Observed in Deprotonated Form Selenium Substituted Uracil

Selenium nucleic acids possess unique properties and have been demonstrated to have a wide range of applications such as DNA X-ray crystallography and novel medical therapies. Yet, as a heavy...