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.     

Conformational Polymorphism in Racemic 2,4-Di-<Emphasis Type="Italic">o</Emphasis>-Benzoyl-6-<Emphasis Type="Italic">o</Emphasis>-Tosyl <Emphasis Type="Italic">myo</Emphasis>-Inositol 1,3,5-Orthoacetate

The title compound, C₂₉H₂₆O₁₀S, yields two conformational polymorphs concomitantly from dichloromethane-methanol mixture; the major polymorph grows as plates (Form I, monoclinic, P2₁/n) and the minor polymorph grows as needles (Form II, triclinic, P-1). The two forms differ mainly in orientation of the tosyl group. In Form I, sulfonyl oxygen of the tosyl group makes intermolecular C −H…O interactions, whereas the same group in Form II is involved in an intramolecular short dipolar S=O…C=O (sulfonyl-carbonyl) contact. The molecular organization and the influence of various weak non-covalent interactions that stabilize these conformers in the crystal lattices are discussed.     

Hydro­gen bonds and C—H⋯O interactions in 2‐(2‐methyl­benzyl)­malonic acid at 150 K

The title compound, C₁₁H₁₂O₄, crystallized in the centrosymmetric space group Pbca with one mol­ecule as the asymmetric unit. The two hydrogen bonds have O_D?O_A distances of 2.667 (2) and 2.628 (2) Å, and O—H?O angles of 179 (2) and 177 (2)°. Each hydrogen bond forms an R(8) cyclic dimer about a center of symmetry. The leading intermolecular C—­H?O interaction has an H?O distance of 2.66 Å and a C—H?O angle of 160°. Taken together with the hydrogen bonds, it results in a three‐dimensional network of inter­actions. The structure is compared with that of a close analog, benzyl­malonic acid.     

Crystal and Molecular Structures of 3-Carboxypropyltriphenylphosphonium Diiodobromide

Complexation in the 3-carboxypropyltriphenylphosphonium bromide–molecular iodine system in chloroform was studied. The maximum number of iodine molecules coordinated by 3-carboxypropyltriphenylphosphonium bromide was established by the spectrophotometric method using a function of the average-iodine number, and the stability constant of the complex was determined. The [(C₆H₅)₃P(CH₂)₃COOH]BrI₂ diiodobromide was studied by X-ray diffraction analysis. The characteristic feature of the crystalline salt was the formation of dimer associates: anionic associates were formed due to the Br···Br intermolecular interactions and cationic associates were formed due to the O···H–O hydrogen bonds. The data obtained were correlated to the results of quantum-chemical calculations.     

Time-Dependent Density Functional Theory Study on the Electronic Excited State of Hydrogen-Bonded Clusters Formed by 2-Hydroxybenzonitrile (<Emphasis Type="Italic">o</Emphasis>-Cyanophenol) and Carbon Monoxide

Time-dependent density functional theory (TDDFT) method has been carried out to investigate excited-state hydrogen-bonding dynamics between 2-hydroxybenzonitrile (o-cyanophenol) and carbon monoxide. We have demonstrated that intermolecular hydrogen bond between 2-hydroxybenzonitrile (o-cyanophenol) and C=O group are significantly strengthened in the electronically excited state by theoretically monitoring the changes of the bond lengths of hydrogen bonds and hydrogen-bonding groups in different electronic states. In this study, we firstly analyze frontier molecular orbitals (MOs). Our results are consistent with the intermolecular hydrogen bond strengthening in the electronically excited state of Coumarin 102 in alcoholic solvents, which has been demonstrated for the first time by Zhao and Han. Moreover, the calculated electronic excitation energies of the hydrogen bonding C=O and O–H groups are markedly red-shifted upon photoexcitation, which illustrates the hydrogen bonds strengthen in the electronically excited state again. And the geometric structures in both ground state and the S₁ state of this hydrogen-bonded complex are calculated using the density functional theory (DFT) and TDDFT methods, respectively.     

