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 calculation of conformations and potentials of internal rotation in polychlorinated biphenyls

Full geometry optimization for all 209 isomers of polychlorinated biphenyls (PCBs) and calculations of internal rotation potentials for 154 isomers have been performed by density functional method B3LYP/6-31G(d, p). Conformations and internal rotation barriers in PCBs were proved to depend on a number of chlorine atoms in ortho-positions and, less, the presence of chlorine atoms in adjacent meta-positions. Subject to the number of chlorine atoms in ortho-and adjacent meta-positions, 209 PCB isomers were classified into 18 groups, within each of them molecules having very close conformations and potentials of internal rotation. It makes possible to evaluate with high accuracy the potential functions of the last 55 PCB molecules for which potential curve calculations have not been made.     

白藜芦醇清除自由基活性的密度泛函理论研究

采用密度泛函理论(DFT)方法,从静态与动态两大方面分析了白藜芦醇分子酚羟基在不同溶剂中清除自由基活性的能力大小.通过白藜芦醇的结构参数、前线轨道理论、3种抽氢反应机制等方面分析了分子活性位与其性质的关系.探讨了白藜芦醇分子不同位置酚羟基清除·OH和·OOH的抗氧化机理,得到了该分子与·OOH发生抽氢反应时的过渡态结构.计算结果表明,在任何溶剂中白藜芦醇分子C(4')位上酚羟基活性最高,发生抽氢反应时反应热最小,是高活性位点.     

Density functional theory study of the beta-carotene radical cation and deprotonated radicals

The beta-carotene radical cation and deprotonated neutral radicals were studied at the density functional theory (DFT) level using different density functionals and basis sets: B3LYP/3-21G, SVWN5/6-31G*, BPW91/DGDZVP2, and B3LYP/6-31G**. The geometries, total energies, spin distributions, and isotropic and anisotropic hyperfine coupling constants of these species were calculated. Deprotonation of the methyl group at the double bond of the cyclohexene ring of the carotenoid radical cation at 5 or 5' produces the most stable neutral radical because of retention of the pi-conjugated system while less stable deprotonation at 9 or 9' and 13 or 13' of the chain methyl groups causes significant distortion of the conjugation. The predicted methyl hyperfine coupling constants of 13-16 MHz of the neutral radicals are in good agreement with the previous electron nuclear double resonance (ENDOR) spectrum of photolyzed beta-carotene on a solid support. DFT calculations on the beta-carotene radical cation in a polar water environment showed that the polar environment does not cause significant changes in the proton hyperfine constants from those in the isolated gas-phase molecule. DFT calculated methyl proton hyperfine coupling constants of less than 7.2 MHz are in agreement with those reported for the radical cation in photosystem II (PS II) and those found in the absence of UV light for the radical cation on a silica alumina matrix.     

ESR方法检测竹红菌素的半醌负离子自由基

从顺磁共振波谱检测到通过竹红菌素的光诱导还原和基态竹红菌素跟脂肪胺的电子转移两条途径所得到的自由基信号, 并由电化学还原得到同一自由基, 确认它为半醌负离子自由基。竹红菌素溶液中加入芳香胺观察不到ESR信号。它的3,10位上与醌基相邻近的羟基离解以后, 无论在基态还是在激发态都观察不到ESR信号。此外, 还从吸收光谱观察到半醌负离子自由基吸收以及竹红菌素跟脂肪胺之间的相互作用。     

Density functional theory study of the role of anions on the oxidative decomposition reaction of propylene carbonate

