On the Formation of Cyclobutane Pyrimidine Dimers in UV‐irradiated DNA: Why are Thymines More Reactive?¶

The reaction pathways for thermal and photochemical formation of cyclobutane pyrimidine dimers in DNA are explored using density functional theory techniques. Although it is found that the thermal [2 + 2] cycloadditions of thymine + thymine (T + T --> T x T), cytosine + cytosine (C + C --> C x C) and cytosine + thymine (C + T --> C x T) all are similarly unfavorable in terms of energy barriers and reaction energies, the excited-state energy curves associated with the corresponding photochemical cycloadditions display differences that--in line with experimental findings--unanimously point to the predominance of T x T in UV-irradiated DNA. It is shown that the photocycloaddition of thymines is facilitated by the fact that the S1 state of the corresponding reactant complex lies comparatively high in energy. Moreover, at a nuclear configuration coinciding with the ground-state transition structure, the excited-state energy curve displays an absolute minimum only for the T + T system. Finally, the T + T system is also associated with the most favorable excited-state energy barriers and has the smallest S2-S0 energy gap at the ground-state transition structure.     

Characterization of the N?H···ON and N?H···NO H‐bonds in nitrosamine dimers

Ab initio molecular orbital and DFT calculations have been carried out for three most stable dimers of parent nitrosamine (NA) in order to elucidate the structures and energetics of the dimers. The structures were optimized using HF, B3LYP, and MP2 methods with 6‐311+G(d,p) and 6‐311++G(2d,2p) basis sets. At the optimized geometries obtained at MP2/6‐311++G(2d,2p) level of theory, the energies were evaluated at QCISD/aug‐cc‐pVDZ and CCSD/aug‐cc‐pVDZ levels. The most stable dimer has two N? H···O?N hydrogen bonds and the least stable dimer has two N? H···N?O hydrogen bonds. The natural bond orbital analysis showed that the lpO(N) → BD*(N? N) and lpO(N) → BD*(N? H_b) interactions play a decisive role in the stabilization of the NH···O(N) hydrogen bonds in dimers. The atoms in molecules results reveal that the intermolecular N? H···O(N) H‐bonds in dimers have electrostatic character. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Cooperative influence of water binding to peptides by N?H···OH2 and CO···HOH hydrogen bonds: Study by Ab Initio calculations

In this article, the geometry structures of hydrogen bond chains of formamide and N‐methylacetamide and their hydrogen‐bonded complexes with water were optimized at the MP2/6‐31G* level. Then, we performed Møller–Plesset perturbation method with 6‐311++g**, aug‐cc‐pvtz basis sets to study the cooperative influence to the total hydrogen bond energy by the N? H ··· OH₂ and C?O ··· HOH hydrogen bonds. On the basis of our results, we found that the cooperativity of the hydrogen‐bonded complexes become weaker as N? H ··· OH₂ and C?O ··· HOH hydrogen bonds replacing N? H ··· O?C hydrogen bonds in protein and peptide. It means that the N? H and C?O bonds in peptide prefer to form N? H ··· O?C hydrogen bond rather than to form C?O ··· HOH and N? H ··· OH₂. It is significant for understanding the structures and properties of the helical or sheet structures of protein and peptide in biological systems. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Theoretical study of the S?H···O blue‐shifted hydrogen bond

Theoretical calculations were performed to study the nature of the hydrogen bonds in the complexes HCHO···HSO, HCOOH···HSO, HCHO···HOO, and HCOOH···HOO. The geometric structures and vibrational frequencies of these four complexes at the MP2/6‐31G(d,p) and MP2/6‐311+G(d,p) levels are calculated by standard and counterpoise‐corrected methods, respectively. The results indicate that in the complexes HCHO···HSO and HCOOH···HSO the S? H bond is strongly contracted. In the S? H···O hydrogen bonds, the calculated blue shifts for the S? H stretching frequencies are in the vicinity of 50 cm^?1. While in the complexes HCHO···HOO and HCOOH···HOO, the O? H bond is elongated and O? H···O red‐shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X? H bond length in the X? H···Y hydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribution, rehybridization, and structural reorganization. Among them hyperconjugation has the effect of elongating the X? H bond. Electron density redistribution and rehybridization belong to the bond shortening effects, while structural reorganization has an uncertain influence on the X? H bond length. In the complexes HCHO···HSO and HCOOH···HSO, the shortening effects dominate which lead to the blue shift of the S? H stretching frequencies. In the complexes HCHO···HOO and HCOOH···HOO where elongating effects are dominant, the O? H···O hydrogen bonds are red‐shifted. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Investigation on the individual contributions of N?H···OC and C?H···OC interactions to the binding energies of β‐sheet models

