Polymorphism for a novel phosphoramidate; NMR and X-ray crystallography

Abstract  

New phosphoramidates with formula 3-NC₅H₄C(O)NHP(O)XY (X=Y=Cl (1), X=Y=NH–C(CH₃)₃ (2a,2b), X=Y=N(C₄H₉)₂ (3), X=Cl, Y=N(C₂H₅)₂ (4) were synthesized and characterized by IR, ¹H-, ¹³C-, ³¹P-NMR spectroscopy and CHN elemental analysis. Surprisingly, the reaction of compound 2a with LaCl₃, 7H₂O in 3:1 M ratio leads to a polymorph of this compound (2b). NMR spectra indicate that ² J(PNH_amide) in 2b (7.0 Hz) is very much greater than in 2a (4.1 Hz), while δ(³¹P) values are identical for both of them. In IR spectra, υ(P=O) is weaker but υ(C=O) is stronger in 2a than in 2b. The structures of 2a, 2b were determined by X-ray crystallography. These compounds form centrosymmetric dimers via two intermolecular P=O……H–N hydrogen bonds. Strong intermolecular N–H…N, N–H…O and weak C–H…O hydrogen bonds lead to a three-dimensional polymeric cluster in the 2a while intermolecular strong N–H……N and weak C–H……O hydrogen bonds form a two-dimensional polymeric chain in 2b.     

Synthesis and Structure of Catena-[Bis(2-Methylimidazole)(μ-Phthalato)cobaltate(II)]

A new coordination compound [Co(Pht)(2-MeIm)₂] (I), where Pht^2–is the deprotonated radical of o-phthalic acid (H₂Pht) and 2-MeIm is 2-methylimidazole, was synthesized. Its structure was established using X-ray diffraction analysis. The crystal is orthorhombic: space group Pca2₁, a= 15.350(3), b= 7.957(2), c= 13.997(3) Å, (calcd.) = 1.505 g/cm³, and Z= 4. The tetrahedral coordination of the Co(II) atom includes two N atoms of two 2-methylimidazole molecules and two oxygen atoms of two carboxyl groups from different acid radicals. The Co–N distances are equal to 2.022(2) and 2.031(2) Å, while the Co–O distances are 1.972(2) and 2.000(2) Å. The carboxyl groups of the Pht^2–radical and the aromatic nucleus form angles of 47.2° and 35.9°, whereas the angle formed by the carboxyl groups themselves is 50.3°. Compound Iis a polymer, which is confirmed by the 1,6-bridging function of the o-phthalic acid radical. The Co···Co distance in a chain is equal to 7.367 Å. Separate chains are united in the crystal into a framework via N–H···O hydrogen bonds.     

Molecular Structure of an Isocytosine Analog: Combined X-ray Structural and Computational Study of 2-Diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone

The structure of 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone has been studied by X-ray crystallography and quantum-chemical calculations. X-ray analysis established that 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone exists exclusively as the lactam tautomer protonated at the N3 ring nitrogen in the solid state. Crystals of 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone are monoclinic (space group P2₁/n); the unit-cell dimensions are: a = 11.0460(8) Å, b = 5.0064(4) Å, c = 22.8358(17) Å, = = 90°, = 90.521(1)°. In the crystal, molecules of 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone are assembled in planar centrosymmetric dimers by strong resonance-assisted N—H···O intermolecular hydrogen bonds from the NH group of one molecule to the C=O of the adjacent molecule (N—H···O distance 2.804 Å). Bond distances and angles are generally similar to those reported for the corresponding tautomer of isocytosine and derivatives. Quantum-chemical calculations on 2-diethylamino-6-methyl-5-n-propyl-4(3H)-pyrimidinone are also reported in order to estimate the relative energies of the possible tautomeric forms; ab initio and DFT results predict the coexistence of the N3 and AH tautomers in the gas phase. There is excellent correspondence between the crystal and the HF/6-311G** or B3LYP/6-31G* calculated structures of the N3 lactam form; the largest deviations between the experimental and computed structures are mostly the effects of strong intermolecular H bonds in the crystal.     

