Electrophilic Center Research Articles

DFT and MP2 Calculations on Tautomers and Water-Assisted Proton Transfer on 1,2,5-Oxadiazol-4,3-diamine

In this work a detailed quantum-chemical comparison of the relative stability of six tautomers of 1,2,5-oxadiazol-4,3-diamine studied in the gas phase and solution. Theoretical calculations are carried out by the density functional theory (DFT/B3LYP) and MP2 methods using the standard 311++G(d,p) basis set. The results indicate that A is the most stable form in the gas phase and also is the predominant tautomer in solution at the DFT and MP2 methods. The transition states of proton transfer reaction are calculated. The variation of dipole moments and charges on atoms are studied in various solvent. Specific solvent effects with addition of one water molecule near the electrophilic centers of tautomer investigated. Also the transition state of proton transfer assisted by a water molecule was investigated.

Rational Engineering of a Flavoprotein Oxidase for Improved Direct Oxidation of Alcohols to Carboxylic Acids.

The oxidation of alcohols to the corresponding carbonyl or carboxyl compounds represents a convenient strategy for the selective introduction of electrophilic carbon centres into carbohydrate-based starting materials. The O2-dependent oxidation of prim-alcohols by flavin-containing alcohol oxidases often yields mixtures of aldehyde and carboxylic acid, which is due to “over-oxidation” of the aldehyde hydrate intermediate. In order to directly convert alcohols into carboxylic acids, rational engineering of 5-(hydroxymethyl)furfural oxidase was performed. In an attempt to improve the binding of the aldehyde hydrate in the active site to boost aldehyde-oxidase activity, two active-site residues were exchanged for hydrogen-bond-donating and -accepting amino acids. Enhanced over-oxidation was demonstrated and Michaelis–Menten kinetics were performed to corroborate these findings.

Xanthohumol prevents dextran sulfate sodium-induced colitis via inhibition of IKKβ/NF-κB signaling in mice.

Xanthohumol (XN), a prenylated chalcone isolated from the hop plant, has been reported to exhibit multiple biological functions including anti-inflammation. However, the pharmacological function of XN on colitis remains unknown. In this study, we investigated the anti-inflammatory effect of synthesized XN and molecular mechanism on dextran sulfate sodium (DSS)-induced experimental colitis. XN attenuated the colitis symptoms along with the prevention of colonic lesions after DSS challenge. XN inhibited the production of pro-inflammatory cytokines, oxidative stress and cyclooxygenase-2 expression in DSS-treated mice. Moreover, XN inhibited the phosphorylation of IκBα, the nuclear translocation of NF-κB subunits and the transcriptional activity of NF-κB in vivo and in vitro. In contrast to XN, isoXN showed much less effects on the kinase activity of IKKβ and IκBα phosphorylation induced by XN in this study, suggesting that an electrophilic carbon center present in XN is critical for the anti-inflammation in colitis, especially inhibition of IKKβ/NF-κB signaling pathway. Consistently, our docking analysis revealed that XN could bind to the active site, presumably at the Cys99 of IKKβ. Taken together, these findings demonstrate a new function of XN to inhibit IKKβ/NF-κB signaling, suggesting XN could be the potential therapeutic agent for the prevention of colitis.

DFT Study of the Strong Solvent Effects in the Cu‐Catalyzed Asymmetric Conjugate Addition Reaction

Significant solvent effects on enantioselection exist in the reaction of Cu‐catalyzed asymmetric conjugate addition of alkylzinc reagents to α,β‐unsaturated carbonyl compounds. Results of our DFT study suggest that solvent effects on enantioselection can be caused by structural changes in the stereodetermining Transition States (TS). We have seen how unconventional hydrogen bonding of the nucleophilic solvent results in a change of the computed optical yield comparable to that caused by well‐known coordination of the solvent to the electrophilic metal center.

Systematic Analysis of Poly(o-aminophenol) Humidity Sensors.

