The interaction of thiocyanate with peptides-A computational study.

According to the Hofmeister series, thiocyanate is the strongest "salting in" anion. In fact, it has a strong denaturant activity against the native state of globular proteins. A molecular level rationalization of the Hofmeister series is still missing, and therefore the denaturant activity of thiocyanate also awaits a robust explanation. In the last years, different types of experimental studies have shown that thiocyanate is capable to directly interact with both polar and nonpolar groups of polypeptide chains. This finding has been scrutinized via a careful computational procedure based on density functional theory approaches. The results indicate that thiocyanate is able to make H-bonds via both the nitrogen and sulfur atom, and to make strong van der Waals interactions with almost all the groups of polypeptide chains, regardless of their polarity.

Modeling Multi-Step Organic Reactions: Can Density Functional Theory Deliver Misleading Chemistry?

Many organic reactions are characterized by a complex mechanism with a variety of transition states and intermediates of different chemical natures. Their correct and accurate theoretical characterization critically depends on the accuracy of the computational method used. In this work, we study a complex ambimodal cycloaddition with five transition states, two intermediates, and three products, and we ask whether density functional theory (DFT) can provide a correct description of this type of complex and multifaceted reaction. Our work fills a gap in that most systematic benchmarks of DFT for chemical reactions have considered much simpler reactions. Our results show that many density functionals not only lead to seriously large errors but also differ from one another in predicting whether the reaction is ambimodal. Only a few of the available functionals provide a balanced description of the complex and multifaceted reactions. The parameters varied in the tested functionals are the ingredients, the treatment of medium-range and nonlocal correlation energy, and the inclusion of Hartree-Fock exchange. These results show a clear need for more benchmarks on the mechanisms of large molecules in complex reactions.

Barrier Heights for Diels-Alder Transition States Leading to Pentacyclic Adducts: A Benchmark Study of Crowded, Strained Transition States of Large Molecules.

Theoretical characterization of reactions of complex molecules depends on providing consistent accuracy for the relative energies of intermediates and transition states. Here we employ the DLPNO-CCSD(T) method with core-valence correlation, large basis sets, and extrapolation to the CBS limit to provide benchmark values for Diels-Alder transition states leading to competitive strained pentacyclic adducts. We then used those benchmarks to test a diverse set of wave function and density functional methods for the absolute and relative barrier heights of these transition states. Our results show that only a few of the tested density functionals can predict the absolute barrier heights satisfactorily, although relative barrier heights are more accurate. The most accurate functionals tested are ωB97M-V, M11plus, ωB97X-V, PBE-D3(0), M11, and MN15 with MUDs from best estimates less than 3.0 kcal. These findings can guide selection of density functionals for future studies of crowded, strained transition states of large molecules.

Antioxidant Activities of Hydroxylated Naphthalenes: The Role of Aryloxyl Radicals.

Herein is delineated a first systematic framework for the definition of structure-antioxidant property relationships in the dihydroxynaphthalene (DHN) series. The results obtained by a combined experimental and theoretical approach revealed that 1,8-DHN is the best performing antioxidant platform, with its unique hydrogen-bonded peri-hydroxylation pattern contributing to a fast H atom transfer process. Moreover, the comparative analysis of the antioxidant properties of DHNs carried out by performing DPPH and FRAP assays and laser flash photolysis experiments, revealed the higher antioxidant power associated with an α-substitution pattern (i. e. in 1,8- and 1,6-DHN) with respect to DHNs exhibiting a ß-substitution pattern (i. e. in 2,6- and 2,7-DHN). DFT calculations and isolation and characterization of the main oligomer intermediates formed during the oxidative polymerization of DHNs supported this evidence by providing unprecedented insight into the generation and fate of the intermediate naphthoxyl radicals, which emerged as the main factor governing the antioxidant activity of DHNs.

Non-covalent small molecule partnership for redox-active films: Beyond polydopamine technology.

