Structure of radical cations of saturated heterocyclic compounds with two heteroatoms as studied by electron paramagnetic resonance, electron-nuclear double resonance, and density functional theory calculations

The radical cations of piperazine, morpholine, thiomorpholine, and thioxane were investigated by electron paramagnetic resonance (EPR) and electron-nuclear double resonance (ENDOR) spectroscopy in a solid Freon matrix. Optimized geometry and magnetic parameters of the radical cations were calculated using a density functional theory (DFT)/Perdew-Burke-Ernzerhof (PBE) method. Both experimental and theoretical results suggest that all the studied species adopt chair (or distorted chair) conformations. No evidence for the boat conformers with intramolecular sigma-bonding between heteroatoms were obtained. In the cases of morpholine and thioxane, the oxygen atoms are characterized by relatively small spin populations, whereas a major part of spin density is located at N and S atoms, respectively. The thiomorpholine radical cation exhibits nearly equal spin population of N and S atoms. In most cases (except for thioxane), the calculated magnetic parameters agree with the experimental data reasonably well.     

Water cluster anions studied by the long-range corrected density functional theory

Long-range corrected density functional theory (LC-DFT) is applied to a series of small water cluster anions(n= 2-6) to compute their vertical detachment energies (VDEs). The LC scheme is shown to eliminate an unphysical overestimation of the electron-water attraction in the hybrid functional by properly accounting for the long-range exchange repulsions. It is shown that a correct correlation energy behavior for a rapidly varying density is also important for describing a spatially extent, excess electron. The one-parameter progressive (OP) correlation functional, which satisfies this condition, leads to a remarkable improvement in the calculated VDE over the conventional one. The LC-BOP method produces highly accurate VDEs with a mean absolute deviation of 13.8 meV from the reference CCSD(T) results, reducing the error of B3LYP by more than 15 times. LC-BOP is found to be more accurate than MP2 which yields an excess electron underbound by 43.6 meV. The effect of basis sets on the calculated VDE is also examined. The aug-cc-pVDZ basis set with an extra diffuse function is found to be more accurate and reliable than the extended Pople-type basis sets used in the previous works. The extrapolation of the calculated VDE of different electron binding motifs is compared with the VDEs of experimentally observed three isomers (Verlet, J. R. R.; Bragg,A. E.; Kammrath, A.; Cheshnovsky, O.; Neumark, D. M. Science 2005, 307, 93).     

Solvation and crystal effects in bilirubin studied by NMR spectroscopy and density functional theory

The open-chain tetrapyrrole compound bilirubin was investigated in chloroform and dimethyl sulfoxide solutions by liquid-state NMR and as solid by (1)H, (13)C, and (15)N magic-angle spinning (MAS) solid-state NMR spectroscopy. Density functional theory (DFT) calculations were performed to interpret the data, using the B3LYP exchange-correlation functional to optimize geometries and to compute NMR chemical shieldings by the gauge-including atomic orbital method. The dependence of geometries and chemical shieldings on the size of the basis sets was investigated for the reference molecules tetramethylsilane, NH(3), and H(2)O, and for bilirubin as a monomer and in clusters consisting of up to six molecules. In order to assess the intrinsic errors of the B3LYP approximation in calculating NMR shieldings, complete basis set estimates were obtained for the nuclear shielding values of the reference molecules. The experimental liquid-state NMR data of bilirubin are well reproduced by a monomeric bilirubin molecule using the 6-311+G(2d,p) basis set for geometry optimization and for calculating chemical shieldings. To simulate the bilirubin crystal, a hexameric model was required. It was constructed from geometry-optimized monomers using information from the X-ray structure of bilirubin to fix the monomeric entities in space and refined by partial optimization. Combining experimental (1)H-(13)C and (1)H-(15)N NMR correlation spectroscopy and density functional theory, almost complete sets of (1)H, (13)C, and (15)N chemical shift assignments were obtained for both liquid and solid states. It is shown that monomeric bilirubin in chloroform solution is formed by 3-vinyl anti conformers, while bilirubin crystals are formed by 3-vinyl syn conformers. This conformational change leads to characteristic differences between the liquid- and solid-state NMR resonances.     

