Identification and conformational study of stable radiation-induced defects in sucrose single crystals using density functional theory calculations of electron magnetic resonance parameters

One of the major stable radiation-induced radicals in sucrose single crystals (radical T2) has been identified by means of density functional theory (DFT) calculations of electron magnetic resonance parameters. The radical is formed by a net glycosidic bond cleavage, giving rise to a glucose-centered radical with the major part of the spin density residing at the C 1 carbon atom. A concerted formation of a carbonyl group at the C 2 carbon accounts for the relatively small spin density at C 1 and the enhanced g factor anisotropy of the radical, both well-known properties of this radical from several previous experimental investigations. The experimentally determined and DFT calculated proton hyperfine coupling tensors agree very well on all accounts. The influence of the exact geometrical configuration of the radical and its environment on the tensors is explored in an attempt to explain the occurrence and characteristics of radical T3, another major species that is most likely another conformation of T2. No definitive conclusions with regard to the actual structure of T3 could be arrived at from this study. However, the results indicate that, most likely, T3 is identical in chemical structure to T2 and that changes in the orientation of neighboring hydroxy groups or changes in the configuration of the neighboring fructose ring can probably not account for the type and size of the discrepancies between T2 and T3.     

Combined electron magnetic resonance and density functional theory study of 10 K X-irradiated beta-D-fructose single crystals

Primary free radical formations in fructose single crystals X-irradiated at 10 K were investigated at the same temperature using X-band Electron Paramagnetic Resonance (EPR), Electron Nuclear Double Resonance (ENDOR) and ENDOR induced EPR (EIE) techniques. ENDOR angular variations in the three principal crystallographic planes and a fourth skewed plane allowed the unambiguous determination of five proton hyperfine coupling tensors. From the EIE studies, these hyperfine interactions were assigned to three different radicals, labeled T1, T1* and T2. For the T1 and T1* radicals, the close similarity in hyperfine coupling tensors suggests that they are due to the same type of radical stabilized in two slightly different geometrical conformations. Periodic density functional theory calculations were used to aid the identification of the structure of the radiation-induced radicals. For the T1/T1* radicals a C3 centered hydroxyalkyl radical model formed by a net H abstraction is proposed. The T2 radical is proposed to be a C5 centered hydroxyalkyl radical, formed by a net hydrogen abstraction. For both radicals, a very good agreement between calculated and experimental hyperfine coupling tensors was obtained.     

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.     

Mercury telluride crystals encapsulated within single walled carbon nanotubes: A density functional study

The structure and binding energies of mercury telluride crystals encapsulated within single walled carbon nanotubes (SWNTs) have been studied using density functional theory. The energies of three different pseudo one‐dimensional crystals of HgTe with 4:4, 3:3, and 2:2 coordination are compared. The initial structure for the 4:4 crystal was a 2 × 2 cubic motif derived from rock salt bulk structure, the 3:3 crystal corresponds to a novel structure found when HgTe was intercalated within SWNTs, and the 2:2 crystal is a chain motif derived from cinnabar (HgS) bulk structure. The isolated 3:3 crystal was found to be the most thermodynamically stable of the three structures. Calculations were performed on the 3:3 crystal inserted into three different SWNTs, (15, 0), (9, 9), and (17, 0), in order to investigate the perturbations on the molecular and electronic structure of the crystal and the SWNT, and the energy of formation of the HgTe@SWNT composites. The calculated structures are in good agreement with the experimental high resolution transmission electron microscopy images of the HgTe@SWNT composite. The calculated binding energies and density of states show that the interaction between nanotubes and the HgTe crystals is noncovalent. Since the energy difference of the “free” 4:4 and 3:3 structures is small and of the order of magnitude of the binding energies with the nanotubes, we carried out calculations on 4:4 HgTe structure inserted in to two different SWNTs, (15, 0) and (17, 0). The calculated binding energies show that, when the 4:4 structure is inserted into the smallest tube, the resultant composite has an energy comparable to the 3:3 structure, suggesting that this polymporph may also be found experimentally. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

An EPR/ENDOR study of the asymmetric hydrogen bond between the quinone electron acceptor and the protein backbone in Photosystem I

