A Comparison of the Properties of Various Fused-Ring Quinones and Their Radical Anions Using Hartree−Fock and Hybrid Hartree−Fock/Density Functional Methods

Systematic High-Accuracy Prediction of Electron Affinities for Biological Quinones

Quinones play vital roles as electron carriers in fundamental biological processes; therefore, the ability to accurately predict their electron affinities is crucial for understanding their properties and function. The increasing availability of cost-effective implementations of correlated wave function methods for both closed-shell and open-shell systems offers an alternative to density functional theory approaches that have traditionally dominated the field despite their shortcomings. Here, we define a benchmark set of quinones with experimentally available electron affinities and evaluate a range of electronic structure methods, setting a target accuracy of 0.1 eV. Among wave function methods, we test various implementations of coupled cluster (CC) theory, including local pair natural orbital (LPNO) approaches to canonical and parameterized CCSD, the domain-based DLPNO approximation, and the equations-of-motion approach for electron affinities, EA-EOM-CCSD. In addition, several variants of canonical, spin-component-scaled, orbital-optimized, and explicitly correlated (F12) Møller-Plesset perturbation theory are benchmarked. Achieving systematically the target level of accuracy is challenging and a composite scheme that combines canonical CCSD(T) with large basis set LPNO-based extrapolation of correlation energy proves to be the most accurate approach. Methods that offer comparable performance are the parameterized LPNO-pCCSD, the DLPNO-CCSD(T₀ ), and the orbital optimized OO-SCS-MP2. Among DFT methods, viable practical alternatives are only the M06 and the double hybrids, but the latter should be employed with caution because of significant basis set sensitivity. A highly accurate yet cost-effective DLPNO-based coupled cluster approach is used to investigate the methoxy conformation effect on the electron affinities of ubiquinones found in photosynthetic bacterial reaction centers. © 2018 Wiley Periodicals, Inc.

DENSITY FUNCTIONAL THEORY STUDY ON THE IONIZATION POTENTIALS AND ELECTRON AFFINITIES OF ADENINE–FORMAMIDE COMPLEXES

The effects of hydrogen bond interactions upon ionization potentials (IPs) and electron affinities (EAs) of adenine–formamide (AF) complexes have been investigated employing the density functional theory B3LYP. It is found that the hydrogen bond interactions between adenine and formamide play a more important role in the process of electron attachment than in the process of electron detachment. Meanwhile, the hydrogen bond interactions facilitate the adiabatical electron detachment and attachment but have different effects on the vertical electron detachment and attachment with different positions of formamide. Furthermore, when the complexes were dissociated to the free monomers, the processes AF - → A - + F and AF + → A + + F are energetically preferable for AF- and AF+, respectively.

The correlation of cathodic peak potentials of vitamin K(3) derivatives and their calculated electron affinities. The role of hydrogen bonding and conformational changes

2-methyl-1,4-naphtoquinone 1 (vitamin K(3), menadione) derivatives with different substituents at the 3-position were synthesized to tune their electrochemical properties. The thermodynamic midpoint potential (E(1/2)) of the naphthoquinone derivatives yielding a semi radical naphthoquinone anion were measured by cyclic voltammetry in the aprotic solvent dimethoxyethane (DME). Using quantum chemical methods, a clear correlation was found between the thermodynamic midpoint potentials and the calculated electron affinities (E(A)). Comparison of calculated and experimental values allowed delineation of additional factors such as the conformational dependence of quinone substituents and hydrogen bonding which can influence the electron affinities (E(A)) of the quinone. This information can be used as a model to gain insight into enzyme-cofactor interactions, particularly for enzyme quinone binding modes and the electrochemical adjustment of the quinone motif.