CpNi(diselenolene)] neutral radical complexes: electron paramagnetic resonance and density functional theory investigations

77Se-enriched CpNi(bds) (bds = 1,2-benzenediselenolate), has been synthesized and its g tensor and 77Se hyperfine tensors have been obtained from its frozen solution electron paramagnetic resonance (EPR) spectrum. These parameters are consistent with those calculated by density functional theory (DFT); it is shown that 10% of the spin is localized on each selenium and that the direction associated to the maximum 77Se couplings is aligned along the gmin direction, perpendicular to the Ni(bds) plane. EPR measurements and DFT calculations are also carried out on the 77Se enriched complex CpNi(dsit) as well on the two dithiolene analogues CpNi(bdt) and CpNi(dmit). The optimized structures of the isolated CpNi(bds) and CpNi(bdt) complexes have been used to generate the idealized dimers (bds)NiCp...CpNi(bds) and (bdt)NiCp...CpNi(bdt) characterized by Cp...Cp overlap. The exchange parameters J calculated at the DFT level for these systems are in reasonable accord with the experimental values. The influence of the geometry of the dimer on its magnetic properties is assessed by calculating the variation of J as a function of the relative orientation of the two Ni(diselenolene) or Ni(dithiolene) planes.     

Hydrogen bond geometries from electron paramagnetic resonance and electron-nuclear double resonance parameters: density functional study of quinone radical anion-solvent interactions

Density functional theory was used to study the impact of hydrogen bonding on the p-benzosemiquinone radical anion BQ(*-) in coordination with water or alcohol molecules. After complete geometry optimizations, (1)H, (13)C, and (17)O hyperfine as well as (2)H nuclear quadrupole coupling constants and the g-tensor were computed. The suitability of different model systems with one, two, four, and 20 water molecules was tested; best agreement between theory and experiment could be obtained for the largest model system. Q-band pulse (2)H electron-nuclear double resonance (ENDOR) experiments were performed on BQ(*-) in D(2)O. They compare very well with the spectra simulated by use of the theoretical values from density functional theory. For BQ(*-) in coordination with four water or alcohol molecules, rather similar hydrogen-bond lengths between 1.75 and 1.78 A were calculated. Thus, the computed electron paramagnetic resonance (EPR) parameters are hardly distinguishable for the different solvents, in agreement with experimental findings. Furthermore, the distance dependence of the EPR parameters on the hydrogen-bond length was studied. The nuclear quadrupole and the dipolar hyperfine coupling constants of the bridging hydrogens show the expected dependencies on the H-bond length R(O.H). A correlation was obtained for the g-tensor. It is shown that the point-dipole model is suitable for the estimation of hydrogen-bond lengths from anisotropic hyperfine coupling constants of the bridging (1)H nuclei for H-bond lengths larger than approximately 1.7 A. Furthermore, the estimation of H-bond lengths from (2)H nuclear quadrupole coupling constants of bridging deuterium nuclei by empirical relations is discussed.     

Valence electronic structure of benzo-2,1,3-chalcogenadiazoles studied by photoelectron spectroscopy and density functional theory

The He I photoelectron spectra of benzo-2,1,3-thia-, selena-, and telluradiazole were measured, and the observed ionization bands were assigned by comparison with the results of DFT calculations. Whereas the B3LYP exchange-correlation functional provided orbital energies that permitted a preliminary assignment by application of Koopman's theorem, a more-accurate interpretation was established by calculation of the vertical ionization energies with the PW91 functional and analysis of the correlation of energy levels along the homologous series. This strategy clarified earlier disagreements in the assignment of the spectrum of benzo-2,1,3-thiadiazole.     

Free radical conformations and conversions in X-irradiated single crystals of L-cysteic acid by electron magnetic resonance and density functional theory studies

Single crystals of L-cysteic acid monohydrate were X-irradiated and studied at 295 K using EPR, ENDOR, and EIE techniques. Three spectroscopically different radicals were observed. These were a deamination radical reduction product (R1), and two oxidation products formed by hydrogen abstraction (radicals R2, R3). R2 and R3 were shown to exhibit the same chemical structure while exhibiting very different geometrical conformations. Cluster DFT calculations at the 6-31G(d,p) level of theory supported the experimental observations for radicals R1 and R2. It was not possible to simulate the R3 radical in any attempted cluster; hence, for this purpose a single molecule approach was used. The precursor radicals for R1, R2, and R3, identified in the low-temperature work on L-cysteic acid monohydrate by Box and Budzinski, were also investigated using DFT calculations. The experimentally determined EPR parameters for the low-temperature decarboxylated cation could only be reproduced correctly within the cluster when the carboxyl group remained in the proximity of the radical. Only one of the two observed low-temperature carboxyl anions (stable at 4 and 48 K) could be successfully simulated by the DFT calculations. Evidence is presented in support of the conclusions that the carboxyl reduction product already is protonated at 4 K and that the irreversible conversion between the two reduction products is brought forward by an umbrella-type inversion of the carboxyl group.     