Hydrogen bonding to the photoaccumulated secondary acceptor radical anion A₁^√− in photosystem (PS) I has been studied using pulsed Q-band ENDOR spectroscopy. With deuterated quinone in protonated PS I particles it is demonstrated that the observed radical anion has only one hydrogen-bond hyperfine coupling (hfc) tensor with tensor components above the 2 MHz range. Below 2 MHz the protein matrix protons dominate and a second weak H-bond could not be detected. The spectral resolution of pulsed Q-band ENDOR is critically required to separate the signals of the H-bond proton from those of the primary chlorophyll acceptor, A₀^√−, which cannot be avoided to be formed to some extent in the photoaccumulation procedure. The determined H-bond hfc tensor of A₁^√− is found to be close to axial symmetry with a small isotropic component, as expected from a predominantly dipolar electron–proton spin interaction in a hydrogen-bond. The principal tensor components are A=(+)7.7, MHz A=(−)4.9 MHz, A_iso=(−)0.7 MHz. The magnitude of the dipolar tensor corresponds to an unusually short H-bond which can be estimated from the point-dipole approximation (1.5±0.1 Å). Based on previous studies with A- and B-branch specific site-directed mutants of the A₁ site of PS I and the chosen photoaccumulation protocol, the observed A₁^√− radical anion can be assigned to the Q_K–A site of the A-branch. The observed H-bond hfc tensor is compared to those determined for related quinone radical anions observed in frozen protic solution as well as in the Q_A site of type II bacterial reaction centers.     

1H NMR, electron paramagnetic resonance, and density functional theory study of dinuclear pentaammineruthenium dicyanamidobenzene complexes

Paramagnetic (1)H NMR and electron paramagnetic resonance (EPR) spectroscopies and density functional theory (DFT) spin density calculations were selectively performed on the [{(NH(3))(5)Ru}(2)(μ-L)](3+,?4+,?5+) complexes, where L is 2,3,5,6-tetrachloro-, 2,5-dichloro-, 2,5-dimethyl-, and unsubstituted 1,4-dicyanamidobenzene dianion, to characterize the electronic structure of these complexes. EPR spectra of the [{(NH(3))(5)Ru}(2)(μ-L)](3+) complexes in N,N'-dimethylformamide at 4 K showed a ruthenium axial signal, and thus the complexes are [Ru(II),L(2-), Ru(III)] mixed-valence systems. DFT spin density calculations of [{(NH(3))(5)Ru}(2)(μ-L)](3+) where L = 1,4-dicyanamidobenzene dianion gave mostly bridging-ligand centered spin distribution for both vacuum and implicit solvent calculations, in poor agreement with EPR, but more realistic results were obtained when explicit electrostatic interactions between solute and solvent were included in modeling. For the [{(NH(3))(5)Ru}(2)(μ-L)](4+) complexes, EPR spectroscopy showed no signal down to 4 K. Nevertheless, solvent-dependent (1)H NMR data and analysis support a [Ru(III),L(2-), Ru(III)] state. Hyperfine coupling constants (A(c)/h) of trans- and cis-ammine and phenyl hydrogens were determined to be 17.2, 3.8, and -1.5 MHz respectively. EPR studies of the [{(NH(3))(5)Ru}(2)(μ-L)](5+) complexes showed a metal-radical axial signal and based on previously published (1)H NMR data, a [Ru(IV),L(2-), Ru(III)] state is favored over a [Ru(III),L(-), Ru(III)] state.     

Ab initio EPR study of S and Se defects in alkali halides

Calculations using density functional theory are performed to study the electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) properties of S and Se impurities in alkali halide lattices. Cluster in vacuo models are used to describe the defect and the lattice surroundings. The trivacancy defect model proposed in the literature is able to reproduce both the experimental principal values and directions of the g tensor for S and Se defects doped in alkali halides. The alternative monovacancy model gives rise to important discrepancies with experiment and can be discarded. For the KCl lattice, the hyperfine tensors of the S and Se molecular ions also agree well with the available experimental data, giving further evidence to the trivacancy model. In addition, for NaCl:S and KCl:S computational results for the ²³Na and ³⁵Cl superhyperfine and quadrupole tensors are compared with experimental ENDOR parameters. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Enantioselective organocatalytic Diels-Alder reactions: a density functional theory and kinetic isotope effects study

The mechanism and enantioselectivity of the organocatalytic Diels-Alder reaction were computationally investigated by density functional theory at the B3LYP/6-31G(d) level of theory. The uncatalyzed Diels-Alder reaction was also studied to explore the effect of the organocatalyst on this reaction in terms of energetics, selectivity, and mechanism. The catalyzed reaction showed improved endo/exo selectivity, and the free energy of activation was significantly lowered in the presence of the catalyst. Both uncatalyzed and catalyzed reactions exhibited concerted asynchronous reaction mechanism with the degree of asynchronicity being more evident in the presence of the catalyst. The Corey's experimentally derived predictive selection rules for the outcome of the organocatalytic Diels-Alder reaction were also theoretically analyzed, and an excellent agreement was found between experiment and theory.     