In this article, the binding energies of 16 antiparallel and parallel β‐sheet models are estimated using the analytic potential energy function we proposed recently and the results are compared with those obtained from MP2, AMBER99, OPLSAA/L, and CHARMM27 calculations. The comparisons indicate that the analytic potential energy function can produce reasonable binding energies for β‐sheet models. Further comparisons suggest that the binding energy of the β‐sheet models might come mainly from dipole–dipole attractive and repulsive interactions and VDW interactions between the two strands. The dipole–dipole attractive and repulsive interactions are further obtained in this article. The total of N? H···H? N and C?O···O?C dipole–dipole repulsive interaction (the secondary electrostatic repulsive interaction) in the small ring of the antiparallel β‐sheet models is estimated to be about 6.0 kcal/mol. The individual N? H···O?C dipole–dipole attractive interaction is predicted to be ?6.2 ± 0.2 kcal/mol in the antiparallel β‐sheet models and ?5.2 ± 0.6 kcal/mol in the parallel β‐sheet models. The individual C^α? H···O?C attractive interaction is ?1.2 ± 0.2 kcal/mol in the antiparallel β‐sheet models and ?1.5 ± 0.2 kcal/mol in the parallel β‐sheet models. These values are important in understanding the interactions at protein–protein interfaces and developing a more accurate force field for peptides and proteins. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Is the Excited‐State H‐atom Transfer in Hypericin Concerted?¶

The excited-state intramolecular H-atom transfer of hypericin (Hyp) was investigated as a function of pH in monodispersed reverse micelles formed by sodium bis(2-ethylhexyl)sulfosuccinate/heptane/water and in complexes with Tb3+ under conditions in which one of the two carbonyl groups of Hyp is incapable of accepting a hydrogen atom. The results of pump-probe transient absorption experiments provide no evidence for a concerted H-atom transfer mechanism.     

A simple model for the band structure and D.C. conductivity of an infinite CO···H?N chain perpendicular to the protein backbone

The¹ Hartree–Fock crystal orbital (CO) method in its linear combination of atomic orbitals form was applied to determine the band structure of histone proteins taking 0.041e charge transfer per nucleotide base from the PO groups of poly(guanilic acid) to the arginine, and lysine side chains in histones (see text). Assuming that there are infinite COs, perpendicular to the main chain, formed by the amide groups of one segment of the protein chain bound together by H‐bonds with the C?O groups of another segment of the chain, we have calculated the band structure. From this, we have determined the mobility using the deformation potential approximation. Multiplying this with the mobile electron concentration due to the charge transfer between the PO groups of DNA and the positive side chains in histones, we have obtained for the direct current (D.C.) electron conductivity σ_fib = 1.07 × 10^?9 Ω^?1 cm for a single fiber and after division by the cross‐section of 9.10 × 10^?16 cm², σ_spec = 1.18 × 10⁶ Ω^?1 cm^?1 for the specific conductivity. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

The Formation of OH*(<Superscript>2</Superscript>Σ<Superscript>+</Superscript>) Radical in the Reaction of Hydrogen with Oxygen behind a Shock Wave in Nonequilibrium Conditions

The mechanism of formation of the electronically excited radical OH*(A²Σ⁺) has been studied by analyzing calculations quantitatively describing the results of shock wave experiments carried out in order to determine the moment of maximum OH* radiation at temperatures T < 1500 K and pressures P ≤ 2 atm in the H₂ + O₂ mixtures diluted by argon when the vibrational nonequilibrium is a factor determining the mechanism and rate of the overall process. In kinetic calculations, the vibrational nonequilibrium of the initial H₂ and O₂ components, the HO₂, OH(X²Π), O₂*(¹Δ) intermediates, and the reaction product H₂O were taken into account. The analysis showed that under these conditions the main contribution to the overall process of OH* formation is caused by the reactions OH + Ar → OH* + Ar, H₂ + HO₂ → OH* + H₂O, H₂ + O*(¹D) → OH* + H, HO² + O → OH* + O² and H + H²O → OH* + H², which occur in the vibrational nonequilibrium mode (their activation barrier is overcome due to the vibrational excitation of reactants), and by H + O₃ → OH* + O₂ and H + H₂O₂ → OH* + H₂O, which are reverse to the reactions of chemical quenching.     