Substrate-binding in quinoprotein ethanol dehydrogenase from pseudomonas aeruginosa studied by electron paramagnetic resonance at 94 GHz

Pyrroloquinoline quinone (2,7,9-tricarboxypyrroloquinoline quinone, PQQ) is one of several quinone cofactors that is utilized in a class of dehydrogenases known as quinoproteins. In this contribution, we have used continuous-wave high-field/high-frequency electron paramagnetic resonance (EPR) at 94 GHz (W-band) to study substrate binding in ethanol dehydrogenase (QEDH) from Pseudomonas aeruginosa, taking advantage of the fact that the enzyme is isolated with a substantial proportion of the PQQ cofactor in the paramagnetic semiquinone form. In the substrate-free enzyme, the principal values of the g-tensor, obtained by spectral simulation are: gx = 2.00585(2), gy = 2.00518(2), and gz = 2.00212(2), giving giso = 2.00438(2). All three principal values of the g-tensor decrease when ethanol is bound to the protein: gx = 2.00574(2), gy = 2.00511(2), and gz = 2.00207(2), giving giso = 2.00431(2). The results represent the first direct evidence for the tight binding of an alcohol to a PQQ-dependent alcohol dehydrogenase and show that ethanol also binds to the enzyme even when the PQQ cofactor is in the semiquinone form. The decrease in g is consistent with an increase in polarity in the immediate vicinity of the PQQ cofactor and probably reflects a changed geometry of the PQQ-Ca2+ complex when ethanol binds.     

Photochemical free radical formation from aliphatic dicarboxylic acids in solution as studied by electron spin resonance spectroscopy

Various free radicals formed during UV.-irradiation of aliphatic dicarboxylic acids in aqueous and methanolic solution are identified by ESR.-spectroscopy. Their structures point to α-cleavage and photoreduction as the dominant primary photochemical decay processes. The relative contributions of these reactions to the overall photodecomposition depend on solvent and degree of α-alkylation of the acid. Emission ESR.-spectra are found for radicals formed by C, CO-bond cleavage of α-dimethyl substituted acids. The polarization is referred to the triplet mechanism of CIDEP. and indicates this cleavage reaction occurs from a triplet molecular state.     

Inhibition and enhancement of resonance as studied by 13C nuclear magnetic resonance spectroscopy

¹³C chemical shifts are reported for a series of 2-substituted 1,3-dimethylbenzenes: comparisons of these values with those for the corresponding monosubstituted benzenes reveal, in some cases, large differences in the para-carbon substituent chemical shifts, which are attributable to steric hindrance of resonance. The questions of steric enhancement of resonance, and methoxy group conformation in certain anisoles are also studied by the ¹³C NMR technique. Studies of selected 2-substituted fluorenes are also reported, and substituent chemical shifts at carbon-7 (traversing eight bonds) of greater than 2ppm are observed. These effects are consistently greater than those reported for the corresponding biphenyl compounds, and are associated with planarity-enforced enhancement of resonance.     

Gamma-irradiated ExtraVit M nutritive supplement studied by electron paramagnetic resonance spectroscopy

An unirradiated and γ-irradiated nutritive supplement named ExtraVit M was studied by electron paramagnetic resonance (EPR) spectroscopy in order to detect stable paramagnetic species following improvement of hygienic quality by γ-radiation. Free radicals were induced by γ-radiation in the studied samples from low absorbed doses, showing a certain sensibility of these samples to the radiation treatment. The EPR spectrum of irradiated ExtraVit M is typical for drugs or nutritive supplements containing high levels of sugars, vitamin C and cellulose.     

Hydrogen radical and hydroxyl radical hydrogen abstraction reaction from formyl fluoride studied with hybrid density functional theory methods

With the goal of reducing flame velocity in combustion reactions, this study focused on the conversion of hydrogen and hydroxyl radicals into relatively unreactive hydrogen and water molecules through the inter-conversion of formyl fluoride to fluoroformyl radicals. Hybrid DFT computational methods were employed to confirm these results. Based on this, the fluoroformyl radical-assisted transformation of the hydrogen and hydroxyl radicals into hydrogen and water molecules was discussed.     

Structure of the ammonia dimer studied by density functional theory

Self-consistent Kohn–Sham density functional calculations have been carried out to study the structure of the ammonia dimer. The local-density approximation yields unusually large binding energy and short internitrogen distance compared with the experimental and more accurate theoretical data. The results from the Becke–Perdew gradient-corrected functionals are generally in good agreement with those at the SCF MP 2 level when the geometry is fully optimized with various large basis sets. With our best estimation, the staggered quasi-linear structure (C_s) is 0.6 kcal/mol lower in energy than the symmetric cyclic one (C_2h). The hydrogen-bonded N—H bond in the staggered quasi-linear structure is found to be 0.008 Å longer than the N—H bond in ammonia. In our calculations, we could not find the minima on the energy surface corresponding to the two asymmetric cyclic structures suggested by microwave spectra and coupled pair functional calculations. © 1994 John Wiley & Sons, Inc.     

