An ONIOM investigation of the effect of conformation on bond dissociation energies in peptides.

In the present study, we use the ONIOM strategy of Morokuma and coworkers to examine the various CH bond dissociation energies (BDEs) of a small peptide (2ONW) and compare these with values obtained for its component individual amino acid residues. To evaluate suitable methods for ONIOM-based geometry optimizations, we test an "internal consistency" approach against full B3-LYP//B3-LYP results, and find B3-LYP/6-31G(d):AM1 to be appropriate. We find that the BDEs at the α-carbon in 2ONW are generally larger than the corresponding values for the individual residues on their own. This is attributed to the constraints of the peptide backbone leading to conformations that are not ideal for captodative stabilization of the resulting α-radicals. At the more flexible ß- and γ-positions, the differences between the BDEs in 2ONW and the individual residues are smaller. Overall, the α-BDEs are smaller than the ß- and γ-BDEs in most cases. Thus, to rationalize the inertness of peptide backbones with respect to α-hydrogen abstraction that is frequently found experimentally, it is necessary to consider alternative protection mechanisms such as the polar effect. © 2018 Wiley Periodicals, Inc.

Carnosine and Carcinine Derivatives Rapidly React with Hypochlorous Acid to Form Chloramines and Dichloramines.

Hypochlorous acid (HOCl) is a highly reactive, toxic species generated by neutrophils via the action of myeloperoxidase in order to destroy invading pathogens. However, when HOCl is produced inappropriately, it can damage host tissue and proteins and plays a role in the initiation and progression of disease. Carnosine, a peptide of ß-alanine and histidine, has been shown to react rapidly with HOCl yielding monochloramines and can undergo intramolecular transchlorination. The current study examines the kinetics and pH dependence of the reactions of carnosine and novel structural derivatives with HOCl and the occurrence of intra- and intermolecular transchlorination processes. We demonstrate that the transchlorination reactions of carnosine are pH dependent, with intramolecular transfer favored at higher pH. Carcinine, having a structure identical to carnosine though lacking the carboxylic acid group of the histidine residue, reacts with HOCl and forms monochloramines though intramolecular transfer reactions are not observed, and this is supported by computational modeling. Novel analogues with one (carnosine+1) and two (carnosine+2) methylene groups in the alkyl chain of the ß-alanine react with HOCl to yield monochloramines that undergo transchlorinations to yield a mixture of mono- and dichloramines. The latter are stable over 24 h. The ability of carnosine and derivatives to react rapidly with HOCl to give long-lived, poorly reactive, species may prevent damage to proteins and other targets at sites of inflammation.

Computational Tale of Two Enzymes: Glycerol Dehydration With or Without B12.

We present a series of QM/MM calculations aimed at understanding the mechanism of the biological dehydration of glycerol. Strikingly and unusually, this process is catalyzed by two different radical enzymes, one of which is a coenzyme-B12-dependent enzyme and the other which is a coenzyme-B12-independent enzyme. We show that glycerol dehydration in the presence of the coenzyme-B12-dependent enzyme proceeds via a 1,2-OH shift, which benefits from a significant catalytic reduction in the barrier. In contrast, the same reaction in the presence of the coenzyme-B12-independent enzyme is unlikely to involve the 1,2-OH shift; instead, a strong preference for direct loss of water from a radical intermediate is indicated. We show that this preference, and ultimately the evolution of such enzymes, is strongly linked with the reactivities of the species responsible for abstracting a hydrogen atom from the substrate. It appears that the hydrogen-reabstraction step involving the product-related radical is fundamental to the mechanistic preference. The unconventional 1,2-OH shift seems to be required to generate a product-related radical of sufficient reactivity to cleave the relatively inactive C-H bond arising from the B12 cofactor. In the absence of B12, it is the relatively weak S-H bond of a cysteine residue that must be homolyzed. Such a transformation is much less demanding, and its inclusion apparently enables a simpler overall dehydration mechanism.

Effect of Hydrogen Bonding and Partial Deprotonation on the Oxidation of Peptides.

