scholarly journals Coordination versus hydrogen bonds in the structures of different tris(pyridin-2-yl)phosphoric triamide derivatives

RSC Advances ◽  
2021 ◽  
Vol 11 (14) ◽  
pp. 8178-8197
Author(s):  
Marjan Sebghati ◽  
Atekeh Tarahhomi ◽  
Marjan Sadat Bozorgvar ◽  
Dan G. Dumitrescu ◽  
Arie van der Lee
Keyword(s):  
Hydrogen Bonds ◽  
Metal Complex ◽  
Crystal Packing ◽  
Phosphoric Triamide ◽  
Improved Model ◽  
Role Of Solvent

Tris(pyridin-2-yl)phosphoric triamide, as a metal complex and purely organic pseudopolymorphs, and the role of solvent/hydrate and substituent in the formation of the crystal packing features, along with an improved model of the MOF structure of Cu(ii)O6 are investigated.

Structural differences/similarities of diastereotopic groups in three new chiral phosphoramides

2021 ◽  
Vol 77 (4) ◽  
pp. 186-196
Author(s):  
Negin Lal Zakaria ◽  
Mehrdad Pourayoubi ◽  
Mahsa Eghbali Toularoud ◽  
Michal Dušek ◽  
Eliska Skorepova
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Crystal Packing ◽  
Mirror Image ◽  
Solution Nmr ◽  
Chiral Amine ◽  
One Dimensional ◽  
Nmr Study ◽  
Structural Differences ◽  
Phosphoric Triamide

The crystal structures of two single-enantiomer amidophosphoesters with an (O)2P(O)(N) skeleton and one single-enantiomer phosphoric triamide with an (N)2P(O)(N) skeleton were studied. The compounds are diphenyl [(R)-(+)-α-4-dimethylbenzylamido]phosphate, (I), and diphenyl [(S)-(−)-α-4-dimethylbenzylamido]phosphate, (II), both C21H22NO3P, and N-(2,6-difluorobenzoyl)-N′,N′′-bis[(R)-(+)-α-ethylbenzyl]phosphoric triamide, C25H28F2N3O2P, (III). The asymmetric units contain two amidophosphoester molecules for (I) and (II), and one phosphoric triamide molecule for (III). In the crystal structures of (I) and (II), molecules are assembled in a similar one-dimensional chiral ribbon architecture, but with almost a mirror-image relationship with respect to each other through N—H...O(P) and C—H...O(P) hydrogen bonds along [010]. In the crystal structure of (III), the chiral tape architecture along [100] is mediated by N—H...O(P) and N—H...O(C) hydrogen bonds, and the tapes are connected into slabs by C—H...O interactions (along the ab plane). The differences/similarities of the two diastereotopic phenoxy groups in (I)/(II) and the two chiral amine fragments in (III) were studied on the grounds of geometry, conformation and contribution to the crystal packing, as well as 1H and 13C signals in a solution NMR study.

A Single-Molecule Perspective on the Role of Solvent Hydrogen Bonds in Protein Folding and Chemical Reactions

ChemPhysChem ◽  
2008 ◽  
Vol 9 (18) ◽  
pp. 2836-2847 ◽  
Author(s):  
Lorna Dougan ◽  
Ainavarapu Sri Rama Koti ◽  
Georgi Genchev ◽  
Hui Lu ◽  
Julio M. Fernandez
Keyword(s):  
Protein Folding ◽  
Hydrogen Bonds ◽  
Chemical Reactions ◽  
Single Molecule ◽  
Role Of Solvent

The structure of {[Co(pht)(bpy)(H2O)]·3H2O} n (pht is phthalate and bpy is 4,4′-bipyridine) and the role of solvent water clusters in structure stability

2014 ◽  
Vol 70 (5) ◽  
pp. 440-444 ◽  
Author(s):  
Miguel Angel Harvey ◽  
Sebastián Suarez ◽  
Fabio Doctorovich ◽  
Fabio D. Cukiernik ◽  
Ricardo Baggio
Keyword(s):  
Hydrogen Bonds ◽  
Water Molecule ◽  
Coordination Polymers ◽  
Water Clusters ◽  
Structure Stability ◽  
Water Molecules ◽  
Solvent Water ◽  
Coordinated Water ◽  
Role Of Solvent

The CoII cation in poly[[aqua(μ-benzene-1,2-dicarboxylato-κ3 O 1,O 2:O 1)(μ-4,4′-bipyridine-κ2 N:N′)cobalt(II)] trihydrate], {[Co(C8H4O4)(C10H8N2)(H2O)]·3H2O} n , is octahedrally coordinated by two N atoms of two 4,4′-bipyridine ligands, three O atoms from phthalate anions and a fourth O atom from a coordinated water molecule. The packing consists of planes of coordination polymers linked by hydrogen bonds mediated by three solvent water molecules; the linkage is achieved by the water molecules forming intricate oligomeric clusters which also involve the O atoms of the phthalate ligands.

