Competition between π–π stacking and hydrogen bonding in (1:2) picrates of 1,5-diamino-3-oxapentane, 1,8-diamino-3,6-dioxaoctane and 1,5-diamino-3-azapentane—solid state studies

Crystallographic studies of (2:1) salts of picric acid with 1,5-diamino-3-oxapentane (1OPICR), 1,8-diamino-3,6-dioxaoctane (2OPICR) and 1,5-diamino-3-azapentane (1NPICR) showed significant conformational change of the picrate ion due to numerous electrostatic, H-bonding and π–π stacking interactions present in the crystal lattice. In particular, intermolecular N–HO H-bonds were found to cause significant twisting of the o-NO₂ groups from the plane of the benzene ring, whereas overlapping of the picrate ions due to electrostatic interactions and π–π stacking caused flattening of the molecule. Analysis of the geometry of 74 picrate ions found in the Cambridge Crystallographic Database, in their various crystallochemical environments, showed that competition between essentially weak but numerous intermolecular interactions of different types led to systematic changes in geometric parameters within the picrate ion. In particular, relations found between the C1–C2–N–O (C1–C6–N–O) torsion angle and the endocyclic C1–C2–C3 (C1–C6–C5) valence angle can be explained on the basis of competition between resonance effects of the o-NO₂ group and π–π stacking.     

X–H rotational-echo double-resonance NMR for torsion angle determination of peptides

C–H and N–H rotational-echo double-resonance (REDOR) NMR is developed for determining torsion angles in peptides. The distance between an X spin such as ¹³C or ¹⁵N and a proton is measured by evolving the proton magnetization under REDOR-recoupled X–H dipolar interaction. The proton of interest is selected through its directly bonded heteronuclear spin Y. The sidechain torsion angle χ₁ is extracted from a ¹³Cβ-detected Hβ–N distance, while the backbone torsion angle φ is extracted from an ¹⁵N-detected H^N–C^′ distance. The approach is demonstrated on three model peptides with known crystal structures to illustrate its utility.     

Infrared depletion spectroscopy of the doubly hydrogen-bonded aniline–(tetrahydrofuran)2 complex produced in supersonic jet

The vibrational frequencies of the N–H stretching modes of aniline after forming a strong doubly H-bonded complex with tetrahydrofuran (THF) are measured with infrared depletion spectroscopy that uses cluster-size-selective resonance-enhanced multiphoton ionization (REMPI) time-of-flight mass spectrometry. Two strong infrared absorption features observed at 3355 and 3488 cm⁻¹ are assigned to the symmetric and antisymmetric N–H stretching vibrations of the 1:2 aniline–THF complex, respectively. The red-shifts of the N–H stretching vibrations of aniline agree with the ab initio calculated (MP2/6-31G**) aniline-(THF)₂ structure in which both aniline N–H bonds interact with the oxygen atom of THF through two hydrogen bonds. The calculated binding energy is found to be 29.6 kJ mol⁻¹ after corrections for basis set superposition error (BSSE) and zero-point energy. The calculated structure revealed that the angle between the N–H bonds in the NH₂ group increased to 112.5° in the aniline–(THF)₂ complex from that of 109.8° in the aniline. The electronic 0–0 band origin for the S₁ ← S₀ transition is observed at 32,900 cm⁻¹ in the aniline–(THF)₂ complex, giving a red-shift of 1129 cm⁻¹ from that of the aniline molecule.     

Synthesis and characterization of [chloro{2(1H)-pyridinethione-S}{tris(pyridin-2-ylthiolato)methyl-C,N,N′,N″]}nickel(II)], [Ni(TPTM)(SPyH)Cl]

