Dinuclear calcium complex with weakly NH...O hydrogen-bonded sulfonate ligands

The novel intramolecularly NH...O hydrogen-bonded Ca(II)-aryl sulfonate complex, [Ca2(SO3-2-t-BuCONHC6H4)2(H2O)4]n(2-t-BuCONHC6H4SO3)2n (1), sulfonate anion, (HNEt3)(SO3-2-t-BuCONHC6H4) (2a), (PPh4)(SO3-2-t-BuCONHC6H4) (2b), (n-Bu4N)(SO3-2-t-BuCONHC6H4) (2c), and sulfonic acid, 2-t-BuCONHC6H4SO3H (3), were synthesized. The structures of 1, 2a, and 2b depict the presence of the formation of NH...O hydrogen bonds between the amide NH and S-O oxygen for a series of compounds as determined by IR and 1H NMR analyses both in the solid state and in the solution state. Thus, the NH...O hydrogen bonds with neutral amide groups are available for investigation of the electronic state of the O- anion. The combined data from the IR and 1H NMR spectra indicate that the sulfonic acid, sulfonate anion, and Ca(II) complex have a substantially weak intramolecular NH...O hydrogen bond between the SO3 oxygen and amide NH. In the detailed comparison with the intense NH...O hydrogen bonds for the carboxylate, weak NH...O hydrogen bonds for sulfonate is due to the strong conjugation of the SO3- group with the lower nucleophilicity.     

Stabilization of calcium- and terbium-carboxylate bonds by NH...O hydrogen bonds in a mononuclear complex: a functional model of the active site of calcium-binding proteins

Novel benzoic acid ligands with bulky amide groups at the ortho position, 2,6-(MeCONH)(2)C(6)H(3)CO(2)H (1) and 2,6-(t-BuCONH)(2)C(6)H(3)CO(2)H (2), and their tris- and tetrakis(carboxylate) complexes with Ca(II) and Tb(III) ions, (NEt(4))(2)[Ca(II)[O(2)C-2,6-(t-BuCONH)(2)C(6)H(3)](4)] (4), [Tb[O(2)C-2,6-(t-BuNHCO)(2)C(6)H(3)](3)(H(2)O)(3)]] (5), and (NMe)(4)[Tb[O(2)C-2,6-(t-BuNHCO)(2)C(6)H(3)](4)(thf)] (6), were synthesized. The formation of the NH...O hydrogen bonds between the amide NH and carboxylate for 2, (NEt(4))[2,6-(t-BuCONH)(2)C(6)H(3)CO(2)] (3), and 4 was determined by (1)H NMR spectroscopy in solution and in the solid state (CRAMPS, IR). The ligand exchange reactions were attempted between 4 and a large excess of 2,4,6- Me(3)C(6)H(3)CO(2)H in chloroform-d solution; however, exchange reaction did not take place, indicating that the Ca(II) ions bound strongly to the carboxylate in 4. The Ca(II) ion binding properties with the benzoate derivatives were also examined using Tb(III) ion as a fluorescence probe. These results indicate that the NH...O hydrogen bonding between the amide NH and the oxygen atom of the carboxylate contributes to strong Ca(II) binding and prevents the dissociation of the calcium-carboxylate bond. The X-ray structural analyses of these complexes revealed that the NH.O hydrogen-bonded carboxylate ligands prefer the chelate-type coordination and create a mononuclear [Ca(O(2)CR)(4)](2)(-) or [Tb(O(2)CR)(4)](-) core with anionic charge, which is known only in the active site of calcium-binding proteins.     