A thin film of poly(o-aminophenol), POAP, has been used as a sensor for various types of toxic and nontoxic gases: a gateway between the digital and physical worlds. We have carried out a systematic mechanistic investigation of POAP as a humidity sensor; how does it sense different gases? POAP has several convenient features such as flexibility, transparency, and suitability for large-scale manufacturing. With an appropriate theoretical method, molecular oligomers of POAP, NH and O functional groups and the perpendicular side of the polymeric body, are considered as attacking sites for humidity sensing. It is found that the NH position of the polymer acts as an electrophilic center: able to accept electronic cloud density and energetically more favorable compared to the O site. The O site acts as a nucleophilic center and donates electronic cloud density toward H2Ovap. In conclusion, only these two sites are involved in the sensing process which leads to strong intermolecular hydrogen bonding, having a 1.96 Å bond distance and ΔE ∼ −35 kcal mol–1. The results suggest that the sensitivity of the sensor improved with the oxidization state of POAP.

Synthesis of 5-Acyl-2-Amino-3-Cyanothiophenes: Chemistry and Fluorescent Properties.

Independent of the substrate structure and reaction conditions, 3-amino-2-cyanothioacrylamides, which contain two active electrophilic centers, were shown to interact with various active halo methylene compounds under mild conditions to afford 5-acyl-2-amino-3-cyanothiophenes as the only products. A series of new polyfunctional thiophene derivatives with a rare combination of functionalities were synthesized, and their photophysical properties were experimentally and computationally investigated. The calculated electronic characteristics of the ground and excited states were compared to the experimental results, which provided a good understanding of the relationship between the optoelectronic properties and the molecular structures. After absorption of light quanta, the systems populate an intramolecular charge-transfer (ICT) Franck-Condon state, and emission occurs from a twisted ICT minimum.

α‐Keto Thioesters as Building Blocks for Accessing γ‐Hydroxybutenolides and Oxazoles

Abstractα‐Keto thioesters, with two electrophilic carbon centres, have been found to react differently with β‐keto esters and isocyanoacetates. They undergo base induced Knoevenagel‐type condensation on the keto carbonyl group with β‐keto esters, followed by intramolecular cyclization and water addition leads to highly substituted γ‐hydroxybutenolides. On the other hand, substituted oxazole derivatives have been obtained using isocyanoacetates via nucleophilic displacement on the thioester carbonyl followed by intramolecular cyclization. Further functionalization of the γ‐hydroxybutenolides is also demonstrated via a BF3.OEt2‐mediated cation‐driven nucleophilic addition of terminal alkynes to access multiply substituted butenolides.magnified image

Theoretical study on the mechanism and selectivity of asymmetric cycloaddition reactions of 3-vinylindole catalyzed by chiral N,N'-dioxide-Ni(II) complex

The mechanism and selectivity of the asymmetric cycloaddition reactions of 3-vinylindole towards methyleneindolinone (Diels–Alder reaction) or ketimine (aza-Diels–Alder reaction) were investigated theoretically by DFT and ONIOM methods. The non-catalytic DA reaction occurred in a two-stage one-step mechanism with the energy barriers of 17.0–29.6kcalmol−1. Reactivity index analysis indicated that the cycloaddition tended to occur by the most nucleophilic terminal C4 center in 3-vinylindole and the most electrophilic Cβ center in methyleneindolinone with lower activation energies, which accounted for the regioseletivity observed in experiment. For non-catalytic reactions, the slightly exo-preference stemmed from the stabilizing π-π stacking of two indole rings in substrates. In the presence of chiral N,N'-dioxide-Ni(II) complex, the bulky ortho-iPr group in aniline of ligand provided sufficient steric shielding around dienophile from the si-face attack in Diels–Alder reaction or re-face attack in aza-Diels–Alder reaction by diene, resulting in predominant products with excellent enantioselectivity (the favorable re-face attack in Diels–Alder reaction or si-face attack in aza-Diels–Alder reaction). A “pocket-like” chiral cavity constructed by chiral catalyst enhanced exo-diastereofacial selectivity significantly by maximizing the overlap of the two indole rings of substrates to avoid unfavorable steric repulsion between indole ring of 3-vinylindole and chiral ligand. Compared with catalytic aza-Diels–Alder reaction of 3-vinylindole and ketimine, the improved catalytic activity of chiral N,N'-dioxide-Ni(II) catalyst in Diels–Alder reaction of 3-vinylindole with methyleneindolinone contributed to the high turnover frequency (TOF=1.05×106s−1). These results were in good agreement with experimental observations.