Structural insights into methyl- or methoxy-substituted 1-(α-aminobenzyl)-2-naphthol structures: the role of C—H...π interactions

2019 ◽  
Vol 75 (2) ◽  
pp. 189-195 ◽  
Author(s):  
Maria Annunziata M. Capozzi ◽  
Giancarlo Terraneo ◽  
Cosimo Cardellicchio
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Methoxy Group ◽  
Crystal Packing ◽  
Molecular Surface ◽  
Methyl Group ◽  
Π Interactions ◽  
Substituted 1 ◽  
Structural Insights

Aminobenzylnaphthols are a class of compounds containing a large aromatic molecular surface which makes them suitable candidates to study the role of C—H...π interactions. We have investigated the effect of methyl or methoxy substituents on the assembling of aromatic units by preparing and determining the crystal structures of (S,S)-1-{(4-methylphenyl)[(1-phenylethyl)amino]methyl}naphthalen-2-ol, C26H25NO, and (S,S)-1-{(4-methoxyphenyl)[(1-phenylethyl)amino]methyl}naphthalen-2-ol, C26H25NO2. The methyl group influenced the overall crystal packing even if the H atoms of the methyl group did not participate directly either in hydrogen bonding or C—H...π interactions. The introduction of the methoxy moiety caused the formation of new hydrogen bonds, in which the O atom of the methoxy group was directly involved. Moreover, the methoxy group promoted the formation of an interesting C—H...π interaction which altered the orientation of an aromatic unit.

The double H-atom acceptability of the P=O group in newXP(O)(NHCH2C6H4-2-Cl)2phosphoramidates [X= C6H5O– and CF3C(O)NH–]: a database analysis of compounds having a P(O)(NHR) group

2012 ◽  
Vol 68 (2) ◽  
pp. o51-o56 ◽  
Author(s):  
Mehrdad Pourayoubi ◽  
Marek Nečas ◽  
Monireh Negari
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Linear Arrangement ◽  
Factors Affecting ◽  
Hydrogen Bond Interactions ◽  
Phosphoric Triamide ◽  
Phosphoryl Groups ◽  
Almost All

In the hydrogen-bond patterns of phenyl bis(2-chlorobenzylamido)phosphinate, C20H19Cl2N2O2P, (I), andN,N′-bis(2-chlorobenzyl)-N′′-(2,2,2-trifluoroacetyl)phosphoric triamide, C16H15Cl2F3N3O2P, (II), the O atoms of the related phosphoryl groups act as double H-atom acceptors, so that the P=O...(H—N)2hydrogen bond in (I) and the P=O...(H—Namide)2and C=O...H—NC(O)NHP(O)hydrogen bonds in (II) are responsible for the aggregation of the molecules in the crystal packing. The presence of a double H-atom acceptor centre is a result of the involvement of a greater number of H-atom donor sites with a smaller number of H-atom acceptor sites in the hydrogen-bonding interactions. This article also reviews structures having a P(O)NH group, with the aim of finding similar three-centre hydrogen bonds in the packing of phosphoramidate compounds. This analysis shows that the factors affecting the preference of the above-mentioned O atom to act as a double H-atom acceptor are: (i) a higher number of H-atom donor sites relative to H-atom acceptor centres in molecules with P(=O)(NH)3, (N)P(=O)(NH)2, C(=O)NHP(=O)(NH)2and (NH)2P(=O)OP(=O)(NH)2groups, and (ii) the remarkable H-atom acceptability of this atom relative to the other acceptor centre(s) in molecules containing an OP(=O)(NH)2group, with the explanation that the N atom bound to the P atom in almost all of the structures found does not take part in hydrogen bonding as an acceptor. Moreover, the differences in the H-atom acceptability of the phosphoryl O atom relative to the O atom of the alkoxy or phenoxy groups in amidophosphoric acid esters may be illustrated by considering the molecular packing of compounds having (O)2P(=O)(NH) and (O)P(=O)(NH)(N)groups, in which the unique N—H unit in the above-mentioned molecules almost always selects the phosphoryl O atom as a partner in forming hydrogen-bond interactions. The P atoms in (I) and (II) are in tetrahedral coordination environments, and the phosphoryl and carbonyl groups in (II) areantiwith respect to each other (the P and C groups are separated by one N atom). In the crystal structures of (I) and (II), adjacent molecules are linkedviathe above-mentioned hydrogen bonds into a linear arrangement parallel to [100] in both cases, in (I) by formingR22(8) rings and in (II) through a combination ofR22(10) andR21(6) rings.

