DFT-calculated structure of protonated tetraphenyl p - tert -butylcalix[4]arene tetraketone

Using DFT calculations, two of the most probable structures (A, B) of the tetraphenyl p-tert-butylcalix[4]arene tetraketone·H₃O⁺ cationic complex species were derived. The hydroxonium ion H₃O⁺, placed in the coordination cavity formed by the calix[4]arene lower-rim groups, is bound by strong hydrogen bonds to the phenoxy oxygen atoms of the calix[4]arene ligand (structures A, B) and also to one carbonyl oxygen (structure B).     

DFT-calculated structure of protonated tetraphenyl <Emphasis Type="Italic">p</Emphasis>-<Emphasis Type="Italic">tert</Emphasis>-butylcalix[4]arene tetraketone

Using DFT calculations, two of the most probable structures (A, B) of the tetraphenyl p-tert-butylcalix[4]arene tetraketone·H₃O⁺ cationic complex species were derived. The hydroxonium ion H₃O⁺, placed in the coordination cavity formed by the calix[4]arene lower-rim groups, is bound by strong hydrogen bonds to the phenoxy oxygen atoms of the calix[4]arene ligand (structures A, B) and also to one carbonyl oxygen (structure B). Correspondence: Emanuel Makrlík, Faculty of Applied Sciences, University of West Bohemia, Pilsen, Czech Republic.     

Contribution to the Protonation of a Calix[4]arene: DFT Calculated Structure of Protonated p-tert -Butylcalix[4]arenetetrakis( N , N -diethylacetamide)

By using DFT calculations, the most probable structure of the p-tert-butylcalix[4]arenetetrakis(N,N-diethylacetamide) · H₃O⁺ complex species was derived. In this complex, the hydroxonium ion H₃O⁺ is predominantly bound by strong hydrogen bonds to three phenoxy oxygens of the ligand and partly to the remaining phenoxy oxygen atom by two somewhat weaker hydrogen bonds. Besides, the H₃O⁺ cation is also bound to two carbonyl oxygens of the mentioned ligand by further two weaker hydrogen bonds.     

Contribution to the Protonation of a Calix[4]arene: DFT Calculated Structure of Protonated <Emphasis Type="Italic">p-tert</Emphasis>-Butylcalix[4]arenetetrakis(<Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-diethylacetamide)

Summary. By using DFT calculations, the most probable structure of the p-tert-butylcalix[4]arenetetrakis(N,N-diethylacetamide) · H₃O⁺ complex species was derived. In this complex, the hydroxonium ion H₃O⁺ is predominantly bound by strong hydrogen bonds to three phenoxy oxygens of the ligand and partly to the remaining phenoxy oxygen atom by two somewhat weaker hydrogen bonds. Besides, the H₃O⁺ cation is also bound to two carbonyl oxygens of the mentioned ligand by further two weaker hydrogen bonds.     

A Proton Complex of p-tert-Butylcalix[4]arene-tetrakis(N,N-dimethylthioacetamide): NMR Evidence and Probable Structure

Using ¹H and ¹³C NMR together with density functional theoretical (DFT) calculations, it is shown that p-tert-butylcalix[4]arene-tetrakis(N,N-dimethylthioacetamide) (1) forms a stable equimolecular complex with proton in the form of hydroxonium ion in nitrobenzene-d ₅. Protons were offered by hydrogen bis(1,2-dicarbollyl) cobaltate (HDCC) and converted to hydroxonium ions by traces of water. The complex 1·H₃O⁺ adopts a slightly asymmetric but rapidly motionally averaged conformation, which is distinctly more cone-like than ligand 1. The hydroxonium ion H₃O⁺ is bound partly to thiocarbonyl sulphur atoms and partly to phenoxy oxygen atoms of 1 by strong hydrogen bonds and other electrostatic interactions.

     

Protonation of electroneutral p-tert-butylcalix[4]arenetetraacetic acid

Abstract  

Using ¹H NMR spectroscopy together with density functional theoretical calculations, it is shown that electroneutral p-tert-butylcalix[4]arenetetraacetic acid forms an equimolar complex with a proton in the form of the H₃O⁺ ion in nitrobenzene-d ₅. Protons were offered by hydrogen bis(1,2-dicarbollyl)cobaltate and converted to hydroxonium ions by traces of water. In the resulting complex, the H₃O⁺ cation is bound by strong hydrogen bonds to two phenoxy oxygen atoms of the parent calix[4]arene ligand and to one carbonyl oxygen of the corresponding COOH group of this ligand.     