Hydro­gen bonds and C—H⋯O ­interactions in the enol tautomer of 4‐­(phenylsulfonyl)spiro­[cyclo­pentane‐1,9′‐[9H]­fluorene]‐2,3‐dione

The title compound, 2‐hydroxy‐1‐(phenyl­sulfonyl)­spiro­[cyclo­pentene‐4,9′‐[9H]­fluoren]‐3‐one, C₂₃H₁₆O₄S, crystallized in the centrosymmetric space group P2₁/n with one mol­ecule as the asymmetric unit. The hydroxyl‐H atom is ordered and participates in a single intramolecular hydrogen bond and in a single intermolecular hydrogen bond, in which the O_D—H distance is 0.90 (2), H?O_A is 2.34 (3), O_D?O_A is 2.987 (2) Å and O_D—H?O_A is 129 (2)°. The intermolecular hydrogen bond forms an R(12) cyclic dimer about a center of symmetry. There are six leading C—H?O interactions. Taken together, these interactions form a three‐dimensional network. Structural comparisons are made with tetrabenzodi­spiro­[4.0.4.3]­tridecatetraene.     

Hydro­gen bonding and C—H⃛O interactions in 2‐[1‐(1‐naphthyl)ethyl]benzoic acid at 150 K

The title acid, C₁₉H₁₆O₂, crystallized in the centrosymmetric space group Pnna with three mol­ecules in the asymmetric unit (apparently the first reported instance of Z′ = 3 in this space group). Four intermolecular hydrogen bonds have O_D?O_A distances of 2.660 (2), 2.594 (2), 2.633 (2) and 2.646 (2) Å, and angles of 177 (2), 179 (2), 175 (2) and 175 (2)°. The four hydrogen bonds form two R(8) cyclic dimers, one about a twofold axis. Five leading intermolecular C—H?O interactions are present. Although first‐ and second‐level graph sets involving these nine interactions are dominated by finite patterns, a three‐dimensional network becomes evident upon analysis of higher‐level graphs. A number of intramolecular C—H?O interactions are also present.     

Syntheses,structures, and properties of two mononuclear cobalt(III) azido complexes containing a tetradentate N-donor Schiff base as end-capping ligand

Two hexacoordinated mononuclear Co(III) compounds of the type cis-[Co(L)(N₃)₂] X [1, X = ClO₄; 2, X = PF₆; L = N,N′-(bis(pyridine-2-yl)benzylidine)-1,4-butanediamine] have been synthesized and characterized by physicochemical and spectroscopic methods. The crystal structures of complexes 1 and 2 both have distorted octahedral geometry with two terminal azides in mutual cis orientations. In the crystalline state, two mononuclear units of 1 are associated by weak C–H…π interactions to produce a dimeric unit, which packs through C–H…O hydrogen bonds and π…π interactions leading to a 2-D continuum. The mononuclear units in 2 are engaged in weak cooperative intermolecular C–H…π interactions and multiple C–H…F hydrogen bonds giving rise to a 3-D network structure. These diamagnetic compounds are redox active and show luminescence in DMF solutions.     

(±)‐cis‐2‐Methyl‐4‐oxo­cyclo­hexane­carboxyl­ic acid: catemeric hydrogen bonding in a δ‐keto acid derived from Hagemann's ester

The title compound, C₈H₁₂O₃, crystallizes as acid‐to‐ketone hydrogen‐bonding catemers, in which hydrogen bonds progress from the carboxyl group of each mol­ecule to the ketone group of a translationally related neighbor [O⋯O = 2.738 (3) Å and O—H⋯O = 153 (4)°]. Four separate hy­drogen‐bonding chains proceed through the cell in centrosymmetrically related pairs along axes lying in the ab plane. Three intermolecular C—H⋯O close contacts exist involving both carboxyl O atoms. Factors contributing to the choice of hydrogen‐bonding mode are discussed.     

