Structure and Magnetic Properties of Glycine Radical in Aqueous Solution at Different pH Values

Intermolecular hydrogen bonding behavior of amino acid radical cations

Amino acid and peptide radicals are of broad interest due to their roles in biochemical oxidative damage, pathogenesis and protein radical catalysis, among others. Using density functional theory (DFT) calculations at the ωB97X-D/def2-QZVPPD//ωB97X-D/def2-TZVPP level of theory, we systematically investigated the hydrogen bonding between water and fourteen α-amino acids (Ala, Asn, Cys, Gln, Gly, His, Met, Phe, Pro, Sel, Ser, Thr, Trp, and Tyr) in both neutral and radical cation forms. For all amino acids surveyed, stronger hydrogen-bonding interactions with water were observed upon single-electron oxidation, with the greatest increases in hydrogen-bonding strength occurring in Gly, Ala and His. We demonstrate that the side chain has a significant impact on the most favorable hydrogen-bonding modes experienced by amino acid radical cations. Our computations also explored the fragmentation of amino acid radical cations through the loss of a COOH radical facilitated by hydrogen bonding. The most favorable pathways provided stabilization of the resulting cationic fragments through hydrogen bonding, resulting in more favorable thermodynamics for the fragmentation process. These results indicate that non-covalent interactions with the environment have a profound impact on the structure and chemical fate of oxidized amino acids.

From the Iron Pentacarbonyl Cation to Heteroleptic η6-arene Carbonyls and bis-η6-arene Cations

Partial ligand substitution at the iron pentacarbonyl radical cation generates novel half-sandwich complexes of the type [Fe(η6-arene)(CO)2]⋅+ (arene=1,3,5-tri-tert-butylbenzene, 1,3,5-trimethylbenzene, benzene and fluorobenzene). Of those, the bulkier 1,3,5-tri-tert-butylbenzene (mes*) derivative [Fe(mes*)(CO)2]⋅+ was fully characterized by XRD analysis, IR, NMR, cw-EPR, Mössbauer spectroscopy and cyclic voltammetry as the [Al(ORF)4]- (RF=C(CF3)3) salt. Chemical electronation, i. e., the single electron reduction, with decamethylferrocene generates neutral [Fe(mes*)(CO)2], whereas further deelectronation under CO-pressure leads to a dicationic three-legged [Fe(mes*)(CO)3]2+ salt with [Al(ORF)4]- counterion. The full substitution of the carbonyl ligands in [Fe(CO)5]⋅+[Al(ORF)4]- mainly resulted in disproportionation reactions, giving solid Fe(0) and the dicationic bis-arene salts [Fe(η6-arene)2]2+([Al(ORF)4]-)2 (arene=1,3,5-trimethylbenzene, benzene and fluorobenzene). Only by employing the very large fluoride bridged anion [F-{Al(ORF)3}2]-, it was possible to isolate an open shell bis-arene cation salt [Fe(C6H6)2]⋅+[F-{Al(ORF)3}2]-. The highly reactive cation was characterized by XRD analysis, cw-EPR, Mössbauer spectroscopy and cyclic voltammetry. The disproportionation of [Fe(C6H6)2]⋅+ salts to give solid Fe(0) and [Fe(C6H6)2]2+ salts was analyzed by a suitable cycle, revealing that the thermodynamic driving force for the disproportionation is a function of the size of the anion used and the polarity of the solvent.

Electron correlation and vibrational effects in predictions of paramagnetic NMR shifts