Protonation of Tetrapropoxy-4-tert-butylcalix[4]arene: NMR Study of Interaction and Probable Structures of the Product

Using ¹H and ¹³C NMR spectroscopy, the interaction of tetrapropoxy-p-tert-butyl-calix[4]arene (1) with H₃O⁺ ions produced by hydrogen bis(1,2-dicarbollyl) cobaltate (HDCC) and traces of water was studied in nitrobenzene-d ₅. It was shown that 1 readily forms an equimolecular complex with H₃O⁺. The equilibrium constant K of its formation is 2.6 at 296 K. Exchange between bound and free 1 is fast even under mild excess of HDCC, the correlation time τ_ex being about 0.13 ms. NMR shows that H₃O⁺ is bound to the aryl-oxygen atoms and this binding forces the calixarene cup to adopt a more open and symmetrical conformation. This conclusion is in full accord with high precision quantum DFT calculations which find one structure of the complex corresponding to a global energy minimum, in which the H₃O⁺ ion is bound to three of the oxygen atoms by strong hydrogen bonds and to the remaining oxygen by two weaker hydrogen bonds. The calixarene part is forced into a C₄ symmetrical opened form.

When stored for weeks, the complex gradually transforms into other forms, most probably its hydrates, according to spectral evidence and DFT calculations.     

Experimental evidence, stability, and the most probable structure of protonated p-tert-butylcalix[4]arenetetrakis(N,N-dimethylacetamide)

Abstract  

From extraction experiments and γ-activity measurements, the extraction constant corresponding to the equilibrium H₃O⁺(aq) + 1·Na⁺(nb) \leftrightarrows \leftrightarrows 1·H₃O⁺ (nb) + Na⁺ (aq) taking place in the two-phase water–nitrobenzene system (1 = p-tert-butylcalix[4]arenetetrakis(N,N-dimethylacetamide); aq = aqueous phase, nb = nitrobenzene phase) was evaluated as log K _ex (H₃O⁺, 1·Na⁺) = −0.1 ± 0.1. Further, the stability constant of the 1·H₃O⁺ complex in water-saturated nitrobenzene was calculated for a temperature of 25 °C as log β _nb (1·H₃O⁺) = 10.9 ± 0.2. By using quantum mechanical DFT calculations, the most probable structure of the 1·H₃O⁺ cationic complex species was derived. In this complex, the hydroxonium ion H₃O⁺ is bound partly to one phenoxy oxygen atom and partly to two carbonyl oxygens of 1 by strong hydrogen bonds and obviously by other electrostatic interactions.     

Protonated Tetramethyl <Emphasis Type="Italic">p</Emphasis>-<Emphasis Type="Italic">tert</Emphasis>-Butylcalix[4]arene Tetraketone: NMR Evidence and Probable Structures

Summary. Both NMR spectra in nitrobenzene-d ₅ and high-precision quantum mechanical DFT calculations proved that tetramethyl p-tert-butylcalix[4]arene tetraketone binds hydroxonium cation H₃O⁺ quite strongly to form an equimolar complex. Three different structures of the resulting complex species were indicated by the NMR spectra and the DFT calculations.     

Protonated Tetramethyl p - tert -Butylcalix[4]arene Tetraketone: NMR Evidence and Probable Structures

Both NMR spectra in nitrobenzene-d ₅ and high-precision quantum mechanical DFT calculations proved that tetramethyl p-tert-butylcalix[4]arene tetraketone binds hydroxonium cation H₃O⁺ quite strongly to form an equimolar complex. Three different structures of the resulting complex species were indicated by the NMR spectra and the DFT calculations.     

Theoretical study on the protonation of cucurbit[6]uril

Abstract  

The most probable structures of the cucurbit[6]uril·H₃O⁺ and cucurbit[6]uril·(H₃O⁺)₂ cationic complex species have been derived by quantum mechanical DFT calculations. In these two complexes, each of the H₃O⁺ ions is bound by three strong linear hydrogen bonds to three carbonyl oxygen atoms of the parent macrocycle.     

