Conformation Of Radicals Research Articles

Theoretical determination of the standard enthalpies of formation of alkyl radicals using the concept of a complete set of homodesmotic reactions

The complete sets of homodesmotic reactions (HDR) for 107 acyclic alkyl free radicals С4-С9 of normal and branched structure were constructed using the graph-theoretic representation and analysis of a tested compound. The absolute enthalpies of the studied compounds and HDR reference structures were calculated using the M062X/cc-pVTZ level of theory. Based on these data, the thermal effects of HDRs were calculated and then applied to determine the standard enthalpies of formation of the studied radicals using the known enthalpies of formation of reference structures. The dissociation energies of BDE C–H and C–CH3 bonds were also calculated. The effect of radical structure on the BDE value is discussed, and a new effect of stabilization of the radical center in the skewed conformation of free radical is established; this effect has not been previously described in the scientific literature.

How the Conformational Movement of the Substrate Drives the Regioselective C–N Bond Formation in P450 TleB: Insights from Molecular Dynamics Simulations and Quantum Mechanical/Molecular Mechanical Calculations

P450 TleB catalyzes the oxidative cyclization of the dipeptide N-methylvalyl-tryptophanol into indolactam V through selective intramolecular C-H bond amination at the indole C4 position. Understanding its catalytic mechanism is instrumental for the engineering or design of P450-catalyzed C-H amination reactions. Using multiscale computational methods, we show that the reaction proceeds through a diradical pathway, involving a hydrogen atom transfer (HAT) from N1-H to Cpd I, a conformational transformation of the substrate radical species, and a second HAT from N13-H to Cpd II. Intriguingly, the conformational transformation is found to be the key to enabling efficient and selective C-N coupling between N13 and C4 in the subsequent diradical coupling reaction. The underlined conformational transformation is triggered by the first HAT, which proceeds with an energy-demanding indole ring flip and is followed by the facile approach of the N13-H group to Cpd II. Detailed analysis shows that the internal electric field (IEF) from the protein environment plays key roles in the transformation process, which not only provides the driving force but also stabilizes the flipped conformation of the indole radical. Our simulations provide a clear picture of how the P450 enzyme can smartly modulate the selective C-N coupling reaction. The present findings are in line with all available experimental data, highlighting the crucial role of substrate dynamics in controlling this highly valuable reaction.

Theoretical Study of Hydroxylation of α- and β-Pinene by a Cytochrome P450 Monooxygenase Model

Previous studies on biocatalytic transformations of pinenes by cytochrome P450 (CYP) enzymes reveal the formation of different oxygenated products from a single substrate due to the multistate reactivity of CYP and the many reactive sites in the pinene scaffold. Up until now, the detailed mechanism of these biocatalytic transformations of pinenes have not been reported. Hereby, we report a systematic theoretical study of the plausible hydrogen abstraction and hydroxylation reactions of α- and β-pinenes by CYP using the density functional theory (DFT) method. All DFT calculations in this study were based on B3LYP/LAN computational methodology using the Gaussian09 software. We used the B3LYP functional with corrections for dispersive forces, BSSE, and anharmonicity to study the mechanism and thermodynamic properties of these reactions using a bare model (without CYP) and a pinene-CYP model. According to the potential energy surface and Boltzmann distribution for radical conformers, the major reaction products of CYP-catalyzed hydrogen abstraction from β-pinene are the doublet trans (53.4%) and doublet cis (46.1%) radical conformer at delta site. The formation of doublet cis/trans hydroxylated products released a total Gibbs free energy of about 48 kcal/mol. As for alpha pinene, the most stable radicals were trans-doublet (86.4%) and cis-doublet (13.6%) at epsilon sites, and their hydroxylation products released a total of ~50 kcal/mol Gibbs free energy. Our results highlight the likely C-H abstraction and oxygen rebounding sites accounting for the multi-state of CYP (doublet, quartet, and sextet spin states) and the formation of different conformers due to the presence of cis/trans allylic hydrogen in α-pinene and β-pinene molecules.

