Synthesis, high-field NMR, X-ray structure, and conformational analysis of a 10-membered diamide disulfide ring

1997 ◽  
Vol 75 (2) ◽  
pp. 140-161 ◽  
Author(s):  
Rabindranath B. Maharajh ◽  
James P. Snyder ◽  
James F. Britten ◽  
Russell A. Bell
Keyword(s):  
Conformational Analysis ◽  
Molecular Modelling ◽  
Density Functional ◽  
Nuclear Overhauser Effect ◽  
Chemical Shifts ◽  
Lone Pair ◽  
Oxidative Cyclization ◽  
Conformational Space ◽  
Aromatic Solvent ◽  
X Ray

N,N′-[Dimethyl-(2,2′-dithiobisacetyl)]ethylenediamine (1) has been synthesized in 30% overall yield from N,N′-dimethylethylenediamine and thioacetic acid by an improved procedure involving simultaneous deprotection and oxidative cyclization with iodine. This cyclic diamide disulfide exists in solution as a mixture of two Z,Z and one Z,E disulfide, and amide ring conformers and has been characterized by nuclear Overhauser effect (NOE), 1H–1H, 1H–13C shift-correlated 2D-NMR and molecular modelling studies. Among the Z,Z ring conformers Z,Z1 and Z,Z2, the former predominates and interconverts with the latter isomer by rotation about the S—S bond with an activation energy of 14.5 ± 1.3 kcal/mol. Coalescence of N-CH3 signals occurred at ca. 127 °C (500 MHz), which corresponded to an approximate barrier to amide rotation of 19.3 kcal/mol. Aromatic solvent-induced shifts in C6D6 corroborated molecular mechanics and NOE predictions of amide stereochemistry. The structure of the Z,E stereoisomer of 1 has been determined by single-crystal X-ray diffraction at 296 K. A large geminal N-CH2 inequivalence (>2 ppm in CDCl3) was observed for the Z,Z conformers. Proton chemical shifts have been calculated for the conformers of 1 and related molecular fragments with DFT/GIAO theory. Absolute chemical shifts are modelled within 0.2 ppm of experiment. The unusual nonequivalence of geminal N-CH2 and S-CH2 protons can be understood as a combination of shielding mechanisms derived from short N-methyl contacts, amide group orientation, and sulfur lone-pair disposition. An implication of these results is the possibility of using α-CH (and eventually α-CH) shifts to probe the local conformational space in cyclic peptides and other conformationally constrained rings. Keywords: amide/disulfide rotamers, conformational analysis, density functional theory, DFT/GIAO NMR shift calculations, methylene nonequivalence, molecular modelling.

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

2020 ◽  
Vol 76 (3) ◽  
pp. 417-426 ◽  
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.

Configurations and conformations of glycosyl sulfoxides

2010 ◽  
Vol 88 (11) ◽  
pp. 1154-1174 ◽  
Author(s):  
Hong Liang ◽  
Micheline MacKay ◽  
T. Bruce Grindley ◽  
Katherine N. Robertson ◽  
T. Stanley Cameron
Keyword(s):  
Solid State ◽  
Dft Calculations ◽  
Gas Phase ◽  
Density Functional ◽  
Lone Pair ◽  
Azido Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Comparison Of The Results ◽  
P Type

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.

scholarly journals Structural Effects of meso-Halogenation on Porphyrins: meso-Xn-ABCD Macrocycles

2021 ◽  
Author(s):  
Keith J Flanagan ◽  
Maximilian Paradiz Dominguez ◽  
Zoi Melissari ◽  
Hans-Georg Eckhardt ◽  
René M Williams ◽  
...  
Keyword(s):  
Conformational Analysis ◽  
Crystal Engineering ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Normal Coordinate ◽  
Functional Theory ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Past ◽  
Meso Position

The use of halogens in the crystal engineering of porphyrin scaffolds has been a topic of strong interest over the past decades. Previously, this was focused on the introduction of a variety of halogens on the meso-phenyl groups of the porphyrin. However, investigations into the effects of direct halogenation of porphyrins at the meso-position on their crystalline architectures have not been conducted to date. Herein we have characterized a series of direct meso-halogenated porphyrins using single crystal X-ray crystallography. This is accompanied by a detailed conformational analysis of all deposited meso-halogenated porphyrins in the CCDC. In this study we have used the Hirshfeld fingerprint plots together with normal-coordinate structural decomposition and determined crystal structures to elucidate the conformation, present intermolecular interactions, and compare respective contacts within the crystalline architectures. Additionally, we have used density functional theory calculations to determine the structure of several halogenated porphyrins. This contrasts conformational analysis with existing X-ray structures and gives a method to characterize samples that are difficult to crystallize.