Hydrogen-bonding interaction in a complex of amino acid with urea studied by DFT calculations

Theoretical studies on hydrogen-bonded complexes between amino acids (glycine, alanine, and leucine) and urea in gas phase have been carried out using density functional theory (DFT) and ab initio methods at the B3LYP/6-311++g** and MP2/6-311++g** theory levels. The structures, binding energy, Chelpg (charges from electrostatic potentials using a grid-based method) charge distribution, and bond characteristics of the mentioned complexes were calculated. Urea is a good H-bond donor and an excellent receptor for highly electronegative atoms like O and N, through the formation of two or more hydrogen bonds. The NH₂ and COOH groups of amino acids can form several different types of H-bonds with urea molecular, as well as C^αH and alkyl side chains. The calculated high binding energy also suggests multiple H-bonds formed in one complex. The OH···O contact is the strongest hydrogen bond interaction with H···O separation around 1.65 Å and its relevant angle close to 176°. The closely linear amide H-bonds NH···O and OH···N strongly stabilize the amino acid–urea complex with H···O separation between 1.89 and 2.38 Å. The weaker CH···O/N H-bonds are also discussed as significant interaction in biological systems involving amino acids.     

Mononuclear Ca(II)-bulky aryl-phosphate monoanion and dianion complexes with ortho-amide groups

Two new mononuclear Ca(II) complexes with aryl dihydrogen phosphate ligands having two strategically oriented bulky amide groups, 2,6-(Ph3CCONH)2C6H3OPO3H2 (1), including one with a phosphate monoanion, (NMe4)[CaII[O2P(OH)OC6H3-2,6-(NHCOCPh3)2]3(NCMe)3] (3), and one with a phosphate dianion, [CaII[O3POC6H3-2,6-(NHCOCPh3)2](H2O)3(MeOH)2] (4). Both are analogues for the NH...O hydrogen bonds in the active site of Ca(II)-containing phosphotransferase. Crystallographic studies of these Ca(II) complexes revealed that the amide NHs are directed to uncoordinated O atoms of the phosphates, and the IR and 1H NMR spectra indicate that strong NH...O hydrogen bonds are formed only in the phosphate dianion state. The ligand exchange reaction of 3 with a non-hydrogen-bonded phosphate ligand shows that the NH...O hydrogen bonds prevent the Ca-O bond from dissociation. A scatter plot analysis comparing the distance of a Ca-O bond with the Ca-O-P angle, the Fourier density analysis, and DFT calculations reveal that a partial degree of covalency in the Ca-O(phosphate) bonds is present.     

A polarizable dipole–dipole interaction model for evaluation of the interaction energies for NH···OC and CH···OC hydrogen‐bonded complexes

In this article, a polarizable dipole–dipole interaction model is established to estimate the equilibrium hydrogen bond distances and the interaction energies for hydrogen‐bonded complexes containing peptide amides and nucleic acid bases. We regard the chemical bonds N? H, C?O, and C? H as bond dipoles. The magnitude of the bond dipole moment varies according to its environment. We apply this polarizable dipole–dipole interaction model to a series of hydrogen‐bonded complexes containing the N? H···O?C and C? H···O?C hydrogen bonds, such as simple amide‐amide dimers, base‐base dimers, peptide‐base dimers, and β‐sheet models. We find that a simple two‐term function, only containing the permanent dipole–dipole interactions and the van der Waals interactions, can produce the equilibrium hydrogen bond distances compared favorably with those produced by the MP2/6‐31G(d) method, whereas the high‐quality counterpoise‐corrected (CP‐corrected) MP2/aug‐cc‐pVTZ interaction energies for the hydrogen‐bonded complexes can be well‐reproduced by a four‐term function which involves the permanent dipole–dipole interactions, the van der Waals interactions, the polarization contributions, and a corrected term. Based on the calculation results obtained from this polarizable dipole–dipole interaction model, the natures of the hydrogen bonding interactions in these hydrogen‐bonded complexes are further discussed. © 2013 Wiley Periodicals, Inc.     