Spin density distribution in mononuclear Rh(0) complexes: A combined experimental and DFT study

The paramagnetic complex [Rh(trop₂dach)]2 was obtained by reduction of the almost planar 16-electron cationic precursor complex, [Rh(trop₂dach)]⁺1 and characterized by EPR spectroscopy [g₁₁ = 2.069, g₂₂ = 2.014, g₃₃ = 1.964, g_iso = 2.016; A(Rh) = (<40, 29, 30)]. The unobservable small nitrogen hyperfine coupling and DFT calculations show that most of the spin density is localized on the hydrocarbon ligand framework and only about 35% on the metal center. DFT calculations on various 17 electron rhodium complexes with carbonyl, olefine, or phosphane ligands like [Rh(CO)₄], [Rh(cod)₂], and [Rh(dppe)₂] reveal that in none of these the spin density at the metal center exceeds 45%. That is all formally Rh(0) complexes reported to date are better described as highly delocalized radicals and an assignment of the formal metal oxidation state is not meaningful.     

Electronic and magnetic properties of substituted BN sheets: a density functional theory study

Using density functional calculations, we investigate the geometries, electronic structures and magnetic properties of hexagonal BN sheets with 3d transition metal (TM) and nonmetal atoms embedded in three types of vacancies: V(B), V(N), and V(B+N). We show that some embedded configurations, except TM atoms in V(N) vacancy, are stable in BN sheets and yield interesting phenomena. For instance, the band gaps and magnetic moments of BN sheets can be tuned depending on the embedded dopant species and vacancy type. In particular, embedment such as Cr in V(B+N), Co in V(B), and Ni in V(B) leads to half-metallic BN sheets interesting for spin filter applications. From the investigation of Mn-chain (C(Mn)) embedments, a regular 1D structure can be formed in BN sheets as an electron waveguide, a metal nanometre wire with a single atom thickness.     

Hydroxyl radical and hydroxide ion in liquid water: a comparative electron density functional theory study

Ab initio density functional theory molecular dynamics simulations of the solvated states of the hydroxyl radical and hydroxide ion are performed using the Becke-Lee-Yang-Parr (BLYP) exchange-correlation functional (Becke, A. D. Phys. Rev. A 1988, 38, 3098. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785). The structures of the solvation shells of the two species are examined. It is found that the OH radical forms a relatively well-defined solvation complex with four neighboring water molecules. Three of these molecules are hydrogen bonded to the OH, while the fourth is hemibonded via a three-electron two-centered bond between the oxygen atoms of the OH and water. The activity and the diffusion mechanism of the OH radical in water is discussed in comparison with the OH- ion. Although the results are partially influenced by the tendency of the BLYP density functional to overestimate hemibonded structure, the present simulations suggest that the widely accepted picture of rapid diffusion of OH radical in water through hydrogen exchange reaction may need to be reconsidered.     

Structure, spectroscopy, and reactivity properties of porphyrin pincers: a conceptual density functional theory and time-dependent density functional theory study

Porphyrin and pincer complexes are both important categories of compounds in biological and catalytic systems. The idea to combine them is computationally investigated in this work. By employment of density functional theory (DFT), conceptual DFT, and time-dependent DFT approaches, structure, spectroscopy, and reactivity properties of porphyrin pincers are systematically studied for a selection of divalent metal ions. We found that the porphyrin pincers are structurally and spectroscopically different from their precursors and are more reactive in electrophilic and nucleophilic reactions. A few quantitative linear/exponential relationships have been discovered between bonding interactions, charge distributions, and DFT chemical reactivity indices. These results are implicative in chemical modification of hemoproteins and understanding chemical reactivity in heme-containing and other biologically important complexes and cofactors.     

Silver chloride supported on Vitamin B1 -Organometallic magnetic catalyst: synthesis,density functional theory study and application in A3-coupling reactions

A highly efficient Fe₃O₄@VitB₁–Ag(I) magnetic catalyst has been obtained using surface modification of Fe₃O₄. To this end, silver chloride was immobilized on Fe₃O₄ nanoparticles via vitamin B₁ biomolecules. The synthesized biocompatible magnetic catalyst was applied in an A³-coupling reaction in the presence of aldehyde, amine and phenyl acetylene under solvent-free conditions and afforded the desired products in excellent yields. Also, interactions between metal and ligand in the Fe₃O₄@VitB₁–Ag(I) were studied using theoretical calculations.     