Protonated Co(III) Complexes with Ethylenediaminetetraacetic and S-Proline-N-Mono-3-propionic Acids. Crystal Structures of (H3O)[Co(HEdta)(CN)] · H2O and [Co(Promp)(HPromp)] · H2O

Crystal structures of [Co(Promp)(Hpromp)] · H₂O (I) (where Promp and Hpromp are deprotonated and monoprotonated anions of S-proline-N-mono-3-propionic acid) and (H₃O)[Co(Hedta)(CN)] · H₂O (II) (where HEdta is monoprotonated anion of ethylenediaminetetraacetic acid) are determined by X-ray diffraction method. The Co coordination octahedron in compound I is formed by two N atoms in trans-positions and by four O atoms of two tridentate ligands, i.e., anions of H₂Promp acid, one of which is fully deprotonated, while the other one has protonated carboxyl group of a six-membered aminopropionate metal cycle. Neutral [Co(Promp)(Hpromp)] complexes and water molecules are united by hydrogen bonds into chains along 2₁ screw axis. Crystals II consist of the complex anions [Co(Hedta)(CN)]⁻, hydroxonium cations, and water molecules. The Co coordination octahedron includes two N atoms and three O atoms of ion of ethylenediaminetetraacetic acid, whose one acetate group is not coordinated but protonated; cyanide ion lies in the NCoN plane. Crystals II contain two types of H₃O⁺ ions that are involved in hydrogen bonds in different way.__________Translated from Koordinatsionnaya Khimiya, Vol. 31, No. 8, 2005, pp. 596–605.Original Russian Text Copyright © 2005 by Poznyak, Burshtein.     

Self‐assembly properties of Salamo‐type trinuclear Cu(II) and Co(II) complexes based on the regulation of H+/OHˉ

A novel naphthalenediol‐based bis(salamo)‐type tetraoxime compound (H₄L) was designed and synthesized. Two new supramolecular complexes, [Cu₃(L)(μ‐OAc)₂] and [Co₃(L)(μ‐OAc)₂(MeOH)₂]·4CHCl₃ were synthesized by the reaction of H₄L with Cu(II) acetate dihydrate and Co(II) acetate dihydrate, respectively, and were characterized by elemental analyses and X‐ray crystallography. In the Cu(II) complex, Cu1 and Cu2 atoms located in the N₂O₂ sites, and are both penta‐coordinated, and Cu3 atom is also penta‐coordinated by five oxygen atoms. All the three Cu(II) atoms have geometries of slightly distorted tetragonal pyramid. In the Co(II) complex, Co1 and Co3 atoms located in the N₂O₂ sites, and are both penta‐coordinated with geometries of slightly distorted triangular bipyramid and distorted tetragonal pyramid, respectively, while Co2 atom is hexa‐coordinated by six oxygen atoms with a geometry of slightly distorted octahedron. These self‐assembling complexes form different dimensional supramolecular structures through inter‐ and intra‐molecular hydrogen bonds. The coordination bond cleavages of the two complexes have occurred upon the addition of the H⁺, and have reformed again via the neutralization effect of the OH^?. The changes of the two complexes response to the H⁺/OH^? have observed in the UV–Vis and ¹H NMR spectra.     

Structure and coordination environment of the zinc complex with vanillin of double-stranded helix

The structure and coordination environment of unusually double-stranded helix of complex [Zn(C₈H₇O₃)₂(H₂O)₂] are studied experimentally and by the density functional theory (DFT) method. The Zn²⁺ ion coordinates six oxygen atoms of deprotonated vanillin and water molecules forming an octahedron. The intermolecular hydrogen bonds and π interactions of the vanillin fragments contributed to the formation of the double-stranded helical supramolecular structure in the crystal. Counterpoise geometric parameters of the calculation agree with the crystal structure determined by experiment. The stabilization energy between the donor and acceptor obtained from an analysis of natural bond orbitals of the indicated six ligand oxygen atoms act as electron donor to Zn²⁺ ion. The results of the density functional theory on the complex demonstrate that the different coordinated oxygen atoms, which have different chemical environment, distort the coordination octahedron. The text was submitted by the authors in English.     

