scholarly journals Integrating Chemical Crystallography into Advanced Undergraduate Laboratories

2014 ◽  
Vol 70 (a1) ◽  
pp. C1382-C1382
Author(s):  
Joseph Tanski
Keyword(s):  
Molecular Structure ◽  
Undergraduate Students ◽  
Scientific Journal ◽  
Molecular Structures ◽  
Module Structure ◽  
Spectroscopic Techniques ◽  
X Ray Crystallography ◽  
Chemical Crystallography ◽  
Structure Of Molecules ◽  
Student Projects

As scientific educators, it is important to mentor students in using state-of-the-art instrumentation and in the communication of new knowledge. Just as chemical crystallography and complimentary spectroscopic techniques such as NMR can be fast, effective tools to experimentally determine the structure of molecules and enhance students learning of molecular structure, they can also provide an inspiring opportunity for students to write short, scientific journal style reports that can be edited and published in collaboration with a mentor. This contribution will focus on incorporating X-ray crystallography into an advanced undergraduate integrated laboratory class as part of a discovery based exercise where the students do not know the identity of their small molecule organic compound, and the publication of the resulting crystal structures. The structures of some recently published examples are shown below. With examples of past student projects and published structures, topics will include: sample choice, the discovery based molecular structure determination lab module, structure validation, analysis and discussion of intermolecular interactions such as hydrogen bonding, π-stacking, halogen-halogen interactions, and C-H···X (X = O, N, halogen) interactions, and the writing of descriptions of crystal and molecular structures for publication in collaboration with undergraduate students. This work was supported by grants from the U.S. National Science Foundation, No. 0521237 & 0911324.

To what degree does handling concrete molecular models promote the ability to translate and coordinate between 2D and 3D molecular structure representations? A case study with Algerian students

2016 ◽  
Vol 17 (4) ◽  
pp. 862-877 ◽  
Author(s):  
Boukhechem Mohamed-Salah ◽  
Dumon Alain
Keyword(s):  
Molecular Structure ◽  
Undergraduate Students ◽  
Bachelor's Degree ◽  
Molecular Structures ◽  
Molecular Models ◽  
Physical Sciences ◽  
Pencil And Paper ◽  
3D Molecular Structure ◽  
2D And 3D ◽  
Concrete Model

This study aims to assess whether the handling of concrete ball-and-stick molecular models promotes translation between diagrammatic representations and a concrete model (orvice versa) and the coordination of the different types of structural representations of a given molecular structure. Forty-one Algerian undergraduate students were requested to answer a pencil and paper questionnaire at the end of their training for a bachelor's degree in physical sciences to test their abilities to translate from Dash-Wedge or Newman representations to 3D ball-and-stick models (andvice versa) of two molecular structures and from one concrete 3D model to the Fischer projection of the molecule. Our results show that concrete molecular models have the potential to be an effective spatial tool to promote visualization, orientation and rotation abilities. However, the handling of the concrete model did not have the same impact on all students and this effectiveness in promoting the spatial abilities required to translate and coordinate between representations was dependent on the representations: it was greater for Dash-Wedge diagrams than for Newman, and was non-existent for the Fischer projection. An implication of our research is that it may be necessary to work with a model over an extensive period of time to improve the mechanisms by which one translates between various representations when the conventions of these representations are varied in nature.

scholarly journals Synthesis, and Molecular Structure Investigations of a New s-Triazine Derivatives Incorporating Pyrazole/Piperidine/Aniline Moieties

Crystals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1500
Author(s):  
Ihab Shawish ◽  
Saied M. Soliman ◽  
Matti Haukka ◽  
Ali Dalbahi ◽  
Assem Barakat ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Dft Calculations ◽  
Nmr Spectra ◽  
Chemical Shifts ◽  
Molecular Structures ◽  
1H And 13C Nmr ◽  
X Ray ◽  
X Ray Crystallography ◽  
Triazine Derivatives ◽  
Structure Investigations