A broadband pulse EPR spectrometer for high-throughput measurements in the X-band

We present an X-band pulse EPR spectrometer with high throughput and excellent sensitivity in the 8.5-11.5GHz range. It is designed for high stability and low noise Fourier Transform measurements for applications in pulse dipolar spectroscopy, pulse hyperfine spectroscopy, and spin relaxation from cryogenic temperatures to room temperature. An arbitrary waveform generator is used to generate pulses of any frequency and shape for multiple resonance experiments or for uniform broadband excitation with bandwidths exceeding 350 MHz. We illustrate the capabilities and performance of the spectrometer by measurements on free radicals and biradicals in solids and liquids. Relaxation times of radicals in liquid solution are measured for fewer than 30,000,000 spins (less than 3 nanomoles per liter). Non-uniform acquisition provides higher throughput for mixtures of radicals with quite different relaxation rates. Conventional DEER measurements on a rigid biradical have good modulation depth. Broadband SIFTER with chirped adiabatic WURST pulses demonstrates versatility for the latest broadband pulse schemes. A broadband ESEEM measurement correlates ESEEM and EPR frequencies which characterize the conformation of a nitroxide radical. The entire EPR spectrum with a width approaching 300 MHz was excited and detected throughout the measurement. The spectrometer supports the operator in tuning, setting up experiments and monitoring their progress so that even novice users consistently can obtain optimal results.

Mechanoresponsive diselenide-crosslinked microgels with programmed ultrasound-triggered degradation and radical scavenging ability for protein protection.

In the context of controlled delivery and release, proteins constitute a delicate class of cargo requiring advanced delivery platforms and protection. We here show that mechanoresponsive diselenide-crosslinked microgels undergo controlled ultrasound-triggered degradation in aqueous solution for the release of proteins. Simultaneously, the proteins are protected from chemical and conformational damage by the microgels, which disintegrate to water-soluble polymer chains upon sonication. The degradation process is controlled by the amount of diselenide crosslinks, the temperature, and the sonication amplitude. We demonstrate that the ultrasound-mediated cleavage of diselenide bonds in these microgels facilitates the release and activates latent functionality preventing the oxidation and denaturation of the encapsulated proteins (cytochrome C and myoglobin) opening new application possibilities in the targeted delivery of biomacromolecules.

Distribution of H^upbeta Hyperfine Couplings in a Tyrosyl Radical Revealed by 263 GHz ENDOR Spectroscopy

^1H ENDOR spectra of tyrosyl radicals (Y^bullet) have been the subject of numerous EPR spectroscopic studies due to their importance in biology. Nevertheless, assignment of all internal ^1H hyperfine couplings has been challenging because of substantial spectral overlap. Recently, using 263 GHz ENDOR in conjunction with statistical analysis, we could identify the signature of the H^{upbeta _2} coupling in the essential Y_{122} radical of Escherichia coli ribonucleotide reductase, and modeled it with a distribution of radical conformations. Here, we demonstrate that this analysis can be extended to the full-width ^1H ENDOR spectra that contain the larger H^{upbeta _1} coupling. The H^{upbeta _2} and H^{upbeta _1} couplings are related to each other through the ring dihedral and report on the amino acid conformation. The 263 GHz ENDOR data, acquired in batches instead of averaging, and data processing by a new “drift model” allow reconstructing the ENDOR spectra with statistically meaningful confidence intervals and separating them from baseline distortions. Spectral simulations using a distribution of ring dihedral angles confirm the presence of a conformational distribution, consistent with the previous analysis of the H^{upbeta _2} coupling. The analysis was corroborated by 94 GHz ^2H ENDOR of deuterated Y_{122}^bullet. These studies provide a starting point to investigate low populated states of tyrosyl radicals in greater detail.