Role of hydrogen-bonds in the crystal packing of three novel strandberg-type polyoxoanion compounds

2018 ◽  
Vol 482 ◽  
pp. 870-877 ◽  
Author(s):  
Shuyun Shi ◽  
Lingyu Chen ◽  
Xunbo Zhao ◽  
Baixiang Ren ◽  
Xiaobing Cui ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Packing

Synthesis and structural study of five new phosphoric triamides: interplay between classical and non-classical intermolecular interactions

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Bahar Bakhshipour ◽  
Atekeh Tarahhomi ◽  
Arie van der Lee
Keyword(s):  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Phosphoric Triamide ◽  
Ft Ir ◽  
Phosphoric Triamides

Abstract Phosphoric triamides are attractive to investigate because of their extensive applications in various fields, especially in medicine. Five new phosphoric triamides with the main parts [N]P(O)[NH]2 and [C(O)NH]P(O)[N]2 have been structurally analyzed by single crystal MoKα/synchrotron-based X-ray diffraction and characterized by spectroscopic methods (FT-IR and 1H, 13C, 31P NMR). Compounds crystallize in orthorhombic (1 with space group Pnma) and monoclinic (2 (P21/a), 3 (C2/c), 4 (P21/n) and 5 (P21/c)) crystal systems. The asymmetric unit of all structures consists of one phosphoric triamide molecule, except for 1 with one half of molecule. X-ray crystallography data reveal that the molecular architectures constructed by classical N—H … O hydrogen bonds are as 1D linear (building the R 2 1 ( 6 ) ${R}\_{2}^{1}(6)$ , C(4) and R 2 2 ( 10 ) / R 2 1 ( 6 ) ${R}\_{2}^{2}(10)/{R}\_{2}^{1}(6)$ motifs, respectively, for 1–3) or dimeric (the R 2 2 ( 8 ) ${R}\_{2}^{2}(8)$ ring motif for 4 and 5). A detailed investigation of the intermolecular interactions using Hirshfeld surface (HS) analysis illustrates that the H … H, O … H/H … O and C … H/H … C contacts for all compounds, and Cl … H/H … Cl and F … H/H … F contacts for 3–5, are the most significant contributors to the crystal packing. Moreover, based on the calculated enrichment ratios (E), the O … H/H … O contacts including the classical N—H … O hydrogen bonds for all structures are considered as favoured contacts.

scholarly journals Neutral and Cationic Chelidonate Coordination Polymers with N,N’-Bridging Ligands

Chemistry ◽  
2021 ◽  
Vol 3 (1) ◽  
pp. 256-268
Author(s):  
Rosa Carballo ◽  
Ana Belén Lago ◽  
Arantxa Pino-Cuevas ◽  
Olaya Gómez-Paz ◽  
Nuria Fernández-Hermida ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Dicarboxylic Acid ◽  
Single Crystals ◽  
Coordination Sphere ◽  
Coordination Polymers ◽  
Crystal Packing ◽  
Water Molecules ◽  
Bridging Ligands ◽  
Bridging Ligand

The biomolecule chelidonic acid (H2chel, 4-oxo-4H-pyran-2,6-dicarboxylic acid) has been used to build new coordination polymers with the bridging N,N’-ligands 4,4′-bipyridine (4,4-bipy) and 1,2-bis(4-pyridyl)ethane (bpe). Four compounds have been obtained as single crystals: 1D cationic coordination polymers [M(4,4-bipy)(OH2)4]2+ with chelidonate anions and water molecules in the second coordination sphere in 1∞[Zn(4,4-bipy)(H2O)4]chel·3H2O (2) and in the two pseudopolymorphic 1∞[Cu(4,4-bipy)(H2O)4]chel·nH2O (n = 3, 4a; n = 6, 4b), and the 2D neutral coordination polymers 2∞[Zn(chel)(4,4-bipy)(H2O)]·2H2O (1) and 2∞[Zn(chel)(bpe)(H2O)]·H2O (3) where the chelidonate anion acts as a bridging ligand. The effects of the hydrogen bonds on the crystal packing were analyzed. The role of the water molecules hosted within the crystals lattices was also studied.

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