Stereoelectronic properties of spiroquinazolinones in differential PDE7 inhibitory activity

A detailed computational study on a series of spiroquinazolinones showing phosphodiesterase 7 (PDE7) inhibitory activity was performed to understand the binding mode and the role of stereoelectronic properties in binding. Our docking studies reproduced the essential hydrogen bonding and hydrophobic interactions for inhibitors of this class of enzymes. The N1 proton of the quinazolinone scaffold was involved in H-bonding to an amide side chain of the conserved glutamine residue in the active site. The central bicyclic ring of the molecules showed hydrophobic and pi-stacking interactions with hydrophobic and aromatic amino acid residues, respectively, present in the PDE7 active site. The docked conformations were optimized with density functional theory (DFT) and DFT electronic properties were calculated. Comparison of molecular electrostatic potential (MEP) plots of inhibitors with the active site of PDE7 suggested that the electronic distribution in the molecules is as important as steric factors for binding of the molecules to the receptor. The hydrogen bonding ability and nucleophilic nature of N1 appeared to be important for governing the interaction with PDE7. For less active inhibitors (pIC(50) < 6.5), the MEP maximum at N1 of the spiroquinazolinone ring was high or low based on the electronic properties of the substituents. All the more active molecules (pIC(50) > 6.5) had MEP highest at N3, not N1. Efficient binding of these inhibitors may need some rearrangement of side chains of active-site residues, especially Asn365. This computational modeling study should aid in design of new molecules in this class with improved PDE7 inhibition.

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.

Quinones as Electron Acceptors. X-Ray Structures, Spectral (EPR, UV−vis) Characteristics and Electron-Transfer Reactivities of Their Reduced Anion Radicals as Separated vs Contact Ion Pairs

Successful isolation of a series of pure (crystalline) salts of labile quinone anion radicals suitable for X-ray crystallographic analysis allows for the first time their rigorous structural distinction as "separated" ion pairs (SIPs) vs "contact" ion pairs (CIPs). The quantitative evaluation of the precise changes in the geometries of these quinones (Q) upon one-electron reduction to afford the anion radical (Q-*) is viewed relative to the corresponding (two-electron) reduction to the hydroquinone (H2Q) via the Pauling bond-length/bond-order paradigm. Structural consequences between such separated and contact ion pairs as defined in the solid state with those extant in solution are explored in the context of their spectral (EPR, UV-vis) properties and isomerization of tightly bound CIPs. Moreover, the SIP/CIP dichotomy is also examined in intermolecular interactions for rapid (self-exchange) electron transfer between Q-* and Q with second-order rate constants of kET approximately equal to 10(8) M-1 s-1, together with the spectral observation of the paramagnetic intermediates [Q,Q-*]leading to 1:1 adducts, as established by X-ray crystallography.

Localized Orbital Corrections for the Calculation of Ionization Potentials and Electron Affinities in Density Functional Theory

This paper describes the extension of a previously reported empirical localized orbital correction model to the correction of ionization potential energies (IP) and electron affinities (EA) for atoms and molecules of first and second row elements. The B3LYP localized orbital correction version of the model (B3LYP-LOC) uses 22 heuristically determined parameters that improve B3LYP DFT IP and EA energy calculations on the G2 data set of 134 molecules from a mean absolute deviation (MAD) from experiment of 0.137 to 0.039 eV. The method significantly reduces the number of outliers and overall MAD to error levels below that achieved with G2 wave function based theory; furthermore, the new model has zero additional computational cost beyond standard DFT calculations. Although the model is heuristic and is based on a multiple linear regression to experimental errors, each of the parameters is justified on physical grounds, and each provides insight into the fundamental limitations of DFT, most importantly the failure of current DFT methods to accurately account for nondynamical electron correlation.