Rotational and fine structure of open-shell molecules in nearly degenerate electronic states. II. Interpretation of experimentally determined interstate coupling parameters of alkoxy radicals.

Rotationally and fine-structure resolved B̃←X̃ laser-induced fluorescence (LIF) spectra of alkoxy radicals have been simulated with a "coupled two-states model" [J. Liu, J. Chem. Phys. 148, 124112 (2018)], in which the nearly degenerate X̃ and à states are considered together. These two electronic states are separated by the "difference potential" and coupled by the spin-orbit (SO) interaction and the Coriolis interaction. Molecular constants determined in fitting the LIF spectra using the coupled two-states model provide quantitative insight into the SO and Coriolis interactions, as well as other intramolecular dynamics, including the pseudo-Jahn-Teller effect. The spectroscopic model also allows semi-quantitative prediction of effective spin-rotation constants using molecular geometry and SO constants, which can be calculated ab initio with considerable accuracy. The dependence of fit values of molecular constants on the size and conformation of alkoxy radicals is discussed.

Laser diagnostics of self-organization of amphiphiles in aqueous solutions on the example of sodium octanoate

In this study, a method of non-contact laser diagnostics of self-organization processes of surfactants in aqueous solutions is proposed. The study of solutions of sodium octanoate using laser Raman and near-IR spectroscopy has shown that spectral bands of stretching vibrations of CC-, CH- and OH-groups (including second overtone of the OH-vibrations) of the surfactant molecules and water, as well as bands of intermolecular vibrations of hydrogen bonds O-H⋯O are sensitive to the change the conformation of the hydrocarbon radical of the surfactant and the dynamics of hydrogen bonds during self-organization of surfactants in solution. It was found that the dependence of the spectral characteristics of these bands on concentration of surfactants has peculiarities in the region of critical premicelle concentration (CPMC), first critical micelle concentration (CMC1) and second critical micelle concentration (CMC2). A method of determining the critical concentrations of surfactants in water based on the revealed peculiarities is proposed. A comparative analysis of the obtained CMC values using laser Raman and IR spectroscopy and those measured by independent contact methods – pH-metry, conductivity, surface tension measurement – has shown a good match of the determined parameters. Advantages of the method of laser diagnostics of surfactant self-organization in water were discussed.

Conformation-Dependent Spin Relaxation Behaviors of 6-Oxoverdazyl Radical Single Crystals

The molecular conformation and packing mode of organic radicals are vital to achieving distinctive electronic, spin relaxation, and magnetic properties. Herein two organic radicals, B2P and B4P, ar...

Conformation of bis-nitroxide polarizing agents by multi-frequency EPR spectroscopy.

The chemical structure of polarizing agents critically determines the efficiency of dynamic nuclear polarization (DNP). For cross-effect DNP, biradicals are the polarizing agents of choice and the interaction and relative orientation of the two unpaired electrons should be optimal. Both parameters are affected by the molecular structure of the biradical in the frozen glassy matrix that is typically used for DNP/MAS NMR and likely differs from the structure observed with X-ray crystallography. We have determined the conformations of six bis-nitroxide polarizing agents, including the highly efficient AMUPol, in their DNP matrix with EPR spectroscopy at 9.7 GHz, 140 GHz, and 275 GHz. The multi-frequency approach in combination with an advanced fitting routine allows us to reliably extract the interaction and relative orientation of the nitroxide moieties. We compare the structures of six bis-nitroxides to their DNP performance at 500 MHz/330 GHz.