Trifluoromethyl: An Amphiphilic Noncovalent Bonding Partner.

The traditional "Fδ- " picture of fluorine suggests that it can only interact with electrophilic centers such as backbone-carbonyl carbon atoms or hydrogen-bond donors in proteins. We show that this view, which neglects polarization, is incomplete and the trifluoromethyl groups can act both as electrophiles and nucleophiles to form noncovalent interactions. The underlying polarization mechanism is based on the anomeric effect and is only fully operative if the geometry is allowed to relax. MP2/aug-cc-pVDZ calculations on model systems demonstrate the effect of the unusual group polarizability of trifluoromethyl. A survey of the Protein Databank reveals more than 600 weak interactions involving a trifluorotoluene moiety. The unique combination of the anomeric effect and the group-polarization process associated with it in CF3 allows its most negative molecular electrostatic potential (MEP) on the surface in contact with a nucleophile to become zero, so that the area of positive MEP on the backside of the carbon atom becomes dominant. However, the reverse polarization is also facile, so that CF3 can also act as an H-bond acceptor for cations such as the guanidinium group of arginine.

Electrophilic Activation of Silicon-Hydrogen Bonds in Catalytic Hydrosilations.

Hydrosilation reactions represent an important class of chemical transformations and there has been considerable recent interest in expanding the scope of these reactions by developing new catalysts. A major theme to emerge from these investigations is the development of catalysts with electrophilic character that transfer electrophilicity to silicon by Si-H activation. This type of mechanism has been proposed for catalysts ranging from Group 4 transition metals to Group 15 main group species. Additionally, other electrophilic silicon species, such as silylene complexes and η3 -H2 SiRR' complexes, have been identified as intermediates in hydrosilation reactions. In this Review, different types of catalysts are compared to highlight the range of hydrosilation mechanisms that feature electrophilic silicon centers. The importance of these catalysts to the development of new hydrosilation reactions is also discussed.

The Chemical Basis of Thiol Addition to Nitro-conjugated Linoleic Acid, a Protective Cell-signaling Lipid

Nitroalkene fatty acids are formed in vivo and exert protective and anti-inflammatory effects via reversible Michael addition to thiol-containing proteins in key signaling pathways. Nitro-conjugated linoleic acid (NO2-CLA) is preferentially formed, constitutes the most abundant nitrated fatty acid in humans, and contains two carbons that could potentially react with thiols, modulating signaling actions and levels. In this work, we examined the reactions of NO2-CLA with low molecular weight thiols (glutathione, cysteine, homocysteine, cysteinylglycine, and β-mercaptoethanol) and human serum albumin. Reactions followed reversible biphasic kinetics, consistent with the presence of two electrophilic centers in NO2-CLA located on the β- and δ-carbons with respect to the nitro group. The differential reactivity was confirmed by computational modeling of the electronic structure. The rates (kon and koff) and equilibrium constants for both reactions were determined for different thiols. LC-UV-Visible and LC-MS analyses showed that the fast reaction corresponds to β-adduct formation (the kinetic product), while the slow reaction corresponds to the formation of the δ-adduct (the thermodynamic product). The pH dependence of the rate constants, the correlation between intrinsic reactivity and thiol pKa, and the absence of deuterium solvent kinetic isotope effects suggested stepwise mechanisms with thiolate attack on NO2-CLA as rate-controlling step. Computational modeling supported the mechanism and revealed additional features of the transition states, anionic intermediates, and final neutral products. Importantly, the detection of cysteine-δ-adducts in human urine provided evidence for the biological relevance of this reaction. Finally, human serum albumin was found to bind NO2-CLA both non-covalently and to form covalent adducts at Cys-34, suggesting potential modes for systemic distribution. These results provide new insights into the chemical basis of NO2-CLA signaling actions.

