Density functional calculations of electronic g-tensors for semiquinone radical anions. The role of hydrogen bonding and substituent effects

A recently developed density functional approach has been used to carry out a systematic computational study of electronic g-tensors for a series of 1,4-semiquinone radical anions. Good agreement with high-field EPR data in frozen 2-propanol is achieved only after taking into account the significant reduction of g-tensor anisotropy caused by hydrogen bonding to solvent molecules. The comparison of various model systems for the first solvation shell suggests two hydrogen bonds from 2-propanol molecules to each of the carbonyl groups of the radical anions, and one additional hydrogen bond to each of the methoxy groups in ubiquinone systems. 2-Propanol makes stronger hydrogen bonds than water and thus influences g-tensor anisotropy more strongly. Substituent effects at the semiquinone are reproduced quantitatively by the calculations. The g-tensor anisotropy is influenced significantly by the conformations of methyl and methoxy substituents, with opposite contributions. Analyses and interpretations of the interrelations between structure, bonding, and spectroscopic data are provided. The relevance of the computational results for the EPR spectroscopy of semiquinone radical anions in photosynthetic reaction centers is discussed.     

Preparation of quaternary pyridinium salts as possible proton conductors

On basis of earlier experimental experience, the transfer of protons in salts of the organic cation-inorganic anion type occurs primarily through directional arrangement of the anion-anion type short hydrogen bonds. The submitted work presents the preparation of quaternary pyridinium salts of inorganic hydrogen anions in the absence of solvent molecules in their crystal structure. These substances can form only the above-described anion-anion type hydrogen bonds; in addition, the absence of solvate anions increases the stability of the prepared compounds. A total of six substituted pyridinium salts were prepared, four of which have not been described yet: 1,2,4,6-tetraphenylpyridinium perchlorate, 1-benzyl-2,4,6-trimethylpyridinium perchlorate, 1,4-dimethylpyridinium hydrogen sulphate, 1,4-dimethylpyridinium dihydrogen phosphate, 1,4-dimethylpyridinium hydrogen sulphate, and 1,2-dimethyl-5-ethylpyridinium dihydrogen phosphate. Three of these substances were characterised by X-ray structural analysis: 1,2,4,6-tetraphenylpyridinium perchlorate crystallises in the orthorhombic system, space group Pbca; 1-benzyl-2,4,6-trimethylpyridinium perchlorate crystallises in the monoclinic system, space group P2₁/c; and 1,4-dimethylpyridinium dihydrogen phosphate crystallises in the monoclinic system, space group C2/c. This structure contains an oriented anion network bond by short anion-anion type hydrogen bonds with the donor acceptor lengths of 2.567(3) Å and 2.557(3) Å and thus fulfils the requirements of a good proton conductor.     

Protein-cofactor interactions and EPR parameters for the Q(H) quinone binding site of quinol oxidase. A density functional study

Recent multifrequency EPR studies of the "high-affinity" quinone binding site of quinol oxidase (Q(H) site) have suggested a very asymmetric hydrogen-bonding environment for the semiquinone radical anion state. Single-sided hydrogen bonding to the O1 carbonyl position was one of the proposals, which contrasts with some previous experimental indications. Here density functional calculations of the EPR parameters (g-tensors, 13C, 1H, and 17O hyperfine tensors) for a wide variety of supermolecular model complexes have been used to provide insight into the detailed relations among structure, environment, and EPR parameters of ubisemiquinone radical anions. A single-sided binding model is not able to account for the experimentally observed low g(x) component of the g-tensor or for the observed magnitude of the asymmetry of the 13C carbonyl HFC tensors. Based on the detailed comparison between computation and experiment, a model with two hydrogen bonds to O1 and one hydrogen bond to O4 is suggested for the Q(H) site, but a model with one more hydrogen bond on each side cannot be excluded. Several general conclusions on the interrelations between EPR parameters and hydrogen bond patterns of ubisemiquinones in proteins are provided.     