Cobalt(III) α-Dimethylglyoximates [Co(DH)2(Py)2]2SiF6 · 10H2O and [Co(DH)2(Thio)2]2SiF6 · 2H2O · C2H5OH: Synthesis and Structure

[Co(DH)₂(Py)₂]₂SiF₆ · 10H₂O and [Co(DH)₂(Thio)₂]₂SiF₆ · 2H₂O · C₂H₅OH complexes are synthesized and characterized by X-ray diffraction analysis. Two radicals of -glyoxime linked by hydrogen O–H···O bonds lie in the equatorial plane of the octahedral Co(III) complexes. Intramolecular (– and N–H···O) and intermolecular (O–H···F, O–H···O, N–H···F, N–H···O, N–H···S) interactions are discovered in the crystal. The influence of nonvalence interactions on the structures is discussed.     

Crystal and Molecular Structure of Bis(O,O"-diisopropyldithiophosphato-S,S")(dimethylglyoximato-N,N")rhodium(III)

The crystal and molecular structure of bis(O,O"-diisopropyldithiophosphato-S,S")(dimethylglyoximato-N,N")rhodium(III) (I) was studied using X-ray diffraction analysis: space group P2₁/c, a = 13.644 Å, b = 10.350 Å, c = 20.906 Å, = 109.02°, Z = 4. The structure was solved by the direct method and anisotropically refined by the full-matrix least-squares method to R = 0.029 using 5447 independent reflections (CAD-4 autodiffractometer, MoK ). Compound I is a mononuclear tris-chelate complex whose three ligands are singly charge anions. The individual molecule of the complex has a noncrystallographic two-fold axis; its Rh atom is coordinated by four S atoms and two N atoms, forming a distorted octahedron. The average coordination bond lengths are Rh–S 2.402 and Rh–N 2.023 Å. The molecules in structureI are joined into infinite chains via weak intramolecular C–H···S hydrogen bonds and intermolecular N–O–H···O–N hydrogen bonds.     

Decavanadates with [Et3NH] and [Me2HN(CH2)2NHMe2]: Variation in protonation state and self-assembly

Synthesis, thermal behaviour and crystal structures of [Et₃NH]₄[V₁₀O₂₆(OH)₂] (1) and [Me₂HN(CH₂)₂NHMe₂]₃[V₁₀O₂₈] · 4H₂O (2) are reported. In the crystal lattice of 1, the anions form discrete dimers via O–H···O hydrogen bonds and the cations are connected to the respective anions through N–H···O hydrogen bonds. On the other hand, 2 forms a complex three-dimensional network due to involvement of the cations, the anions and the lattice water in O–H···O and N–H···O hydrogen bonds.     

Synthesis,structure and spectroelectrochemical property of (2,2′-bipyridine)–metal (M = Pt,Pd) dichloride with 4,4′-bis(fluorous-ponytail) on bipyridine

The 4,4′-bis(R_fCH₂OCH₂)-2,2′-bpy ligands [R_f = n-C₃F₇ (1a), HCF₂(CF₂)₃ (1b)] were prepared and then treated with [MCl₂(CH₃CN)₂] (M = Pt or Pd) to result in the corresponding metal complexes, [MCl₂(4,4′-bis(R_fCH₂OCH₂)-2,2′-bpy)] (M = Pt 2a–b; Pd 3a–b). Both ligands and metal complexes were fully characterized by multi-nuclei NMR (¹H, ¹⁹F and ¹³C), FTIR, and mass (GC/MS or HR-FAB) methods. The X-ray structures of 2a–b and 3a–b were studied. With terminal CF₃, the structures of 2a and 3a exhibit disordered polyfluorinated regions in solid state. With terminal HCF₂, the structures of 2b and 3b show a π–π stacking of the bpy planes, five-membered C–H···O hydrogen bond and an unusual intramolecular blue-shifting C–H···F–C hydrogen bond system, whereas without terminal HCF₂, the structures of 2a and 3a show the similar π–π stacking, five-membered C–H···O hydrogen bond and typical orientation of polyfluorinated ponytails, but not the C–H···F–C hydrogen bond system. The CV and UV/Vis studies were also carried out.     