The compound, [chloro{2(1H)-pyridinethione-S}{tris(pyridin-2-ylthiolato)methyl-C,N,N′,N″]}nickel(II)], [Ni(TPTM)(SPyH)Cl], was isolated from the reaction between NiCl₂ · 6H₂O and tris(pyridin-2-ylthiolato)methane in aqueous EtOH. X-ray crystallography at 120 K revealed an octahedral arrangement about Ni with a tetradentate tris(pyridin-2-ylthio)methyl-C,N,N,N ligand, a monodentate 2(1H)-pyridinethione-S ligand and a chloride. The 2(1H)-pyridinethione-S ligand was derived from tris(pyridin-2-ylthio)methane probably via an acid catalysed hydrolysis reaction. Intramolecular N–H–Cl and C–H–Cl interactions help to cement the molecular structure. Weak C–H–Cl and C–H–S hydrogen bonding interactions link molecules of [Ni(TPTM)(SPyH)Cl] into a 3D array. EPR and UV spectra, and Hartree–Fock theoretical calculations are reported.     

Ab initio calculations on blocked Pro-Ala dipeptides

The effect of the chirality of the amino acid at position i + 2 on a β-turn was investigated by a grid scan ab initio calculation on the Ac- -Pro- -Ala-NH₂ and Ac- -Pro- -Ala-NH₂ blocked dipeptides. Th6-31G basis set was used to estimate the effect of the alanyl side chain on the conformation of the peptide backbone in a blocked dipeptide as a simple, but complete model for a reverse turn. This study provides a quantum mechanical evaluation of the ability of the NH at the i + 3 residue to form the H-bond that closes the 10 membered ring which stabilizes the turn. The lowest energy of all 64 probed conformations of the -Ala containing peptide corresponded to a good type II β-turn with a hydrogen bond distance between the acetyl oxygen and the amide terminal hydrogen of 2.21 Å. A comparison with the nonblocked dipeptide ab initio study indicates that the presence of the end blocks enhances the propensity of the -Ala-containing dipeptide for a type II β-turn, but does not seem to enhance the propensity of the -Ala-containing dipeptide for a type I β-turn. The energies and geometric parameters for the lowest four optimized conformations identified by the grid scan search for each molecule have been calculated.     

Comparison of calculated DFT/B3LYP and experimental C and O NMR chemical shifts, ab initio HF/6-31G* optimised structures, and single crystal X-ray structures of some substituted methyl 5β-cholan-24-oates

Single crystal X-ray structures (monoclinic space group P2₁) for methyl 3-oxo-5β-cholan-24-oate and methyl 3,12-dioxo-5β-cholan-24-oate have been solved and compared with HF/6-31G* optimised structures. In the crystalline packings the side chains are connected with weak OC(sp³)HO-type of interactions between C25–H and C24–O–C25 and the keto ends with weak C(sp³)HO=C-type of interactions between C4–H and O=C3. The orientations of the side chains, which steric configurations are of great importance to the biological activity of the molecules, are compared with the experimental structure of methyl 3-hydroxy-5β-cholan-24-oate. Probable reasons for the observed differences are discussed. In addition, ¹³C and ¹⁷O NMR chemical shifts of methyl 3-oxo-5β-cholan-24-oate and methyl 3,12-dioxo-5β-cholan-24-oate as well as the epimeric methyl 3-hydroxy-5β-cholan-24-oate and methyl 3β-hydroxy-5β-cholan-24-oate have been calculated (DFT/B3LYP/6-311G*) and compared with the experimental values by linear regression analyses. In general, the correspondence between the theoretical and experimental parameters is good or excellent.     

Design and synthesis of enantiopure 1-[1(S)-(2-pyridyl)alkyl]-2(R)-isopropylaziridines, new ligands for asymmetric catalysis

Enantiopure 1-(2-pyridyl)alkyl aziridines were designed as bidentate ligands for asymmetric catalysis. Their synthesis involved the addition of organometallic reagents to the imine prepared from 2-pyridinealdehyde and an enantiopure β-aminoalcohol, followed by cyclisation of the β-aminoalcohol moiety to the aziridine ring. Two such ligands (N–N)* were prepared from (S)-valinol and converted to the complexes (η³-allyl)(N–N)*Pd⁺SbF₆⁻, one of which was characterised by X-ray crystallography. Modest enantioselectivities were achieved in a representative Pd-catalysed allylic substitution reaction.     