Studies on Photoinduced H-Atom and Electron Transfer Reactions of o-Naphthoquinones by Laser Flash Photolysis

The quenching of the triplets of 1,2-naphthoquinone (NQ) and 1,2-naphthoquinone-4-sulfonic acid sodium salt (NQS) by various electron and H-atom donors was investigated by laser flash photolysis measurement in acetonitrile and benzene. The results showed that the reactivities and configurations of 3NQ* (3NQS*) are governed by solvent polarity. All the quenching rate constants (kq) measured in benzene are larger than those in acetonitrile. The SO3Na substituent at the C-4 position of NQS makes 3NQS* more reactive than 3NQ* in electron/H-atom transfer reactions. Large differences of kq values were discovered in H-atom transfer reactions for alcohols and phenols, which can be explained by different H-abstraction mechanisms. Detection of radical cations of amines/anilines in time-resolved transient absorption spectra confirms an electron transfer mechanism. Triplets are identified as precursors of formed radical anions of NQ and NQS in photoinduced reactions. The dependence of electron transfer rate constants on the free energy changes (DeltaG) was treated by using the Rehm-Weller equation. For the four anilines with different substituents on the para or meta position of amidocyanogen, good correlation between log kq values with Hammett sigma constants testifies the correctness of empirical Hammett equation. Charge density distributions, adiabatic ionization/affinity potentials and redox potentials of NQ (NQS) and some quenchers were studied by quantum chemistry calculation.

An Unusual Reaction of the Natural Compound Benaphthamycin B: Theoretical Study of a Model System

The surprising and complex transformation of benaphthamycin B to give quinone 2a is investigated theoretically with a model compound, 1,5-dihydroxy-4-methoxy-2,3-dimethylanthraquinone (3). The detailed study is performed using both DFT and perturbation theory under inclusion of solvent effects. Several individual steps (reduction and hydrolysis, water elimination, ether cleavage, and oxidation) of the proposed reaction cascade calculated at the PCM-MP2/6-31G(d)//B3LYP/6-31G(d) level of theory are presented and discussed. It is shown that the key step, the ether cleavage as an S(N)2 reaction leading to the anthrone 12a, possesses a smaller activation barrier compared to the alternative process yielding 12b. Therefore, the formation of the thermodynamically preferred model quinone 13a is also the kinetically favored pathway: The results of the calculated model reaction should also be valid for benaphthamycin B (1).

Ab initio and semiempirical study of structure and electronic spectra of hydroxy substituted naphthoquinones

The geometries of hydroxy derivatives of 1,4-naphthoquinone (NQ), viz., 2-hydroxy-1,4-naphthoquinone (2HNQ), 5-hydroxy-1,4-naphthoquinone (5HNQ), and 5,8-dihydroxy-1,4-naphthoquinone (DHNQ), have been optimized using the semiempirical and ab initio theoretical methods. Semiempirical methods used for the optimization are Austin Model 1 (AM1) and Zerner's Intermediate Neglect of Differential Overlap/1(ZINDO/1). For ab initio calculations the 6-31G* basis set is used. The electronic spectra of 1,4-naphthoquinone and its hydroxy derivatives are calculated using the semiempirical Zerner's Intermediate Neglect of Differential Overlap/Spectroscopy (ZINDO/S) method employing the geometries optimized at AM1, ZINDO/1 and ab initio levels and compared with their electronic absorption spectra measured by us. For hydroxy substituted systems, such calculations for spectral assignments are made for the first time. It is found that though the predictions of the three theoretical methods for the geometries are similar, the predictions of the ZINDO/S method using the ZINDO/1 optimized geometries, are better for the transition wavelengths in the visible region of the hydroxy substituted naphthoquinones, especially for 5HNQ and DHNQ.