The oxidative decomposition mechanism of the lithium battery electrolyte solvent propylene carbonate (PC) with and without PF(6)(-) and ClO(4)(-) anions has been investigated using the density functional theory at the B3LYP/6-311++G(d) level. Calculations were performed in the gas phase (dielectric constant ε = 1) and employing the polarized continuum model with a dielectric constant ε = 20.5 to implicitly account for solvent effects. It has been found that the presence of PF(6)(-) and ClO(4)(-) anions significantly reduces PC oxidation stability, stabilizes the PC-anion oxidation decomposition products, and changes the order of the oxidation decomposition paths. The primary oxidative decomposition products of PC-PF(6)(-) and PC-ClO(4)(-) were CO(2) and acetone radical. Formation of HF and PF(5) was observed upon the initial step of PC-PF(6)(-) oxidation while HClO(4) formed during initial oxidation of PC-ClO(4)(-). The products from the less likely reaction paths included propanal, a polymer with fluorine and fluoro-alkanols for PC-PF(6)(-) decomposition, while acetic acid, carboxylic acid anhydrides, and Cl(-) were found among the decomposition products of PC-ClO(4)(-). The decomposition pathways with the lowest barrier for the oxidized PC-PF(6)(-) and PC-ClO(4)(-) complexes did not result in the incorporation of the fluorine from PF(6)(-) or ClO(4)(-) into the most probable reaction products despite anions and HF being involved in the decomposition mechanism; however, the pathway with the second lowest barrier for the PC-PF(6)(-) oxidative ring-opening resulted in a formation of fluoro-organic compounds, suggesting that these toxic compounds could form at elevated temperatures under oxidizing conditions.     

Density functional theory predicts the barriers for radical fragmentation in solution

[reaction: see text] N-Methoxypyridyl radicals formed by one-electron reduction of the corresponding cationic heterocycles undergo N-O bond cleavage. Experimental activation free energies for a series of these bond fragmentations are compared to corresponding barriers determined from electronic structure calculations. The DFT barriers agree well with those from experiment, being smaller than the latter values by an average value of ca. 1 kcal/mol, for rate constants varying over almost 3 orders of magnitude, or within ca. 3 kcal/mol over 8 orders of magnitude of rate constant. For a model compound, the B3PW91/6-31+G hybrid density functional method is also found to be in good agreement with the MCSCF-MRMP2 method. One of the reactions is found by DFT to have no minimum for the reactant radical, consistent with a truly barrierless reaction.     

Density functional theory study of conformation-dependent properties of neutral and radical cationic L-tyrosine and L-tryptophan

Conformation-dependent properties of L-tyrosine and L-tryptophan in neutral and radical cations were studied by using the density functional theory (DFT) with a new density functional M05-2X. The results are compared with those obtained by using the conventional DFT (B3LYP). Results obtained by both types of DFT were in qualitative accord, including the existence of two conformational subgroups and their subgroup-dependent adiabatic ionization energy and hydrogen bonding. On the other hand, quantitative differences were found between the two DFT methods as well: the M05-2X method successfully reproduced experimental adiabatic ionization energy, whereas the B3LYP functional consistently yielded significantly lower values by 0.2-0.3 eV. More importantly, natural bond orbital (NBO) analysis for cationic conformers showed that all conformers of L-tyrosine and L-tryptophan undergo charge localization upon ionization regardless of the presence of intramolecular hydrogen bonding, unlike the case of L-phenylalanine that was treated earlier by other studies. Different degrees of charge localization among all three aromatic amino acids are explained by employing a simple model in which the aromatic amino acid is assumed to consist of two submoieties of distinct cationic core: the backbone and aromatic side chain. The difference in adiabatic ionization energy between these two submoieties is found to govern the degree of charge localization.     

Density functional calculations on dissociation reactions of radical anions of 5-fluorouracil derivatives

Fragmentation reactions upon electron attachment to 5-fluorouracil with CH2R substituents at N1 have been evaluated by means of density functional calculations. The present results show that electron attachment to R = F, HC=O or CN derivatives follows a stepwise pathway with radical anions as intermediates. For these compounds, the most stable species formed is the pi radical anion which bears an unpaired spin density at the C6=C5-C4=O pi-conjugated system of the uracil ring. Cleavage of the N1-CH2R or N1CH2-R bond of these intermediates proceeds through the mixing of the pi and sigma states by means of proper geometrical fluctuations along the reaction coordinate. No sigma radical anion could be characterised on any of these sigma basal potential surfaces. A noticeable decrease in the activation energy for the N1-CH2R bond dissociation was observed for R = H-C=O or CN. Therefore, such derivatives with unsaturated groups positioned vicinal to the N1-C1' bond are identified as targets for the development of novel radiation-activated antitumour drugs. On the other hand, the electron transfer to the compounds with R = Cl, Br is dissociative, i.e. it occurs without the mediation of radical anions. For compounds with R = halides or R = NO2, the fragmentation of the N1CH2-R bond is the preferred dissociation pathway.     