Structural features of 4,4′-diaminooctafluorobiphenyl

Molecules of C₁₂H₄F₈N₂ crystallize in the orthorhombic space group P2₁2₁2₁ with cell constants a=9.200(1), b=10.896(1), c=23.178(3) Å and V=2323.4(5) ų. There are two molecules in the asymmetric unit which have D₂ symmetry. However these two molecules have C₂ symmetry in central C–C bonds, separately. Intramolecular steric repulsions between F atoms and N–HF hydrogen bonds have very much affected the molecular conformation. The mean dihedral angle between intramolecular phenyl rings is 119.2(1)°. The N–C bonds have lengths 1.363(4)–1.407(4) Å with a mean of 1.388 Å. This is shorter than the conventional C–N (1.47(1) Å) bond length due to π-electron delocalizations (F.H. Allen, O. Kennard, D.G. Watson, L. Brammer, A.G. Orpen, R. Taylor, J. Chem. Soc. Perkin Trans. II (1987) S1–S19).

The molecular structure of the title compound was also investigated by IR spectroscopy. It was shown that the IR spectra are in agreement with the crystal structure. On the other hand, theoretical and semi-emprical molecular mechanic calculations were carried out to obtain the most probable low-energy conformations by using MM3, PM3 and AM1 programs.     

Dynamic, electrooptical and energetic nonequivalency of NH bonds in 1:1 and 1:2 complexes of aminopyridines with proton acceptors

The influence of the –NH₂ group position in the pyridine ring on the proton donor ability of N–H groups in hydrogen bonding as well as on the spectral behaviour of stretching and bending vibrations of aminopyridines has been studied. The proton donor ability was shown to increase in the row: meta-, ortho-, and para-aminopyridines. It was established tha N–H bonds in ortho-aminopyridine were not equivalent, and the evaluation of their dynamic nonequivalence was made.

The influence of temperature on the spectral characteristics of the absorption bands of the stretching vibrations of amine groups in the free and hydrogen bonded molecules in CCl₄ has been studied (in temperature range 290–330 K), the formation constants of the complexes have been determined, enthalpy of the 1:1 complexes formation (−ΔH₁) between ortho- and meta-aminopyridines with dimethylformamide, dimethylsulphoxide and hexamethylphosphoramide has been calculated in temperature range 290–330 K. The 1:2 complexes of ortho-, meta- and para-aminopyridines with acetonitrile, tetrahydrofurane, dimethylsulphoxide, hexamethylphosphoramide were studied at the indoor temperature. Enthalpy of the 1:2 complex (−ΔH₂) was estimated on the basis of ‘intensity rule’; −ΔH₁=ΔB^1/2 assuming that parameter does not depend on the composition of a complex.

The vibrational and electrooptical tasks were solved for the free and H-bounded molecules of aminopyridines as well as its complexes of the 1:1 and 1:2 compositions. Dynamic, electrooptical and energetic nonequivalency of NH bonds of aminogroups in aminopyridines was studied quantitatively. The independent calculations of dynamic constants proved mentioned above nonequivalency of NH bonds.

Correlations between spectral characteristics of the absorption bands, geometric, dynamic and electrooptical parameters of –NH₂ group in aminopyridines in the free and hydrogen bonded molecules have been established. Those correlations allow to determine the most important molecular characteristics obtained on the basis of spectral measurements in the range of the absorption bands of the stretching vibrations of aminogroup.     

A molecular dynamics study of the pentacyclo-undecane cage amino acid tripeptide

In this paper, we report on the conformational profile of the pentacyclo-undecane (PCU) cage tripeptide carried out by molecular dynamics (MD) simulation using water as an explicit solvent. The MD solution phase studies carried on the model peptide analogues (A)=Ac–Ala–Ala–Ala–NHMe; (B)=Ac–Cage–Cage–Cage–NHMe; (C)=Ac–Ala–Cage–Ala–NHMe and (D)=Ac–Ala–Pro–Ala–NHMe, are used as a complimentary technique to the corresponding gas phase simulated annealing (SA) study previously carried out in our laboratory. No significant structural changes were observed over the MD trajectories. However, the results reported here provide further evidence that the (PCU) cage amino acid exhibits C_7eq, C_7aq, _R and _L conformations, and the theoretical results suggest that the PCU cage amino acid is a strong β-turn inducer. These results support the prediction that when the PCU cage residues are in the (i) and (i+2) positions, the β-turn can be extended in either direction to form anti-parallel β-pleated sheets, thereby forming the basis of the mechanism for the folding back of the chain in a cross-β-turn structure.     