Photoreactions of p-quinones with dimethyl sulfide and dimethyl sulfoxide in aqueous acetonitrile. goerner@mpi-muelheim.mpg.de

The effects of dimethyl sulfide (DMS) and dimethyl sulfoxide (DMSO) on the photoreactions of 1,4-benzoquinone (BQ), 1,4-naphthoquinone (NQ), 9,10-anthraquinone (AQ) and several derivatives in acetonitrile/water were studied. The observed triplet state of the quinones is quenched and the rate constant is close to the diffusion-controlled limit for reactions of most quinones with DMS and lower with DMSO. Semiquinone radical anions (Q*-) produced by electron transfer from sulfur to the triplet quinone were detected. For both DMS and DMSO the yield of Q*- is similar, being generally low for BQ and NQ, substantial for AQ and largest for chloranil. The specific quencher concentrations and the effects of quinone structure and redox potentials on the time-resolved photochemical properties are discussed.     

Effects of static and dynamic perturbations on isotropic hyperfine coupling constants in some quinone radicals

The effects of solvent dielectric response on the isotropic hyperfine coupling constants of the 1,4-benzoquinone, 1,4-naphthoquinone and 9,10-anthraquinone anions and 1,4-naphthalenediol cation radicals were studied by electron spin resonance (ESR) spectroscopy and by the theoretical density functional method within the polarizable continuum model. Experimental results demonstrate that the isotropic hyperfine coupling constants can be obtained with high accuracy and that the effects of solvent impurities can be minimized by careful sample preparation. The results obtained correlate well with theoretical predictions from density functional theory calculations. For 1,4-naphthalenediol both the solvent dielectric response as well as rotational averaging of the hydroxy groups were calculated. The overall results highlight the importance of static and dynamic perturbations to the couplings and aid in the assignation process of the couplings to specific magnetic nuclei.     

Quinone sensitized electron transfer photooxidation of nucleic acids: chemistry of thymine and thymidine radical cations in aqueous solution

The 2-methyl-1,4-naphthoquinone (MQ) sensitized photooxidation of nucleic acid derivatives has been studied by laser flash photolysis and steady state methods. Thymine and thymidine, as well as other DNA model compounds, quench triplet MQ by electron transfer to give MQ radical anions and pyrimidine or purine radical cations. Although the pyrimidine radical cations cannot be directly observed by flash photolysis, the addition of N,N,N',N'-tetramethyl-1,4-phenylenediamine (TMPD) results in the formation of the TMPD radical cation via scavenging of the pyrimidine radical cation. The photooxidation products for thymine and thymidine are shown to result from subsequent chemical reactions of the radical cations in oxygenated aqueous solution. The quantum yield for substrate loss at limiting substrate concentrations is 0.38 for thymine and 0.66 for thymidine. The chemistry of the radical cations involves hydration by water leading to C(6)-OH adduct radicals of the pyrimidine and deprotonation from the N(1) position in thymine and the C(5) methyl group for thymidine. Superoxide ions produced via quenching of the quinone radical anion with oxygen appear to be involved in the formation of thymine and thymidine hydroperoxides and in the reaction with N(1)-thyminyl radicals to regenerate thymine. The effects of pH were examined in the range pH 5-8 in both the presence and absence of superoxide dismutase. Initial C(6)-OH thymine adducts are suggested to dehydrate to give N(1)-thyminyl radicals.     

Application of rhodanine,fluorene and semicarbazide hydrochloride as new spectrophotometric reagents for quinones

New selective and sensitive Spectrophotometric methods for quinone determination are described. Quinone samples are treated with either methanolic solution of rhodanine, fluorene in ammoniacal media or aqueous semicarbazide hydrochloride solution. Semicarbazide is the most sensitive reagent for the determination of 1,4-benzoquinone, 1,4-naphthoquinone and 2-methyl-1,4-naphthoquinone. Quinones substituted with electron withdrawing groups are better determined using rhodanine. The average recovery is 99.1%, 98.7% and 99.2% using rhodanine, fluorene and semicarbazide as reagents, respectively.     

Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu Peptide

The vibrational spectrum of the Ala-Leu-Ala-Leu peptide in solution, computed from first-principles simulations, shows a prominent band in the amide I region that is assigned to stretching of carbonyl groups. Close inspection reveals combined but slightly different contributions by the three carbonyl groups of the peptide. The shift in their exact vibrational signature is in agreement with the different probabilities of these groups to form hydrogen bonds with the solvent. The central carbonyl group has a hydrogen bond probability intermediate to the other two groups due to interchanges between different hydrogen-bonded states. Analysis of the interaction energies of individual water molecules with that group shows that shifts in its frequency are directly related to the interactions with the water molecules in the first hydration shell. The interaction strength is well correlated with the hydrogen bond distance and hydrogen bond angle, though there is no perfect match, allowing geometrical criteria for hydrogen bonds to be used as long as the sampling is sufficient to consider averages. The hydrogen bond state of a carbonyl group can therefore serve as an indicator of the solvent’s effect on the vibrational frequency.     