scholarly journals A New Approach Using Aromatic-Solvent-Induced Shifts in NMR Spectroscopy to Analyze β-Lactams with Various Substitution Patterns

Synlett ◽  
2019 ◽  
Vol 31 (02) ◽  
pp. 158-164 ◽  
Author(s):  
Leticia Chavelas-Hernández ◽  
Jonathan R. Valdéz-Camacho ◽  
Luis G. Hernández-Vázquez ◽  
Blanca E. Dominguez-Mendoza ◽  
María G. Vasquez-Ríos ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Nmr Spectroscopy ◽  
1H Nmr Spectroscopy ◽  
Density Functional ◽  
Chemical Shifts ◽  
Density Functional Theory Calculations ◽  
Aromatic Solvent ◽  
Functional Theory ◽  
New Approach ◽  
Lactam Ring

The chemical shifts of protons depend not only on the properties of the solute molecule but also on the medium in which the solute resides. A series of β-lactams with various substitution patterns were synthesized to study aromatic-solvent-induced shifts (ASISs) in chloroform and benzene by using 1H NMR spectroscopy. The results agreed with those obtained by theoretical density functional theory calculations. The protons of the β-lactam ring are the most affected by the ASIS effect, and they tend to overlap due to the anisotropic effect of benzene.

13C and 19F solid-state NMR and X-ray crystallographic study of halogen-bonded frameworks featuring nitrogen-containing heterocycles

2017 ◽  
Vol 73 (3) ◽  
pp. 157-167 ◽  
Author(s):  
Patrick M. J. Szell ◽  
Shaina A. Gabriel ◽  
Russell D. D. Gill ◽  
Shirley Y. H. Wan ◽  
Bulat Gabidullin ◽  
...  
Keyword(s):  
Solid State ◽  
Density Functional ◽  
Halogen Bond ◽  
Chemical Shifts ◽  
Halogen Bonding ◽  
Structural Features ◽  
Magic Angle Spinning ◽  
Magic Angle ◽  
X Ray ◽  
Donor And Acceptor

Halogen bonding is a noncovalent interaction between the electrophilic region of a halogen (σ-hole) and an electron donor. We report a crystallographic and structural analysis of halogen-bonded compounds by applying a combined X-ray diffraction (XRD) and solid-state nuclear magnetic resonance (SSNMR) approach. Single-crystal XRD was first used to characterize the halogen-bonded cocrystals formed between two fluorinated halogen-bond donors (1,4-diiodotetrafluorobenzene and 1,3,5-trifluoro-2,4,6-triiodobenzene) and several nitrogen-containing heterocycles (acridine, 1,10-phenanthroline, 2,3,5,6-tetramethylpyrazine, and hexamethylenetetramine). New structures are reported for the following three cocrystals, all in the P21/c space group: acridine–1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C6F3I3·C13H9N, 1,10-phenanthroline–1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C6F3I3·C12H8N2, and 2,3,5,6-tetramethylpyrazine–1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C6F3I3·C8H12N2. 13C and 19F solid-state magic-angle spinning (MAS) NMR is shown to be a convenient method to characterize the structural features of the halogen-bond donor and acceptor, with chemical shifts attributable to cocrystal formation observed in the spectra of both nuclides. Cross polarization (CP) from 19F to 13C results in improved spectral sensitivity in characterizing the perfluorinated halogen-bond donor when compared to conventional 1H CP. Gauge-including projector-augmented wave density functional theory (GIPAW DFT) calculations of magnetic shielding constants, along with optimization of the XRD structures, provide a final set of structures in best agreement with the experimental 13C and 19F chemical shifts. Data for carbons bonded to iodine remain outliers due to well-known relativistic effects.

scholarly journals Synthesis Single Crystal X-ray Structure DFT Studies and Hirshfeld Analysis of New Benzylsulfanyl-Triazolyl-Indole Scaffold

Crystals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 685 ◽  
Author(s):  
Ahmed T. A. Boraei ◽  
Saied M. Soliman ◽  
Sammer Yousuf ◽  
Assem Barakat
Keyword(s):  
Density Functional Theory ◽  
Dft Calculations ◽  
Single Crystal ◽  
13C Nmr ◽  
Density Functional ◽  
Chemical Shifts ◽  
Functional Theory ◽  
X Ray ◽  
Reactivity Descriptors ◽  
Hirshfeld Analysis

