Configurations and conformations of glycosyl sulfoxides

X-ray crystallographic studies of two axial glycosyl sulfoxides having RS configurations (derivatives of phenyl 2-azido-2-deoxy-1-thio-α-d-galactopyranoside S-oxide) show that they adopt anti conformations in the solid state, in contrast to previous observations and assumptions. Density functional theory (DFT) calculations at the B3lYP6–311G+(d,p)/6–31G(d) level confirm that anti conformations of both phenyl and methyl RS glycosyl sulfoxides of 2-azido-2-deoxy-α-d-pyranosides are more stable than exo-anomeric conformations in the gas phase. 1D NOE measurements indicate that the more polar exo-anomeric conformers are only populated to a slight extent in solution. The anti conformations are distorted so that the glycosyl substituents are closer to being eclipsed with H1. This distortion allows S n → σ* overlap if the sulfur lone pair is a p-type lone pair. Evidence for this overlap comes from short C1–S bond distances, as short as the comparable bond distances in the X-ray crystal structure and in the results from DFT calculations for the SS glycoside, which does adopt the expected exo-anomeric conformation, both in the solid state and in solution, and has normal n → σ* overlap. For 2-deoxy derivatives not bearing a 2-azido group, gas-phase DFT calculations at the same level indicate that the anti- and exo-anomeric conformers have comparable stabilities. Comparison of the results of the two series shows that electronegative substituents in equatorial orientations at C2 destabilize conformations with parallel S–O arrangements, the conformation favored by having an endocyclic C–O dipole antiparallel to the S–O dipole, by about 2.5 kcal mol–1 (1 cal = 4.184 J). An equatorial glycosyl sulfoxide, (SS) phenyl 3,4,6-tri-O-acetyl-2-deoxy-2-phthalimido-1-thio-β-d-glucopyranoside S-oxide, also adopts an anti conformation in the solid state as shown by X-ray diffraction. It also adopts this conformation in solution, in contrast to studies of other equatorial glycosyl sulfoxides.

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Conformational behaviour of 3-methyl-4-(4-methylbenzoyl)-1-phenyl-pyrazol-5-one: a sudden story of three desmotropes

RSC Advances ◽

10.1039/c5ra11858a ◽

2015 ◽

Vol 5 (90) ◽

pp. 73859-73867 ◽

Cited By ~ 3

Author(s):

Vanya B. Kurteva ◽

Boris L. Shivachev ◽

Rositsa P. Nikolova ◽

Svetlana D. Simova ◽

Liudmil M. Antonov ◽

...

Keyword(s):

Solid State ◽

Nmr Spectroscopy ◽

Dft Calculations ◽

Gas Phase ◽

X Ray Diffraction ◽

X Ray

The conformational behaviour of 3-methyl-4-(4-methylbenzoyl)-1-phenyl-pyrazol-5-one was studied using a combination of X-ray diffraction, NMR spectroscopy in solution and the solid state, and DFT calculations in the gas phase.

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Investigation of Solvatomorphism and Its Photophysical Implications for Archetypal Trinuclear Au3(1-Methylimidazolate)3

Molecules ◽

10.3390/molecules26154404 ◽

2021 ◽

Vol 26 (15) ◽

pp. 4404

Author(s):

Shengyang Guan ◽

David C. Mayer ◽

Christian Jandl ◽

Sebastian J. Weishäupl ◽

Angela Casini ◽

...

Keyword(s):