A New Inclusion Compound between 2,4,5,7,9,10-hexachloro-1,3,6,8-tetrakis (4-methoxyphenylthio)pyrene Host and Cyclohexane Guest Stabilized by C–H···π and C–H···Cl Interaction

Crystal structure analysis shows the 2,4,5,7,9,10-hexachloro-1,3,6,8-tetrakis-(4-methoxyphenylthio) pyrene host and its cyclohexane guest in the Pnma crystal lattice. The crystal data and refinement parameter for the title compound are: a = 15.864(3), b = 30.455(6), c = 9.231(5) Å, V = 4459.2 (14) ų. For Z = 4 and M _w = 1045.76, the calculate density Dcal = 1.558 g/cm³. The C–H···π interaction and C–H Cl interaction stabilized the inclusion of cyclohexane molecules. The S···Cl weak interaction assembled the host molecules into a two-dimensional layer structure, and a three-dimensional structure was obtained by connecting the layers with C–H···O hydrogen bonding.Electronic Supplementary Material Supplementary material is available for this article at ^*Supplementary data: crystallographic data (atomic coordinates, anisotropic displacement parameters, selected bond distance and angles) for the structures in this paper have been deposited with the Cambridge Crystallographic Data Center with CCDC 270603 as supplementary publication.     

Structure of Complexes Formed in the CuX2–Cu–N-Allylisoquinolinium Chloride System (X = Cl,Br)

The crystals of N-allylisoquinolinium chlorides of the compositions [C₉H₇N(C₃H₅)]₂Cu^IICl₄ (I), [C₉H₇N(C₃H₅)]Cu^ICl₂ · H₂O (II), and [C₉H₇N(C₃H₅)]Cu^ICl_1.43Br_0.57 · H₂O (III) were prepared by alternating-current electrosynthesis. X-ray diffraction analysis (using diffractometer models DARCH1 for I, STOE for II, and KUMA/CCD for III, MoK radiation) showed that the crystals of I are monoclinic, space group P2₁/n, a = 14.91(1) Å, b = 10.41(1) Å, c = 16.90(1) Å, = 109.73(8)°, V = 2470(8) ų, Z = 4. The crystals of isostructural compounds II and III are triclinic, space group P, Z = 2; crystals II: a = 7.2446(6) Å, b = 7.4379(6) Å, c = 12.110(1) Å, = 80.95(1)°, = 85.55(1)°, = 86.60(1)°, V = 641.8(2) ų; crystals III: a = 7.253(2) Å, b = 7.459(4) Å, c = 12.151(5) Å, = 80.82(4)°, = 83.73(3)°, = 86.81(4)°, V = 644.6(9) ų. The structure of I is composed of Cu^IICl₄ ^2– tetrahedra and N-allylisoquinolinium cations united by C–H···Cl hydrogen bonds in corrugated layers. The crystal structures of -complexesII and III are built of [C₉H₇(C₃H₅)]₂Cu₂ ^IX₄ dimers, which form layers along the c axis due to the C–H···X hydrogen bonds. An important role in the structure formation is played by water molecules, which crosslink the organometallic layers to form a three-dimensional framework through the O–H···X contacts.     