Tetrel, pnictogen and chalcogen bonds identified in the gas phase before they had names: a systematic look at non-covalent interactions

The terms tetrel bond, pnictogen bond and chalcogen bond were coined recently to describe non-covalent interactions involving group 14, 15 and 16 atoms, respectively, acting as the electrophilic site that seeks a nucleophilic region of another molecule, for example a non-bonding electron pair or π-electron pair of a Lewis base. Many complexes containing these non-covalent bonds were identified and characterised in isolation in the gas phase by rotational and vibrational spectroscopy long before they were given these names. In this article, the geometries so determined for selected examples of complexes of each type are rationalised in terms of the molecular electrostatic surface potentials of the component molecules. Examples of chalcogen-bonded complexes considered are based mainly on sulfur dioxide, with the region near the sulfur atom as the electrophilic site that interacts with n-electron and π-electron pairs for a range of simple Lewis base molecules. For tetrel bonds, the examples discussed involve the carbon atom of carbon dioxide as the electrophilic centre, while for pnictogen bonds the central nitrogen of the closely related molecule nitrous oxide is chosen. Geometrical similarities within each series allow simple definitions of each type of non-covalent bond that are conformal with that recently advanced for the halogen bond, a related non-covalent interaction.

Nucleophilicity and electrophilicity of the C(sp3)-H bond: methane and ethane binary complexes with iodine.

The occurrence of stable van der Waals complexes of small saturated hydrocarbons with molecular iodine is assessed in order to investigate the ability of sp3-hybridized carbon atoms to act as either electron donors or electron acceptors depending on the ligand orientation. Systematic ab initio potential energy surface exploration of methane-I2 and ethane-I2 model dimers was followed by thorough characterization. Despite modest evidence of whole-adduct polarization, the resulting interactions feature a dominant dispersive character. The noncovalent interaction descriptors employed comprise NBO, AIM, NCI, and source function analyses. The relevance of bonding C-H orbitals in donor-acceptor interactions involving saturated hydrocarbons is highlighted. The results here presented corroborate existing literature regarding the electrophilicity of the aliphatic C-H group, and also indicate that the nucleophilic character of C(sp3) shares a dependence on electron withdrawing/donating substituents similar to that extensively documented for σ-holes. Indeed, the sole difference between the two, aside from the nucleophilicity/electrophilicity switch, seems to lie in their directionality. Nucleophilic sites on C(sp3) are not limited to the outermost region of C along a covalent bond axis, but can also engage electrophiles via the bifurcation plane of a CH2 unit. Since valence electrons on these carbon atoms are engaged in covalent bonds, they can only interact with polarizing ligands via the electron density accumulation/depletion in the four corresponding σ orbitals. These, however, do not seem to interact individually with the accompanying electrophile. Source function and NCI results suggest instead that nucleophilic carbon centres participate in the noncovalent bond themselves by drawing electron density from their shared electron pairs.

<i>o</i>-（ヒドロシリル）（ボリル）ベンゼンの反応：ホウ素原子によるケイ素-水素結合の分子内活性化

Hydrosilanes are versatile reagents in organic synthetic chemistry as well as oraganosilicon chemistry. Since the Si-H bond is rather inert, its activation is generally required. Recently electrophilic activation of the Si-H bond by a strong Lewis acid such as triarylboranes has received much attention. The highly electrophilic boron center interacts with the hydrogen on the silicon, which renders the Si-H bond polarized. We report here the intramolecular electrophilic activation of a Si-H bond by an ortho boryl group in o-(hydrosilyl)(dimesitylboryl)benzenes, which leads to (i) dehydrogenative condensation with alcohols and amines and (ii) mesityl-H ligand exchange between the silicon atom and the boron atom to form the o-(silyl)(hydroboryl)benzene intermediates. The o-(silyl)(hydroboryl)benzene intermediates undergo (i) hydroboration to carbonyl compounds and (ii) intramolecular B-H/C-H dehydrogenative cyclization to form the dibenzosilaborins.

Reversible C-C bond formation at a triply cyclometallated platinum(iv) centre.