In a recent computational study, we found that hydrogen bonding/partial deprotonation facilitates subsequent electron transfer from amides to HO•. We have now analyzed these and related reactions with a glycine derivative as a model peptide, investigating not only reaction energies but also barriers for the individual steps. We find that partial deprotonation not only assists subsequent electron transfer (a sequential proton-loss electron-transfer (SPLET)-type reaction pathway) but also promotes sequential hydrogen-atom transfer (HAT, in a sequential proton-loss hydrogen-atom-transfer (SPLHAT)-type process), both being potential alternatives to direct HAT as routes for peptide oxidation. Each of these alternative pathways is calculated to have energy requirements that make them accessible and competitive. These oxidative processes may produce α-carbon-centered peptide radicals that, through deprotonation, are readily oxidized to the corresponding imines. We have also examined the possibility of competing reactions of amino acid side chains by comparing reactions of the glycine model with those of an analogous valine derivative. We find that, while the side chains of amino acids are more reactive toward direct HAT, a preceding partial deprotonation instead continues to favor the SPLET- and SPLHAT-type reactions, leading to the production of α-carbon-centered peptide radicals. Taken together, these processes have broad implications that impact many aspects of the science and utility of peptides.

Solvation of the Glycyl Radical.

The effect of adding explicit water molecules to the neutral (N) and zwitterionic (Z) forms of the glycyl radical has been examined. The results show that a minimum of three water molecules is required to stabilize the Z radical as a local minimum, with an energy gap of 123 kJ mol-1 between the N and Z forms at this point, in favor of the N form. Increasing the number of water molecules to ∼20 leads to a converged Z-N energy difference of ∼50 kJ mol-1 still in favor of the N form, even though the radical is not considered fully solvated from a structural point of view. Thus, energetic convergence is determined mainly by solvation of the polar functional groups, and a complete coverage of the entire molecule is not necessary. Because aqueous closed-shell glycine exists as a zwitterion while aqueous glycyl radical prefers the neutral form, the conversion between the two necessitates a change along the hydrogen-abstraction reaction pathway. In this regard, the transition structure for α-hydrogen abstraction by the ·OH radical has greater resemblance to glycine than to the glycyl radical. Overall, the barrier for hydrogen abstraction from Z glycine is larger than that from the N isomer, and this might act to provide some protection against radical damage to the free amino acid in the (aqueous) biological environment.

On the inclusion of post-MP2 contributions to double-hybrid density functionals.

In this study, we explore the effect of supplementing the DuT spin-component-scaled double-hybrid density functional method with post-second-order Møller-Plesset-type theory (MP2) correlation terms. We find that the inclusion of additional MP3 correlation energies has almost no effect on the performance. Further addition of correlation effects from MP4 generally leads to a small improvement in the performance. However, we find that the inclusion of the higher-order perturbative correlation effects does not rectify some major shortcomings of DuT for more challenging systems, and the use of MP4, in fact, leads to a significant deterioration in the performance in some cases. We also find that the use of correlation energies from CCSD(T) instead of those from MP3 and MP4 does not lead to a substantial improvement over the MP4-based method, both in general and in some difficult cases that we have examined. An additional observation is that, for large systems that are dominated by noncovalent interactions, DuT and the two MPn-based post-MP2 double-hybrid density functional theory (DFT) procedures all benefit from the inclusion of dispersion corrections. Overall, our investigation suggests that the current generation of MP2-based double-hybrid DFT methods may already be providing close to the optimal performance that can be achieved with the double-hybrid methodology paired with spin-component-scaling. Development of even better double hybrids is an active research field, and we hope that our study provides valuable insights. We recommend the continuing use of existing MP2-based double-hybrid methods as a bridging level between hybrid density functional procedures and high-level wave-function-based procedures.

Factors influencing the formation of polybromide monoanions in solutions of ionic liquid bromide salts.