Structure and properties of dibutylamine complexes with aluminum and gallium halides: The role of hydrogen bonds

Reactions of aluminum and gallium halides MX₃ (M = Al, Ga; X = Cl, Br) with dibutylamine in benzene solutions were studied by calorimetry, dielectrometry, and cryoscopy. The formation of molecular complexes Bu₂NH·MX₃ (1:1), 2Bu₂NH·MX₃ (2:1) and 6Bu₂NH·MX₃ (6:1) was established. In the 1:1 complexes, the donor-acceptor bond is formed by the lone electron pair of the nitrogen atom and a vacant orbital of the metal. Hydrogen bonds strongly affect the structure and properties of the 2:1 and 6:1 complexes. Complexes of the composition 2Bu₂NH·MX₃ are present in solution as six-membered metallacycle with a four-coordinate metal atom, and the second amine molecule linked with the complex Bu₂NH·MX₃ with N-H···N and N-H···X hydrogen bonds.     

Structure and proton-donating ability of trifluoro-<Emphasis Type="Italic">N</Emphasis>-(2-phenylacetyl)methanesulfonamide

According to the data of quantum-chemical calculations and IR spectroscopy the trifluoro-N-(2-phenylacetyl)methanesulfonamide CF₃SO₂NHC(O)CH₂Ph in the isolated state and in inert media exists in the form of two conformers with the syn- and antiperiplanar orientation of the C=O and N-H bonds. Its self-associates in the CCl₄ solution and in molecular crystals constitute cyclic dimers formed by the NH···O=S bonds and chain dimers with the NH···O=C bonds. As a hydrogen bond donor, trifluoro-N-(2-phenylacetyl)methanesulfonamide is stronger than N-methyltrifluoromethanesulfonamide. Its pK _a in methanol is 5.45, that is 5 pK units lower than for amides CF₃SO₂NHR and 2 pK units higher than for imide (CF₃SO₂)₂NH.     

Remarkable shifts of Csp2-H and O-H stretching frequencies and stability of complexes of formic acid with formaldehydes and thioformaldehydes

Thirty-six stable complexes of formic acid with formaldehydes and thioformaldehydes were determined on the potential energy surface, in which the XCHO···HCOOH complexes are found to be more stable than the XCHS···HCOOH counterparts, with X = H, F, Cl, Br, CH₃, NH₂. All complexes are stabilized by hydrogen bonds, and their contribution to the total stabilization energy of the complexes increases in going from C-H···S to C-H···O to O-H···S and finally to O-H···O. Remarkably, a significant blueshift of C_sp2-H bond by 81–96 cm⁻¹ in the C_sp2-H···O hydrogen bond has hardly ever been reported, and a considerable redshift of O-H stretching frequency by 206–544 cm⁻¹ in the O-H···O/S hydrogen bonds is also predicted. The obtained results in our present work and previous literatures support that a distance contraction and a stretching frequency blueshift of C-H bond involving hydrogen bond depend mainly on its polarity and gas phase basicity of proton acceptor, besides the rearrangement of electron density due to complex formation. Markedly, we suggest the ratio of deprotonation enthalpy to proton affinity (R _c) as an indicator to prospect for classification of hydrogen bonds. The symmetry adapted perturbation theory results show a larger role of attractive electrostatic term in XO-n as compared to that in XS-n and the electrostatic interaction is overwhelming dispersion or induction counterparts in stabilizing XO-n and XS-n , with n = 1, 2, 3. © 2019 Wiley Periodicals, Inc.     

Theoretical study of the S?H···O blue‐shifted hydrogen bond

Theoretical calculations were performed to study the nature of the hydrogen bonds in the complexes HCHO···HSO, HCOOH···HSO, HCHO···HOO, and HCOOH···HOO. The geometric structures and vibrational frequencies of these four complexes at the MP2/6‐31G(d,p) and MP2/6‐311+G(d,p) levels are calculated by standard and counterpoise‐corrected methods, respectively. The results indicate that in the complexes HCHO···HSO and HCOOH···HSO the S? H bond is strongly contracted. In the S? H···O hydrogen bonds, the calculated blue shifts for the S? H stretching frequencies are in the vicinity of 50 cm^?1. While in the complexes HCHO···HOO and HCOOH···HOO, the O? H bond is elongated and O? H···O red‐shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X? H bond length in the X? H···Y hydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribution, rehybridization, and structural reorganization. Among them hyperconjugation has the effect of elongating the X? H bond. Electron density redistribution and rehybridization belong to the bond shortening effects, while structural reorganization has an uncertain influence on the X? H bond length. In the complexes HCHO···HSO and HCOOH···HSO, the shortening effects dominate which lead to the blue shift of the S? H stretching frequencies. In the complexes HCHO···HOO and HCOOH···HOO where elongating effects are dominant, the O? H···O hydrogen bonds are red‐shifted. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Crystal structures of two Ca(II) complexes with imidazole-4,5-dicarboxylate and water ligands