The oxidation of the tribenzylphosphine derivative of the doubly cylcometallated platinum(ii) complex of diphenylpyridine, 1, with PhICl2 led, as a first step, to the formation of a highly electrophilic metal centre which attacked the benzyl phosphine to give a triply cyclometallated species as the arenium ion. The highly acidic arenium ion protonated unreacted starting 1, a reaction that could be supressed by the addition of water, and gave the neutral species 2(t). Octahedral complex 2(t) was induced to reductively couple, with two five-membered rings coupling to give square planar complex 5 containing a nine-membered ring. The crystal structure of 5 showed the nine-membered ring to span trans across the square planar metal accompanied by considerable distortion: the P-Pt-N bond angle is 155.48(5)°. Oxidation of 5 with PhICl2 resulted in the addition of two chlorides and a change of the nine-membered ring ligand coordination to cis at an octahedral centre, still with considerable distortions: the P-Pt-N bond angle in the crystal structure of 6 is 99.46(5)°. Treatment of 2(t) with AgBF4 also induced a coupling to give a nine-membered ring, and the fluxional three coordinate complex 7. A mono-methylated version of 1, Me-1, was prepared and similar reactions were observed. The presence of the methyl group allowed us to observe selectivity in the coupling reaction to give the nine-membered ring, with two products (a-Me-7 and b-Me7) being initially formed in the ratio 7 : 1. The concentrations of two products changed with time giving a final ratio of 1 : 8 at room temperature (half-life 48 hours), the equilibration being made possible by a reversible C-C bond forming reaction. Reaction of complexes 7 with CO or hydrogen left the nine-membered ring intact, though oxidative degradation resulted in decomplexation of the phosphine donor, accompanied by formation of a P[double bond, length as m-dash]O group.

Theoretical insights into the sites and mechanisms for base catalyzed esterification and aldol condensation reactions over Cu.

Condensation and esterification are important catalytic routes in the conversion of polyols and oxygenates derived from biomass to fuels and chemical intermediates. Previous experimental studies show that alkanal, alkanol and hydrogen mixtures equilibrate over Cu/SiO2 and form surface alkoxides and alkanals that subsequently promote condensation and esterification reactions. First-principle density functional theory (DFT) calculations were carried out herein to elucidate the elementary paths and the corresponding energetics for the interconversion of propanal + H2 to propanol and the subsequent C-C and C-O bond formation paths involved in aldol condensation and esterification of these mixtures over model Cu surfaces. Propanal and hydrogen readily equilibrate with propanol via C-H and O-H addition steps to form surface propoxide intermediates and equilibrated propanal/propanol mixtures. Surface propoxides readily form via low energy paths involving a hydrogen addition to the electrophilic carbon center of the carbonyl of propanal or via a proton transfer from an adsorbed propanol to a vicinal propanal. The resulting propoxide withdraws electron density from the surface and behaves as a base catalyzing the activation of propanal and subsequent esterification and condensation reactions. These basic propoxides can readily abstract the acidic Cα-H of propanal to produce the CH3CH(-)CH2O* enolate, thus initiating aldol condensation. The enolate can subsequently react with a second adsorbed propanal to form a C-C bond and a β-alkoxide alkanal intermediate. The β-alkoxide alkanal can subsequently undergo facile hydride transfer to form the 2-formyl-3-pentanone intermediate that decarbonylates to give the 3-pentanone product. Cu is unique in that it rapidly catalyzes the decarbonylation of the C2n intermediates to form C2n-1 3-pentanone as the major product with very small yields of C2n products. This is likely due to the absence of Brønsted acid sites, present on metal oxide catalysts, that rapidly catalyze dehydration of the hemiacetal or hemiacetalate over decarbonylation. The basic surface propoxide that forms on Cu can also attack the carbonyl of a surface propanal to form propyl propionate. Theoretical results indicate that the rates for both aldol condensation and esterification are controlled by reactions between surface propoxide and propanal intermediates. In the condensation reaction, the alkoxide abstracts the weakly acidic hydrogen of the Cα-H of the adsorbed alkanal to form the surface enolate whereas in the esterification reaction the alkoxide nucleophilically attacks the carbonyl group of a vicinal bound alkanal. As both condensation and esterification involve reactions between the same two species in the rate-limiting step, they result in the same rate expression which is consistent with experimental results. The theoretical results indicate that the barriers between condensation and esterification are within 3 kJ mol-1 of one another with esterification being slightly more favored. Experimental results also report small differences in the activation barriers but suggest that condensation is slightly preferred.