Tautomeric properties, conformations and structure of N-(2-hydroxy-5-chlorophenyl) salicylaldimine

The crystal structure of N-(2-hydroxy-5-chlorophenyl) salicylaldimine (C₁₃H₁₀NO₂Cl) was determined by X-ray analysis. It crystallizes orthorhombic space group P2₁2₁2₁ with a=12.967(2) Å, b=14.438(3) Å, c=6.231(3) Å, V=1166.5(6) Å³, Z=4, D_c=1.41 g cm⁻³ and μ(MoK)=0.315 mm⁻¹. The title compound is thermochromic and the molecule is nearly planar. Both tautomeric forms (keto and enol forms in 68(3) and 32(3)%, respectively) are present in the solid state. The molecules contain strong intramolecular hydrogen bonds, N1–H1O1/O2 (2.515(1) and 2.581(2) Å) for the keto form and O1–H01N1 for the enol one. There is also strong intermolecular O2–HO1 hydrogen bonding (2.599(2) Å) between neighbouring molecules. Minimum energy conformations AM1 were calculated as a function of the three torsion angles, θ₁(N1–C7–C6–C5), θ₂(C8–N1–C7–C6) and θ₃(C9–C8–N1–C7), varied every 10°. Although the molecule is nearly planar, the AM1 optimized geometry of the title compound is not planar. The non-planar conformation of the title compound corresponding to the optimized X-ray structure is the most stable conformation in all calculations.     

Theoretical studies on the BN substituted fullerenes C70−2x(BN)x (x=1–3)—isoelectronic equivalents of C70

The equilibrium structures and relative stabilities of BN-doped fullerenes C_70−2x(BN)_x (x=1–3) have been studied at the AM1 and MNDO level. The most stable isomers of C_70−2x(BN)_x have been found out and their electronic properties have been predicted. The calculation results show that the BN substituted fullerenes C_70−2x(BN)_x have considerable stabilities, though they are less stable than their all carbon analog. For C₆₈BN, the isomers whose BN is located in the most chemically active bonds of C₇₀ (namely B and A) are among the most stable species, of which B is predicted to be the ground state. The stabilities of C₆₈BN decrease and the dipole moments increase with increasing the distance between the heteroatoms. For C₆₆(BN)₂, the lowest energy species is the isomer in which the B–N–B–N bond is formed; For C₆₄(BN)₃, the most stable species should have three BN units located in the same hexagon to form B–N–B–N–B–N ring. The ionization potentials and the affinity energies of the most stable species of BN-doped C₇₀ are almost the same as those of C₇₀ because of the isoelectronic relationship. The ionization potentials and affinity energies depend on the relative position of the heteroatoms in C₆₈BN, the chemical reactivities of the isomers whose heteroatoms are well separated should differ significantly from their all carbon analog.     

Synthesis, structural characterization and ab initio calculation of dipyridyltetraazathiapentalene: a highly conjugative polycyclic molecule with hypervalent N–S–N bond

A highly conjugative polyheterocyclic compound, tetraazathiapentalene fused with pyridine rings, was synthesized by reacting 2-aminopyridine with carbon disulfide. The single crystal X-ray determination reveals that the molecule crystallizes in monoclinic space group C2/c, with the following unit cell dimensions: a=11.062(2), b=9.030(1), c=20.898(5) Å, β=102.98(1)°, V=2034.00(3) Å³, Z=8, and that a hypervalent N–S–N bond exists in the molecule. Ab initio calculations predict its IR and ¹H NMR spectra that are coincident with the experimental ones and reveal the bonding nature of the hypervalent N–S–N bond and the electronic structure of the molecule.     

