Enthalpy-entropy correlations in reactions of 2,4-dinitrophenyl benzoate with phenols in the presence of potassium hydrogen carbonate and with potassium phenoxides in dimethylformamide

Temperature dependences of the relative reactivity of substituted phenols RC₆H₄OH in the presence of potassium hydrogen carbonate and of potassium phenoxides RC₆H₄O⁻K⁺ toward 2,4-dinitrophenyl benzoate in dimethylformamide were studied using the competitive reactions technique. Correlation analysis of the relative rate constants k _R/k _H and differences in the activation parameters (ΔΔH ^≠ and ΔΔS ^≠) of competitive reactions revealed the existence of two isokinetic series for each type of nucleophiles. The mechanism of transesterification was interpreted in terms of an approach based on analysis of the effect of substituent in the nucleophile on the activation parameters.     

Catalytic Mechanism of the Arylsulfatase Promiscuous Enzyme from Pseudomonas Aeruginosa

To elucidate the working mechanism of the “broad substrate specificity” by the Pseudomonas aeruginosa aryl sulfatase (PAS) enzyme, we present here a full quantum chemical study performed at the density functional level. This enzyme is able to catalyze the hydrolysis of the original p‐nitrophenyl‐sulfate (PNPS) substrate and the promiscuous p‐nitrophenyl‐phosphate (PNPP) one with comparable reaction kinetics. Based on the obtained results, a multistep mechanism including activation of the nucleophile, the nucleophilic attack, and the cleavage of the S? O (P? O) bond is proposed. Regarding the phosphate monoester, the results indicate that only some steps of the promiscuous reaction are identical to those in the native process. Differences concern mainly the last step in which the His115 residue acts as a general base to accept the proton by the O atom of the FGly51 in the PNPS, whereas in PNPP, the Asp317 protonated residue works as a general acid to deliver a proton by a water molecule to the oxygen atom of the C? O bond. The shapes of the relative potential‐ energy surface (PES) are similar in the two examined cases but the rate‐determining step is different (nucleophile attack vs. nucleophile activation). The influence of the dispersion contributions on the investigated reactions was also taken into account.     

Hydrogen‐bonded supramolecular motifs in 2‐amino‐4,6‐dimethoxypyrimidinium picrate and pyrimethaminium picrate dimethyl sulfoxide solvate

In the crystal structures of 2‐amino‐4,6‐dimethoxypyrimidinium 2,4,6‐trinitrophenolate (picrate), C₆H₁₀N₃O₂⁺·C₆H₂N₃O₇⁻, (I), and 2,4‐diamino‐5‐(4‐chlorophenyl)‐6‐ethylpyrimidin‐1‐ium (pyrimethaminium or PMN) picrate dimethyl sulfoxide solvate, C₁₂H₁₄ClN₄⁺·C₆H₂N₃O₇⁻·C₂H₆OS, (II), the 2‐amino‐4,6‐dimethoxypyrimidine and PMN cations are protonated at one of the pyrimidine N atoms. The picrate anion interacts with the protonated cations through bifurcated N—H...O hydrogen bonds, forming R₂¹(6) and R₁²(6) ring motifs. In (I), Z′ = 2. In (II), two inversion‐related PMN cations are connected through a pair of N—H...N hydrogen bonds involving the 4‐amino group and the uncharged N atom of the pyrimidine ring, forming a cyclic hydrogen‐bonded R₂²(8) motif. In addition to the pairing, the O atom of the dimethyl sulfoxide solvent molecule bridges the 2‐amino and 4‐amino groups on both sides of the paired bases, resulting in a self‐complementary …DADA… array of quadruple hydrogen‐bonding patterns.     

N‐{3‐[(2‐Ammonioethyl)amino]propyl}ethane‐1,2‐diaminium tris(trifluoromethanesulfonate): a salt of a folded triply protonated tetramine

The structure of a trifluoromethanesulfonate salt of a nontypical triply protonated linear tetramine, C₇H₂₃N₄³⁺·3CF₃SO₃⁻, with a layered crystal structure is presented. One N atom remains unprotonated. The conformation of the cation is enforced by intra‐ and intermolecular hydrogen bonds. The crystal structure is built of ca 10 Å deep layers, within which cations and anions are hydrogen bonded. Each layer is only weakly bound to its neighbours. This study shows a rare example of an unsymmetrically protonated polyamine and the relation between the lack of protonation, intramolecular hydrogen bonding and the conformation of the cation.     