Alkali metal ion catalysis and inhibition in alkaline ethanolysis of O-Y-substituted-phenyl O-phenyl thionocarbonates: contrasting M+ ion effects upon changing electrophilic centre from C=O to C=S

Pseudo-first-order rate constants (kobsd) were measured for nucleophilic substitution reactions of O-Y-substituted-phenyl O-phenyl thionocarbonates (4a–4h) with alkali metal ethoxides (EtOM, M = Li, Na, or K) in anhydrous ethanol at 25.0 ± 0.1 °C. Plots of kobsd vs. [EtOM] exhibited upward curvature for the reaction of O-4-nitrophenyl O-phenyl thionocarbonate (4a) with EtOK in the presence of 18-crown-6-ether (18C6), but showed downward curvature for the reaction with EtOLi, indicating that the reaction is catalyzed by the 18C6-crowned K+ ion, but is inhibited by Li+ ion. The kobsd values were dissected into kEtO− and kEtOM, the second-order rate constant for the reaction with dissociated EtO− and ion-paired EtOM, respectively. The reactivity of EtOM toward 4a increases in the order EtOLi < EtONa < EtO− < EtOK < EtOK/18C6, which is in contrast to that reported previously for the corresponding reaction of 4-nitrophenyl phenyl carbonate (a C=O analogue of 4a), e.g., EtO− ≈ EtOK/18C6 < EtOLi < EtONa < EtOK. The reaction mechanism, including the transition-state model and the origin of the contrasting reactivity patterns found for the reactions of the C=O and C=S compounds, are discussed.

Stable Di- and Tri-coordinated Carbon(II) Supported by an Electron-Rich β-Diketiminate Ligand.

Complexes of the ubiquitous β-diketiminates (NacNac) ligands have been reported with most elements of the periodic table, including Group 14 Si, Ge, Sn, and Pb. The striking absence of carbon representatives has been attributed to the extreme electrophilicity of the putative C-NacNac adducts. An electron enriched 2,4-(dimethylamino)diketiminato backbone is described, which allowed for the synthesis and isolation of such stable pyrimidin-1,3-diium and pyrimidinium-2-ylidene salts. Structural and preliminary reactivity studies are reported, including an air-stable gold complex. An unforeseen original class of stable N-heterocyclic carbenes and, more generally, the potential of electron-rich NacNac patterns for taming highly electrophilic centers are showcased.

Activation of surface oxygen sites on an iridium-based model catalyst for the oxygen evolution reaction

The oxygen evolution reaction (OER) is of prime importance in multiple energy storage devices; however, deeper mechanistic understanding is required to design enhanced electrocatalysts for the reaction. Current understanding of the OER mechanism based on oxygen adsorption on a metallic surface site fails to fully explain the activity of iridium and ruthenium oxide surfaces, and the drastic surface reconstruction observed for the most active OER catalysts. Here we demonstrate, using La2LiIrO6 as a model catalyst, that the exceptionally high activity found for Ir-based catalysts arises from the formation of active surface oxygen atoms that act as electrophilic centres for water to react. Moreover, with the help of transmission electron microscopy, we observe drastic surface reconstruction and iridium migration from the bulk to the surface. Therefore, we establish a correlation between surface activity and surface stability for OER catalysts that is rooted in the formation of surface reactive oxygen.

Cyanide anion sensing mechanism of 1,3,5,7-tetratolyl aza-BODIPY: Intramolecular charge transfer and partial configuration change

The cyanide anion sensing mechanism of 1,3,5,7-tetratolyl aza-BODIPY (1) has been rigorously investigated using density functional theory and time dependent-density functional theory methods. Mulliken charge distribution and Natural Bond Orbital analysis reveals that cyanide addition may occur at both electrophilic centers with equal probability. The molecular orbital analysis reveals that first excited state (S1) of 1 is a local excited state with π-π∗ transition, whereas for 2 (the cyano form of 1), S1, a charge-separation state, is found to be responsible for the intramolecular charge transfer (ICT) process which in conjunction with partial configuration change induces fluorescence stimulation in 2.