Crystal Structure of 4,7,13,16,21,24-Hexaoxa-1,10-diazoniabicyclo[8.8.8]hexacosane Triaquachlorolithium Dichloride

The crystal adduct (1 :1) 4,7,13,16,21,24-hexaoxa-1,10-diazoniabicyclo[8.8.8]hexacosane triaquachlorolithium dichloride, [H₂(Crypt-222)]²⁺ · 2Cl^– · [LiCl(H₂O)₃] (I), was synthesized and studied using X-ray diffraction analysis. Structure I (space group R3, a = 7.922 Å, c = 37.207 Å, Z = 3) was solved by direct methods and anisotropically refined by the full-matrix least-squares method to R = 0.034 for 1363 independent reflections (CAD4 autodiffractometer, MoK ). Crystal I consists of disordered 2.2.2-cryptand dications, chloride anions, and tetrahedral [LiCl(H₂O)₃] complexes. All of them lie on threefold axes. There are tridentate ⁺N–H (···O)₃ hydrogen bonds in the [H₂(Crypt-222)]²⁺ dication. The crystal structure of adduct I contains a complex interionic hydrogen bonding system.     

Synthesis,Crystal and Molecular Structures of [Co(MH)2(Thio)2][BF4] · H2O and [Co(DH)2(NH3)2][BF4]

Crystal structures of [Co(MH)₂(Thio)₂][BF₄] · H₂O (I) and [Co(DH)₂(NH₃)₂][BF₄] (II), where MH^– is H₃C–C(NOH)–C(NO^–)–H and DH^– is H₃C–C(NOH)–C(NO^–)–CH₃, were determined by X-ray diffraction. The crystals are monoclinic, space group C2/c, unit cell parameters (for I and II, respectively): a = 22.018(2) Å, b = 7.943(1) Å, c = 11.681(1) Å, = 92.68(1)° and a = 21.436(2) Å, b = 6.400(2) Å, c = 12.389(2) Å, = 113.13(1)°. In both cases, the Co(III) coordination polyhedron is a centrosymmetrical trans-octahedron, N₄S₂ for I and N₆ for II. In the crystals of I and II, the complex cations and the outer-sphere [BF₄]^– anions (and the crystal water molecules in I) form elaborate hydrogen bonding system.     

Interaction of Phosphorus Iminoilides with Metal Acetates. Crystal and Molecular Structure of Cu[(2-O–)(5-NO2)C6H3N–CH=CH–+PPh3]2 · 2CHCl3

The structure of the Cu[(2-O^–)(5-NO₂)C₆H₃N–CH=CH–⁺PPh₃]₂ complex with the CuN₂O₂ coordination core of distorted square-planar geometry was established by X-ray diffraction analysis. The molecules in the crystal structure of the Cu[(2-O^–)(5-NO₂)C₆H₃N–CH=CH–⁺PPh₃]₂ · 2CHCl₃ solvate are bound via hydrogen bonds of two types, namely, C(sp ²)–H···O and C(sp ³)–H···O.     

Ritter reactions. VIII. Inclusion compounds formed betweenN-(5H-Dibenzo[a,d]cycloheptyl)acetamides and dioxane

5H-Dibenzo[a, d]cyclohepten-5-ol2 and its saturated analogue4 undergo Ritter reactions with acetonitrile and sulfuric acid to afford the acetamide derivatives3 or5 respectively. Both products form unstable inclusion compounds when crystallised from dioxane. The crystal structure of the dioxane compound of3 is reported. This material [(C₁₇H₁₅NO)·(C₄H₈O₂)₂,Pnma,a=9.616(1),b=23.280(2),c=10.298(1) Å,Z=4,R=0.054] has the amide molecules arranged in parallel chains by means of intermolecular –N–HO=C hydrogen bonds. The inclusion compound is stabilised by means of –C–HO-hydrogen bonds. Each dioxane molecule is involved in five such interactions to neighbouring molecules of3 and dioxane.Author for correspondence. Supplementary Data relating to this article are deposited with the British Library as supplementary publication No. SUP 82173 (5 pages).     