Probing the reactivity of microhydrated α‐nucleophile in the anionic gas‐phase SN2 reaction

To probe the kinetic performance of microsolvated α‐nucleophile, the G2(+)_M calculations were carried out for the gas‐phase S_N2 reactions of monohydrated and dihydrated α‐oxy‐nucleophiles XO^?(H₂O)_{n = 1,2} (X = HO, CH₃O, F, Cl, Br), and α‐sulfur‐nucleophile, HSS^?(H₂O)_{n = 1,2}, toward CH₃Cl. We compared the reactivities of hydrated α‐nucleophiles to those of hydrated normal nucleophiles. Our calculations show that the α‐effect of monohydrated and dihydrated α‐oxy‐nucleophiles will become weaker than those of unhydrated ones if we apply a plot of activation barrier as a function of anion basicity. Whereas the enhanced reactivity of monohydrated and dihydrated ROO^? (R = H, Me) could be observed if compared them with the specific normal nucleophiles, RO^? (R = H, Me). This phenomena can not be seen in the comparisons of XO^?(H₂O)_{n = 1,2} (X = F, Cl, Br) with ClC₂H₄O^?(H₂O)_{n = 1,2}, a normal nucleophile with similar gas basicity to XO^?(H₂O)_{n = 1,2}. These results have been carefully analyzed by natural bond orbital theory and activation strain model. Meanwhile, the relationships between activation barriers with reaction energies and the ionization energies of α‐nucleophile are also discussed. © 2015 Wiley Periodicals, Inc.     

Hydrogen‐bonding patterns in pyrimethaminium dinitrate

The title compound, 2,4‐diamino‐5‐(4‐chloro­phen­yl)‐6‐ethyl­pyrimidine‐1,3‐diium dinitrate, C₁₂H₁₅ClN₄²⁺·2NO₃⁻, contains two crystallographically independent pyrimethamine (PMN) mol­ecules, which differ in the relative orientations of the pyrimidine and benzene rings and of the eth­yl substitutents. In both pyrimethamine mol­ecules, all the pyrimidine N atoms are protonated, unlike most related compounds, in which only one pyrimidine N atom is protonated. The two pyrimethamine moieties are bridged by a variety of N—H⋯O(nitrate) inter­actions, including some three‐centre hydrogen bonds.     

Ropinirole hydro­chloride,a dopamine agonist

Ropinirole hydro­chloride, or diethyl[2‐(2‐oxo‐2,3‐dihydro‐1H‐indol‐4‐yl)ethyl]ammonium chloride, C₁₆H₂₅N₂O⁺·Cl⁻, belongs to a class of new non‐ergoline dopamine agonists which bind specifically to D2‐like receptors with a selectivity similar to that of dopamine (D3 > D2 > D4). The N atom in the ethyl­amine side chain is protonated and there is a hydrogen bond between it and the Cl⁻ ion. In the crystal structure, two cations and two anions form inversion‐related cyclic dimers via N—H⋯Cl hydrogen bonds.     

Hydrogen bonding in the inner-salt zwitterion and in two different charged forms of 5,6-bis(2-pyridyl)pyrazine-2,3-dicarboxylic acid