HPLC와 DPPH radical 소거능 측정 방법의 결합에 의한 약용 식물 추출물의 항산화 활성 비교

Natural anti-oxidative compounds have important disease prevention and food preservation properties, in addition to anti-bacterial, anti-inflammation, anti-cancer, and skin whitening effects. High-performance liquid chromatography (HPLC), with an ultra vilolet (UV) detector coupled to a reverse phase C18 column and an online measurement system for 1, 1-diphenyl-2-picryl hydrazyl (DPPH) radicals, was used to search for potent antioxidative compounds in crude extracts. The online HPLCDPPH assay was then applied to confirm antioxidative compounds in water extracts from Radix of Pueraria lobata, Rhizoma of Zingiber officinale, Fructus of Chaenomeles sinensis, Cortex of Ulmus pumila, and Radix of Astragalus membranaceus. To determine the yields of the extracts, the Brix% of each extract solution was measured using a refractometer. When the relative DPPH radical scavenging ability values of the water extracts were compared with those of a positive control (ascorbic acid), the water extracts of P. lobata, C. sinensis, and U. pumila were 7.77%, 4.71%, and 4.19%, respectively. The results suggest that this method provides a useful assay for rapid measurement of DPPH radical scavenging abilities and conformation of antioxidative compounds in natural products. Moreover, it can reduce the time spent on the separation of active compounds from natural materials, such as medicinal plants, in addition to the use of reagents for separation.

Radical Reaction Control in the AdoMet Radical Enzyme CDG Synthase (QueE): Consolidate, Destabilize, Accelerate.

Controlling radical intermediates and thus catalysing and directing complex radical reactions is a central feature of S‐adensosylmethionine (SAM)‐dependent radical enzymes. We report ab initio and DFT calculations highlighting the specific influence of ion complexation, including Mg2+, identified as a key catalytic component on radical stability and reaction control in 7‐carboxy‐7‐deazaguanine synthase (QueE). Radical stabilisation energies (RSEs) of key intermediates and radical clock‐like model systems of the enzyme‐catalysed rearrangement of 6‐carboxytetrahydropterin (CPH4), reveals a directing role of Mg2+ in destabilising both the substrate‐derived radical and corresponding side reactions, with the effect that the experimentally‐observed rearrangement becomes dominant over possible alternatives. Importantly, this is achieved with minimal disruption of the thermodynamics of the substrate itself, affording a novel mechanism for an enzyme to both maintain binding potential and accelerate the rearrangement step. Other mono and divalent ions were probed with only dicationic species achieving the necessary radical conformation to facilitate the reaction.

Protonation-induced change in the conformation, crystal structure and property of triarylmethyl carbocation radical

We report a new triarylmethyl carbocation radical which was easily synthesized via ⿿one-pot⿿ approach. Interestingly, this ⿿cis⿿ triarylmethyl carbocation radical converted to the ⿿trans⿿ one upon protonation. Such an obviously conformational change is triggered by the intermolecular hydrogen bond interaction involving one exocyclic ⿿keto⿿ oxygen atom and the protonated pyridinium nitrogen atom. Two triarylmethyl carbocation radical crystals were characterized by the elemental analysis and single crystal X-ray diffraction. A change in conformation also brings about change in crystal structure, phosphorescence and magnetic susceptibility properties.

Radiation-induced radicals in different polymorphic modifications of d -mannitol: Structure, conformations and dosimetric implications

Abstract The structure and conformation of radicals produced by X-ray irradiation of three polymorphic forms of d -mannitol were investigated using EPR spectroscopy. In all the cases, primary species were identified as radicals resulting from hydrogen abstraction from position 3 or 4 of the mannitol molecule. It was found that molecular packing in crystals of different polymorphic modifications had noticeable effect on the conformation of radicals observed after irradiation at room temperature and the dehydration of the primary radicals occurring at 400 K. The radicals trapped in stable modifications (β- and δ-forms) were found to be very stable at room temperature. Relatively high radical yields and remarkable stability of radicals suggest that d -mannitol can be used as an EPR dosimeter or irradiation marker.

Lithium Formate for EPR Dosimetry (2): Secondary Radicals in X-Irradiated Crystals.