Electronic structure calculations are fundamentally important for the interpretation of nuclear magnetic resonance (NMR) spectra from paramagnetic systems that include organometallic and inorganic compounds, catalysts, or metal-binding sites in proteins. Prediction of induced paramagnetic NMR shifts requires knowledge of electron paramagnetic resonance (EPR) parameters: the electronic g tensor, zero-field splitting D tensor, and hyperfine A tensor. The isotropic part of A, called the hyperfine coupling constant (HFCC), is one of the most troublesome properties for quantum chemistry calculations. Yet, even relatively small errors in calculations of HFCC tend to propagate into large errors in the predicted NMR shifts. The poor quality of A tensors that are currently calculated using density functional theory (DFT) constitutes a bottleneck in improving the reliability of interpretation of the NMR spectra from paramagnetic systems. In this work, electron correlation effects in calculations of HFCCs with a hierarchy of ab initio methods were assessed, and the applicability of different levels of DFT approximations and the coupled cluster singles and doubles (CCSD) method was tested. These assessments were performed for the set of selected test systems comprising an organic radical, and complexes with transition metal and rare-earth ions, for which experimental data are available. Severe deficiencies of DFT were revealed but the CCSD method was able to deliver good agreement with experimental data for all systems considered, however, at substantial computational costs. We proposed a more computationally tractable alternative, where the A was computed with the coupled cluster theory exploiting locality of electron correlation. This alternative is based on the domain-based local pair natural orbital coupled cluster singles and doubles (DLPNO-CCSD) method. In this way the robustness and reliability of the coupled cluster theory were incorporated into the modern formalism for the prediction of induced paramagnetic NMR shifts, and became applicable to systems of chemical interest. This approach was verified for the bis(cyclopentadienyl)vanadium(II) complex (Cp₂V; vanadocene), and the metal-binding site of the Zn²⁺ → Co²⁺ substituted superoxide dismutase (SOD) metalloprotein. Excellent agreement with experimental NMR shifts was achieved, which represented a substantial improvement over previous theoretical attempts. The effects of vibrational corrections to orbital shielding and hyperfine tensor were evaluated and discussed within the second-order vibrational perturbation theory (VPT2) framework.

Photoredox Cross-Dehydrogenative Coupling of N-Aryl Glycines Mediated by Mesoporous Graphitic Carbon Nitride: An Environmentally Friendly Approach to the Synthesis of Non-Proteinogenic α-Amino Acids (NPAAs) Decorated with Indoles

Indole-decorated glycine derivatives are prepared through an environmentally benign cross-dehydrogenative coupling between N-aryl glycine analogues and indoles (yield of ≤81%). Merging heterogeneous organocatalysis and photocatalysis, C–H functionalization has been achieved by selective C-2 oxidation of N-aryl glycines to afford the electrophilic imine followed by Friedel–Crafts alkylation with indole. The sustainability of the process has been taken into account in the reaction design through the implementation of a metal-free recyclable heterogeneous photocatalyst and a green reaction medium. Scale-up of the benchmark reaction (gram scale, yield of 69%) and recycling experiments (over seven runs without a loss of efficiency) have been performed to prove the robustness of the protocol. Finally, mechanistic studies were conducted employing electron paramagnetic resonance spectroscopy to unveil the roles of the photocatalyst and oxygen in the formation of odd-electron species.

pH-Controlled Intramolecular Decarboxylative Cyclization of Biarylacetic Acids: Implication on Umpolung Reactivity of Aroyl Radicals

A simple approach for the intramolecular aroylation of electron-rich arenes under mild conditions has been developed. A pH-controlled polarity umpolung strategy can be used to synthesize different fluorenones, which are important building blocks for biological applications. Unlike previous acylation reactions involving nucleophilic aroyl radicals, this approach likely relies on in situ generated electrophilic aroyl radicals. Detailed mechanistic and computational investigations provide detailed insights into the reaction mechanism and support the hypothesis of a pH-mediated umpolung.

Reactions of methyl, hydroxyl and peroxyl radicals with the DOTA chelating agent used in medical imaging

The mechanism of reaction of DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) with ·CH₃, CH₃O₂· and ·OH radicals were studied. The radicals were formed in situ radiolytically. The methyl radicals react orders of magnitude slower with DOTA and with M^III(DOTA)^- than the hydroxyl radicals. The various final products were identified and mechanisms for their formation are proposed. CH₃O₂· radicals do not react, or react too slowly to be observed, with DOTA and with M^III(DOTA)^- as long as the central cation is not oxidized by the peroxyl radical. The results imply that synthesis of the M^III(DOTA)^-(M^III = radioisotope) complexes in a water-organic solvent (ethanol or 2-propanol or acetonitrile) mixture is not only kinetically desired but the so formed complex also decreases the radiolytic decomposition of DOTA.