Molecular orbital theory of the hydrogen bond. 25. Water–uracil complexes in excited n → π states

Hydrogen bonding of uracil with water in excited n → π* states has been investigated by means of ab initio SCF -CI calculations on uracil and water–uracil complexes. Two low-energy excited states arise from n → π* transitions in uracil. The first is due to excitation of the C₄? O group, while the second is associated with excitation of the C₂? O group. In the first n → π* state, hydrogen bonds at O₄ are broken, so that the open water–uracil dimer at O₄ dissociates. The “wobble” dimer, in which a water molecule is essentially free to move between its position in an open structure at N₃? H and a cyclic structure at N₃? H and O₄ in the ground state, collapses to a different “wobble” dimer at N₃? H and O₂ in the excited state. The third dimer, a “wobble” dimer at N₁? H and O₂, remains intact, but is destabilized relative to the ground state. Although hydrogen bonds at O₂ are broken in the second n → π* state, the three water–uracil dimers remain bound. The “wobble” dimer at N₁? H and O₂ changes to an excited open dimer at N₁? H. The “wobble” dimer at N₃? H and O₄ remains intact, and the open dimer at O₄ is further stabilized upon excitation. Dimer blue shifts of n → π* bands are nearly additive in 2:1 and 3:1 water:uracil structures. The fates of the three 2:1 water:uracil trimers and the 3:1 water:uracil tetramer in the first and second n → π* states are determined by the fates of the corresponding excited dimers in these states.     

trans‐4‐Acetylcyclo­hexane­carboxyl­ic acid and ()‐trans‐2‐acetyl­cyclo­hexane­carboxyl­ic acid: hydrogen‐bonding patterns in two isomeric keto acids

Both title compounds, C₉H₁₄O₃, display carboxyl‐dimer hydrogen‐bonding patterns. The 4‐acetyl isomer adopts a chiral conformation with negligible disordering of the methyl and carboxyl groups and forms centrosymmetric dimers across the b and c edges of the chosen cell [O?O = 2.667 (3) Å and O—H?O = 175°]. Intermolecular C—H?O close contacts were found for both carbonyl groups. In the 2‐acetyl isomer, there is no intramolecular interaction between the carboxyl and acetyl groups and the hydrogen bonding involves centrosymmetric carboxyl dimerization across the ab and ac faces of the chosen cell [O?O = 2.668 (2) Å and O—H?O = 173°]. The carboxyl group is negligibly disordered, but significant rotational disordering was found for the acetyl methyl group. An intermolecular C—H?O close contact was found involving the ketone group.     

Ferrocene compounds. XXXIV. 1′‐(tert‐Butoxycarbonylamino)ferrocene‐1‐carboxylic acid

Heteroannularly substituted ferrocene derivatives can act as model systems for various hydrogen‐bonded assemblies of biomol­ecules formed, for instance, by means of O—H⋯O and N—H⋯O hydrogen bonding. The crystal structure analysis of 1′‐(tert‐butoxy­carbonyl­amino)­ferrocene‐1‐carbox­ylic acid, [Fe(C₁₀H₁₄NO₂)(C₆H₅O₂)] or (C₅H₄COOH)Fe(C₅­H₄NHCOOC(CH₃)₃, reveals two independent mol­ecules within the asymmetric unit, and these are joined into discrete dimers by two types of intermolecular hydrogen bonds, viz. O—H⋯O and N—H⋯O. The –COOH and –NHCOOR groups are archetypes for dimer formation via two eight‐membered rings. The O—H⋯O hydrogen bonds [2.656 (3) and 2.663 (3) Å] form a cyclic carboxylic acid dimer motif. Another eight‐membered ring is formed by N—H⋯O hydrogen bonds [2.827 (3) and 2.854 (3) Å] between the N—H group and an O atom of another carbamoyl moiety. The dimers are assembled in a herring‐bone fashion in the bc plane.     