Crystal Structure ◽

Solid State ◽

Density Functional ◽

Bulk Material ◽

Variable Temperature ◽

Active Phase ◽

Solvent Free ◽

X Ray Diffraction ◽

X Ray ◽

Aurophilic Interactions

A new solvatomorph of [Au3(1-Methylimidazolate)3] (Au3(MeIm)3)—the simplest congener of imidazolate-based Au(I) cyclic trinuclear complexes (CTCs)—has been identified and structurally characterized. Single-crystal X-ray diffraction revealed a dichloromethane solvate exhibiting remarkably short intermolecular Au⋯Au distances (3.2190(7) Å). This goes along with a dimer formation in the solid state, which is not observed in a previously reported solvent-free crystal structure. Hirshfeld analysis, in combination with density functional theory (DFT) calculations, indicates that the dimerization is generally driven by attractive aurophilic interactions, which are commonly associated with the luminescence properties of CTCs. Since Au3(MeIm)3 has previously been reported to be emissive in the solid-state, we conducted a thorough photophysical study combined with phase analysis by means of powder X-ray diffraction (PXRD), to correctly attribute the photophysically active phase of the bulk material. Interestingly, all investigated powder samples accessed via different preparation methods can be assigned to the pristine solvent-free crystal structure, showing no aurophilic interactions. Finally, the observed strong thermochromism of the solid-state material was investigated by means of variable-temperature PXRD, ruling out a significant phase transition being responsible for the drastic change of the emission properties (hypsochromic shift from 710 nm to 510 nm) when lowering the temperature down to 77 K.

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The structure of 1-formyl-3-phenyl-Δ2-pyrazoline in the gas phase (DFT calculations), in solution (NMR) and in the solid state (X-ray crystallography)

Journal of Molecular Structure ◽

10.1016/j.molstruc.2003.10.041 ◽

2004 ◽

Vol 689 (3) ◽

pp. 251-254 ◽

Cited By ~ 14

Author(s):

I. Alkorta ◽

J. Elguero ◽

A. Fruchier ◽

N. Jagerovic ◽

G.P.A. Yap

Keyword(s):

Solid State ◽

Dft Calculations ◽

Gas Phase ◽

Solution Nmr ◽

X Ray ◽

X Ray Crystallography

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A tale of hydrogen abstraction, initially detectedviaX-ray diffraction

Acta Crystallographica Section C Structural Chemistry ◽

10.1107/s2053229614003234 ◽

2014 ◽

Vol 70 (3) ◽

pp. 250-255 ◽

Cited By ~ 1

Author(s):

Alice K. Hui ◽

Chun-Hsing Chen ◽

Adam M. Terwilliger ◽

Richard L. Lord ◽

Kenneth G. Caulton

Keyword(s):

Solid State ◽

Density Functional ◽

Computational Study ◽

Hydrogen Abstraction ◽

Open Shell ◽

X Ray Diffraction ◽

Neutral Radical ◽

X Ray ◽

Chloride Ligand ◽

Synthetic Reaction

Reaction of a bis-tetrazinyl pyridine pincer ligand, btzp, with a vanadium(III) reagent gives not a simple adduct but dichlorido{3-methyl-6-[6-(6-methyl-1,2,4,5-tetrazin-3-yl-κN2)pyridin-2-yl-κN]-1,4-dihydro-1,2,4,5-tetrazin-1-yl-κN1}oxidovanadium(IV) acetonitrile 2.5-solvate, [V(C11H10N9)Cl2O]·2.5CH3CN, a species which X-ray diffraction reveals to have one H atom added to one of the two tetrazinyl rings. This H atom was first revealed by a short intermolecular N...Cl contact in the unit cell and subsequently established, from difference maps, to be associated with a hydrogen bond. One chloride ligand has also been replaced by an oxide ligand in this synthetic reaction. This formula for the complex, [V(Hbtzp)Cl2O], leaves open the question of both ligand oxidation state and spin state. A computational study of all isomeric locations of the H atom shows the similarity of their energies, which is subject to perturbation by intermolecular hydrogen bonding found in X-ray work on the solid state. These density functional calculations reveal that the isomer with the H atom located as found in the solid state contains a neutral radical Hbtzp ligand and tetravalentd1V center, but that these two unpaired electrons are more stable as an open-shell singlet and hence antiferromagnetically coupled.

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Synthesis, Crystal Structure, Thermal Analysis, and DFT Calculations of Molecular Copper(II) Chloride Complexes with Bitopic Ligand 1,1,2,2-tetrakis(pyrazol-1-yl)ethane

Crystals ◽

10.3390/cryst9040222 ◽

2019 ◽

Vol 9 (4) ◽

pp. 222

Author(s):

Lider ◽

Sukhikh ◽

Smolentsev ◽

Semitut ◽

Filatov ◽

...