OH�� Radical Production Induces Direct Enhancement of the Amylo?d �� Protein/Chondroitin Sulfate Binding: Inhibition by Potentially Radical Scavengers, a Biochromatographic and Thermodynamic Model

??-Amyloid (A??) is a major component of the senile plaques characteristic of Alzheimer disease (AD). Chondroitin sulfate (CS) and glycoaminoglycan (GAG) are also localized throughout the senile plaques in AD. In previous studies, the interaction of the A?? protein with CS immobilized on a chromatographic support and the role of aluminum and copper cations was studied using a molecular chromatographic approach [1, 2]. Here, we demonstrated the direct implication of OH· radical formation on this binding via a novel analytical procedure. The binding of A?? amyloid on CS was accompanied by an OH· radical uptake. The A?¨CCS complex was stabilized by the OH· radical via the creation of about one to two hydrogen bonds. The addition in the medium of a radical scavenger allowed decreasing the A??/CS association and thus confirmed the positive role of these compounds in amyloidosis.     

Detection and Determination of Released Ions in the Presence of Nanoparticles: Selectivity or Strategy?

Metallic nanoparticles can release ionic species, but also both species can occur in the same samples. Therefore, there is a need of efficient and cost‐effective methods to determine these ionic species in the presence of the corresponding nanoparticles. Electroanalytical techniques open the door to this selective detection of NPs and their ions. In this work, a methodology that allows the direct determination of ionic silver (Ag⁺) in the presence of silver nanoparticles based on anodic stripping voltammetry was implemented. Silver nanoparticles were determined, after acidic digestion of the sample, by difference with respect to the total content of silver. The method was validated in terms of specific identification of silver ions, linearity, working range, limit of detection, limit of quantification, recovery, repeatability and ruggedness. All parameters are adequate for an analytical method following Eurachem recommendations. The validated method was used to determine the concentration of Ag⁺ and total silver in two commercial products of colloidal silver. The results were compared with those obtained by atomic absorption spectrometry in combination with an ultrafiltration step for isolation of ionic silver. There were no significant differences in the results. The proposed methodology benefits from the intrinsic selectivity of the electroanalysis methods, allowing to eliminate the steps of pretreatments of the samples, which are necessary in other techniques. The novelty of the article lies in the direct determination of Ag (I) ions in the presence of AgNPs, without the use of previous separation steps.     

Effect of Al?H···H?O dihydrogen bond on the reaction between diphenylmethanol and pyrazolate‐bridged dialuminum complex. An ONIOM DFT/AM1 study

To elucidate the nature of the Al? H···H? O dihydrogen bond and its effect on the reaction between diphenylmethanol and pyrazolate‐bridged dialuminum complex, a theoretical study was carried out using the ONIOM(B3LYP/6‐31+G(d,p):AM1) method. Calculations indicate that this reaction is a two‐step process. The first step is nucleophilic addition and the resulting intermediate is stabilized by an Al? H···H? O dihydrogen bond. Topology analyses based on the “atoms‐in‐molecules” theory show that the Al? H···H? O dihydrogen bond in dialuminum intermediate is stronger than normal hydrogen bond. This step is not barrierless, which is contrary to the result predicted by using simplified model. The second step, eliminating a molecule of dihydrogen, requires an activation free energy of 9.9 kcal/mol in gas phase, which implies the simplified model underestimates the energy barrier of this elimination step. ONIOM calculations also show that, using the simplified model without zero‐point energy correction, the dihydrogen bonding strength has been underestimated and unreliable results have been obtained. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Tetrabutylammonium salt of the B24F224− anion. Two B12F112− icosahedra linked by a 2c–2e B?B bond and surrounded by a sheath of CH· · ·FB hydrogen bonds