Isotope effect in the formation of hydrogen peroxide by the sonolysis of light and heavy water

The kinetics of the formation of hydrogen peroxide by the sonolysis of light and heavy water in argon and oxygen atmospheres was investigated. The sonochemical reaction has a zero order with respect to hydrogen peroxide (H₂O₂, D₂O₂, or DHO₂). The measurement of the kinetic isotope effect (α), defined as the ratio of the reaction rates in H₂O and D₂O, carried out under argon gave a value of 2.2±0.3. The observed isotope effect decreases with an increase in the concentration of light water in H₂O−D₂O mixtures. No isotope effect is displayed in the oxygen atmosphere (α=1.05±0.10). The isotope effect is determined presumably by the mechanism of sonochemical decomposition of water molecules, which includes the H₂O−Ar^* and D₂O−Ar^* energy exchange (where Ar^* are argon atoms in the³P_2.0 excited state) in the nonequilibrium plasma generated by a shock wave, arising upon a cavitation collapse. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 645–649, April, 2000.     

Analysis of relaxation on polypropyleneglycols above vitrification temperature

The dielectric spectra of polypropyleneglycols H-(C₃H₆O) _{N p} -OH (PPGs), where N _p = 1, 2, 3, 7, 12, 17, 20, 34, 69, were analyzed in terms of the Dissado Hill (DH) cluster model above the vitrification temperatures. In PPGs, the structural clusters are associates formed by intra- and intermolecular hydrogen bonds. The activation processes of cleavage and formation of intermolecular hydrogen bonds in clusters, when the total number of intermolecular hydrogen bonds changes, are characterized by the parameter n _DH. The fluctuation processes of simultaneous exchange of molecules between adjacent clusters correspond to redistributions of intermolecular hydrogen bonds between clusters, when only the position but not the total number of intermolecular hydrogen bonds changes, and are characterized by the parameter m _DH. The relaxation time τ_DH at 303 K and 423 K and the parameters n _DH and m _DH of the dielectric spectra were calculated. The activation energies of relaxation in the range 210–323 K were determined. The mean statistic squares of the dipole moments of clusters 〈μ_c²〉 and di-PG, PPG-425 (N _p = 7), and PPG-2025 (N _p = 34) molecules 〈μ_m²〉 at 303 K and 423 K were calculated. The number of the units of the oxypropylene chains involved in relaxation was determined. The dependence of the parameters of the DH model, relaxation energies, 〈μ_c²〉 and 〈μ_m²〉 on N _p were studied.     

Crystal Structure of A Molecular Complex Compound of Antimony(III) Fluoride with L-Leucine

Single crystal X-ray diffraction analysis is used to determine the crystal structure of a newly synthesized molecular complex compound of antimony(III) fluoride with L-leucine of the composition SbF₃(C6H₁₃NO₂) (orthohombic crystal system: a = 5.7948(8) ?, b = 6.2433(9) ?, c = 28.594(4) ?, Z = 4, P2₁2₁2₁ space group). The structure consists of SbF₃ molecules and L-leucine bound into polymer chains by bidentate bridging carboxyl groups of amino acid molecules. Weak Sb…F(1)^b bonds combine the adjacent chains into polymer ribbons organized by N-H…. F and N-H…. O hydrogen bonds into a framework.     

Synthesis,characterization, and X-ray crystal structures of zinc(II) complexes with schiff bases 2-[(2-isopropylaminoethylimino)methyl]-5-methoxyphenol and N,N-dimethyl-N′-(1-pyridin-2-ylethylidene)ethane-1,2-diamine

Two new zinc(II) complexes, [ZnBr₂L¹] (I) and [ZnBr₂L²] (II), where L¹ is 2-[(2-isopropylaminoethylimino)methyl]-5-methoxyphenol and L² is N,N-dimethyl-N′-(1-pyridin-2-yl-ethylidene)ethane-1,2-diamine, were prepared and characterized using elemental analysis, FT-IR spectroscopy, and X-ray single-crystal diffraction. In complex I, the Zn(II) atom is coordinated by one phenolic O and one imino N atoms of L¹ and two Br atoms, forming a tetrahedral coordination geometry. In complex II, the Zn(II) atom is in a trigonal bipyramidal coordination geometry with the equatorial plane formed by the imino N atom of L² and two Br atoms and with the two axial positions occupied by one pyridine N and one amino N atoms of L². In the crystal structure of I, the mononuclear zinc complex molecules are linked through intermolecular N-H…O and N-H…Br hydrogen bonds, forming chains running along the y axis. The chains are further linked via intermolecular C-H…Br hydrogen bonds. In the crystal structure of II, the mononuclear zinc complex molecules are linked through intermolecular C-H…Br hydrogen bonds, forming a 3D network.     