HYPOTHESIS: The possibility to use hexamethylenediamine (HMDA) to impart film forming ability to natural polymers including eumelanins and plant polyphenols endowed with biological activity and functional properties has been recently explored with the aim to broaden the potential of polydopamine (PDA)-based films overcoming their inherent limitations. 5,6-dihydroxyindole-2-carboxylic acid, its methyl ester (MeDHICA) and eumelanins thereof were shown to exhibit potent reducing activity. EXPERIMENTS: MeDHICA and HMDA were reacted in aqueous buffer, pH 9.0 in the presence of different substrates to assess the film forming ability. The effect of different reaction parameters (pH, diamine chain length) on film formation was investigated. Voltammetric and AFM /SEM methods were applied for analysis of the film redox activity and morphology. HPLC, MALDI-MS and 1HNMR were used for chemical characterization. The film reducing activity was evaluated in comparison with PDA by chemical assays and using UV stressed human immortalized keratinocytes (HaCat) cells model. FINDINGS: Regular and homogeneous yellowish films were obtained with moderately hydrophobic properties. Film deposition was optimal at pH 9, and specifically induced by HMDA. The film consisted of HMDA and monomeric MeDHICA accompanied by dimers/small oligomers, but no detectable MeDHICA/HMDA covalent conjugation products. Spontaneous assembly of self-organized networks held together mainly by electrostatic interactions of MeDHICA in the anion form and HMDA as the dication is proposed as film deposition mechanism. The film displayed potent reducing properties and exerted significant protective effects from oxidative stress on HaCaT.

Disentangling the Puzzling Regiochemistry of Thiol Addition to o-Quinones.

The addition of thiol compounds to o-quinones, as exemplified by the biologically relevant conjugation of cysteine to dopaquinone, displays an anomalous 1,6-type regiochemistry compared to the usual 1,4-nucleophilic addition, for example, by amines, which has so far eluded intensive investigations. By means of an integrated experimental and computational approach, herein, we provide evidence that the addition of glutathione, cysteine, or benzenethiol to 4-methyl-o-benzoquinone, modeling dopaquinone, proceeds by a free radical chain mechanism triggered by the addition of thiyl radicals to the o-quinone. In support of this conclusion, DFT calculations consistently predicted the correct regiochemistry only for the proposed thiyl radical-quinone addition pathway. These results would prompt a revision of the commonly accepted mechanisms for thiol-o-quinone conjugation and stimulate further work aimed at assessing the impact of the free radical processes in biologically relevant thiol-quinone interactions.

Mining for encrypted peptide antibiotics in the human proteome.

The emergence of drug-resistant bacteria calls for the discovery of new antibiotics. Yet, for decades, traditional discovery strategies have not yielded new classes of antimicrobial. Here, by mining the human proteome via an algorithm that relies on the sequence length, net charge, average hydrophobicity and other physicochemical properties of antimicrobial peptides, we report the identification of 2,603 encrypted peptide antibiotics that are encoded in proteins with biological function unrelated to the immune system. We show that the encrypted peptides kill pathogenic bacteria by targeting their membrane, modulate gut and skin commensals, do not readily select for bacterial resistance, and possess anti-infective activity in skin abscess and thigh infection mouse models. We also show, in vitro and in the two mouse models of infection, that encrypted antibiotic peptides from the same biogeographical area display synergistic antimicrobial activity. Our algorithmic strategy allows for the rapid mining of proteomic data and opens up new routes for the discovery of candidate antibiotics.

Proton-Sensitive Free-Radical Dimer Evolution Is a Critical Control Point for the Synthesis of Δ2,2'-Bibenzothiazines.