The structure of compound I: poly-diaqua(μ-imidazole-4,5-dicarboxylato-N,O; -O′; -O′′, -O′′′) calcium(II) monohydrate [Ca(C₅H₂N₂O₄)(H₂O)₂·H₂O] is built of molecular sheets in which imidazole-4,5-dicarboxylate ligands bridge the metal ions using both carboxylate groups, each bidentate. Ca(II) is coordinated by six oxygen atoms and one hetero-ring nitrogen atom distributed at the apices of a capped tetragonal bipyramid. The basal plane of the pyramid is formed by two carboxylate oxygen atoms [d(Ca–O2?=?2.374(1)?Å, d(Ca–O4)?=?2.412(1)?Å] and two water oxygen atoms [d(Ca–O5)?=?2.384(1)?Å, d(Ca–O6)?=?2.455(1)?Å], the capped position is occupied by the carboxylate oxygen atom O3 [d(Ca–O3)?=?2.325(1)?Å], the hetero-ring nitrogen atom [d(Ca–N2)?=?2.523(1)?Å] and the carboxylate oxygen atom O4 [d(Ca–O2)?= 2.412(1)?Å] form the apices of the prism. The solvation water molecule plays a significant role in a framework of hydrogen bonds responsible for the stability of the crystal. The structure of compound II: trans-tetraquadi(H-imidazole-4,5-dicarboxylato-N,O) calcium(II) monohydrate, [Ca(C₅H₃N₂O₄)₂(H₂O)₄·H₂O] consists of monomers in which the Ca(II) ion is located on a centre of symmetry. The coordination around the Ca(II) is a strongly deformed pentagonal bipyramidal with the imidazole-4,5-dicarboxylate (4,5-IDA) ligands in the trans arrangement forming a dihedral angle of 68.3°. An imidazole-ring nitrogen atom [d(Ca–N)?=?2.632(2)?Å] and one carboxylate O atom [d(Ca–O)?=?2.531(2)?Å] from each ligand coordinate to the metal ion. The coordination is completed by four water oxygen atoms [d(Ca–O)?=?2.393(2)?Å] and [d(Ca–O)?=?2.367(2)?Å]. The coordinated water molecules act as hydrogen bond donors and acceptors to the unbonded carboxylate oxygen atoms in adjacent monomers giving rise to a three-dimensional molecular network.     

Conformational analysis of 2-methyl-1,3,2-dioxaborinane in the presence of an ammonia molecule

Nonempirical quantum chemical methods RHF//STO-3G, 3-21G and 6-31G(d) were used for the investigation of the conformational properties of molecular complexes of 2-methyl-1,3,2-dioxaborinane with ammonia (1:1). Two types of possible associates are revealed: with donor-acceptor N→B bond and with intermolecular NH···O hydrogen bond. Their calculated relative stability and conformational behavior are determined not only by the spatial orientation of the donor and the acceptor but also by the concepts of the used calculation approach.     