Influence of the Side Chain in the Structure and Fragmentation of Amino Acids Radical Cations

The conformational properties of ionized amino acids (Gly, Ala, Ser, Cys, Asp, Gln, Phe, Tyr, and His) have been theoretically analyzed using the hybrid B3LYP and the hybrid-meta MPWB1K functionals as well as with the post-Hartree Fock CCSD(T) level of theory. As a general trend, ionization is mainly localized at the -NH2 group, which becomes more planar and acidic, the intramolecular hydrogen bond in which -NH2 acts as proton donor being strengthened upon ionization. For this reason, the so-called conformer IV(+) becomes the most stable for nonaromatic amino acid radical cations. Aromatic amino acids do not follow this trend because ionization takes place mainly at the side chain. For these amino acids for which ionization of the side chain prevails over the -NH2 group, structures III(+) and II(+) become competitive. The Cα-X fragmentations of the ionized systems have also been studied. Among the different decompositions considered, the one that leads to the loss of COOH(•) is the most favorable one. Nevertheless, for aromatic amino acids fragmentations leading to R(•) or R(+) start being competitive. In fact, for His and Tyr, results indicate that the fragmentation leading to R(+) is the most favorable process.

Development and Validation of the B3LYP/N07D Computational Model for Structural Parameter and Magnetic Tensors of Large Free Radicals

Extensive calculations on a large set of free radicals containing atoms of the second and third row show that the B3LYP/N07D computational model provides remarkably accurate structural parameters and magnetic tensors at reasonable computational costs. The key of this success is the optimization of core-valence s functions for hyperfine coupling constants, while retaining (and even improving) the good performances of the parent 6-31+G(d,p) basis set for valence properties through reoptimization of polarization and diffuse p functions.

New developments of a multifrequency virtual spectrometer: stereo-electronic, dynamical, and environmental effects on chiroptical spectra

Computational spectroscopy has recently evolved from a field reserved for specialists toward a general tool allowing interpretations and analyses of experimental results. However, the current practice of providing tables of transitions for rigid geometries, possibly tuned by phenomenological broadening, is by far too naive. In order to improve this situation in the last few years we have been developing a general, robust, and user-friendly virtual spectrometer (VS) able to complement experimental studies for complex systems in condensed phases. The VS is based on flexible graphical pre- and postprocessing tools interfaced with general number-crunching software. This last tool is rooted in several electronic structure methodologies (DFT, TD-DFT, post-Hartree-Fock), powerful discrete/continuum models for describing environmental effects, and general vibrational and vibronic models. These last topics are the main focus of this work, which sketches our latest developments related to effective inclusion of anharmonic contributions, together with time-independent and/or time-dependent descriptions of vibronic transitions including Franck-Condon, Herzberg-Teller, and Duschinsky effects. Some test cases are described in some detail with the aim of showing the role of different effects in ruling vibrational (VCD) and electronic (ECD, CPL) chiral spectroscopies.

Extension of the AMBER Force Field for Nitroxide Radicals and Combined QM/MM/PCM Approach to the Accurate Determination of EPR Parameters of DMPO-H in Solution

A computational strategy that combines both time-dependent and time-independent approaches is exploited to accurately model molecular dynamics and solvent effects on the isotropic hyperfine coupling constants of the DMPO-H nitroxide. Our recent general force field for nitroxides derived from AMBER ff99SB is further extended to systems involving hydrogen atoms in β-positions with respect to NO-moiety. The resulting force-field has been employed in a series of classical molecular dynamics simulations, comparing the computed EPR parameters from selected molecular configurations to the corresponding experimental data in different solvents. The effect of vibrational averaging on the spectroscopic parameters is also taken into account, by second-order vibrational perturbation theory involving semidiagonal third energy derivatives together first and second property derivatives.

Accurate structure, thermodynamics, and spectroscopy of medium-sized radicals by hybrid coupled cluster/density functional theory approaches: the case of phenyl radical

The coupled-cluster singles doubles model with perturbative treatment of triples (CCSD(T)) coupled with extrapolation to the complete basis-set limit and additive approaches represent the "golden standard" for the structural and spectroscopic characterization of building blocks of biomolecules and nanosystems. However, when open-shell systems are considered, additional problems related to both specific computational difficulties and the need of obtaining spin-dependent properties appear. In this contribution, we present a comprehensive study of the molecular structure and spectroscopic (IR, Raman, EPR) properties of the phenyl radical with the aim of validating an accurate computational protocol able to deal with conjugated open-shell species. We succeeded in obtaining reliable and accurate results, thus confirming and, partly, extending the available experimental data. The main issue to be pointed out is the need of going beyond the CCSD(T) level by including a full treatment of triple excitations in order to fulfil the accuracy requirements. On the other hand, the reliability of density functional theory in properly treating open-shell systems has been further confirmed.