Crystal structure of a calcium(II) complex with pyrazine-2,3-dicarboxylate,nitrate and water ligands

The structure of catena-[tris(aquo-O)(nitrato-O,O′)(µ-hydrogen pyrazine-2,3-dicarboxylato-O,N–O′,N′)calcium(II)][tetra(aquo-O)(μ-hydrogen pyrazine-2,3-dicarboxylato-O,N–O′,N′) calcium(I)] nitrate, {Ca[H(2,3-PZDC)](H₃O)₃(NO₃)}{Ca[H(2,3-PZDC)](H₂O)₄}⁺ (NO₃)^?, is composed of molecular ribbons in which calcium atoms are bridged by both N,O-bonding moieties of singly deprotonated ligand molecules. The hydrogen atom donated by one carboxylic group is linked by a short intramolecular hydrogen bond of 2.37 Å to an oxygen atom of the second carboxylic group of the same ligand. Two crystallographically independent Ca(II) ions exhibit different coordination modes. One is coordinated by two bonding moieties of the bridging ligand molecules, three water oxygen atoms and two oxygen atoms of a nitrate ligand. The other calcium ion is chelated by two bonding moieties donated by the bridging ligand molecules and four water oxygen atoms, forming a positively charged assembly with a nitrate anion located nearby. The coordination polyhedron of the first calcium ion is a strongly deformed bicapped pentagonal bipyramid with nine-coordinated atoms; the second calcium ion is also in a strongly deformed pentagonal bipyramid with one apex on one side of the equatorial plane and two apices on the other. Coordinated water oxygen atoms act as donors in a hydrogen-bond network.     

New Type of Neutral Binuclear Spin-Crossover Complex of Iron(III) with Twist of Two Disulfide Bridges as a Product of Electrochemical Oxidation of [FeIII(5Cl-thsa)2]− Anions

As a result of the electrochemical oxidation process, the [Fe^III(5Cl-thsa)₂]⁻ spin-crossover (SCO) anion with N₂S₂O₂ coordination sphere transforms into N₄O₂-coordinated Fe^III SCO neutral binuclear complex 2 with twist of two disulfide bridges. Each dimeric complex is a binuclear double-stranded helicate with similar chirality of both Fe centers. The crystal structure of the complex 2 ⋅ 3H₂O at 100 K has a monoclinic C2/c space group and contains large cavities (about 21.5 % of the unit cell volume) half-filled by 3 water molecules per one dimer. The N₄O₂ coordination of iron(III) with two oxygen atoms (−O⁻) of phenoxy groups, two imine-type (−N_im=) nitrogen atoms of azomethine groups, one amidrazone-type (=N_amidH) nitrogen atom and one ionized terminal group (−N_ionizH) of nitrogen has not been observed in CCDC so far. The oxidation state of the iron atoms in the dimeric complex was confirmed by ⁵⁷Fe Mössbauer spectroscopy on 90 % enriched ⁵⁷Fe sample. Mössbauer spectra and dc magnetic measurements demonstrated the partial HS-HS→LS-LS SCO in the 185–225 K temperature range. The details of the structure of complex 2 and the features of its magnetic properties were refined by theoretical analysis based on DFT calculations. The B3LYP* functional correctly predicting the energy of the spin-crossover process was revealed.     

Exploring the Interactions of Atomic Oxygen on Silver Clusters with Hydrogen

The interactions between Ag_nO^-(n=1-8) and H₂ (or D₂) were explored by combination of the mass spectroscopy experiments and density function theory (DFT) calculations. The experiments found that all oxygen atoms in Ag_nO^-(n=1-8) are inert in the interactions with H₂ or D₂ at the low temperature of 150 K, which is in contrast to their high reactivity with CO under the same condition. These observations are parallel with the preferential oxidation (PROX) of CO in excess hydrogen catalyzed by dispersed silver species in the condensed phase. Possible reaction paths between Ag_nO^-(n=1-8) and H₂ were explored using DFT calculations. The results indicated that adsorption of H₂ on any site of Ag_nO^-(n=1-8) is extremely weak, and oxidation of H₂ by any kind of oxygen in Ag_nO^-(n=1-8) has an apparent barrier strongly dependent on the adsorption style of the "O". These experiments and theoretical results about cluster reactions provided molecule-level insights into the activity of atomic oxygen on real silver catalysts.     