5,6-Bis(2-pyridyl)­pyrazine-2,3-di­carboxyl­ic acid exists as an inner-salt zwitterion, 3-carboxy-5-(2-pyridinio)-6-(2-pyridyl)­pyrazine-2-carboxyl­ate, (Ia), C₁₆H₁₀N₄O₄. The adjacent pyridine and pyridinium rings are almost coplanar due to the presence of an intramolecular hydrogen bond involving the pyridine N atom and the NH H atom of the pyridinium group. In the crystal of (Ia), symmetry-related mol­ecules are hydrogen bonded via the carboxyl­ic acid OH group and one of the carboxyl­ate O atoms to form a polymer, which exhibits a channel-type structure. In the HCl, HClO₄ and HPF₆ salts, 6-­carboxy-5-carboxyl­ato­pyrazine-2,3-diyldi-2-pyridinium chloride 2.25-hydrate, (II), C₁₆H₁₁N₄O₄⁺·Cl⁻·2.25H₂O, 6-­carboxy-5-carboxyl­ato­pyrazine-2,3-diyldi-2-pyridinium perchlor­ate trihydrate, (IIIa), C₁₆H₁₁N₄O₄⁺·ClO₄⁻·3H₂O, and 6-car­boxy-5-carboxyl­ato­pyrazine-2,3-diyldi-2-pyridinium hexa­fluoro­phosphate trihydrate, (IIIb), C₁₆H₁₁N₄O₄⁺·PF₆⁻·3H₂O, both pyridine rings are protonated. In the perchlorate form, and in the isomorphous hexa­fluoro­phosphate form, the mol­ecule possesses C₂ symmetry, with has a symmetrical intramolecular hydrogen bond involving the adjacent carboxyl­ate and carboxyl­ic acid substituents. In the crystals of the chloride and perchlorate (or hexa­fluoro­phosphate) salts, hydrogen-bonded polymers are formed which are three-dimensional and one-dimensional, respectively.     

A novel two‐dimensional zinc(II) coordination polymer with 6‐mercaptonicotinic acid

The novel title Zn^II coordination polymer, poly[bis(μ‐6‐thioxo‐1,6‐dihydropyridine‐3‐carboxylato‐κ²S:O)zinc(II)], [Zn(C₆H₄NO₂S)₂]_n, consists of two crystallographically independent zinc centers and two 6‐mercaptonicotinate (Hmna⁻) ligands. Each Zn^II atom is four‐coordinated and lies at the center of a distorted tetrahedral ZnS₂O₂ coordination polyhedron, bridged by four Hmna⁻ ligands to form a two‐dimensional (4,4)‐network. Each Hmna⁻ ion acts as a bridging bidentate ligand, coordinating to two Zn^II atoms through the S atom and a carboxyl O atom. The metal centers reside on twofold rotation axes. The coordination mode of the S atoms and N—H...O hydrogen‐bonding interactions between the protonated N atoms and the uncoordinated carboxyl O atoms give the extended structure a wavelike form.     

A Unified Mechanism to Account for Manganese- or Ruthenium-Catalyzed Nitrile α-Olefinations by Primary or Secondary Alcohols: A DFT Mechanistic Study

Acceptorless dehydrogenative coupling (ADC) reactions generally involve a nucleophile (e.g., amine) as a coupling partner. Intriguingly, it has been reported that nitriles could also act as nucleophiles in ADC reactions, achieving the α-olefination of nitriles with primary or secondary alcohols by employing a manganese or ruthenium pincer complex as the catalyst, respectively. Although different mechanisms have been postulated for the two catalytic systems, the results of our DFT mechanistic study, reported herein, have allowed us to propose a unified mechanism to account for both nitrile α-olefinations. The reactions take place in four stages, namely alcohol dehydrogenation, nitrile activation to generate a nucleophilic metal species, coupling of an aldehyde or ketone with the metal species to form a C−C bond and to transfer a nitrile (C^α−)H atom to the carbonyl group, and dehydration by transferring the protonic (N−)H to the hydroxy group. A notable feature of the coupling stage is the activation of water or alcohol to give an intermediate featuring an OH⁻- or OR⁻-like group that activates a nitrile C^α−H bond. Moreover, the mechanism can even be applied to the base (KOtBu, modeled by the (KOtBu)₄ cluster)-catalyzed Knoevenagel condensation of nitriles with ketones, which further indicates the generality of the mechanism and the resemblance of the metal pincer complexes to the (KOtBu)₄ base. We expect these in-depth mechanistic insights and the finding of the resemblance of the metal pincer complexes to the (KOtBu)₄ cluster could assist the development of new ADC reactions.     