Density functional study of methyl radical association kinetics

Rate constants of the prototypical methyl-methyl radical association reaction are calculated on the basis of variational transition-state theory with a variable reaction coordinate and a multifaceted dividing surface. The potential energies required in the Monte Carlo integrations are evaluated directly using the M06 and M06-L density functionals. The rate constants are calculated at the canonical, microcanonical, and E,J-resolved microcanonical levels. The best prediction of rate constants is based on the potential energies calculated by the M06-L density functional; these agree with experimental data quantitatively from 300 to 1000 K. This study shows that density functional theory can be accurate enough for calculating rate constants of reactions with loose transition states, whereas previously only multireference wave function methods, which are more complicated and more expensive, had been demonstrated to be sufficiently accurate. The application of density functional theory for the loose transition states will allow larger and complicated systems to be studied efficiently.     

Density functional theory study of formaldehyde oligomers

Hydrogen‐bonded formaldehyde oligomers (dimer to pentamer) are studied using density functional theory (DFT), the B3LYP method, and the 6‐311+G* basis set. Many‐body interaction energies are obtained to study the contribution of many‐body terms to binding energy. The basis set superposition error (BSSE)‐corrected total energies are ?229.08170, ?343.61410, ?458.16660, and ?572.70901 hartrees for dimer, trimer, tetramer, and pentamer, respectively, with corresponding binding energies ?2.55, ?4.86, ?6.99, and ?9.49 kcal/mol. Two‐body energies have been found to contribute significantly to the total binding energy in dimer to pentamer, whereas higher‐order interaction energies are negligible. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Density functional theory study of BnC clusters

B_nC clusters (n = 3–10) were studied at the density functional theory (DFT) (B3LYP)/6‐311G** level of theory. The calculations predicted that the most stable configurations of the B_nC clusters are the (n + 1)‐membered cyclic structures. For boron–carbon clusters, the configurations containing greater numbers of three‐membered boron rings are more favorable, except for the B₇C and B₉C clusters. Through molecular orbital analysis of these B_nC clusters, we have concluded that π‐electron delocalization plays a crucial role in the stability of n + 1‐membered cyclic structures. In this paper, the relative stability of each cluster is discussed based on their single atomic‐binding energies. The capability of clusters to obtain or lose an electron was also discussed, based on their vertical electron detachment energies (VDEs), adiabatic electron detachment energies (ADEs), vertical electron affinities (VEAs) and adiabatic electron affinities (AEAs). Copyright © 2011 John Wiley & Sons, Ltd.     

Density functional theory investigation of physical properties of the OCCN radical and the cation

Structural and thermodynamic properties for the OCCN radical and its cation were estimated with hybrid, gradient-corrected and local density functional theory methods by using three various Gaussian type basis sets. It was estimated that the radical structure should be a zig-zag structure, which corresponds to the sp² hybridization of the carbonyl carbon, while the OCCN cation is linear. The radical ionization potential should be between 8.7 and 9.1 eV with the enthalpy of formation at approximately 51 kcal/mol. It was computed in the infrared spectra that there were two strong absorptions at 1863 and 2080 cm⁻¹ for the CO and the CN functionalities and they should be observable for the OCCN radical.     

Density functional and ab initio study of the free radical MgNC

A new “non-terrestrial” molecule present in the envelope of the carbon star IRC + 10216 was described for the first time in 1986. Recently, this molecule was identified as the free radical MgNC, the first Mg-containing molecule in space. We present here the first density functional study performed on this radical, as well as on its isomer MgCN and the transition state connecting these species. It is shown that the optimum geometry obtained at the Becke3LYP/6-311+G(3df) level leads to the most exact rotational constants B_e and B_o calculated up to now. It is also shown that the energy differences between the three species are completely in agreement with the best ab initio calculations available. Furthermore, it is shown that the popular MP2 method fails for this system in the same way that has been demonstrated for other radicals.     