The secondary radiation-induced radicals in lithium formate monohydrate were studied using electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR) and ENDOR-induced EPR (EIE) techniques complemented with periodic density functional theory (DFT) calculations. Single crystals of lithium formate monohydrate were X irradiated at 77 K and at room temperature. The main radicals present after irradiation at 77 K are the CO(2)(•-) radical (R1), the recently identified protonated electron-gain product, HCOOH(•-) (R2) (Krivokapić et al., Radiat Res 2014: 181:503-11), and a different geometrical conformation of this latter radical, a species that, up until now, has remained unidentified (R3). The successful quantum chemical modeling of R3 confirmed its structure and also provided a possible mechanism for its formation. After irradiation at 295 K, the crystals were investigated both shortly after irradiation and after storage for eight months at room temperature in ambient environments. After long-term storage the CO(2)(•-) radical had significantly decayed and the EPR spectra were dominated by two minority radicals. Both of these radicals are most likely formate-centered π-radicals, and based on the observed EPR parameters (g- and hyperfine coupling tensors) tentative candidates are the CO(•-) radical and the dimer formed by the CO(2)(•-) radical and a neighboring formate molecule yielding the radical (-)O(2)C·O·(•)CH·O(-).

Radical sites in humic acids: A theoretical study on protocatechuic and gallic acids

Protocatechuic and gallic acids (PCA/GA) were used as models for studying the radical sites in humic acids. Neutral, anionic, and anion radical conformers were investigated by means of density functional theory in gas phase and solvent, respectively. For the most stable radical structures electron spin density and EPR parameters such as g-tensors and isotropic hyperfine coupling constants (HFCCs) were calculated using the B3LYP functional. Additionally, the performance of several other popular functionals of the DFT theory including BP86, B97D, M06, TPSS, TPSSh and B2PLYP was evaluated. Obtained g-tensors are strongly anisotropic having two principal components (gxx, gyy) lying in the plane of the aromatic ring. The difference between the g-tensors of PCA and GA anion radicals are minimal. Inclusion of environmental effects (explicit consideration of hydrogen bonds plus continuum solvation) has a significant impact on g-tensor components and HFC constants shifting their values closer to available experimental data. In summary, good agreement of the B3LYP results with experiment is obtained and from the set of the additional DFT functionals used only the hybrid variant of the TPSSh functional provides good results. The calculated values of g-tensors and HFCCs support the hypothesis that polyphenolic fragments are main sources of transient and native radical sites in structurally complex humic acids.

Open-shell pair interaction energy decomposition analysis (PIEDA): Formulation and application to the hydrogen abstraction in tripeptides

An open-shell extension of the pair interaction energy decomposition analysis (PIEDA) within the framework of the fragment molecular orbital (FMO) method is developed. The open-shell PIEDA method allows the analysis of inter- and intramolecular interactions in terms of electrostatic, exchange-repulsion, charge-transfer, dispersion, and optional polarization energies for molecular systems with a radical or high-spin fragment. Taking into account the low computational cost and scalability of the FMO and PIEDA methods, the new scheme provides a means to characterize the stabilization of radical and open-shell sites in biologically relevant species. The open-shell PIEDA is applied to the characterization of intramolecular interactions in capped trialanine upon hydrogen abstraction (HA) at various sites on the peptide. Hydrogen abstraction reaction is the first step in the oxidative pathway initiated by reactive oxygen or nitrogen species, associated with oxidative stress. It is found that HA results in significant geometrical reorganization of the trialanine peptide. Depending on the HA site, terminal interactions in the radical fold conformers may become weaker or stronger compared to the parent molecule, and often change the character of the non-covalent bonding from amide stacking to hydrogen bonding.