4‐Carboxypiperidinium 1‐carboxycyclobutane‐1‐carboxylate

The title salt, C₆H₁₂NO₂⁺·C₆H₇O₄⁻ or ISO⁺·CBDC⁻, is an ionic ensemble assisted by hydrogen bonds. The amino acid moiety (ISO or piperidine‐4‐carboxylic acid) has a protonated ring N atom (ISO⁺ or 4‐carboxypiperidinium), while the semi‐protonated acid (CBDC⁻ or 1‐carboxycyclobutane‐1‐carboxylate) has the negative charge residing on one carboxylate group, leaving the other as a neutral –COOH group. The –⁺NH₂– state of protonation allows the formation of a two‐dimensional crystal packing consisting of zigzag layers stacked along a separated by van der Waals distances. The layers extend in the bc plane connected by a complex network of N—H...O and O—H...O hydrogen bonds. Wave‐like ribbons, constructed from ISO⁺ and CBDC⁻ units and described by the graph‐set symbols C₃³(10) and R₃³(14), run alternately in opposite directions along c. Intercalated between the ribbons are ISO⁺ cations linked by hydrogen bonds, forming rings described by the graph‐set symbols R₆⁶(30) and R₄²(18). A detailed analysis of the structures of the individual components and the intricate hydrogen‐bond network of the crystal structure is given.     

Anilinium dihydrogen phosphate

The triclinic structure of the title compound, C₆H₈N⁺·H₂PO₄⁻, with three symmetry‐independent structural units (Z′ = 3), is formed of separate organic and inorganic layers alternating along the b axis. The building blocks of the inorganic layer are deformed H₂PO₄ tetrahedra assembled into infinite ladders by short and hence strong hydrogen bonds. The anilinium cations forming the organic layer are not hydrogen bonded to one another, but they are anchored by four N—H...O crosslinks between the dihydrogen phosphate chains of adjacent ladders. Two H atoms of each –NH₃ group then form one normal and one bifurcated N—H...O hydrogen bond to the P=O oxygens of two tetrahedra of one chain, while the third H atom is hydrogen bonded to the nearest O atom of an adjacent chain belonging to another dihydrogen phosphate ladder.     

Addition of carbon nucleophiles to arene-chromium complexes

The electrophilic reactivity of arenes coordinated to the chromium tricarbonyl unit has been developed into several distinct methods for coupling carbon nucleophiles with aromatic rings. Addition of the nucleophile produces stable η⁵-cyclohexadienyl chromium complexes which can be oxidized to induce loss of the endo hydrogen and the metal, overall nucleophilic substitution for hydrogen. Alternatively, the intermediate can be protonated and the resulting cyclohexa-1,3-diene can be detached from the chromium, effecting nucleophilic addition with reduction of one double bond. If a halogen (F, Cl) is present as a ring substituent, and if the nucleophile can migrate about the arene ligand, then loss of halide can occur parallel with classical nucleophilic aromatic substitution for halogen in electron-deficient haloarenes.With substituted arenes, the regioselectivity of addition becomes important and is often very high. Particularly useful are strong resonance donor substituents (RO-, R₂N-, F-) where selectivity for meta attack is high. Indole provides an excellent example of selective activation, as the six-membered ring complexes selectively and is then susceptible to nucleophilic substitution, predominantly at the 4 and 7 positions.Substitution for halogen is a somewhat limited process and depends upon the nature of the nucleophile. Very reactive nucleophiles add to unsubstituted positions and are often slow to isomerize to the ipso position from which loss of halide can occur.     

2,4‐Diamino‐6‐methyl‐1,3,5‐triazin‐1‐ium trifluoroacetate

Crystals of the title compound, C₄H₈N₅⁺·C₂F₃O₂⁻, are built up of singly protonated 2,4‐diamino‐6‐methyl‐1,3,5‐triazin‐1‐ium cations and trifluoroacetate anions. The CF₃ group of the anion is disordered. The oppositely charged ions interact via almost linear N—H...O hydrogen bonds, forming a CF₃COO⁻...C₄H₈N₅⁺ unit. Two units related by an inversion centre interact through a pair of N—H...N hydrogen bonds, forming planar (CF₃COO⁻...C₄H₈N₅⁺...C₄H₈N₅⁺·CF₃COO⁻) aggregates that are linked by a pair of N—H...O hydrogen bonds into chains running along the c axis.     