Accurate structure, thermodynamic and spectroscopic parameters from CC and CC/DFT schemes: the challenge of the conformational equilibrium in glycine

The structures, relative stabilities, and infrared spectra of the six low-energy conformers of glycine have been characterized using a state-of-the-art quantum-mechanical approach allowing the bond distances, conformational enthalpies and vibrational frequencies to be determined well within the chemical accuracy. Transition state structures governing interconversion among the different energy minima have also been characterized. In detail, the gas-phase thermodynamic properties (at 15 K and 410 K) of the glycine conformers considered have been obtained with a 1 kJ mol(-1) accuracy, and it has been shown that the employment of DFT geometries usually reduces such accuracy by at most 0.1 kJ mol(-1). Regarding molecular structures, the use of two different composite schemes allowed us to further confirm the suitability of a rather cost-effective approach and provide geometrical parameters with an overall accuracy better than 0.002 Å for distances and 1 degree for angles. Thanks to a hybrid CC/DFT approach, the infrared spectra of all conformers considered and of several deuterated isotopologues have been reproduced (when experimental data were available) or predicted with an accuracy of 10 cm(-1). Finally, the joint thermodynamic and spectroscopic investigation allowed us to shed some light on the possible observation of elusive conformers. On the whole, the high accuracy of the computational results allows us to draw a fully consistent interpretation of the available experimental data and to obtain a more complete characterization of the potential energy surface of glycine.

Towards an accurate description of anharmonic infrared spectra in solution within the polarizable continuum model: reaction field, cavity field and nonequilibrium effects

We present a newly developed and implemented methodology to perturbatively evaluate anharmonic vibrational frequencies and infrared (IR) intensities of solvated systems described by means of the polarizable continuum model (PCM). The essential aspects of the theoretical model and of the implementation are described and some numerical tests are shown, with special emphasis towards the evaluation of IR intensities, for which the quality of the present method is compared to other methodologies widely used in the literature. Proper account of an incomplete solvation regime in the treatment of the molecular vibration is also considered, as well as inclusion of the coupling between the solvent and the probing field (cavity field effects). In order to assess the quality of our approach, comparison with experimental findings is reported for selected cases.

Zero-point vibrational corrections to isotropic hyperfine coupling constants in polyatomic molecules

The present work addresses isotropic hyperfine coupling constants in polyatomic systems with a particular emphasis on a largely neglected, but a posteriori significant, effect, namely zero-point vibrational corrections. Using the density functional restricted-unrestricted approach, the zero-point vibrational corrections are evaluated for the allyl radical and four of its derivatives. In addition for establishing the numerical size of the zero-point vibrational corrections to the isotropic hyperfine coupling constants, we present simple guidelines useful for identifying hydrogens for which such corrections are significant. Based on our findings, we critically re-examine the computational procedures used for the determination of hyperfine coupling constants in general as well as the practice of using experimental hyperfine coupling constants as reference data when benchmarking and optimizing exchange-correlation functionals and basis sets for such calculations.

Halogen bonds between 2,2,6,6-tetramethylpiperidine-N-oxyl radical and CxHyFzI species: DFT calculations of physicochemical properties and comparison with hydrogen bonded adducts

Structural, thermodynamic, and magnetic properties of adducts between the 2,2,6,6-tetramethylpiperidine-N-oxyl radical and representative hydrogen and halogen bond donors in solution have been investigated by an integrated computational tool including hybrid density functionals and discrete-continuum solvent models. From a quantitative point of view, the computed values show a fair agreement with experiment when environmental effects are taken into the proper account. From a more general point of view, our analysis points out a number of analogies, but also some difference, between hydrogen and halogen bond, which have been interpreted in terms of the various effects tuning thermodynamic and spectroscopic parameters.

Interplay of Intrinsic, Environmental, and Dynamic Effects in Tuning the EPR Parameters of Nitroxides: Further Insights from an Integrated Computational Approach

The role of stereoelectronic, environmental, and short-time dynamic effects in tuning the hyperfine and gyromagnetic tensors of a prototypical nitroxide spin probe has been investigated by an integrated computational approach based on extended Lagrangian molecular dynamics and discrete-continuum solvent models. Trajectories were generated in two protic solvents as well as in the gas phase for reference; structural analysis of the dynamics, and comparison with optimized solute-solvent clusters, allowed for the identification of the prevailing solute-solvent hydrogen-bonding patterns and helped to define the strategy for the computation of magnetic parameters. This was performed in a separate step, on a large number of frames, by a high-level DFT approach coupling the PBE0 hybrid functional with a tailored basis set and with proper account of specific and bulk solvent effects. Remarkable changes in solvation networks are found on going from aqueous to methanol solution, thus providing a rationalization of indirect experimentally available evidence. The computed magnetic parameters are in satisfactory agreement with the available measured values and allow for an unbiased evaluation of the role of different effects in tuning the overall EPR observables. Apart from their intrinsic interest, our results pave the route toward the development of tunable detection protocols based on specific spectroscopic signatures.