The B₂₄F₂₂⁴⁻ anion, which was formed as a minor by‐product when the B₁₂H₁₂²⁻ anion was treated with F₂ in liquid HF, has been isolated as its N(n‐Bu)₄⁺ salt and characterized by ¹⁰B, ¹¹B, and ¹⁹F NMR spectroscopy, electrospray mass spectrometry, cyclic voltammetry, single‐crystal X‐ray diffraction, and calculations at the DFT level of theory. The B₂₄F₂₂⁴⁻ anion has idealized D₅ symmetry and consists of two B₁₂F₁₁²⁻ icosahedra linked by a 2c–2e boron–boron single bond with a B B distance of 1.725(4) Å. In the solid state, the anion interacts with eight N(n‐Bu)₄⁺ cations via a network of 34 CH···FB hydrogen bonds with H· · ·F distances that range from 2.26 to 2.55 Å. These hydrogen bonds were successfully modeled by DFT calculations, which showed that the hydrogen bonds probably have a measurable, albeit subtle, effect on the structure of the B₂₄F₂₂⁴⁻. © 2006 Wiley Periodicals, Inc. Heteroatom Chem 17:181–187, 2006; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20220     

Photosensitized Structural Modifications of the Lens Protein α‐Crystallin: Do All Modifications Impair Chaperone‐like Activity?¶

Among chaperone-like functioning proteins, the lens alpha-crystallins are of particular interest because they are not renewed, and even minor alterations can hurt their function of maintaining the proper refractive index and avoiding cataract formation in the lens. Several reports have suggested the occurrence of remarkable structural modifications in lens proteins in the presence of endogenous and exogenous sensitizers upon exposure to light. In particular, it has been shown in vitro that hypericin, the active ingredient of Hypericum, can bind to and, in the presence of light, cause the photopolymerization of alpha-crystallin. On the basis of these results it has also been suggested that a subsequent significant impairment of the protein function can occur. Using absorption and emission spectroscopic techniques, as well as circular dichroism, we have studied the structural modifications of alpha-crystallin resulting from its interaction with hypericin after irradiation with visible light. To investigate the chaperone-like function of alpha-crystallin, the heat-induced aggregation kinetics of another lens protein, betaLow-crystallin, was monitored by measuring the apparent absorption due to scattering at 360 nm as a function of time, and no apparent damage to its functional role was observed. Spectroscopic results, on the contrary, show a prominent reduction in both tryptophan and hypericin fluorescence emission intensity after light irradiation, suggesting an alteration in the tryptophan microenvironment and a high degree of packing of the chromophore due to photoinduced modification of the molecular framework. Control experiments on alpha-crystallin structurally modified by light in the presence of hypericin indicated that the protein still retains its ability to chaperone both lens crystallins and insulin.     

Isotactic Regulation in the Radical Polymerization of Calcium Methacrylate: Is Multiple Chelation the Key to Stereocontrol?

Accurate quantum chemistry is used to explain the origins of isospecificity in radical polymerization of calcium methacrylate hydrate (CaMA). Distonic radical–cation interactions are shown to be crucial in determining the reactivity of different coordination structures. Cation coordination to the terminal and incoming monomer side chains reduces radical-cation separation, enhancing the reactivity of these modes over the stereocontrolling terminal-penultimate binding modes. This explains why Lewis acid-mediated radical polymerization often fails to produce highly isotactic polymer for common monomers such as methyl methacrylate. However, theoretical calculations suggest that the poly(CaMA) terminus forms a chelated bridging scaffold in N,N-dimethylformamide (DMF), which involves the terminal, penultimate and incoming monomer carboxylate groups. This scaffold simultaneously activates the incoming monomer toward propagation and regulates the relative orientation of the terminal and penultimate side chains. The bridging scaffold is disrupted in more polar solvents and/or if alternative nonchelating counter-cations are employed, leading to loss of isotactic control. These results suggest that higher levels of isotactic control may be achievable if reaction conditions are optimized to favor bridging scaffold formation. The broader importance of these findings to stereocontrol in radical polymerization is also discussed. © 2019 Wiley Periodicals, Inc. J. Polym. Sci. 2020 , 58, 52–61     