Nitropyrazoles 15. Synthesis and some transformations of 1-(2,4-dinitrophenyl)-4-methyl-3,5-dinitropyrazole

The method for preparation of 1-(2,4-dinitrophenyl)-4-methyl-3,5-dinitropyrazole has been developed. Due to the larger CH-acidity of 4-Me-group compared to 1,4-dimethyl-3,5-dinitropyrazole, 1-(2,4-dinitrophenyl)-4-methyl-3,5-dinitropyrazole is capable of reacting with substituted benzaldehydes to afford 4-[(E)-2-arylvinyl]-1-(2,4-dinitrophenyl)-3,5-dinitropyrazoles. Under the action of nucleophiles, dinitrophenyl group is detached from the former compounds leading to previously unknown N-unsubstituted 4-[(E)-2-arylvinyl]-3,5-dinitropyrazoles.     

Bis­(melaminium) dl‐malate tetrahydrate

The crystal structure of the title melaminium salt, bis(2,4,6‐tri­amino‐1,3,5‐triazin‐1‐ium) dl ‐malate tetrahydrate, 2C₃H₇N₆⁺·C₄H₄O₅²⁻·4H₂O, consists of singly protonated melaminium residues, dl ‐malate dianions and water mol­ecules. The melaminium residues are connected into chains by four N—H⃛N hydrogen bonds, and these chains form a stacking structure along the c axis. The dl ‐malate dianions form hydrogen‐bonded chains and, together with hydrogen‐bonded water mol­ecules, form a layer parallel to the (100) plane. The conformation of the malate ion is compared with an ab initio molecular‐orbital calculation. The oppositely charged moieties, i.e. the stacks of melaminium chains and hydrogen‐bonded dl ‐malate anions and water mol­ecules, form a three‐dimensional polymeric structure, in which N—H⃛O hydrogen bonds stabilize the stacking.     

Helical catena‐poly[[tris(1H‐benzimidazole‐κN3)cobalt(II)]‐μ‐maleato‐κ3O,O′:O′′]

The crystal structure of the title compound, [Co(C₄H₂O₄)(C₇H₆N₂)₃]_n, consists of polymeric chains of the Co^II complex. Two maleate dianions and three benz­imidazole ligands coordinate to the Co^II atom with a distorted octahedral geometry. The maleate dianions bridge neighbouring Co^II atoms via both terminal carboxylic acid groups, one of which is monodentate and the other bidentate, to form a helical structure of alternating maleate dianions and Co^II atoms, with a pitch height of 9.2667 (17) Å. The absolute structure has been determined, and the crystal contains only right‐handed helices. Intrahelical N—H⋯O hydrogen bonds stabilize the helical structure, while interhelical N—H⋯O hydrogen bonds link neighbouring helices to form the supramolecular structure.     

Synthesis of 4,6-dinitro-3-R-benzo[d]isoxazoles and their transformations under the action of nucleophiles

A new procedure was developed for the preparation of 4,6-dinitro-3-R-benzo[d]isoxazoles (R are derivatives of the aldehyde group) based on 2,4,6-trinitrophenylacetaldehyde. The resulting compounds are characterized by the regiospecific substitution of the nitro group at position 4 under the action of anionic nucleophiles RS^–, RO^–, F^–, or N₃ ^–, which allowed the development of a new method for the preparation of previously unknown 4-Nu-6-nitro-3-R-benzo[d]isoxazoles (Nu is the residue of a nucleophile). At the same time, oxidative nucleophilic substitution under the action of anions of some -dicarbonyl compounds leads to the replacement of the hydrogen atom at position 7 with the corresponding C-nucleophiles.     

Ambident Nucleophilic Substitution: Understanding Non-HSAB Behavior through Activation Strain and Conceptual DFT Analyses

The ability to understand and predict ambident reactivity is key to the rational design of organic syntheses. An approach to understand trends in ambident reactivity is the hard and soft acids and bases (HSAB) principle. The recent controversy over the general validity of this principle prompted us to investigate the competing gas-phase S_N2 reaction channels of archetypal ambident nucleophiles CN⁻, OCN⁻, and SCN⁻ with CH₃Cl (S_N2@C) and SiH₃Cl (S_N2@Si), using DFT calculations. Our combined analyses highlight the inability of the HSAB principle to correctly predict the reactivity trends of these simple, model reactions. Instead, we have successfully traced reactivity trends to the canonical orbital-interaction mechanism and the resulting nucleophile–substrate interaction energy. The HOMO–LUMO orbital interactions set the trend in both S_N2@C and S_N2@Si reactions. We provide simple rules for predicting the ambident reactivity of nucleophiles based on our Kohn–Sham molecular orbital analysis.