Electron transfer in a radical ion pair: quantum calculations of the solvent reorganization energy

Results are presented for an investigation of intermolecular electron transfer (ET) in solution by means of quantum calculations. The two molecules that are involved in the ET reaction form a solvent-separated radical ion pair. The solvent plays an important role in the ET between the two molecules. In particular, it can give rise to specific solute-solvent interactions with the solutes. An example of specific interactions is the formation of a hydrogen bond between a protic solvent and one of the molecules involved in the ET. We address the study of this system by means of quantum calculations on the solutes immersed in a continuum solvent. However, when the solvent can give rise to hydrogen bond formation with the negatively charged ion after ET, we explicitly consider solvent molecules in the solute cavity, determining the hydrogen bond energetic contribution to the overall interaction energy. Solute-solvent pair distribution functions, showing the different arrangement of solvent molecules before and after ET in the first solvation shell, are reported. We provide results of the solvent reorganization energy from quantum calculations for both the two isolated fragments and the ion pair in solution. Results are in agreement with available experimental data.     

A new type of palladium(0) complex having both electron-withdrawing and -donating sites in a ligand: 5,8-dihydro- and 5,8,9,10-tetrahydro-1,4-naphthoquinone complexes

A new type of palladium(0) complex, (5,8-dihydro-1,4-naphthoquinone)Pd(PPh₃)₂ and (5,8,9,10-tetrahydro-1,4-naphthoquinone)Pd(PPh₃)₂, having both olefin and quinone or dihydro-quinone sites in a ligand molecule was prepared. IR and ¹H NMR spectroscopic studies of these complexes suggested that it is the quinone or dihydro-quinone CC bond which is complexed to Pd. Ligand exchange reactions showed that the stability order of the olefinic quinone complexes was as follows: (1,4-naphthoquinone)Pd(PPh₃)₂ > (5,8-dihydro-1,4-naphthoquinone) Pd(PPh₃)₂>(5,8,9,10-tetrahydro-1,4-naphthoquinone)Pd(PPh₃)₂.     

吩噻嗪、N-甲基吩噻嗪及其自由基正离子的结构和电子光谱的理论研究

用INDO系列方法对吩噻嗪、N-甲基吩噻嗪及其自由基正离子进行了几何构型优化, 中性分子为蝶状折叠形, 自由基正离子为平面构型。以优化构型为基础,计算了上述四种分子、离子的电荷密度、自旋密度、键序和电子光谱, 对光谱进行理论指认的同时, 讨论了从中性分子到离子谱带红移的原因。所有理论计算值均与实验值一致。     

Intermolecular Hydrogen Bonds Formed Between Amino Acid Molecules in Aqueous Solution Investigated by Temperature-jump NanosecondTime-resolved Transient Mid-IR Spectroscopy

Carboxyl (COO?) vibrational modes of two amino acids histidine and glycine in D2O solution were investigated by temperature-dependent FTIR spectroscopy and temperature-jump nanosecond time-resolved IR di?erence absorbance spectroscopy. The results show that hydrogen bonds are formed between amino acid molecules as well as between the amino acid molecule and the solvent molecules. The asymmetric vibrational frequency of COO? around 1600-1610 cm?1 is blue shifted when raising temperature, indicating that the strength of the hydrogen bonds becomes weaker at higher temperature. Two bleaching peaks at 1604 and 1612 cm?1 were observed for histidine in response to a temperature jump from 10 ±C to 20 ±C. The lower vibrational frequency at 1604 cm?1 is assigned to the chain COO? group which forms the intermolecular hydrogen bond with NH3+ group, while the higher frequency at 1612 cm?1 is assigned to the end COO? group forming hydrogen bonds with the solvent molecules. This is because that the hydrogen bonds in the former are expected to be stronger than the latter. In addition the intensities of these two bleaching peaks are almost the same. In contrast, only the lower frequency at 1604 cm?1 bleaching peak has been observed for glycine. The fact indicates that histidine molecules form a dimer-like intermolecular chain while glycine forms a relatively longer chain in the solution. The rising phase of the IR absorption kinetics in response to the temperature-jump detected at 1604 cm?1 for histidine is about 30§10 ns, within the resolution limit ofour instrument, indicating that breaking or weakening the hydrogen bond is a very fast process.     