The Keto–Enol Tautomerism of Biliverdin in Bacteriophytochrome: Could it Explain the Bathochromic Shift in the Pfr Form?†

Phytochromes are ubiquitous photoreceptors found in plants, eukaryotic algae, bacteria and fungi. Particularly, when bacteriophytochrome is irradiated with light, a Z‐to‐E (photo)isomerization takes place in the biliverdin chromophore as part of the Pr‐to‐Pfr conversion. This photoisomerization is concomitant with a bathochromic shift in the Q‐band. Based on experimental evidence, we studied a possible keto–enol tautomerization of BV, as an alternative reaction channel after its photoisomerization. In this contribution, the noncatalyzed and water‐assisted reaction pathways for the lactam–lactim interconversion through consecutive keto–enol tautomerization of a model BV species were studied deeply. It was found that in the absence of water molecules, the proton transfer reaction is unable to take place at normal conditions, due to large activation energies, and the endothermic formation of lactim derivatives prevents its occurrence. However, when a water molecule assists the process by catalyzing the proton transfer reaction, the activation free energy lowers considerably. The drastic lowering in the activation energy for the keto–enol tautomerism is due to the stabilization of the water moiety through hydrogen bonds along the reaction coordinate. The absorption spectra were computed for all tautomers. It was found that the UV–visible absorption bands are in reasonable agreement with the experimental data. Our results suggest that although the keto–enol equilibrium is likely favoring the lactam tautomer, the equilibrium could eventually be shifted in favor of the lactim, as it has been reported to occur in the dark reversion mechanism of bathy phytochromes.     

Does the Sign of the Cu–Gd Magnetic Interaction Depend on the Number of Atoms in the Bridge?

Several theoretical investigations with CASSCF methods confirm that the magnetic behavior of Cu–Gd complexes can only be reproduced if the 5d Gd orbitals are included in the active space. These orbitals, expected to be unoccupied, do present a low spin density, which is mainly due to a spin polarization effect. This theory is strengthened by the experimental results reported herein. We demonstrate that Cu–Gd complexes characterized by Cu–Gd interactions through single‐oxygen and three‐atom bridges consisting of oxygen, carbon, and nitrogen atoms, present weak ferromagnetic exchange interactions, whereas complexes with bridges made of two atoms, such as the nitrogen–oxygen oximato bridge, are subject to weak antiferromagnetic exchange interactions. Therefore, a bridge with an odd number of atoms induces a weak ferromagnetic exchange interaction, whereas a bridge with an even number of atoms supports a weak antiferromagnetic exchange interaction, as observed in pure organic compounds and also, as in this case, in metal–organic compounds with an active spin polarization effect.     

Radical Cations of Phenyl‐Substituted Aziridines: What Are the Conditions for Ring Opening?

Radical cations were generated from different phenyl-substituted aziridines by pulse radiolysis in aqueous solution containing TlOH.+, N3. or SO4.- as oxidants or in n-butyl chloride, by 60Co gamma radiolysis in Freon matrices at 77 K, and in some cases by flash photolysis in aqueous solution. Depending on the substitution pattern of the aziridines, two different types of radical cations are formed: if the N atom carries a phenyl ring, the aziridine appears to retain its structure after oxidation and the resulting radical cation shows an intense band at 440-480 nm, similar to that of the radical cation of dimethylaniline. Conversely, if the N atom carries an alkyl substituent while a phenyl ring is attached to a C-atom of the aziridine, oxidation results in spontaneous ring opening to yield azomethine ylide radical cations which have broad absorptions in the 500-800 nm range. In aqueous solution the two types of radical cations are quenched by O2 with different rates, whereas in n-butyl chloride, the ring-closed aziridine radical cations are not quenchable by O2. The results of quantum chemical calculations confirm the assignment of these species and allow to rationalize the different effects that phenyl rings have if they are attached in different positions of aziridines. In the pulse radiolysis experiments in aqueous solution, the primary oxidants can also be observed, whereas in n-butyl chloride a transient at 325 nm remains unidentified. In the laser flash experiments, both types of radical cations were also observed.