Six different bromide salts - tetraethylammonium bromide ([N2,2,2,2]Br, Br), 1-ethyl-1-methylpiperidinium bromide ([C2MPip]Br, Br), 1-ethyl-1-methylpyrrolidinium bromide ([C2MPyrr]Br, Br), 1-ethyl-3-methylimidazolium bromide ([C2MIm]Br, Br), 1-ethylpyridinium bromide ([C2Py]Br, Br), and 1-(2-hydroxyethyl)pyridinium bromide ([C2OHPy]Br, Br) - were studied in regards to their capacity to form polybromide monoanion products on addition of molecular bromine in acetonitrile solutions. Using complementary spectroscopic and computational methods for the examination of tribromide and pentabromide anion formation, key factors influencing polybromide sequestration were identified. Here, we present criteria for the targeted synthesis of highly efficient bromine sequestration agents.

Hydrogen-atom attack on phenol and toluene is ortho-directed.

The reaction of H + phenol and H/D + toluene has been studied in a supersonic expansion after electric discharge. The (1 + 1') resonance-enhanced multiphoton ionization (REMPI) spectra of the reaction products, at m/z = parent + 1, or parent + 2 amu, were measured by scanning the first (resonance) laser. The resulting spectra are highly structured. Ionization energies were measured by scanning the second (ionization) laser, while the first laser was tuned to a specific transition. Theoretical calculations, benchmarked to the well-studied H + benzene → cyclohexadienyl radical reaction, were performed. The spectrum arising from the reaction of H + phenol is attributed solely to the ortho-hydroxy-cyclohexadienyl radical, which was found in two conformers (syn and anti). Similarly, the reaction of H/D + toluene formed solely the ortho isomer. The preference for the ortho isomer at 100-200 K in the molecular beam is attributed to kinetic, not thermodynamic effects, caused by an entrance channel barrier that is ∼5 kJ mol(-1) lower for ortho than for other isomers. Based on these results, we predict that the reaction of H + phenol and H + toluene should still favour the ortho isomer under elevated temperature conditions in the early stages of combustion (200-400 °C).

Restricted-Open-Shell G4(MP2)-Type Procedures.

In the present study, we have reformulated the G4(MP2) and G4(MP2)-6X procedures for use with a restricted-open-shell (RO) formalism. We find that the resulting ROG4(MP2) and ROG4(MP2)-6X procedures generally perform comparably to the original unrestricted (U) variants, including their performance on radicals. Our analysis suggests that this is due mainly to the inclusion of empirical parameters that overcome the slightly less good performance of the U variants. However, a major practical advantage of ROG4(MP2) and ROG4(MP2)-6X is that they can be used in a wider range of computational chemistry software packages than the U analogs. We have demonstrated the importance of this aspect with a large-scale ROG4(MP2)-6X computation for the dissociation of the dodecahedryl dimer (C20H19)2.

Role of Hydrogen Bonding on the Reactivity of Thiyl Radicals: A Mass Spectrometric and Computational Study Using the Distonic Radical Ion Approach.

Experimental and computational quantum chemistry investigations of the gas-phase ion-molecule reactions between the distonic ions +H3N(CH2)nS• (n = 2-4) and the reagents dimethyl disulfide, allyl bromide, and allyl iodide demonstrate that intramolecular hydrogen bonding can modulate the reactivity of thiyl radicals. Thus, the 3-ammonium-1-propanethiyl radical (n = 3) exhibits the lowest reactivity of these distonic ions toward all substrates. Theoretical calculations on this distonic ion highlight that its most stable conformation involves a six-membered ring configuration, and that it has the strongest intramolecular hydrogen bond. In addition, the calculations indicate that the barrier heights for radical abstraction by this hydrogen-bond-stabilized 3-ammonium-1-propanethiyl radical are the highest among the systems examined, consistent with the experimental observations.

Rapid additive-free selenocystine-selenoester peptide ligation.

We describe an unprecedented reaction between peptide selenoesters and peptide dimers bearing N-terminal selenocystine that proceeds in aqueous buffer to afford native amide bonds without the use of additives. The selenocystine-selenoester ligations are complete in minutes, even at sterically hindered junctions, and can be used in concert with one-pot deselenization chemistry. Various pathways for the transformation are proposed and probed through a combination of experimental and computational studies. Our new reaction manifold is also showcased in the total synthesis of two proteins.