Density functional theory study of NO adsorbed in A-zeolite

Density functional theory was employed to investigate the adsorption site and hyperfine interactions of nitric oxide adsorbed in Na-LTA (previous name NaA) zeolite. Three different cluster models of increasing complexity were used to represent the zeolite network: (1) a six-membered ring terminated by hydrogen atoms with one sodium ion above the ring, (2) as model 1 with the addition of three sodium ions located at the centers of three imagined four-membered rings adjacent to the six-membered ring, and (3) as model 2 with the addition of the three four-membered rings adjacent to the six-membered ring. Calculations on the largest system (model 3) showed very good agreement with measured electronic Zeeman interaction couplings, 14N hyperfine coupling tensors, and 23Na hyperfine and nuclear quadruple coupling tensors of the S = 1/2 Na+...N-O adsorption complex when the position of the sodium ion was relaxed. The optimized geometry of the complex agreed nicely with that estimated experimentally, except for the Na-N distance, where the present results indicate that the distance deduced from previous ENDOR experiments may be underestimated by as much as 0.5 angstroms.     

Binding modes in metal ion complexes of quinones and semiquinone radical anions: electron-transfer reactivity.

9,10-Phenanthrenequinone (PQ) and 1,10-phenanthroline-5,6-dione (PTQ) form 1:1 and 2:1 complexes with metal ions (M (n+)=Sc (3+), Y (3+), Mg (2+), and Ca (2+)) in acetonitrile (MeCN), respectively. The binding constants of PQ--M (n+) complexes vary depending on either the Lewis acidity or ion radius of metal ions. The one-electron reduced species (PTQ(-)) forms 1:1 complexes with M (n+), and PQ(-) also forms 1:1 complexes with Sc(3+), Mg(2+), and Ca(2+), whereas PQ(-) forms 1:2 complexes with Y(3+) and La(3+), as indicated by electron spin resonance (ESR) measurements. On the other hand, semiquinone radical anions (Q(-) and NQ(-)) derived from p-benzoquinone (Q) and 1,4-naphthoquinone (NQ) form Sc(3+)-bridged pi-dimer radical anion complexes, Q(-)--(Sc(3+))(n)--Q and NQ(-)--(Sc(3+))(n)-NQ (n=2 and 3), respectively. The one-electron reduction potentials of quinones (PQ, PTQ, and Q) are largely positively shifted in the presence of M (n+). The rate constant of electron transfer from CoTPP (TPP(2-)=dianion of tetraphenylporphyrin) to PQ increases with increasing the concentration of Sc(3+) to reach a constant value, when all PQ molecules form the 1:1 complex with Sc(3+). Rates of electron transfer from 10,10'-dimethyl-9,9'-biacridine [(AcrH)(2)] to PTQ are also accelerated significantly by the presence of Sc(3+), Y(3+), and Mg(2+), exhibiting a first-order dependence with respect to concentrations of metal ions. In contrast to the case of o-quinones, unusually high kinetic orders are observed for rates of Sc(3+)-promoted electron transfer from tris(2-phenylpyridine)iridium(III) [Ir(ppy)(3)] to p-quinones (Q): second-order dependence on concentration of Q, and second- and third-order dependence on concentration of Sc(3+) due to formation of highly ordered radical anion complexes, Q()--(Sc(3+))(n)--Q (n=2 and 3).     

Density functional theory study of single-wall platinum nanotubes

Single-wall platinum nanotubes (SWPtN) were studied using spin-polarized density functional theory calculations. These nanotubes consist of 5-, 6-, and 8-Pt atoms coiling around the tubular axis forming 3.54–4.73 Å in diameter and 0.7–1.4 nm and infinite in length. Two types of wall structures, square and triangular, were investigated. The results show that triangular nanotubes are more stable. Our results suggest that it is also feasible to synthesize the 5- and 8-atom triangular nanotubes as the 6-atom Pt nanotubes were found experimentally. These SWPtN may provide a new dimension in the catalytic applications of platinum.     

Density functional theory study of the oxidation reaction in the gas and aqueous phase of allyl methyl disulfide with hydroxyl radical

Structural Chemistry - An in silico analysis of the oxidation mechanism of allyl methyl disulfide (AMDS) by hydroxyl radical was achieved at DFT level using B3LYP, CAM-B3LYP, M06-2X, and BMK...     

Density functional theory study of the photosensitization mechanisms of indigo

The triplet excited state properties and photosensitization mechanisms of indigo were investigated based on density functional theory calculations. The solvent effects on the photosensitization mechanisms of indigo have also been considered. The thermodynamic feasibility of the possible ¹O₂ and O₂·⁻-photogeneration pathways by triplet excited state indigo in different solvents was explored, in order to gain some deeper insights into the photosensitization characters of the dye.