Keyword(s):

Dft Calculations ◽

Coordination Compounds ◽

Density Functional ◽

Water Molecules ◽

X Ray Diffraction ◽

Chloride Complexes ◽

Functional Theory ◽

X Ray ◽

Lattice Water ◽

Ir Bands

Two binuclear coordination compounds of Cu(II) chloride with the bitopic ligand 1,1,2,2-tetrakis(pyrazol-1-yl)ethane (Pz4) of the composition [Cu2(µ2Pz4)(DMSO)2Cl4]·4H2O and [Cu2(µ2Pz4)(DMSO)2Cl4]∙2DMSO were prepared and characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis, single-crystal X-ray diffraction, and powder diffraction analysis. It was shown that in contrast to silver(I) and copper(II) nitrates, copper(II) chloride forms discrete complexes instead of coordination polymers. The supramolecular structure of the complex [Cu2(µ2Pz4)(DMSO)2Cl4]·4H2O with lattice water molecules is formed by OH···Cl and OH···O hydrogen bonds. Density functional theory (DFT) calculations of vibrational frequencies of the ligand and its copper(II) complex allowed for assigning IR bands to specific vibrations.

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Conformational polymorphism in a Schiff-base macrocyclic organic ligand: an experimental and theoretical study

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768110029514 ◽

2010 ◽

Vol 66 (5) ◽

pp. 527-543 ◽

Cited By ~ 11

Author(s):

Leonardo Lo Presti ◽

Raffaella Soave ◽

Mariangela Longhi ◽

Emanuele Ortoleva

Keyword(s):

Schiff Base ◽

Solid State ◽

Dft Calculations ◽

Gas Phase ◽

Phase Ii ◽

Density Functional ◽

Organic Ligand ◽

Stable Phase ◽

Stable Form ◽

Molecular Conformations

Polymorphism in the highly flexible organic Schiff-base macrocycle ligand 3,6,9,17,20,23-hexa-azapentacyclo(23.3.1.111,15.02,6.016,20)triaconta-1(29),9,11,13,15(30),23,25,27-octaene (DIEN, C24H30N6) has been studied by single-crystal X-ray diffraction and both solid-state and gas-phase density functional theory (DFT) calculations. In the literature, only solvated structures of the title compound are known. Two new polymorphs and a new solvated form of DIEN, all obtained from the same solvent with different crystallization conditions, are presented for the first time. They all have P\bar 1 symmetry, with the macrocycle positioned on inversion centres. The two unsolvated polymorphic forms differ in the number of molecules in the asymmetric unit Z′, density and cohesive energy. Theoretical results confirm that the most stable form is (II°), with Z′ = 1.5. Two distinct molecular conformations have been found, named `endo' or `exo' according to the orientation of the imine N atoms, which can be directed towards the interior or the exterior of the macrocycle. The endo arrangement is ubiquitous in the solid state and is shared by two independent molecules which constitute an invariant supramolecular synthon in all the known crystal forms of DIEN. It is also the most stable arrangement in the gas phase. The exo form, on the other hand, appears only in phase (II°), which contains both the conformers. Similarities and differences among the occurring packing motifs, as well as solvent effects, are discussed with the aid of Hirshfeld surface fingerprint plots and correlated to the results of the energy analysis. A possible interconversion path in the gas phase between the endo and the exo conformers has been found by DFT calculations; it consists of a two-step mechanism with activation energies of the order of 30–40 kJ mol−1. These findings have been related to the empirical evidence that the most stable phase (II°) is also the last appearing one, in accordance with Ostwald's rule.

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On the nature of M–CO(lone pair)⋯π(arene) interactions in the solid state of fluorinated oxaphosphirane complexes

CrystEngComm ◽

10.1039/c5ce01331c ◽

2015 ◽

Vol 17 (35) ◽

pp. 6736-6743 ◽

Cited By ~ 8

Author(s):

Cristina Murcia-García ◽

Antonio Bauzá ◽

Antonio Frontera ◽

Rainer Streubel

Keyword(s):

Solid State ◽

Dft Calculations ◽

Lone Pair ◽

X Ray ◽

High Level

The X-ray structures of several oxaphosphirane tungsten(0) complexes exhibit interesting intramolecular W–CO(lone pair)ċπ(arene) interactions that have been rationalized by means of high-level DFT calculations and the CSD.