Syntheses, structural determination and binding studies of nine-coordinate mononuclear (EnH2)1.5 [ErIII(Ttha)] · 3H2O and (EnH2)[ErIII(Egta)(H2O)]2 · 6H2O

In this work, the title complexes, (EnH₂)_1.5[Er^III(Ttha)] · 3H₂O (I) and (EnH₂)[Er^III(Egta)(H₂O)]₂ · 6H₂O (II), where En = ethylenediamine, H₆Ttha = triethylenetetramine-N,N,N′,N″,N″’,N″′-hexaacetic acid, H₄Egta = ethyleneglycol-bis-(2-aminoethylether)-N,N,N′,N′-tetraacetic acid, have been successfully synthesized. Their structures have been characterized by IR spectroscopy and single-crystal X-ray diffraction techniques. The X-ray diffraction reveals that I is nine-coordinated and crystallizes in the monoclinic crystal space group P2/n with cell dimensions a = 17.6058(16), b = 9.6249(9), c = 20.560(2) ?, β = 109.7440(10)°, and V = 3279.1(5) ?³. Compound II is also nine-coordinated and crystallizes in the monoclinic crystal space group P2₁/n with the cell dimensions a = 12.938(6), b = 12.651(5), c = 14.943(6) ?, β = 105.441(5)°, and V = 2357.5(17) ?³. In I, each EnH₂²⁺ cation connects three adjacent [Er^III(Egta)(H₂O)]⁻ complex anions through hydrogen bonds, while in I, there are two types of EnH₂ ²⁺ anions. One is highly symmetrical, forming hydrogen bonds with two neighboring [Er^III(Ttha)]³⁻ complex anions. The other anion connects three adjacent [Er^III(Ttha)]³⁻ complex anions through hydrogen bonds. These hydrogen bonds lead to the formation of 2D ladder-like layer structure.     

Crystal Structure of Diaqua(1,2-bis(2-(o-hydroxyphenoxy)ethyloxy)ethane)(perchlorato-O)strontium Perchlorate Hydrate

The aqua complex of podand 1,2-bis(2-(o-hydroxyphenoxy)ethyloxy)ethane (L) with strontium perchlorate of the composition [Sr(ClO₄)L(H₂O)₂]⁺ · ClO₄ ^– · H₂O (I) was synthesized and studied using X-ray diffraction analysis: space group P2₁/c, a = 16.195 Å, b = 11.382 Å, c = 16.646 Å, = 117.01°, Z = 4. The structure was solved by direct method and anisotropically refined by the full-matrix least-squares method to R = 0.069 for 4278 independent reflections (CAD4 autodiffractometer, MoK ). Structure I contains complex cation [Sr(ClO₄)L(H₂O)₂]⁺ of the host–guest type. The Sr²⁺ cation (coordination number 9) is coordinated to all six O atoms of the L podand, O atom of a disordered ClO₄ ^– ligand, and two O atoms of two water molecules. The coordination polyhedron of Sr²⁺ is irregular; in a rough approximation, it can be described as a face-centered cube. The crystal structure of I contains an infinite three-dimensional network of the O–H···O hydrogen bonds joining the complex cations, ClO₄ ^– anions, and molecules of crystallization water.     

Effect of intermolecular =C–HO interaction on the crystal structure and vibrational properties of 2,6-dimethyl-4-nitropyridine N-oxide

The crystal structure of 2,6-dimethyl-4-nitropyridine N-oxide (DMNPO) has been determined at ambient temperature. The compound crystallizes as a monoclinic structure, space group P2/n, with 12 molecules per unit cell. The unit cell contains three non-equivalent formula units. The nitro group is not coplanar with the pyridine ring. Through a system of =C–HO hydrogen bonds the molecules are arranged into a two-dimensional network of layers parallel to the axc plane.The IR and Raman spectra, measured in the 3500–100 cm⁻¹ region at ambient temperature, are correlated with X-ray structural data. The assignment of IR and Raman bands is given. The appearance of characteristic vibrational features in the spectra of this compound and the observed shifts of the =C–H and N–O IR active stretching modes, when the sample is dissolved in CCl₄, is discussed in terms of the relatively strong =C–HO hydrogen bonds present in this crystal.     