Gas-phase structure and reactivity of the keto tautomer of the deoxyguanosine radical cation.

Guanine radical cations are formed upon oxidation of DNA. Deoxyguanosine (dG) is used as a model, and the gas-phase infrared (IR) spectroscopic signature and gas-phase unimolecular and bimolecular chemistry of its radical cation, dG˙(+), A, which is formed via direct electrospray ionisation (ESI/MS) of a methanolic solution of Cu(NO3)2 and dG, are examined. Quantum chemistry calculations have been carried out on 28 isomers and comparisons between their calculated IR spectra and the experimentally-measured spectra suggest that A exists as the ground-state keto tautomer. Collision-induced dissociation (CID) of A proceeds via cleavage of the glycosidic bond, while its ion­molecule reactions with amine bases occur via a number of pathways including hydrogen-atom abstraction, proton transfer and adduct formation. A hidden channel, involving isomerisation of the radical cation via adduct formation, is revealed through the use of two stages of CID, with the final stage of CID showing the loss of CH2O as a major fragmentation pathway from the reformed radical cation, dG˙(+). Quantum chemistry calculations on the unimolecular and bimolecular reactivity are also consistent with A being present as a ground-state keto tautomer.

Outcome-changing effect of polarity reversal in hydrogen-atom-abstraction reactions.

We have examined hydrogen-atom-abstraction reactions for combinations of electrophilic/nucleophilic radicals with electrophilic/nucleophilic substrates. We find that reaction between an electrophilic radical and a nucleophilic substrate is relatively favorable, and vice versa, but the reactions between a radical and a substrate that are both electrophilic or both nucleophilic are relatively unfavorable, consistent with the literature reports of Roberts. As a result, the regioselectivity for the abstraction from a polar substrate can be reversed by reversing the polarity of the attacking radical. Our calculations support Roberts' polarity-reversal-catalysis concept and suggest that addition of a catalyst of appropriate electrophilicity/nucleophilicity can lead to an enhancement of the reaction rate of approximately 5 orders of magnitude. By exploiting the control over regioselectivity associated with the polar nature of the radical and the substrate, we demonstrate the possibility of directing the regioselectivity of hydrogen abstraction from amino acid derivatives and simultaneously providing a significant rate acceleration.

H and D attachment to naphthalene: spectra and thermochemistry of cold gas-phase 1-C10H9 and 1-C10H8D radicals and cations.

Excitation spectra of the 1H-naphthalene (1-C10H9) and 1D-naphthalene (1-C10H8D) radicals, and their cations, are obtained by laser spectroscopy and mass spectrometry of a skimmed free-jet expansion following an electrical discharge. The spectra are assigned on the basis of density functional theory calculations. Isotopic shifts in origin transitions, vibrational frequencies and ionization energies were found to be well reproduced by (time-dependent) density functional theory. Absolute bond dissociation energies, ionization energies and proton affinities were calculated using high-level quantum chemical methods.

Effect of protonation state and interposed connector groups on bond dissociation enthalpies of alcohols and related systems.

High-level quantum chemical procedures have been used to study how the C-H bond dissociation enthalpies (BDEs) of alcohols and related systems are affected by changes to their protonation state. The high-level procedures used have been determined from a benchmark of 25 neutral, protonated, and deprotonated substituted methanes. The benchmark calculations suggest that the experimental C-H BDEs for CH3NH2 and CH3SH should be reassessed. We confirm previous findings that protonation increases the BDEs of alcohols, while deprotonation decreases the BDEs. For the prototypical alcohol, methanol, reducing the strength of the proton donor or acceptor leads to a smaller change in the BDE, and a smooth variation of C-H bond strength with the extent of protonation or deprotonation is observed. Changes in the BDE with protonation state are reduced for alcohols with a connector group separating the oxygen center and the site of C-H bond scission. These changes are rationalized through introduction of three new quantities, termed the effect of protonation state on dissociation energies, the alcohol radical connector energy, and the alcohol molecule connector energy. Gas-phase acidities and proton affinities for all relevant alcohols have been computed and compared with experiment. The agreement between theory and experiment is generally reasonable, with just one notable outlier (the proton affinity of CH3CH2CH2OH). In this case, we suggest that the experimental value should be reevaluated.