A1 Reduction in Intact Cyanobacterial Photosystem I Particles Studied by Time-Resolved Step-Scan Fourier Transform Infrared Difference Spectroscopy and Isotope Labeling

Time-resolved step-scan Fourier transform infrared (FTIR) difference spectroscopy, with 5 mus time resolution, has been used to produce P700(+)A(1)(-)/P700A(1) FTIR difference spectra in intact photosystem I particles from Synechococcus sp. 7002 and Synechocystis sp. 6803 at 77 K. Corresponding spectra were also obtained for fully deuterated photosystem I particles from Synechococcus sp. 7002 as well as fully (15)N- and (13)C-labeled photosystem I particles from Synechocystis sp. 6803. Static P700(+)/P700 FTIR difference spectra at 77 K were also obtained for all of the unlabeled and labeled photosystem I particles. From the time-resolved and static FTIR difference spectra, A(1)(-)/A(1) FTIR difference spectra were constructed. The A(1)(-)/A(1) FTIR difference spectra obtained for unlabeled trimeric photosystem I particles from both cyanobacterial strains are very similar. There are some mode frequency differences in spectra obtained for monomeric and trimeric PS I particles. However, the spectra can be interpreted in an identical manner, with the proposed band assignments being compatible with all of the data obtained for labeled and unlabeled photosystem I particles. In A(1)(-)/A(1) FTIR difference spectra obtained for unlabeled photosystem I particles, negative bands are observed at 1559 and 1549-1546 cm(-)(1). These bands are assigned to amide II protein vibrations, as they downshift approximately 86 cm(-)(1) upon deuteration and approximately 13 cm(-)(1) upon (15)N labeling. Difference band features at 1674-1677(+) and 1666(-) cm(-)(1) display isotope-induced shifts that are consistent with these bands being due to amide I protein vibrations. The observed amide modes suggest alteration of the protein backbone (possibly in the vicinity of A(1)) upon A(1) reduction. A difference band at 1754(+)/1748(-) cm(-)(1) is observed in unlabeled spectra from both strains. The frequency of this difference band, as well as the observed isotope-induced shifts, indicate that this difference band is due to a 13(3) ester carbonyl group of chlorophyll a species, most likely the A(0) chlorophyll a molecule that is in close proximity to A(1). Thus A(1) reduction perturbs A(0), probably via a long-range electrostatic interaction. A negative band is observed at 1693 cm(-)(1). The isotope shifts associated with this band are consistent with this band being due to the 13(1) keto carbonyl group of chlorophyll a, again, most likely the 13(1) keto carbonyl group of the A(0) chlorophyll a that is close to A(1). Semiquinone anion bands are resolved at approximately 1495(+) and approximately 1414(+) cm(-)(1) in the A(1)(-)/A(1) FTIR difference spectra for photosystem I particles from both cyanobacterial strains. The isotope-induced shifts of these bands could suggest that the 1495(+) and 1414(+) cm(-)(1) bands are due to C-O and C-C modes of A(1)(-), respectively.

Cyclic perfluorocarbon radicals and anions having high global warming potentials (GWPs): structures, electron affinities, and vibrational frequencies

Adiabatic electron affinities, optimized molecular geometries, and IR-active vibrational frequencies have been predicted for small cyclic hydrocarbon radicals C(n)H(2)(n)(-)(1) (n = 3-6) and their perfluoro counterparts C(n)F(2)(n)(-)(1) (n = 3-6). Total energies and optimized geometries of the radicals and corresponding anions have been obtained using carefully calibrated (Chem. Rev. 2002, 102, 231) density functional methods, namely, the B3LYP, BLYP, and BP86 functionals in conjunction with the DZP++ basis set. The predicted electron affinities show that only the cyclopropyl radical tends to bind electrons among the hydrocarbon radicals studied. The trend for the perfluorocarbon (PFC) radicals is quite different. The electron affinities increase with expanding ring size until n = 5 and then slightly decrease at n = 6. Predicted electron affinities of the hydrocarbon radicals using the B3LYP hybrid functional are 0.24 eV (C(3)H(5)/C(3)H(5)(-)), -0.19 eV (C(4)H(7)/C(4)H(7)(-)), -0.15 eV (C(5)H(9)/C(5)H(9)(-)), and -0.11 eV (C(6)H(11)/C(6)H(11)(-)). Analogous electron affinities of the perflurocarbon radicals are 2.81 eV (C(3)F(5)/C(3)F(5)(-)), 3.18 eV (C(4)F(7)/C(4)F(7)(-)), 3.34 eV (C(5)F(9)/C(5)F(9)(-)), and 3.21 eV (C(6)F(11)/C(6)F(11)(-)).