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Intra- and intermolecular interactions in a series of chlorido-tricarbonyl-diazabutadienerhenium(I) complexes: structural and theoretical studies

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s2052520620004333 ◽

2020 ◽

Vol 76 (3) ◽

pp. 417-426 ◽

Cited By ~ 2

Author(s):

Reza Kia ◽

Azadeh Kalaghchi

Keyword(s):

Intermolecular Interactions ◽

Density Functional ◽

Metal Carbonyl ◽

Lone Pair ◽

Carbonyl Complexes ◽

X Ray Diffraction ◽

Functional Theory ◽

X Ray ◽

Covalent Interaction ◽

Metal Carbonyl Complexes

A series of new chlorido-tricarbonylrhenium(I) complexes bearing alkyl-substituted diazabutadiene (DAB) ligands, namely N,N′-bis(2,4-dimethylbenzene)-1,4-diazabutadiene (L1), N,N′-bis(2,4-dimethylbenzene)-2,3-dimethyl-1,4-diazabutadiene (L2), N,N′-bis(2,4,6-trimethylbenzene)-2,3-dimethyl-1,4-diazabutadiene (L3) and N,N′-bis(2,6-diisopropylbenzene)-1,4-diazabutadiene (L4), were synthesized and investigated. The crystal structures have been fully characterized by X-ray diffraction and spectroscopic methods. Density functional theory, natural bond orbital and non-covalent interaction index methods have been used to study the optimized geometry in the gas phase and intra- and intermolecular interactions in the complexes, respectively. The most important studied interactions in these metal carbonyl complexes are n→π*, n→σ* and π→π*. Among complexes 1–4, only 2 shows interesting intermolecular n→π* interactions due to lp(C[triple-bond]O)...π* and lp(Cl)...π* (lp = lone pair) contacts.

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Structure and conformational analysis of a bidentate pro-ligand, C21H34N2S2, from powder synchrotron diffraction data and solid-state DFTB calculations

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768109027244 ◽

2009 ◽

Vol 65 (5) ◽

pp. 639-646 ◽

Cited By ~ 6

Author(s):

Edward E. Ávila ◽

Asiloé J. Mora ◽

Gerzon E. Delgado ◽

Ricardo R. Contreras ◽

Luis Rincón ◽

...

Keyword(s):

Solid State ◽

Diffraction Data ◽

Density Functional ◽

Simulated Annealing Algorithm ◽

Theoretical Calculations ◽

Tight Binding ◽

Van Der Waals Interactions ◽

Am1 Calculations ◽

X Ray Diffraction ◽

X Ray

The molecular and crystalline structure of ethyl 1′,2′,3′,4′,4a′,5′,6′,7′-octahydrodispiro[cyclohexane-1,2′-quinazoline-4′,1′′-cyclohexane]-8′-carbodithioate (I) was solved and refined from powder synchrotron X-ray diffraction data. The initial model for the structural solution in direct space using the simulated annealing algorithm implemented in DASH [David et al. (2006). J. Appl. Cryst. 39, 910–915] was obtained performing a conformational study on the fused six-membered rings of the octahydroquinazoline system and the two spiran cyclohexane rings of (I). The best model was chosen using experimental evidence from 1H and 13C NMR [Contreras et al. (2001). J. Heterocycl. Chem. 38, 1223–1225] in combination with semi-empirical AM1 calculations. In the refined structure the two spiran rings have the chair conformation, while both of the fused rings in the octahydroquinazoline system have half-chair conformations compared with in-vacuum density-functional theory (DFT) B3LYP/6-311G*, DFTB (density-functional tight-binding) theoretical calculations in the solid state and other related structures from X-ray diffraction data. Compound (I) presents weak intramolecular hydrogen bonds of the type N—H...S and C—H...S, which produce delocalization of the electron density in the generated rings described by graph symbols S(6) and S(5). Packing of the molecules is dominated by van der Waals interactions.

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