The mechanism of the acid-dependent interring dehydrogenation in the conversion of the single-bonded 3-phenyl-2H-1,4-benzothiazine dimer 2 to the Δ2,2'-bi(2H-1,4-benzothiazine) scaffold of red hair pigments is disclosed herein. Integrated chemical oxidation and oxygen consumption experiments, coupled with electron paramagnetic resonance (EPR) analyses and DFT calculations, allowed the identification of a key diprotonated free-radical intermediate, which was implicated in a remarkable oxygen-dependent chain process via peroxyl radical formation and evolution to give the Δ2,2'-bi(2H-1,4-benzothiazine) dimer 3 by interring dehydrogenation. The critical requirement for strongly acidic conditions was rationalized for the first time by the differential evolution channels of isomeric peroxyl radical intermediates at the 2- versus 3-positions. These results offer for the first time a rationale to expand the synthetic scope of the double interring dehydrogenation pathway for the preparation of novel symmetric double-bond bridged captodative heterocycles.

Luminescent cis-Iridium(III) Complex Based on a Bis(6,7-dimethoxy-3,4-dihydroisoquinoline) Platform Featuring an Unusual cis Orientation of the C∧N Ligands: From a Theoretical Approach to a Deep Red LEEC Device.

By pursuing the strategy of manipulating natural compounds to obtain functional materials, in this work, we report on the synthesis and characterization of a luminescent cationic iridium complex (cis-1), designed starting from the catecholic neurotransmitter dopamine, exhibiting the unusual cis arrangement of the C∧N ligands. Through an integrated experimental and theoretical approach, it was possible to delineate the optoelectronic properties of cis-1. In detail, (a) a series of absorption maxima in the range 300-400 nm was assigned to metal-to-ligand charge transfer and weak and broad absorption maxima at longer wavelengths (400-500 nm) were ascribable to spin-forbidden transitions with a mixed character; (b) there was an intense red phosphorescence with emission set in the range 580-710 nm; and (c) a highest occupied molecular orbital was mainly localized on the metal and the 2-phenylpiridine ligand and a lowest unoccupied molecular orbital was localized on the N∧N ligand, with a ΔH-L set at 2.20 eV. This investigation allowed the design of light-emitting electrochemical cell (LEEC) devices endowed with good performance. The poor literature reporting on the use of cis-iridium(III) complexes in LEECs prompted us to investigate the role played by the selected cathode and the thickness of the emitting layer, as well as the doping effect exerted by ionic liquids on the performance of the devices. All the devices exhibited a deep red emission, in some cases, quite near the pure color (devices #1, #4, and #8), expanding the panorama of the iridium-based red-to-near-infrared LEEC devices. The characteristics of the devices, such as the brightness reaching values of 162 cd/m2 for device #7, suggested that the performances of cis-1 are comparable to those of trans isomers, opening new perspective toward designing a new set of luminescent materials for optoelectronic devices.

An ab initio study of Cu-based delafossites as an alternative to nickel oxide in photocathodes: effects of Mg-doping and surface electronic features.

CuMO2 delafossites (M = Al, Ga, and Cr) are p-type semiconductor oxides that have been recently proposed as the electrode in p-type dye-sensitized solar cells (p-DSSC) which is an alternative to the standard, low-performing nickel oxide. To assess this potential application of delafossites, we report here a DFT-based investigation of the structural and electronic properties of CuAlO2, CuGaO2 and CuCrO2. In particular, we address the role of Mg doping to obtain the p-type semiconducting character: the substitution of an M3+ cation with Mg2+ is easier with Ga than with Al and Cr, and, in all cases, the hole introduced by Mg2+ leads to the formation of Cu2+ species. Moreover, we address surface electronic features in order to characterize the most exposed delafossite surface termination and, more importantly, to predict the valence band maximum energy value, which determines the p-DSSC open circuit potential. From analysis of all our results, CuGaO2 emerges as the most promising system that can boost the development of new photocathodes for p-DSSCs.

Characterization and Fate of Hydrogen-Bonded Free-Radical Intermediates and Their Coupling Products from the Hydrogen Atom Transfer Agent 1,8-Naphthalenediol.