Formation, solution structure and reactivity of alkylperoxo complexes of titanium

A detailed in situ ¹³C and ¹H NMR spectroscopic characterization of the following families of alkylperoxo complexes of titanium is presented: Ti(η²-OOtBu)_n(OiPr)_4−n, where n = 1–4; binuclear complexes [(iPrO)₃Ti(μ-OiPr)₂Ti(OiPr)₂(η²-OOtBu)] and [(η²-OOtBu)(iPrO)₂Ti(μ-OiPr)₂Ti(OiPr)₂(η²-OOtBu)]; complexes with β-diketonato ligands: Ti(LL)₂(OEt)(η²-OOtBu), Ti(LL)₂(OiPr)(η²-OOtBu), Ti(LL)₂(η²-OOtBu)₂, Ti(LL)₂(OtBu)(η¹-OOtBu), where HLL = acetylacetone, dipivaloylmethane. These alkylperoxo complexes could not be isolated due to their instability and were studied in situ at low temperatures. Whereas the side-on (η²) coordination mode of tert-butylperoxo ligand is generally preferable, the end-on (η¹) coordination caused by spatial hindrance from surrounding bulky ligands is found in two cases. The quantitative data on the reactivity of alkylperoxo complexes found towards sulfides and alkenes were obtained. The system TiO(acac)₂/tBuOOH in C₆H₆ was reinvestigated using ¹³C and ¹H NMR spectroscopy. The structure of the complex Ti(acac)₂{CH₃C(O)(OOtBu)COO} actually formed in this system was elucidated. Four types of titanium(IV) alkylperoxo complexes were detected in the Sharpless–Katsuki catalytic system using ¹³C NMR spectroscopy.     

3D H-bonding networks self-assembly from pyridinium derivatives and bis(maleonitriledithiolato)zincate(II)

The two ion-pair complexes, [pyH]₂[Zn(mnt)₂] (1) and [4,4′-bipyH₂]-[Zn(mnt)₂] (2), were synthesized, where mnt²⁻ denotes maleonitriledithiolate, and [pyH]⁺, [4,4′-bipyH₂]²⁺ represent pyridinium and diprotonated 4,4′-bipyridinium, respectively. Their single crystal structures show that there are strong bifurcated H-bonding interactions between the cations of the pyridinium derivative and the [Zn(mnt)₂]²⁻ anions in both 1 and 2. The bifurcated H-bonding interactions between the N–H of the pyridiniums and the CN groups of the mnt²⁻ ligands give rise to a 2D layered H-bonding network, the adjacent layers come together in such way as mutual embrace to give a tight pack, thus 2D hydrogen-bonding sheets further develop into 3D H-bonding networks through weak C–HS and ππ stacking interactions in 1. As for 2, the cations and anions connect into several types of H-bonding macrorings ([2+2], [3+3] and [4+4]), these H-bonding macrorings fuse to extend into 2D layered structure, the interpenetration between [3+3] and [4+4] type H-bonding macrorings in the adjacent layers give further rise to novel 3D extended H-bonding networks, in which there are clearly parallel stacks of cations and the chelate rings of anions.     

The synthesis and spectroscopic properties of some but-2-yne tungsten complexes of the type [WIX(CO){Ph2P(CH2)PPh2}(η-MeC2Me)] (X = Cl, Br, I, NO2, NO3, NCS or OH)

Reaction of the cationic complex [WI(CO)(NCMe){Ph₂P(CH₂)PPh₂}(η²-MeC₂ME)][BF₄] with an equimolar amount of MX (MX = NaCl, NaBr, NaI, KNO₂, KNO₃, NaNCS or KOH) in acetone at room temperature gave the neutral complex [WIX(CO){Ph₂P(CH₂)PPh₂}(η²-MeC₂Me)] (1–7) in good yield. Complexes 1–7 have been characterized by elemental analysis (C, H and N), IR and ¹H NMR spectroscopy.     

