Nonequilibrium free-energy relations for thermal changes

The Jarzynski equality and the Crooks fluctuation theorem enable the calculation of the change in a system's free energy from nonequilibrium path integrals. These relations consider processes where the system is driven out of equilibrium by a mechanical external agent while remaining in contact with a thermal reservoir at a fixed temperature. We generalize these relations to describe processes driven by any type of external agent, be it thermal or mechanical. Attention is given to the case of a system, initially in equilibrium, that is driven through a temperature change by a heat reservoir. The results are cast in a form applicable to experiments.     

Direct Observation of Alkyl Chain Interdigitation in Conjugated Polyquarterthiophene Self‐Organized on Graphite Surfaces

A solution processible polymer—poly(3,3‴‐didodecylquaterthiophene) (PQT‐12) is investigated at the liquid/solid interface using the scanning tunneling microscopy (STM). Two‐dimensional ordered films made up of self‐assembled domains, with dimensions of 100 nm × 50 nm adsorbed on highly oriented pyrolytic graphite (HOPG) were formed. These domains consist of parallel lamellar polymer chains, with the alkyl chains forming interdigitated structures, along with U‐shaped and closed ring segments of the polymer chains. A polymer chain packing model is proposed herein, which attempts to propose a correlation between the packing of long chains and charge mobilities. These STM results could help in understanding the relationship between the extended conjugation and molecular organization of the PQT‐12 chains.

     

Conformational Dynamics of Human ALKBH2 Dioxygenase in the Course of DNA Repair as Revealed by Stopped-Flow Fluorescence Spectroscopy

Elucidation of physicochemical mechanisms of enzymatic processes is one of the main tasks of modern biology. High efficiency and selectivity of enzymatic catalysis are mostly ensured by conformational dynamics of enzymes and substrates. Here, we applied a stopped-flow kinetic analysis based on fluorescent spectroscopy to investigate mechanisms of conformational transformations during the removal of alkylated bases from DNA by ALKBH2, a human homolog of Escherichia coli AlkB dioxygenase. This enzyme protects genomic DNA against various alkyl lesions through a sophisticated catalytic mechanism supported by a cofactor (Fe(II)), a cosubstrate (2-oxoglutarate), and O₂. We present here a comparative study of conformational dynamics in complexes of the ALKBH2 protein with double-stranded DNA substrates containing N1-methyladenine, N3-methylcytosine, or 1,N6-ethenoadenine. By means of fluorescent labels of different types, simultaneous detection of conformational transitions in the protein globule and DNA substrate molecule was performed. Fitting of the kinetic curves by a nonlinear-regression method yielded a molecular mechanism and rate constants of its individual steps. The results shed light on overall conformational dynamics of ALKBH2 and damaged DNA during the catalytic cycle.     

Formation of Catalytically Active Nanoparticles under Thermolysis of Silver Chloroplatinate(II) and Chloroplatinate(IV)

The thermal behaviour of Ag₂[PtCl₄] and Ag₂[PtCl₆] complex salts in inert and reducing atmospheres has been studied. The thermolysis of compounds in a helium atmosphere is shown to occur in two stages. At the first stage, the complexes decompose in the temperature range of 350–500 °C with the formation of platinum and silver chloride and the release of chlorine gas. At the second stage, silver chloride is sublimated in the temperature range of 700–900 °C, while metallic platinum remains in the solid phase. In contrast to the thermolysis of Ag₂[PtCl₆], the thermal decomposition of Ag₂[PtCl₄] at 350 °C is accompanied by significant heat release, which is associated with disproportionation of the initial salt to Ag₂[PtCl₆], silver chloride, and platinum metal. It is confirmed by DSC measurements, DFT calculations of a suggested reaction, and XRD. The thermolysis of Ag₂[PtCl₄] and Ag₂[PtCl₆] compounds is shown to occur in a hydrogen atmosphere in two poorly separable steps. The compounds are decomposed within 170–350 °C, and silver and platinum are reduced to a metallic state, while a metastable single-phase solid solution of Ag_0.67Pt_0.33 is formed. The catalytic activity of the resulting nanoalloy Ag_0.67Pt_0.33 is studied in the reaction of CO total (TOX) and preferential (PROX) oxidation. Ag_0.67Pt_0.33 enhanced Pt nano-powder activity in CO TOX, but was not selective in CO PROX.     

Synthesis of 4-Aminopyrazol-5-ols as Edaravone Analogs and Their Antioxidant Activity

One of the powerful antioxidants used clinically is Edaravone (EDA). We synthesized a series of new EDA analogs, 4-aminopyrazol-5-ol hydrochlorides, including polyfluoroalkyl derivatives, via the reduction of 4-hydroxyiminopyrazol-5-ones. The primary antioxidant activity of the compounds in comparison with EDA was investigated in vitro using ABTS, FRAP, and ORAC tests. In all tests, 4-Amino-3-pyrazol-5-ols were effective. The lead compound, 4-amino-3-methyl-1-phenylpyrazol-5-ol hydrochloride (APH), showed the following activities: ABTS, 0.93 TEAC; FRAP, 0.98 TE; and ORAC, 4.39 TE. APH and its NH-analog were not cytotoxic against cultured normal human fibroblasts even at 100 μM, in contrast to EDA. According to QM calculations, 4-aminopyrazolols were characterized by lower gaps, IP, and η compared to 4-hydroxyiminopyrazol-5-ones, consistent with their higher antioxidant activities in ABTS and FRAP tests, realized by the SET mechanism. The radical-scavenging action evaluated in the ORAC test occurred by the HAT mechanism through OH bond breaking in all compounds, directly dependent on the dissociation energy of the OH bond. All the studied compounds demonstrated the absence of anticholinesterase activity and moderate inhibition of CES by some 4-aminopyrazolols. Thus, the lead compound APH was found to be a good antioxidant with the potential to be developed as a novel therapeutic drug candidate in the treatment of diseases associated with oxidative stress.     