1,8-Naphthalenediol (dihydroxynaphthalene, 1,8-DHN) has been shown to be a potent hydrogen atom transfer (HAT) antioxidant compound because of the strong stabilization of the resulting free radical by intramolecular hydrogen bonding. However, the properties, reactivity, and fate of the 1,8-DHN phenoxyl radical have remained so far uncharted. Herein, we report an integrated experimental and computational characterization of the early intermediates and dimer products that arise by the oxidation of 1,8-DHN. Laser flash photolysis (LFP) studies of HAT from 1,8-DHN to the cumyloxyl and aminoxyl radicals showed the generation of a transient species absorbing at 350, 400, and >600 nm attributable to the 1,8-DHN phenoxyl radical. Peroxidase/H2O2 oxidation of 1,8-DHN was found to proceed via an intense blue intermediate (λmax 654 nm) preceding precipitation of a black melanin-like polymer. By halting the reaction in the early stages, three main dimers featuring 2,2'-, 2,4'-, and 4,4'-bondings could be isolated and characterized in pure form. Density functional theory calculations supported the generation of the 1,8-DHN phenoxyl radical and its subsequent coupling via the 2- and 4-positions giving extended quinone dimers with intense transitions in the visible range, consistent with UV-vis and LFP data. Overall, these results allowed to elucidate the mechanism of oxidative polymerization of 1,8-DHN of possible relevance to melanogenesis in fungi and other processes of environmental and astrochemical relevance.

Structural Basis of Polydopamine Film Formation: Probing 5,6-Dihydroxyindole-Based Eumelanin Type Units and the Porphyrin Issue.

The role of 5,6-dihydroxyindole (DHI)-based oligomers, including porphyrin-like tetramers, in polydopamine (PDA) film formation was addressed by a comparative structural investigation against model polymers from DHI and its 2,7'-dimer. MALDI-MS data showed that (a) PDA is structurally different from DHI melanin and does not contain species compatible with DHI-based oligomers as primary building blocks; (b) PDA films and precipitate display a single main peak at m/ z 402 in common; (c) no species matching the range of m/ z values expected for cyclic porphyrin-type tetramers was detected in DHI melanin produced in the presence or in the absence of folic acid (FA) as templating agent, nor by oxidation of the 2,7'-dimer of DHI as putative precursor. 15N NMR resonances and Raman spectra predicted by extensive DFT calculations on porphyrin-type structures at various oxidation levels did not match spectral data for PDA or DHI melanin. Notably, unlike PDA, which gave structurally homogeneous films on quartz on atomic force microscopy (AFM) and micro-Raman spectroscopy, DHI melanin did not form any adhesive deposit after as long as 24 h. It is concluded that PDA film deposition involves structural components unrelated to DHI-based oligomers or porphyrin-type tetramers, which, on mechanism-based analysis, may arise by quinone-amine conjugation leading to polycyclic systems with extensive chain breakdown.

Replacing Nitrogen by Sulfur: From Structurally Disordered Eumelanins to Regioregular Thiomelanin Polymers.

The oxidative polymerization of 5,6-dihydroxybenzothiophene (DHBT), the sulfur analog of the key eumelanin building block 5,6-dihydroxyindole (DHI), was investigated to probe the role of nitrogen in eumelanin build-up and properties. Unlike DHI, which gives a typical black insoluble eumelanin polymer on oxidation, DHBT is converted to a grayish amorphous solid (referred to as thiomelanin) with visible absorption and electron paramagnetic resonance properties different from those of DHI melanin. Mass spectrometry experiments revealed gradational mixtures of oligomers up to the decamer level. Quite unexpectedly, nuclear magnetic resonance (NMR) analysis of the early oligomer fractions indicated linear, 4-, and 7-linked structures in marked contrast with DHI, which gives highly complex mixtures of partially degraded oligomers. Density functional theory (DFT) calculations supported the tendency of DHBT to couple via the 4- and 7-positions. These results uncover the role of nitrogen as a major determinant of the structural diversity generated by the polymerization of DHI, and point to replacement by sulfur as a viable entry to regioregular eumelanin-type materials for potential applications for surface functionalization by dip coating.