Benzylsulfanyl-triazolyl-indole scaffold was synthesized through coupling of 4-amino-5-(1H-indol-2-yl)-1,2,4-triazol-3(2H)-thione and benzyl bromide in EtOH under basic conditions (K2CO3). The benzylation direction was deduced from the 13C NMR signal found at 35.09 ppm, assigned for the methylene carbon of the benzyl group, this value indicates that the benzyl group attacks sulfur, not nitrogen. 1H NMR, 13C NMR, COSY, HMQC, HRMS and X-ray single crystal diffraction analysis were used for structure assignment. The desired compound accomplished in good yield. Hirshfeld analysis revealed the importance of the short N...H (1.994–2.595 Ǻ), S…H (2.282 Ǻ) and C…H (2.670 Ǻ) contacts as well as the weak π-π stacking interactions in the molecular packing of benzylthio-triazolyl-indole scaffold. Its electronic and structural aspects were predicted using density functional theory (DFT) calculations and the reactivity descriptors as well. The Uv-Vis spectral bands were assigned based on the time-dependant density functional theory TD-DFT calculations, while the gauge-including atomic orbitals (GIAO) method was used to predict the 1H and 13C NMR chemical shifts.

NMR, IR, Mössbauer and quantum chemical investigations of metalloporphyrins and metalloproteins

2001 ◽  
Vol 05 (03) ◽  
pp. 323-333 ◽  
Author(s):  
LORI K. SANDERS ◽  
WILLIAM D. ARNOLD ◽  
ERIC OLDFIELD
Keyword(s):  
Chemical Shift ◽  
Electric Fields ◽  
Heme Proteins ◽  
Density Functional ◽  
Chemical Shifts ◽  
Coupling Constants ◽  
Chemical Shift Tensors ◽  
X Ray ◽  
X Ray Crystallography ◽  
Isotropic Chemical Shifts

We review contributions made towards the elucidation of CO and O 2 binding geometries in respiratory proteins. Nuclear magnetic resonance, infrared spectroscopy, Mössbauer spectroscopy, X-ray crystallography and quantum chemistry have all been used to investigate the Fe –ligand interactions. Early experimental results showed linear correlations between 17 O chemical shifts and the infrared stretching frequency (νCO) of the CO ligand in carbonmonoxyheme proteins and between the 17 O chemical shift and the 13CO shift. These correlations led to early theoretical investigations of the vibrational frequency of carbon monoxide and of the 13 C and 17 O NMR chemical shifts in the presence of uniform and non-uniform electric fields. Early success in modeling these spectroscopic observables then led to the use of computational methods, in conjunction with experiment, to evaluate ligand-binding geometries in heme proteins. Density functional theory results are described which predict 57 Fe chemical shifts and Mössbauer electric field gradient tensors, 17 O NMR isotropic chemical shifts, chemical shift tensors and nuclear quadrupole coupling constants (e2qQ/h) as well as 13 C isotropic chemical shifts and chemical shift tensors in organometallic clusters, heme model metalloporphyrins and in metalloproteins. A principal result is that CO in most heme proteins has an essentially linear and untilted geometry (τ = 4 °, β = 7 °) which is in extremely good agreement with a recently published X-ray synchrotron structure. CO / O 2 discrimination is thus attributable to polar interactions with the distal histidine residue, rather than major Fe–C–O geometric distortions.

CONFORMATIONAL ANALYSIS OF NEVIRAPINE IN SOLUTIONS BASED ON NMR SPECTROSCOPY AND QUANTUM CHEMICAL CALCULATIONS

2006 ◽  
Vol 05 (04) ◽  
pp. 913-924 ◽  
Author(s):  
V. VAILIKHIT ◽  
P. BUNSAWANSONG ◽  
S. TECHASAKUL ◽  
S. HANNONGBUA
Keyword(s):  
Conformational Analysis ◽  
Reverse Transcriptase ◽  
Density Functional ◽  
Chemical Shifts ◽  
Complex Structure ◽  
Density Functional Theory Calculations ◽  
Transcriptase Inhibitor ◽  
Nmr Chemical Shifts ◽  
Solvation Free Energies ◽  
Hiv 1

The conformational analysis of HIV-1 Reverse Transcriptase Inhibitor, nevirapine, 11-cyclopropyl-5,-11dihydro-4-methyl-6H-dipyrido[3,2-b2′,3′-e][1,4]diazepin-6-one, was investigated using ab initio and density functional theory calculations. The fully optimized structures and rotational potential energies of the nitrogen and carbon bonds in the cyclopropyl ring (C15-N11-C17-C19, α) were examined in detail. Geometries obtained from all applied calculations show similarities to the complex structure with HIV-1 reverse transcriptase. To obtain more information on the structure, conformational minima of nevirapine, optimized at the B3LYP/6-31G** level, were calculated for the 1H, 13C, and 15N-NMR chemical shifts at the B3LYP/6-311++G** level using the GIAO approach in DMSO and chloroform IEFPCM solvation models. The calculated 1H, 13C-NMR chemical shifts agree well with the experimental data, which indicates that the geometry of nevirapine in solution is similar to that of the molecule in the inhibition complex. Solvation free energies (ΔG sol ) of nevirapine in DMSO and chloroform were also obtained.

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