Cooperative influence of water binding to peptides by N?H···OH2 and CO···HOH hydrogen bonds: Study by Ab Initio calculations

In this article, the geometry structures of hydrogen bond chains of formamide and N‐methylacetamide and their hydrogen‐bonded complexes with water were optimized at the MP2/6‐31G* level. Then, we performed Møller–Plesset perturbation method with 6‐311++g**, aug‐cc‐pvtz basis sets to study the cooperative influence to the total hydrogen bond energy by the N? H ··· OH₂ and C?O ··· HOH hydrogen bonds. On the basis of our results, we found that the cooperativity of the hydrogen‐bonded complexes become weaker as N? H ··· OH₂ and C?O ··· HOH hydrogen bonds replacing N? H ··· O?C hydrogen bonds in protein and peptide. It means that the N? H and C?O bonds in peptide prefer to form N? H ··· O?C hydrogen bond rather than to form C?O ··· HOH and N? H ··· OH₂. It is significant for understanding the structures and properties of the helical or sheet structures of protein and peptide in biological systems. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Synthesis,crystal structure and other properties of the complexes of Er(III), Yb(III) and Lu(III) with 4,4′-bipyridine and dichloroacetates

A novel mixed-ligand complexes of Er(III), Yb(III) and Lu(III) with title ligands were prepared and characterized by chemical and elemental analysis and IR spectroscopy, conductivity (in methanol, dimethyloformamide and dimethylsulphoxide). The thermal properties of complexes in the solid state were studied. The mode of metal–ligand coordination was discussed. The title compounds are isomorphic and isostructural in solid state. All atoms in studied compounds lie in general positions but occurrence of inversion on the midpoint of the bond linking two pyridine rings leads to existence in asymmetric unit one complex molecule and half of outer coordination sphere 4-bpy molecule. All chelating carboxylate groups are symmetrically bonded to the metal cations. The molecules of studied compounds are connected to the three dimensional network via O–H···O and O–H···N intermolecular hydrogen bonds. In the structures also exist C–H···O, C–H···Cl weak hydrogen bonds and π····π stacking interactions.     

Nitrogen versus sulfur acylation in sugar thioureas: regioselectivity and conformational consequences

The influence of steric and electronic effects in the regioselectivity of base-catalysed acetylation reactions of sugar thioureas and the structural and conformational properties of the resulting products have been investigated. Bulky alkyl substituents favoured S-acetylation, whereas aryl substituents directed acylation at nitrogen. The conformational properties of both the S- and N-acetyl compounds are governed by the existence of a strong six-membered NH···OC intramolecular hydrogen bond that locks the pseudoamide bonds in a rigid configurational arrangement.     

MgSO4·11H2O and MgCrO4·11H2O based on time‐of‐flight neutron single‐crystal Laue data

Hexaaquamagnesium(II) sulfate pentahydrate, [Mg(H₂O)₆]SO₄·5H₂O, and hexaaquamagnesium(II) chromate(II) pentahydrate, [Mg(H₂O)₆][CrO₄]·5H₂O, are isomorphous, being composed of hexaaquamagnesium(II) octahedra, [Mg(H₂O)₆]²⁺, and sulfate (chromate) tetrahedral oxyanions, SO₄²⁻ (CrO₄²⁻), linked by hydrogen bonds. There are two symmetry‐inequivalent centrosymmetric octahedra: M1 at (0, 0, 0) donates hydrogen bonds directly to the tetrahedral oxyanion, T1, at (0.405, 0.320, 0.201), whereas the M2 octahedron at (0, 0, ) is linked to the oxyanion via five interstitial water molecules. Substitution of Cr^VI for S^VI leads to a substantial expansion of T1, since the Cr—O bond is approximately 12% longer than the S—O bond. This expansion is propagated through the hydrogen‐bonded framework to produce a 3.3% increase in unit‐cell volume; the greatest part of this chemically induced strain is manifested along the b* direction. The hydrogen bonds in the chromate compound mitigate ∼20% of the expected strain due to the larger oxyanion, becoming shorter (i.e. stronger) and more linear than in the sulfate analogue. The bifurcated hydrogen bond donated by one of the interstitial water molecules is significantly more symmetrical in the chromate analogue.     