Application of the atoms in molecules theory and computational chemistry in mass spectrometry analysis of 1,4-naphthoquinone derivatives

Mass spectrometry analysis of 2-(acylamino)-1,4-naphthoquinone derivatives was carried out using electrospray ionization ion source in combination with tandem mass spectrometry. Protonated molecules were dissociated by application of the collision-induced dissociation (CID), and the protonation sites were suggested on the basis of the HOMO, molecular electrostatic potential map (MEP), proton affinity, and Fukui functions calculated by B3LYP/6-31+G(d,p). The main fragmentation mechanisms undergone by the protonated ions were elucidated on the basis of energy, geometry, and topology analysis of equilibrium geometries. Compounds exhibiting only aliphatic hydrogens at the lateral chain undergo interesting ketene elimination. On the other hand, only the benzoylium ion formation is detected for 2-benzoylamino-1,4-naphthoquinone. The bonds geometric and atoms in molecules parameters give evidence that acidic hydrogen atoms play an important role in the fragmentation pathways.     

Solvation structure of hydroxyl radical by Car-Parrinello molecular dynamics

Car-Parrinello molecular dynamics simulations of a hydroxyl radical in liquid water have been performed. Structural and dynamical properties of the solvated structure have been studied in details. The partial atom-atom radial distribution functions for the hydrated hydroxyl do not show drastic differences with the radial distribution functions for liquid water. The OH is found to be a more active hydrogen bond donor and acceptor than the water molecule, but the accepted hydrogen bonds are much weaker than for the hydroxide OH- ion. The first solvation shell of the OH is less structured than the water's one and contains a considerable fraction of water molecules that are not hydrogen bonded to the hydroxyl. Part of them are found to come closer to the solvated radical than the hydrogen bonded molecules do. The lifetime of the hydrogen bonds accepted by the hydroxyl is found to be shorter than the hydrogen bond lifetime in water. A hydrogen transfer between a water molecule and the OH radical has been observed, though it is a much rarer event than a proton transfer between water and an OH- ion. The velocity autocorrelation power spectrum of the hydroxyl hydrogen shows the properties both of the OH radical in clusters and of the OH- ion in liquid.     

The structure of the hydrated electron. Part 1. Magnetic resonance of internally trapping water anions: a density functional theory study

Density functional theory is used to rationalize magnetic parameters of hydrated electron trapped in alkaline glasses as observed using electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) spectroscopies. To this end, model water cluster anions (n=4-8 and n=20, 24) that localize the electron internally are examined. It is shown that hyperfine coupling tensors of H/D nuclei in the water molecules are defined mainly by the cavity size and the coordination number of the electron; the water molecules in the second solvation shell play a relatively minor role. An idealized model of the hydrated electron (that is usually attributed to L. Kevan) in which six hydroxyl groups arranged in an octahedral pattern point toward the common center is shown to provide the closest match to the experimental parameters, such as isotropic and anisotropic hyperfine coupling constants for the protons (estimated from ESEEM), the second moment of the EPR spectra, and the radius of gyration. The salient feature is the significant transfer (10-20%) of spin density into the frontal O 2p orbitals of water molecules. Spin bond polarization involving these oxygen orbitals accounts for small, negative hyperfine coupling constants for protons in hydroxyl groups that form the electron-trapping cavity. In Part 2, these results are generalized for more realistic geometries of core anions obtained using a dynamic one-electron mixed quantum/classical molecular dynamics model.     

Charge separation in mesoporous aluminosilicates

EPR spectroscopy has been used to investigate spontaneous and/or photo-induced electron transfer between adsorbed organic molecules and the mesoporous aluminosilicate MCM-41 host. Spontaneous electron transfer occurs from the host to electron acceptor molecules with sufficiently favourable reduction potentials (TCNE, TCNQ, 1,4-benzoquinone, 1,4-naphthaquinone and 1,4-anthraquinone), provided the MCM-41 contains aluminium and the radical anion yield correlates with the aluminium content of the host. The semiquinone radical anions are interacting strongly with exposed Al³⁺ sites, whereas the TCNE and TCNQ radical anions are loosely bound and can be washed from the host. Radical cation formation is observed when electron donor molecules with favourable oxidation potentials are adsorbed in MCM-41 containing aluminium, and the radical cations formed interact with exposed Al³⁺ sites. This work shows that aluminium-containing MCM-41 contains both electron donating and electron accepting sites which may intervene in intra-molecular charge separation processes in adsorbed organic molecules.     