Molecular and crystal structures of N,N′-propylene- and N,N′-phenylene-diylbis [3-(1-aminoethyl)-6-methyl-2H-pyran-2,4(3H)-dione]

Two macrocyclic ligands, N,N′-propylene-diylbis[3-(1-aminoethyl)-6-methyl-2H-pyran-2,4(3H)-dione] I and N,N′-phenylene-diylbis[3-(1-aminoethyl)-6-methyl-2H-pyran-2,4(3H)-dione] II, have been prepared by the condensation of dehydroacetic acid (3-acetyl-4-hydroxy-6-methyl-2H-pyran-2-one) with 1,2-phenylenediamine and 1,3-propylenediamine. They have been characterized by means of elemental analysis, IR spectroscopy as well as by X-ray crystallography. The molecular structures of the compounds I and II can be described as consisting of two β-enaminone-2-pyrone rings interlaced with either alkyl chain in I or phenyl ring in II. The X-ray studies confirmed the existence of strong N–HO intramolecular hydrogen bonds in both structures. Their lengths are in accordance to lengths of RAHB intramolecular hydrogen bonds in 1,3-diketones, aryl-hydrazones, β-enaminones and related heterodienes (2.5–2.6 Å) [P. Gilli, V. Bertolasi, V. Ferretti and G. Gilli, J. Am. Chem. Soc., 122 (2000) 10405].     

Reactions of metalloalkynes VII. Protonation of ruthenium ethyne-1,2-diyl complexes

The acid–base chemistry of some ruthenium ethyne-1,2-diyl complexes, [{Ru(CO)₂(η-C₅H₄R)}₂(μ₂-CC)] (R=H, Me) has been investigated. Initial protonation of [{Ru(CO)₂{η-C₅H₄R}}₂(μ₂-CC)] gave the unexpected complex cation, crystallised as the BF₄ salt, [{Ru(CO)₂(η-C₅H₄R}}₃(μ₃-CC)][BF₄] (R=Me structurally characterised). This synthesis proved to be unreliable but subsequent, careful protonation experiments gave excellent yields of the protonated ethyne-1,2-diyl complexes, [{Ru(CO)₂{η-C₅H₄R)}₂(μ₂-η¹:η²-CCH)](BF₄) (R=Me structurally characterised) which could be deprotonated in high yield to return the starting ethyne-1,2-diyl complexes.     

Quantum mechanical study of tautomerism of methimazole and the stability of methimazole–I2 complexes

DFT and ab initio theoretical methods were used to calculate the relative stability of tautomers in the methimazole (MMI). The calculations show that the thione form of MMI 1 is more stable than the thiol tautomer in good agreement with the experimental results. The DFT and ab initio calculations were also used to determine the stability of MMI–I₂ complexes. All methods suggest that the methimazole in the MMI–I₂ complex exists almost exclusively as the thione tautomer. The Gibbs free energy difference between planar and perpendicular forms of thione tautomer of MMI–I₂ complex indicates that the planar form is the predominant complex. The counterpoise corrected Gibbs free energy also shows that the MMI–I₂(plan.) complex is more stable than the MMI–I₂(perp.) complex. These predictions are in good agreement with the experimental results. By using the natural bond orbital (NBO) approach, the effects of charge transfer interactions on the stability of MMI–I₂ complexes were investigated. The LP₃(S)→σ*(I–I) and LP₃(I)→σ*(N–H) charge transfer interactions may be very important in the stability of the planar form. The results show that the LP₃(S)→σ*(I–I) charge transfer interaction causes a greater increase in the σ*(I–I) antibond occupation number, and concomitantly, a greater increase in the corresponding I–I bond length in the planar complex with respect to the perpendicular complex. The LP₃(S)→σ*(I–I) charge transfer interaction is assisted by NHI intermolecular hydrogen bonding. The atom in molecule (AIM) analysis shows that the charge density and its Laplacian at the SI bond critical point of the planar complex is greater than the perpendicular complex.