Hydrogen from formic acid through its selective disproportionation over sodium germanate--a non-transition-metal catalysis system.

A robust catalyst for the selective dehydrogenation of formic acid to liberate hydrogen gas has been designed computationally, and also successfully demonstrated experimentally. This is the first such catalyst not based on transition metals, and it exhibits very encouraging performance. It represents an important step towards the use of renewable formic acid as a hydrogen-storage and transport vector in fuel and energy applications.

Accurate quantum chemical energies for tetrapeptide conformations: why MP2 data with an insufficient basis set should be handled with caution.

High-level quantum chemical calculations have been carried out for biologically-relevant conformers of tetrapeptides. Our results indicate potential problems if the widely-applied MP2 approach is used in such situations with basis sets of insufficient size. Efficient alternatives are discussed.

Hierarchy of relative bond dissociation enthalpies and their use to efficiently compute accurate absolute bond dissociation enthalpies for C-H, C-C, and C-F bonds.

We have used the high-level W1X-2 and G4(MP2)-6X procedures to examine the performance of a variety of computationally less demanding quantum chemistry methods for the calculation of absolute bond dissociation enthalpies (BDEs) and a hierarchy of relative bond dissociation enthalpies. These include relative bond dissociation enthalpies (RBDEs), deviations from additivity of RBDEs (DARBDEs), and deviations from pairwise additivity of RBDEs (DPARBDEs). The absolute magnitudes of these quantities decrease in the order BDE > RBDE > DARBDE > DPARBDE, and overall, theoretical procedures are better able to describe these quantities in the same order. In general, the performance of the various types of procedures improves in the order pure DFT → hybrid DFT → double-hybrid DFT → composite procedures, as expected. Overall, we find M06-L to be the best-performing pure DFT procedure and M06-2X to be the best among the hybrid DFT methods. A promising observation is that even many pure and hybrid DFT procedures give DARBDE and DPARBDE values that are reasonably accurate. This can be exploited by using reference BDEs calculated at a higher-level of theory, in combination with DARBDE or DPARBDE values obtained at a lower level, to produce BDEs and RBDEs with an accuracy that is close to the directly calculated higher-level values. Strongly π-electron-withdrawing or π-electron-donating groups, however, sometimes represent challenges to these approximation methods when the substrate contains several of these substituents.

Evaluation of the heats of formation of corannulene and C60 by means of high-level theoretical procedures.

In this study, we address the issues associated with predicting usefully accurate heats of formation for moderately-sized molecules such as corannulene and C(60). We obtain a high-level theoretical heat of formation for corannulene through the use of reaction schemes that conserve increasingly larger molecular fragments between the reactants and products. The reaction enthalpies are obtained by means of the high-level, ab initio W1h thermochemical protocol, while accurate experimental enthalpies of formation for the other molecules involved in the reactions are obtained from the Active Thermochemical Tables (ATcT) network. Our best theoretical heat of formation for corannulene (Δ(f)H°(298)[C(20)H(10)(g)] = 485.2 ± 7.9 kJ mol(-1)) differs significantly from the currently accepted experimental value (Δ(f)H°(298)[C(20)H(10)(g)] = 458.5 ± 9.2 kJ mol(-1)), and this suggests that re-examination of the experimental data may be in order. We have used our theoretical heat of formation for corannulene to obtain a predicted heat of formation of C(60) through reactions that involve only corannulene and planar polyacenes. Current experimental values span a range of ~200 kJ mol(-1). Our reaction enthalpies are obtained by means of double-hybrid density functional theory in conjunction with a large quadruple-ζ basis set, while accurate experimental heats of formation (or our theoretical value in the case of corannulene) are used for the other molecules involved. Our best theoretical heat of formation for C(60) (Δ(f)H°(298)[C(60)(g)] = 2521.6 kJ mol(-1)) suggests that the experimental value adopted by the NIST thermochemical database (Δ(f)H°(298)[C(60)(g)] = 2560 ± 100 kJ mol(-1)) should be revised downward.