Fourier transform infrared and Raman spectra, vibrational assignment and density functional theory calculations of naphthazarin

FT Raman and FTIR spectra of Naphthazarin (5,8-dihydroxy-1,4-naphthoquinone) and its deuterated analogue are recorded. Comparison between the spectra obtained by two techniques, a series of density functional theory (DFT) calculations and the spectral behavior upon deuteration were used for the assignment of the vibrational spectra of this compound. The calculated vibrational frequencies by the B3LYP, B3PW91, G96LYP, G96P86, and MPWLYP density functionals are generally consistent with the observed spectra. Infrared and Raman vibrational transitions predicted by B3LYP/6-311++G** are reported for the titled compound and its deuterated analogous and the assignments are discussed. All experimental and theoretical results support a relatively weak hydrogen bond in naphthazarin (NZ), compared with that in the enol form of normal beta-diketones. The observed nuOH/nuOD and gammaOH/gammaOD appear at about 3060/2220 and 790/560 cm(-1), respectively, which are consistent with the calculated hydrogen bond geometry and proton chemical shift results. Two bands at about 350 and 290 cm(-1) are assigned to the O...O stretching modes belong to A1 and B2 species, respectively.     

Rigid macrocyclic triamides as anion receptors: anion-dependent binding stoichiometries and 1H chemical shift changes

The cyclic triamide of 3'-amino-3-biphenylcarboxlic acid is readily synthesized in a stepwise manner and represents a novel class of anion receptors with a large central cavity. This macrocycle binds more strongly to tetrahedral anions than spherical or planar anions in organic solvents. The binding stoichiometries for anions with symmetrical charge distribution depend on the solvent polarity, while tetrahedral p-tosylate binds to the macrocycle with 1:1 stoichiometry in all solvents studied. The (1)H NMR chemical shift changes of the protons lining the interior of the macrocycle's central cavity also depend on the geometry of the bound anion. The importance of the convergent array of hydrogen bond donors for anion binding by the macrocycle was confirmed by control studies with an acyclic triamide and a macrocycle with intramolecular hydrogen bonds.     

Interactions of guanine and guanosine hydrates with quinones: a laser flash photolysis and magnetic field effect study

Laser flash photolysis and an external magnetic field have been used to study the interaction of two quinone molecules, namely, 9,10-anthraquinone (AQ) and 2-methyl 1,4-naphthoquinone, commonly known as menadione (MQ), with one of the DNA bases, guanine (G) and its nucleoside guanosine hydrate (dG). In organic homogeneous medium, it has been observed that G undergoes a predominant hydrogen (H) abstraction reaction with both the quinones while dG supports photoinduced electron transfer (PET) along with H abstraction. On the other hand, in SDS medium, G supports PET with AQ but not with MQ. However, behavior of dG remains unperturbed toward AQ and MQ with the change in medium. All of these observations have been explained on the basis of stabilization of radical ion pair and difference in size of the quinones, which can affect the distance of approach among the interacting molecules.     

Isolation and Characterization of Radical Anions Derived from a Boryl‐Substituted Diphosphene

Radical anions of a diphosphene with two boryl substituents were isolated and characterized by single‐crystal X‐ray diffraction, electron spin resonance (ESR), and UV/Vis absorption spectroscopy as well as DFT calculations. Structural analysis of the radical anions revealed an elongation of the P=P bond and a contraction of the B−P bonds relative to the neutral diphosphene. The UV/Vis spectra of these radical anions showed a strong absorption in the visible region, which was assigned to SOMO‐related transitions on the basis of DFT calculations. The ESR spectra revealed that the hyperfine coupling constant with the phosphorus nuclei is the smallest that has been reported thus far. The results of the DFT calculations furthermore suggest that this should be attributed to a soaking of electron spin to the vacant p orbitals of the boryl substituents.