Odd carbon long linear chains HC2n+1H (n = 4-11): properties of the neutrals and radical anions

The optimized geometries, adiabatic electron affinities, vertical electron affinities, vertical electron detachment energies (for the anions), and IR-active vibrational frequencies have been predicted for the long linear carbon chains HC(2)(n)()(+1)H (n = 4-11). The B3LYP density functional combined with DZP and TZ2P basis sets was used in this theoretical study. These methods have been extensively calibrated versus experiment for the prediction of electron affinities (Chem. Rev. 2002, 102, 231). The computed physical properties are discussed and compared with the even carbon chains HC(2)(n)()H. The predicted electron affinities form a remarkably regular sequence: 2.12 eV (HC(9)H), 2.42 eV (HC(11)H), 2.66 eV (HC(13)H), 2.85 eV (HC(15)H), 3.01 eV (HC(17)H), 3.14 eV (HC(19)H), 3.25 eV (HC(21)H), and 3.35 eV (HC(23)H). These electron affinities are as much as 0.4 eV higher than those for analogous even carbon chains. The predicted structures display an intermediate cumulene-polyacetylene type of bonding, with the inner carbons appearing cumulenic and the outer carbons polyacetylenic.

What is the nature of polyacetylene neutral and anionic chains HC(2n)H and HC(2n)H(-) (n = 6-12) that have recently been observed?

The optimized geometries, adiabatic electron affinities, and IR-active vibrational frequencies have been predicted for the long linear carbon chains HC(2n)H. The B3LYP density functional combined with the DZP basis set was used in this theoretical study. The computed physical properties are discussed. The predicted electron affinities form a remarkably regular sequence: 1.78 (HC(12)H), 2.08 (HC(14)H), 2.32 (HC(16)H), 2.53 (HC(18)H), 2.69 (HC(20)H), 2.83 (HC(22)H), and 2.95 eV (HC(24)H). The predicted structures display an alternating triple and very short single bond pattern, with the degree of bond alternation significantly less for the radical anions.

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.

Density functional calculated spin densities and hyperfine couplings for hydrogen bonded 1,4-naphthosemiquinone and phyllosemiquinone anion radicals: a model for the A1 free radical formed in photosystem I

The B3LYP hybrid density functional method is used to calculate spin densities and hyperfine couplings for the 1,4-naphthosemiquinone anion radical and a model of the phyllosemiquinone anion radical. The effect of hydrogen bonding on the spin density distribution is shown to lead to a redistribution of pi spin density from the semiquinone carbonyl oxygens to the carbonyl carbon atoms. The effect of in plane and out of plane hydrogen bonding is examined. Out of plane hydrogen bonding is shown to give rise to a significant delocalisation of spin density on to the hydrogen bond donor heavy atom. Excellent agreement is observed between calculated and experimental hyperfine couplings. Comparison of calculated hyperfine couplings with experimental determinations for the A1 phyllosemiquinone anion radical present in Photosystem I (PS I) of higher plant photosynthesis indicates that the in vivo radical may have a hydrogen bond to the O4 atom only as opposed to hydrogen bonds to each oxygen atom in alcohol solvents. The hydrogen bonding situation appears to be the reverse of that observed for QA in the bacterial type II reaction centres where the strong hydrogen bond occurs to the quinone O1 oxygen atom. For different types of reaction centre the presence or absence of the non-heme Fe(II) atom may well determine which type of hydrogen bonding situation prevails at the primary quinone site which in turn may influence the direction of subsequent electron transfer.