Magnetostructural Correlation for Rational Design of Mn(II) Hybrid-Spin Complexes

The magnetic properties of a series of manganese(II) diacetylacetonate and dihexafluoroacetylacetonate hybrid-spin complexes with neutral pyridine-based organic radicals were characterized theoretically by DFT calculations. Three stable radicals, in which a radical group is bound in either para or meta position with respect to the pyridine nitrogen atom, were considered. The correct stable structures and multiplets of the complexes were obtained by full geometry optimization starting from an ideal structure. A total of three important geometry descriptors of the complexes were monitored and related to their magnetic characteristics. These structural parameters are (i) the torsion angle governing the conjugation of the organic radical m-PyNO (anti versus gauche), (ii) the coordination geometry of the acetyl acetonate ligands around the metal ion (square versus rhombic), and (iii) the relative orientation of the organic radical with respect to the acetyl acetonate plane (parallel versus perpendicular). It was found that the magnetic properties are not sensitive to the orientation of the radicals with respect to the equatorial plane but do depend on the conformation of the organic radicals. Even a spin switch between the ferromagnetic (S = (7)/(2)) and antiferromagnetic (S = (3)/(2)) ground state was found to be feasible for one of the complexes upon variation of the organic radical geometry, namely, the dihedral angle between the organic radical moiety and the pyridine ring. The pattern of molecular orbital overlap was determined to be the key factor governing the exchange coupling in the modeled systems. Bonding π-type overlap provides antiferromagnetic coupling in all complexes of the para radicals. In the meta analogues, the spins are coupled through the σ orbitals. A low-spin ground state occurs whenever a continuous σ-overlap pathway is present in the complex. Ferromagnetic interaction requires σ-π orthogonality of the pyridine atomic orbitals and/or π-antibonding Mn-pyridine natural orbital overlap. Using an estimate of the donor-acceptor energy stabilization, the affinity of a given Mn(II) d-orbital to mix with the sp(2) orbital from pyridine can be predicted.

Influence of γ irradiation on the conformation of free radicals in polytetrafluoroethylene

A study has been made of the spectra of electron paramagnetic resonance and of experimental curves of accumulation of free radicals in polytetrafluoroethylene at different temperatures and radiation doses. It has been found that at a temperature of 60°C, the curve of accumulation of stabilized radicals goes through the maximum and thereafter drops exponentially. The change in the parameters of intermolecular interaction causes the transformation of a standardly shaped accumulation curve with saturation to a nonmonotonic curve with a maximum.

Carboxyl-Catalyzed Prototropic Rearrangements in Histidine Peptide Radicals upon Electron Transfer: Effects of Peptide Sequence and Conformation

We report an unusual prototropic rearrangement in gas-phase radicals formed by collisional electron transfer from cesium atoms to protonated peptides HAL, AHL, and ALH at 50 keV. The rearrangement depends on the peptide amino acid sequence and presence or steric accessibility of a free carboxyl group. Upon electron transfer, protonated HAL and ALH rearrange to tautomers that are detected as nondissociated anions in charge-reversal mass spectra. The isomerization is minor in protonated ALH and virtually absent in HAL amide. Electron structure calculations indicate that the gas-phase ions are preferentially protonated in the His imidazole ring and consist of multiple conformers that differ in their hydrogen bonding patterns. Electron transfer to protonated HAL and AHL triggers an exothermic and dynamically barrierless transfer of the carboxyl proton onto the C-2' position of the His ring that occurs on a 120-240 ns time scale. The kinetics of this isomerization are controlled by internal rotations in the radicals to assume conformations favoring the proton transfer. The radical conformations also affect subsequent proton migrations in zwitterionic His imidazoline intermediates that reform the COOH group and result in His ring isomerization. This autocatalytic prototropic rearrangement in gas-phase peptide radicals is analogous to enzyme catalytic reactions involving His and acidic amino acid residues. In contrast to HAL and AHL, the C-2' position is sterically inaccessible in ALH radicals. These radicals undergo proton migrations to the His ring C-5' positions that have moderate energy barriers and are less efficient. RRKM calculations on the combined B3LYP and PMP2/6-311++G(2d,p) potential energy surface of the ground doublet electronic state of the peptide radicals provided rate constants that were quantitatively consistent with the dissociations observed in the gas phase. The formation of minor sequence z(1) and z(2) fragments from AHL was interpreted as occurring in the first excited state of the radical.