Eumelanin broadband absorption develops from aggregation-modulated chromophore interactions under structural and redox control.

Eumelanins, the chief photoprotective pigments in man and mammals, owe their black color to an unusual broadband absorption spectrum whose origin is still a conundrum. Excitonic effects from the interplay of geometric order and disorder in 5,6-dihydroxyindole (DHI)-based oligomeric/polymeric structures play a central role, however the contributions of structural (scaffold-controlled) and redox (π-electron-controlled) disorder have remained uncharted. Herein, we report an integrated experimental-theoretical entry to eumelanin chromophore dynamics based on poly(vinyl alcohol)-controlled polymerization of a large set of 5,6-dihydroxyindoles and related dimers. The results a) uncover the impact of the structural scaffold on eumelanin optical properties, disproving the widespread assumption of a universal monotonic chromophore; b) delineate eumelanin chromophore buildup as a three-step dynamic process involving the rapid generation of oxidized oligomers, termed melanochromes (phase I), followed by a slow oxidant-independent band broadening (phase II) leading eventually to scattering (phase III); c) point to a slow reorganization-stabilization of melanochromes via intermolecular redox interactions as the main determinant of visible broadband absorption.

Antimicrobial potency of cationic antimicrobial peptides can be predicted from their amino acid composition: Application to the detection of "cryptic" antimicrobial peptides.

Cationic antimicrobial peptides (CAMPs) are essential components of innate immunity. Here we show that antimicrobial potency of CAMPs is linearly correlated to the product CmHnL where C is the net charge of the peptide, H is a measure of its hydrophobicity and L its length. Exponents m and n define the relative contribution of charge and hydrophobicity to the antimicrobial potency. Very interestingly the values of m and n are strain specific. The ratio n/(m+n) can vary between ca. 0.5 and 1, thus indicating that some strains are sensitive to highly charged peptides, whereas others are particularly susceptible to more hydrophobic peptides. The slope of the regression line describing the correlation "antimicrobial potency"/"CmHnL product" changes from strain to strain indicating that some strains acquired a higher resistance to CAMPs than others. Our analysis provides also an effective computational strategy to identify CAMPs included inside the structure of larger proteins or precursors, which can be defined as "cryptic" CAMPs. We demonstrate that it is not only possible to identify and locate with very good precision the position of cryptic peptides, but also to analyze the internal structure of long CAMPs, thus allowing to draw an accurate map of the molecular determinants of their antimicrobial activity. A spreadsheet, provided in the Supplementary material, allows performing the analysis of protein sequences. Our strategy is also well suited to analyze large pools of sequences, thus significantly improving the identification of new CAMPs and the study of innate immunity.

Kaxiras's Porphyrin: DFT Modeling of Redox-Tuned Optical and Electronic Properties in a Theoretically Designed Catechol-Based Bioinspired Platform.

A detailed computational investigation of the 5,6-dihydroxyindole (DHI)-based porphyrin-type tetramer first described by Kaxiras as a theoretical structural model for eumelanin biopolymers is reported herein, with a view to predicting the technological potential of this unique bioinspired tetracatechol system. All possible tautomers/conformers, as well as alternative protonation states, were explored for the species at various degrees of oxidation and all structures were geometry optimized at the density functional theory (DFT) level. Comparison of energy levels for each oxidized species indicated a marked instability of most oxidation states except the six-electron level, and an unexpected resilience to disproportionation of the one-electron oxidation free radical species. Changes in the highest energy occupied molecular orbital (HOMO)⁻lowest energy unoccupied molecular orbital (LUMO) gaps with oxidation state and tautomerism were determined along with the main electronic transitions: more or less intense absorption in the visible region is predicted for most oxidized species. Data indicated that the peculiar symmetry of the oxygenation pattern pertaining to the four catechol/quinone/quinone methide moieties, in concert with the NH centers, fine-tunes the optical and electronic properties of the porphyrin system. For several oxidation levels, conjugated systems extending over two or more indole units play a major role in determining the preferred tautomeric state: thus, the highest stability of the six-electron oxidation state reflects porphyrin-type aromaticity. These results provide new clues for the design of innovative bioinspired optoelectronic materials.