Effective method to compute vibrationally resolved optical spectra of large molecules at finite temperature in the gas phase and in solution

The authors present a new method for the computation of vibrationally resolved optical spectra of large molecules, including the Duschinsky rotation of the normal modes and the effect of thermal excitation. The method automatically selects the relevant vibronic contributions to the spectrum, independently of their frequency, and it is able to provide fully converged spectra with moderate computational times, both in vacuo and in solution. By describing the electronic states in the frame of the density functional theory and its time-dependent extension, they computed the room temperature absorption spectra of coumarin C153 and trans-stilbene in cyclohexane and the phosphorescence spectrum of porphyrazine in gas phase, showing that the method is fast and efficient. The comparison with experiment for trans-stilbene and coumarin C153 is very satisfactory, confirming the progress made toward a reliable method for the computation and interpretation for the optical spectra of large molecules.

Effects of ionization on N-glycylglycine peptide: Influence of intramolecular hydrogen bonds

The ionization effects on 28 conformations of N-glycylglycine are analyzed by means of the hybrid B3LYP and the hybrid meta-MPWB1K density functionals and by single-point calculations at the CCSD(T) level of theory. The most favorable process observed corresponds to the ionization of the only neutral conformation that presents a OH...NH2 intramolecular hydrogen bond, which leads to CO2 elimination after a spontaneous proton transfer from -COOH to NH2. The remaining neutral structures evolve to 20 different conformations of N-glycylglycine radical cation, which lie about 25-40 kcal/mol higher than the decarboxylated [NH3CH2CONHCH2]+*...[CO2] complex. Structural changes induced by ionization depend on the intramolecular hydrogen bonds of the initial conformation, since they determine the nature of the electron hole formed. In most cases, ionization takes place at the terminal -NH2 and -CO of the amide bond, which produces a strengthening of the peptide bond and the formation of new -NH2...OC(amide) and -NH2...OCOH hydrogen bonds. However, if -NH2 and -CO(amide) simultaneously act as proton acceptor in the neutral conformation, ionization is mainly localized at the carboxylic group, which produces a strengthening of the -COOH...OC(amide) bond. Both functionals lead to similar trends and compare well with CCSD(T) results except for a few cases for which B3LYP provides a too delocalized picture of the electron hole and consequently leads to artificial geometry reorganization.

Complete structural and magnetic characterization of biological radicals in solution by an integrated quantum mechanical approach: Glycyl radical as a case study

An integrated quantum mechanical approach for the structural and magnetic characterization of flexible free radicals in solution has been applied to a model of the glycyl radical engaged in peptidic chains. The hyperfine couplings computed using hybrid density functionals and purposely tailored basis sets are in good agreement with experiment when vibrational averaging effects from low frequency motions and solvent effects (both direct H bonding and bulk) are taken into the proper account. The g tensor shows a smaller dependence on the specific form of the density functional, the extension of the basis set over a standard double-zeta+polarization level, vibrational averaging, and bulk solvent effects. However, hydrogen bridges with solvent molecules belonging to the first solvation shell play a significant role. Together with their intrinsic interest, our results show that a comprehensive and reliable computational approach is becoming available for the complete characterization of open-shell systems of biological interest in their natural environment.

Effects of pathological mutations on the stability of a conserved amino acid triad in retinoschisin

A three-dimensional model has been calculated for the discoidin domain of retinoschisin (RS1), the protein involved in the X-linked juvenile retinoschisis. The model allows for a mapping of the pathological retinoschisis missense mutations and a rationale for the structural effects of an evolutionary conserved surface exposed triad (W122-R200-W163). Molecular dynamics simulations of the triad mutants models, together with ab initio energy calculations of the complexes corresponding to the triad show that the observed pathological mutations sensibly destabilize local interactions and the entire fold. Moreover the presented model reveals evidence of a putative site for membrane association.