Characterization of the N?H···ON and N?H···NO H‐bonds in nitrosamine dimers

Ab initio molecular orbital and DFT calculations have been carried out for three most stable dimers of parent nitrosamine (NA) in order to elucidate the structures and energetics of the dimers. The structures were optimized using HF, B3LYP, and MP2 methods with 6‐311+G(d,p) and 6‐311++G(2d,2p) basis sets. At the optimized geometries obtained at MP2/6‐311++G(2d,2p) level of theory, the energies were evaluated at QCISD/aug‐cc‐pVDZ and CCSD/aug‐cc‐pVDZ levels. The most stable dimer has two N? H···O?N hydrogen bonds and the least stable dimer has two N? H···N?O hydrogen bonds. The natural bond orbital analysis showed that the lpO(N) → BD*(N? N) and lpO(N) → BD*(N? H_b) interactions play a decisive role in the stabilization of the NH···O(N) hydrogen bonds in dimers. The atoms in molecules results reveal that the intermolecular N? H···O(N) H‐bonds in dimers have electrostatic character. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Photoinduced switching of intramolecular hydrogen bond between amide NH and carboxyl oxygen

In this study, we synthesized two novel carboxylic acid and carboxylate compounds, both of which had an amide group linked with an azomethine moiety to introduce photoinduced switching of the intramolecular NH...O hydrogen bond. We suggest that the cis-carboxylate compound forms a stronger intramolecular NH...O hydrogen bond than the cis-carboxylic acid compound.     

Strong asymmetric hydrogen bonding in 2‐(oxamoylamino)ethylammonium oxamate–oxamic acid (1/1)

The title compound, C₄H₁₀N₃O₂⁺·C₂H₂NO₃⁻·C₂H₃NO₃, contains at least 11 distinct hydrogen‐bond interactions showing a great variety of bond strengths. The shortest and strongest hydrogen bond [O...O = 2.5004 (12) Å] is found between the uncharged oxamic acid molecule and the oxamate monoanion. The grouping formed by such a strong hydrogen bond can thus be considered as a hydrogen bis(oxamate) monoanion. It lacks crystallographic symmetry and the two oxamate groups have different conformations, showing an asymmetric hydrogen‐bond interaction. Significantly, the asymmetry allows us to draw a direct comparison of site basicity for the two inequivalent carboxylate O atoms in the planar oxamate anion. The constituent molecular ions of (I) form ribbons, where all amide and carboxylate groups are coplanar. Graph‐set analysis of the hydrogen‐bonded networks reveals the R²₂(10) and R²₂(9) homodromic nets as important structure‐directing motifs, which appear to be a common feature of many oxamate‐containing compounds.     

Hydrogen‐bonded complexes of nicotine with simple alcohols

Ab initio and density functional theory studies have been performed on the hydrogen‐bonded complexes of neutral and protonated nicotine with ethanol, methanol, and trifluromethanol to explore their relative stability in a systematic way. Among all the hydrogen‐bonded nicotine complexes considered here, protonated forms in nicotine–ethanol and nicotine–methanol, and neutral form in nicotine–trifluromethanol complexes have been found to be the most stable. In the former two complexes, the proton attached to the pyrrolidine nitrogen acts as a strong hydrogen bond donor, whereas the pyrrolidine nitrogen atom acts as a hydrogen bond acceptor in the latter case. Neutral complex of nicotine with trifluromethanol has been found to possess a very short hydrogen bond (1.57 Å) and basis set superposition error corrected hydrogen bond energy value of 19 kcal/mol. The nature of the various hydrogen bonds formed has been investigated through topological aspects using Bader's atoms in molecules theory. From the calculated topological results, excellent linear correlation is shown to exist among the hydrogen bond length, electron density, and its Laplacian at the bond critical points for all the complexes considered. The natural bond orbital analysis has been carried out to investigate the charge transfer in the nicotine alcohol complexes. In contrast to the blue shifting behavior that is generally exhibited by other C? H···O hydrogen bonds involving sp³ carbon atom, the C? H···O hydrogen bond in the protonated nicotine–ethanol and methanol complexes has been found to be proper with red shifting in nature. © 2011 Wiley Periodicals, Inc.