Hot spot mapping of protein surfaces with TEMPOL: Bovine pancreatic RNase A as a model system.

TEMPOL spin-label has been used to identify surface exposure of protein nuclei from NMR analysis of the induced paramagnetic relaxation enhancements (PRE). The absence of linear dependence between atom depths and observed PRE reveals that specific mechanisms drive the approach of the paramagnet to the protein surface. RNase A represents a unique protein system to explore the fine details of the information offered by TEMPOL induced PRE, due to the abundance of previous results, obtained in solution and in the crystal, dealing with surface dynamics behavior of this protein. MD simulations in explicit solvent have been performed, also in the presence of TEMPOL, in order to delineate the role of intermolecular hydrogen bonds (HB) on PRE extents. Comparison of our results with the ones obtained from multiple solvent crystal structure (MSCS) studies yields information on the specificities that these two techniques have for characterizing protein-ligand interactions, a fundamental step in the development of reliable surface druggability predictors.

Stability of melamine-exfoliated graphene in aqueous media: quantum-mechanical insights at the nanoscale.

In recent experiments, melamine (1,3,5-triazine-2,4,6-triamine) has been proposed as an effective exfoliating agent to obtain high quality graphene from graphite. After washing out the melamine in excess, small amounts (ppm) are still needed to stabilize the dispersion of graphene flakes in aqueous media. To understand the origin of this behaviour, we investigated the melamine-graphene-water system and the fundamental interactions that determine its structure and energetics. To disentangle the subtle interplay of hydrogen-bonding and dispersive forces we used state-of-the-art ab initio calculations based on density functional theory. First, we focused on the case of water molecules interacting with melamine-graphene assemblies at different melamine coverages. We found that water-melamine interactions provide the driving force for washing off the melamine from graphene. Then, we addressed the interaction of single and double layers of water molecules with the graphene surface in the presence of an adsorbed melamine molecule. We found that this melamine acts as a non-covalent anchor for keeping a number of water molecules conveniently close to the graphene surface, thus helping its stabilization in aqueous media. Our analysis helps understanding how competing weak forces can lead to a stable graphene water suspension thanks to small amounts of adsorbed melamine. From our results, we derive simple indications on how the water-graphene interfacial properties can be tuned via non-covalent adsorption of small functional molecules with H-bond donor/acceptor groups. These new hints can be helpful to prepare stable graphene dispersions in water and so to unlock graphene potential in aqueous environments.

Trichocyanines: a Red-Hair-Inspired Modular Platform for Dye-Based One-Time-Pad Molecular Cryptography.

Current molecular cryptography (MoCryp) systems are almost exclusively based on DNA chemistry and reports of cryptography technologies based on other less complex chemical systems are lacking. We describe herein, as proof of concept, the prototype of the first asymmetric MoCryp system, based on an 8-compound set of a novel bioinspired class of cyanine-type dyes called trichocyanines. These novel acidichromic cyanine-type dyes inspired by red hair pigments were synthesized and characterized with the aid of density functional theory (DFT) calculations. Trichocyanines consist of a modular scaffold easily accessible via an expedient condensation of 3-phenyl- or 3-methyl-2H-1,4-benzothiazines with N-dimethyl- or o-methoxyhydroxy-substituted benzaldehyde or cinnamaldehyde derivatives. The eight representative members synthesized herein can be classified as belonging to two three-state systems tunable through four different control points. This versatile dye platform can generate an expandable palette of colors and appears to be specifically suited to implement an unprecedented single-use asymmetric molecular cryptography system. With this system, we intend to pioneer the translation of digital public-key cryptography into a chemical-coding one-time-pad-like system.