Dynamic and electrooptical properties of FH…F and FH…N hydrogen bridges

The dynamic and electrooptical parameters of the hydrogen bridges in (HF)₂, FH…FCD₃, FH…NCH, and FH…NCCH₃ complexes were calculated by the MINDO/3 method. Relationships between these parameters have been found. These parameters for the F−H…Y bridges mainly coincide with the relationships previously established for the hydrogen O−H…Y bridges. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1067–1069, May, 1997.     

Hydrogen bonds in dimers of 3-hydroxy-2-methyl-4-pyrone. AIM analysis

According to quantum topological analysis performed at the MP2/6-311++G** level the intramolecular hydrogen bond OH⋯O=C in 3-hydroxy-2-methyl-4-pyrone (maltol) is weak and has ionic nature. This bond is broken upon formation of H-complex of maltol with phosgene and with increase the polarity of medium. The chain dimer of maltol is stabilized by weak intermolecular bonds OH⋯O=C and CH⋯O=C of ionic character, whereas the cyclic dimer by two medium in strength intermolecular hydrogen bonds OH⋯O=C. Original Russian Text ? E.P. Doronina, T.N. Aksamentova, N.N. Chipanina, S.A. Mukha, S.A. Medvedeva, 2009, published in Zhurnal Obshchei Khimii, 2009, vol. 79, No. 2, pp. 308–313.     

Hydrogen‐bonded networks in 1‐(4‐methoxyphenyl)‐2,2‐dimethylpropan‐1‐ol

The asymmetric unit of the title compound, C₁₂H₁₈O₂, contains two independent molecules. They differ only slightly in conformation but form completely different intermolecular hydrogen‐bonded arrays. One molecule exhibits disorder in the hydroxy group region, but this does not influence the formation of hydrogen bonds. The bulky tert‐butyl group on one side of the carbinol C atom and the benzene ring on the other side promote the formation of discrete dimeric motifs via hydrogen‐bridged hydroxy groups. Dimers are further joined by strong hydroxy–methoxy O—H...O bonds to form chains with dangling alcohol groups. Weaker intermolecular C—H...O interactions mediate the formation of a two‐dimensional network.     

The synergistic co‐operation of N—H…O=P hydrogen bonds and C—H…OX weak intermolecular interactions (X is =P or —C) in the (CH3O)2P(O)(NH–NHC6F5) amidophosphoester: a combined X‐ray crystallographic and theoretical study

The asymmetric unit of O,O′‐dimethyl [(2,3,4,5,6‐pentafluorophenyl)hydrazinyl]phosphonate, C₈H₈F₅N₂O₃P, is composed of two symmetry‐independent molecules with significant differences in the orientations of the C₆F₅ and OMe groups. In the crystal structure, a one‐dimensional assembly is mediated from classical N—H…O hydrogen bonds, which includes R₂²(8), D(2) and some higher‐order graph‐set motifs. By also considering weak C—H…O=P and C—H…O—C intermolecular interactions, a two‐dimensional network extends along the ab plane. The strengths of the hydrogen bonds were evaluated using quantum chemical calculations with the GAUSSIAN09 software package at the B3LYP/6‐311G(d,p) level of theory. The LP(O) to σ*(NH) and σ*(CH) charge‐transfer interactions were examined according to second‐order perturbation theory in natural bond orbital (NBO) methodology. The hydrogen‐bonded clusters of molecules, including N—H…O and C—H…O interactions, were constructed as input files for the calculations and the strengths of the hydrogen bonds are as follows: N—H…O [R₂²(8)] > N—H…O [D(2)] > C—H…O. The decomposed fingerprint plots show that the contribution portions of the F…H/H…F contacts in both molecules are the largest.