Synthesis and Crystal Structure of Diaqua(2.2.2-Cryptand)strontium Dichloride Trihydrate

Absract—Diaqua(2.2.2-Cryptand)strontium dichloride trihydrate [Sr(2.2.2-Crypt)(H₂O)₂]²⁺ · 2Cl^– · 3H₂O (I) was prepared and studied by X-ray diffraction. The triclinic structure of I (space group P , a = 9.152 Å, b = 10.140 Å, c = 15.219 Å, = 88.84°, = 88.19°, = 87.62°, Z = 2) was solved by the direct method and refined by full-matrix least-squares calculations in the anisotropic approximation to R = 0.050 for 4188 independent reflections (CAD4 automated diffractometer, CuK radiation). The structure contains the [Sr(2.2.2-Crypt)(H₂O)₂]²⁺ host–guest cation. The Sr²⁺ cation resides in the 2.2.2-cryptand cavity and is coordinated by all eight heteroatoms (6O + 2N) of the cryptand ligand and by two O atoms of water molecules. The Sr²⁺ coordination polyhedron (C.N. 10) is a highly distorted dibase-centered two-cap trigonal prism. The crystal structure of I contains a branched system of ion–ion (intermolecular) hydrogen bonds O(w)–H···Cl^–, which connect the complex cations, the Cl^– anions, and the crystal water molecules to form infinite thick layers parallel to the yz plane.     

Ferrocene Compounds. XXVII. Synthesis and Structure of 2-(Ferrocenylmethyl)propane-1,3-diol

The title compound was obtained by reduction of diethyl (ferrocenylmethyl)malonate with lithium aluminium hydride in diethyl ether. The structure of this novel ferrocene derivative was assigned by means of elemental analysis, IR, [¹H]NMR, and [¹³C]NMR spectroscopy. The structure was also confirmed by a single crystal X-ray study. The compound crystallizes in monoclinic P2₁/a space group with unit cell dimensions: a = 9.7360(6), b = 27.040(5), c = 14.767(3) Å, = 103.835(6)°, V = 3774.8(11) ų, Z = 12. The asymmetric unit contains three crystallographically independent molecules. In the ferrocenyl moieties, the Fe–C bond distance values are in the range 2.006(5)—2.051(3) Å and C–C distances in the range 1.366(7)–1.425(4) Å. The cyclopentadienyl rings in each of the molecules are mutually twisted by about 13° from the eclipsed conformation. The hydroxyl groups are involved in the intermolecular O–H...O hydrogen bond formation with O-O distances in the range 2.686(3)–2.801(4) Å forming infinite two-dimensional network in a [0 0 1] plane. The crystal structure is additionally stabilized by C–H-O weak intermolecular hydrogen bonds.     

Cooperative N–H···N,N–H···O,and O–H···N bonded molecular dimers of two new 3,5-diaryl-1<Emphasis Type="Italic">H</Emphasis>-pyrazoles

Two new 3,5-diaryl-1H-pyrazoles: 3(5)-(4-tert-butylphenyl)-5(3)-(naphthalene-2-yl)-1H-pyrazole (1) and 5-(4-(benzyloxy)phenyl)-3-(furan-2-yl)-1H-pyrazole (2) were synthesized and characterized. Two strong ions peaks [2M]⁺ and [2M + Na]⁺ observed in the ESI–MS spectra are attributed to the dimerization process in solution formed by intermolecular N–H···N hydrogen bonds. The crystal structures have been determined by X-ray crystal structure analysis. Compound 1 exists as a pair of tautomers 1a and 1b, and its dimer [R ₂²(6) motif] is formed by the tautomers 1a and 1b. Compound 2 only exists as a 2a tautomer, and interesting intermolecular N–H···O and O–H···N hydrogen bonds link two pyrazoles and two methanol molecules, leading to the formation of an R ₄⁴(10) dimer motif.