Novel Copper(II) Complexes with Dipinodiazafluorene Ligands: Synthesis,Structure, Magnetic and Catalytic Properties

The reactions of CuX₂ (X = Cl, Br) with dipinodiazafluorenes yielded four new complexes [CuX₂L₁]₂ (X = Cl (1), Br (2), L₁ = (1R,3R,8R,10R)-2,2,9,9-Tetramethyl-3,4,7,8,9,10-hexahydro-1H-1,3:8,10-dimethanocyclopenta [1,2-b:5,4-b’]diquinolin-12(2H)-one) and [(CuX₂)₂L₂]n (X = Cl (3), Br (4), L₂ = (1R,3R,8R,10R,1’R,3’R,8’R,10’R)-2,2,2’,2’,9,9,9’,9’-Octamethyl-1,1’,2,2’,3,3’,4,4’,7,7’,8,8’,9,9’,10,10’-hexadecahydro-1,3:1’,3’:8,10:8’,10’-tetramethano-12,12’-bi(cyclopenta [1,2-b:5,4-b’]diquinolinylidene). The complexes were characterized by IR and EPR spectroscopy, HR-ESI-MS and elemental analysis. The crystal structures of compounds 1, 2 and 4 were determined by X-ray diffraction (XRD) analysis. Complexes 1–2 have a monomeric structure, while complex 4 has a polymeric structure due to additional coordinating N,N sites in L₂. All complexes contain a binuclear fragment {Cu₂(μ-X)_2×2} (X = Cl, Br) in their structures. Each copper atom has a distorted square-pyramidal coordination environment formed by two nitrogen atoms and three halogen atoms. The Cu-N_ax distance is elongated compared to Cu-N_eq. The EPR spectra of compounds 1–4 in CH₃CN confirm their paramagnetic nature due to the d⁹ electronic configuration of the copper(II) ion. The magnetic properties of all compounds were studied by the method of static magnetic susceptibility. For complexes 1 and 2, the effective magnetic moments are µ_eff ≈ 1.87 and 1.83 µ_B (per each Cu²⁺ ion), respectively, in the temperature range 50–300 K, which are close to the theoretical spin value (1.73 µ_B). Ferromagnetic exchange interactions between Cu(II) ions inside {Cu₂(μ-X)₂X₂} (X = Cl, Br) dimers (J/k_B ≈ 25 and 31 K for 1 and 2, respectively) or between dimers (θ′ ≈ 0.30 and 0.47 K for 1 and 2, respectively) were found at low temperatures. For compounds 3 and 4, the magnetic susceptibility is well described by the Curie–Weiss law in the temperature range 1.77–300 K with µ_eff ≈ 1.72 and 1.70 µ_B for 3 and 4, respectively, and weak antiferromagnetic interactions (θ ≈ −0.4 K for 3 and −0.65 K for 4). Complexes 1–4 exhibit high catalytic activity in the oxidation of alkanes and alcohols with peroxides. The maximum yield of cyclohexane oxidation products reached 50% (complex 3). Based on the data on the study of regio- and bond-selectivity, it was concluded that hydroxyl radicals play a decisive role in the oxidation reaction. The initial products in reactions with alkanes are alkyl hydroperoxides.     

Synthesis of Spin-Labeled Ibuprofen and Its Interaction with Lipid Membranes

Ibuprofen is a non-steroidal anti-inflammatory drug possessing analgesic and antipyretic activity. Electron paramagnetic resonance (EPR) spectroscopy could be applied to study its interaction with biological membranes and proteins if its spin-labeled analogs were synthesized. Here, a simple sequence of ibuprofen transformations—nitration, esterification, reduction, Sandmeyer reaction, Sonogashira cross-coupling, oxidation and saponification—was developed to attain this goal. The synthesis resulted in spin-labeled ibuprofen (ibuprofen-SL) in which the spin label TEMPOL is attached to the benzene ring. EPR spectra confirmed interaction of ibuprofen-SL with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers. Using ²H electron spin echo envelope modulation (ESEEM) spectroscopy, ibuprofen-SL was found to be embedded into the hydrophobic bilayer interior.     

Water as the Key to Proto‐Aragonite Amorphous CaCO3

Temperature and pH value can affect the short‐range order of proto‐structured and additive‐free amorphous calcium carbonates (ACCs). Whereas a distinct change occurs in proto‐vaterite (pv) ACC above 45 °C at pH 9.80, proto‐calcite (pc) ACC (pH 8.75) is unaffected within the investigated range of temperatures (7–65 °C). IR and NMR spectroscopic studies together with EXAFS analysis showed that the temperature‐induced change is related to the formation of proto‐aragonite (pa) ACC. The data strongly suggest that the binding of water molecules induces dipole moments across the carbonate ions in pa‐ACC as in aragonite, where the dipole moments are due to the symmetry of the crystal structure. Altogether, a (pseudo‐)phase diagram of the CaCO₃ polyamorphism in which water plays a key role can be formulated based on variables of state, such as the temperature, and solution parameters, such as the pH value.     

Check on a nonlocal Maxwellian theory of sound propagation in fluid-saturated rigid-framed porous media

A macroscopic nonlocal theory of sound propagation in homogeneous rigid-framed porous media permeated with a viscothermal fluid has been recently proposed in this journal. It accounts for the first time for the full temporal and spatial dispersion effects, independently of the nature of the microgeometry. In this paper this new Maxwellian theory is validated in the case of sound propagation in cylindrical circular tubes, by showing that it matches exactly the long-known direct Kirchhoff–Langevin’s solutions.