Structure and electron paramagnetic resonance parameters of the manganese site of concanavalin A studied by density functional methods

The EPR parameters of the manganese site in the saccharide-binding protein concanavalin A have been studied by density functional methods, with an emphasis on metal (⁵⁵Mn) and ligand (¹H and ¹⁷O) hyperfine couplings, in comparison with high-field EPR and ENDOR data. Results for gradient-corrected and hybrid functionals with different exact-exchange admixture have been compared with experiment for the ⁵⁵Mn and the ¹H ligand hyperfine coupling and have been predicted for ¹⁷O hyperfine coupling based on comparison with experiment for the related [Mn(H₂O)₆]²⁺. Appreciable exact-exchange admixture in the hybrid functional is needed to obtain an adequate spin-density distribution and thus near-quantitative agreement with experimental EPR parameters. The common use of experimental proton hyperfine coupling tensors together with the point-dipole approximation for determination of bond lengths is evaluated by explicit calculations.     

Predicting 9Be nuclear magnetic resonance chemical shielding tensors utilizing density functional theory

The structures of a series of beryllium containing complexes have been optimized at the B3LYP/6-31G(d) level and their (9)Be magnetic shielding values have been determined using B3LYP/6-311G+g(2d,p) and the gauge-including atomic orbital (GIAO) method. The calculated chemical shifts are in excellent agreement with experimental values. The performance of a variety of NMR methods (SGO, IGAIM, CSGT) were also examined but were found to be inferior to the GIAO method at the chosen level of theory employed. The theoretical method has been utilized to predict the beryllium chemical shifts of structurally characterized complexes for which no measured (9)Be NMR spectrum exists, and to investigate a literature complex with an unusual (9)Be NMR chemical shift. A new standard for beryllium NMR in nonaqueous solvents has been suggested.     

Structures of tetrafluorocyclopropene, hexafluorocyclobutene, octafluorocyclopentene and related perfluoroalkene radical anions revealed by electron spin resonance spectroscopic and computational studies

Isotropic and anisotropic ESR spectra were observed for the radical anions of hexafluorocyclobutene (c-C(4)F(6)(-)), octafluorocyclopentene (c-C(5)F(8)(-)) and perfluoro-2-butene (CF(3)CF=CFCF(3)(-)) in gamma-irradiated plastically crystalline neopentane, tetramethylsilane (TMS) and TMS-d(12) matrices, or the rigid 2-methyltetrahydrofuran (MTHF) matrix. The isotropic spectra of c-C(4)F(6)(-) and c-C(5)F(8)(-) are characterized by three different sets of pairs of (19)F nuclei with the isotropic hyperfine (hf) splittings of 15.2 (2F), 6.5 (2F), 1.1 (2F) mT for c-C(4)F(6)(-) and 14.7 (2F), 7.4 (2F), 1.0 (2F) mT for c-C(5)F(8)(-). By comparison with the results of ab initio quantum chemical computations, the large triplet (19)F hf splittings of ca. 15 mT are assigned to the two fluorines attached to the C=C bond. The UHF, B3LYP and MP2 computations predict that the geometrical structures of the perfluoroalkenes are strongly distorted by one-electron reduction to form their radical anions; c-C(3)F(4)(-): C(2) symmetry ((2)A state) <-- C(2)(v) ((1)A(1)), c-C(4)F(6)(-): C(1) ((2)A) <-- C(2)(v) ((1)A(1)) and c-C(5)F(8)(-): C(1) ((2)A) <-- C(s) ((1)A'). The structural distortion arises from a mixing of the pi* and higher-lying sigma* orbitals at the C=C carbons similar to that previously found for CF(2)=CF(2)(-) with a C(2)(h) distortion. The isotropic (19)F hf splittings computed with the B3LYP method with 6-311+G(2df,p) basis set for the geometry optimized by the UHF and/or MP2 methods are within 6% error of the experimental values. The experimental anisotropic spectra of c-C(4)F(6)(-), c-C(5)F(8)(-) and CF(2)=CF(2)(-) were satisfactorily reproduced by the ESR spectral simulation method using the computed hf principal values and orientation of (19)F nuclei. In addition, the electronic excitation energies and oscillator strengths for the CF(2)=CF(2)(-), c-C(3)F(4)(-), c-C(4)F(6)(-) and c-C(5)F(8)(-) radical anions were computed for the first time by TD-DFT methods.