Structures, reductive dechlorination, and electron affinities of selected polychlorinated dibenzo-p-dioxins: density functional theory study

Density functional theory calculations were performed to obtain the structures, vertical electron affinities, and adiabatic affinities of 15 polychlorinated dibenzo-p-dioxins (PCDDs), including several extremely toxic congeners. A three-parameter hybrid density functional, B3LYP, was utilized with two different basis sets, 6-311G(d,p) and 6-311+G(2d,2p). The optimized structures of all PCDDs under consideration were planar, while all corresponding anions attained nonplanar geometries. One of the C-Cl bonds on each PCDD anion was considerably elongated, and the dechlorination of PCDDs occurred as the departing chlorine bent off the aromatic ring plane for effective pi-sigma orbital mixing. The characteristic electron energy-dependent regioselective chloride ion loss channels for 1,2,3,7,8-pentaCDD were elucidated by transition-state theory calculations. The relative low-energy barrier for the dechlorination of 1,2,3,7,8-pentaCDD indicated the high likelihood of obtaining reductive dechlorination (RD) products that are more toxic than the parent species. The calculated vertical electron affinities of PCDDs are consistent with the available experimental attachment energies, and the positive adiabatic electron affinities suggest that PCDDs may act as electron acceptors in living cells.     

Molecular conformations of a partially halogenated ether: A study based on infrared spectroscopy and density functional theory calculations

A new partially halogenated ether (ClCF₂CF(CF₃)OCF₂CH₃) has been synthesized and characterized using DSC, GC, ¹H and ¹⁹F NMR, IR. The experimental infrared spectra of this “flexible” molecule have been successfully interpreted on the basis of reliable Density Functional Theory calculations. An efficient method useful for the identification of the many stable conformers has been developed and applied. Infrared spectra of the stable conformers have been simulated after full geometry optimization. The results obtained allow detection of conformation-sensitive bands, making possible the interpretation of fine details in the spectra.     

Aqueous coordination chemistry and photochemistry of uranyl(VI) oxalate revisited: a density functional theory study

Using density functional theory (DFT) calculations, we revisited a classical problem of uranyl(VI) oxalate photochemical decomposition. Photoreactivities of uranyl(VI) oxalate complexes are found to correlate largely with ligand-structural arrangements. Importantly, the intramolecular photochemical reaction is inhibited when oxalate is bound to uranium exclusively in chelate binding mode. Previously proposed mechanisms involving a UO(2)(C(2)O(4))(2)(2-) (1:2) complex as the main photoreactive species are thus unlikely to apply, because the two oxalic acids are bound to uranium in a chelating binding mode. Our DFT results suggest that the relevant photoreactive species are UO(2)(C(2)O(4))(3)(4-) (1:3) and (UO(2))(2)(C(2)O(4))(5)(6-) (2:5) complexes binding uranium in an unidentate fashion. These species go through decarboxylation upon excitation to the triplet state, which ensues the release of CO(2) and reduction of U(vi) to U(v). The calculations also suggest an alternative intermolecular pathway at low pH via an electron transfer between the excited state *UO(2)(2+) and hydrogen oxalate (HC(2)O(4)(-)) which eventually leads to the production of CO and OH(-) with no net reduction of U(VI). The calculated results are consistent with previous experimental findings that CO is only detected at low pH while U(IV) is detected only at high pH.     

1-Cyclohepta-2,4,6-trienyl-selanes--a 77Se NMR study: indirect nuclear 77Se--13C spin-spin coupling constants and application of density functional theory (DFT) calculations

1-Cyclohepta-2,4,6-trienyl-selanes Se(C(7)H(7))(2) (2c), R--Se--C(7)H(7) with R = Bu, (t)Bu, Ph, 4-F--C(6)H(4) (12a,b,c,d) were prepared by the reaction of the corresponding silanes, Si(SeMe(3))(2) and R--Se--SiMe(3), respectively, with tropylium bromide C(7)H(7)Br. In spite of the low stability of the selanes even in dilute solutions and at low temperature, they could be characterised by their (1)H, (13)C and (77)Se NMR parameters. Coupling constants (1)J((77)Se,(13)C) were measured and calculated by DFT methods at the B3LYP/6-311+G(d,p) level of theory. The comparison of experimental and calculated coupling constants (1)J((77)Se,(13)C) included numerous selenium carbon compounds with largely different Se--C bonds, revealing a satisfactory agreement. Both the spin-dipole (SD) and the paramagnetic spin-orbital (PSO) terms contributed significantly to the spin-spin coupling interaction, in addition to the Fermi contact (FC) term.