Theoretical study on the protonation of bambus[6]uril

Abstract  

Quantum mechanical density functional theory (DFT) calculations were used to derive the most probable structures of the bambus[6]uril·H₃O⁺ and bambus[6]uril·(H₃O⁺)₂ cationic complex species. In these two complexes, each of the considered H₃O⁺ ions is bound by three strong linear hydrogen bonds to the three corresponding carbonyl oxygens of the parent macrocyclic receptor.     

Water-rich molybdotellurates: Preparation and crystal structure of Li6[TeMo6O24] · 18 H2O and Li6[TeMo6O24] · Te(OH)6 · 18 H2O

Li₆[TeMo₆O₂₄] · 18 H₂O is triclinic (space group P1 , a = 1 041.7(1), b = 1 058.6(1), c = 1 070.8(1) pm, α = 61.08(1), β = 60.44(1), γ = 73.95(1)°). Single crystal X-ray structure analysis (Z = 1, 295 K, 317 parameters, 3 973 reflections, R_g = 0.0250) revealed an infinite branched chain of edge-sharing Li coordination polyhedra to be the prominent structural feature. One of the four crystallographically independent Li⁺ is coordinated octahedrally. The coordination polyhedra of the remaining Li⁺ are distorted trigonal bipyramids. Only three unique oxygen atoms (O(9), O(10), O(12)) of the centrosymmetric [TeMo₆O₂₄]^6? anion are bound to Li⁺. The further positions in the coordination spheres of the Li⁺ are occupied by water molecules. Intermolecular hydrogen bonds involve mainly oxygen atoms of the [TeMo₆O₂₄]^6? anion as nearly equivalent proton acceptors without regard to their different bonding modes to Te and Mo, respectively. Li₆[TeMo₆O₂₄] · Te(OH)₆ · 18 H₂O crystallizes monoclinically in space group P2₁/n with Z = 4, a = 994.1(3), b = 2 344.8(10), c = 1 764.9(4) pm, and β = 91.36(4)°. Single crystal structure analysis with least squares refinement of 627 parameters (5 900 reflections, 295 K) converged to R_g = 0.0324. There are six unique Li⁺ cations. The coordination polyhedra of Li(1), Li(2), Li(3), and Li(4) are linked by common edges to yield an eight membered centrosymmetric strand. The coordination polyhedra of the remaining two Li⁺ sites (Li(5), Li(6)) are connected to a dimeric unit via a common corner. All oxygen atoms of the Te(OH)₆ molecule are involved in the coordination of Li⁺. However, only three oxygen atoms (O(13), O(18), O(23)) of the [TeMo₆O₂₄]^6? anion which lacks crystallographic symmetry are involved in the coordination of Li⁺. The oxygen atoms of the anion act as proton acceptors in hydrogen bonds of predominantly medium strength. Te(OH)₆ molecules and [TeMo₆O₂₄]^6? anions connected by strong hydrogen bonds form an infinite chain.     

First‐ and second‐ sphere coordination of the uranyl ion by bis­[2‐(2‐hydroxy­phenoxy)­ethoxy]­ethane

Uranyl nitrate hexahydrate reacts with bis­[2‐(2‐hydroxy­phenoxy)­ethoxy]­ethane (C₁₈H₂₂O₆), denoted LH₂ hereafter, in the presence of triethylamine to give ­triethylammonium aqua[2,2′‐(3,6‐dioxaoctane‐1,8‐diyldioxy)diphenolato‐κ²O,O′](nitrato‐κ²O,O′)dioxouranium(VI), (Et₃NH)[UO₂(H₂O)L(NO₃)], which possesses a symmetry plane. The uranyl ion is coordinated to the two phenoxide O atoms, a nitrate ion and a water mol­ecule (first sphere); the water mol­ecule is itself held in the crown ether chain by hydrogen‐bonding interactions, thus ensuring second‐sphere coordination by the ligand L.