In this work, we synthesized two new s-triazine incorporates pyrazole/piperidine/aniline moieties. Molecular structure investigations in the light of X-ray crystallography combined with Hirshfeld and DFT calculations were presented. Intermolecular interactions controlling the molecular packing of 4-(3,5-dimethyl-1H-pyrazol-1-yl)-N-phenyl-6-(piperidin-1-yl)-1,3,5-triazin-2-amine; 5a and N-(4-bromophenyl)-4-(3,5-dimethyl-1H-pyrazol-1-yl)-6-(piperidin-1-yl)-1,3,5-triazin-2-amine; 5b were analyzed using Hirshfeld calculations. The most dominant interactions are the H...H, N...H and H...C contacts in both compounds. The N...H and H...C interactions in 5a and the N...H, Br...H and H...H interactions in 5b are the most important. In addition, DFT calculations were used to compute the molecular structures of 5a and 5b; then, their electronic properties, as well as the 1H- and 13C-NMR spectra, were predicted. Both compounds are polar where 5a (1.018 Debye) has lower dipole moment than 5b (4.249 Debye). The NMR chemical shifts were calculated and very good correlations between the calculated and experimental data were obtained (R2 = 0.938–0.997).

Synthesis, characterization, and the molecular structures of two new kinds of stilbene

2006 ◽  
Vol 84 (6) ◽  
pp. 867-873 ◽  
Author(s):  
Yan-Hong Liu ◽  
Tong-Lai Zhang ◽  
Jian-Guo Zhang ◽  
Li Yang ◽  
Jin-Yu Guo ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Thermal Decomposition ◽  
High Heat ◽  
Molecular Structures ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Decomposition Processes ◽  
Ft Ir ◽  
C Nmr

We report in this study the synthesis, crystal culture, and single-crystal X-ray crystallography of two new kinds of double stilbene, which were readily prepared from trinitro-p-xylene and p-tolualdehyde in the presence of piperidine. We found that these triclinic crystals belong to the space group P-1. These compounds were also investigated using FT-IR, 1H NMR, 13C NMR, and MS spectroscopy techniques. The thermal decomposition processes of the compounds were tested by DSC and TG-DTG at a heating rate of 10  C/min. These results indicate that the compounds have high heat-resistant stability.Key words: polynitrostilbene, molecular structure, thermal decomposition.

scholarly journals Copper(II) Complexes with Tetradentate Piperazine-Based Ligands: DNA Cleavage and Cytotoxicity

Inorganics ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 12
Author(s):  
Sebastian Doniz Kettenmann ◽  
Yvonne Nossol ◽  
Febee R. Louka ◽  
Julia R. Legrande ◽  
Elise Marine ◽  
...  
Keyword(s):  
Dna Cleavage ◽  
Molecular Structures ◽  
Spectroscopic Techniques ◽  
Cleavage Rate ◽  
X Ray Crystallography ◽  
Mechanistic Pathway ◽  
Nitrophenyl Phosphate ◽  
Oxidative Pathway ◽  
Spectrophotometric Titrations ◽  
Acetonitrile Solutions

Five-coordinate Cu(II) complexes, [Cu(Ln)X]ClO4/PF6, where Ln = piperazine ligands bearing two pyridyl arms and X = ClO4− for Ln = L1 (1-ClO4), L2 (2-ClO4), L3 (3-ClO4), and L6 (6-ClO4) as well as [Cu(Ln)Cl]PF6 for Ln = L1 (1-Cl), L4 (4-Cl), and L5 (5-Cl) have been synthesized and characterized by spectroscopic techniques. The molecular structures of the last two complexes were determined by X-ray crystallography. In aqueous acetonitrile solutions, molar conductivity measurements and UV-VIS spectrophotometric titrations of the complexes revealed the hydrolysis of the complexes to [Cu(Ln)(H2O)]2+ species. The biological activity of the Cu(II) complexes with respect to DNA cleavage and cytotoxicity was investigated. At micromolar concentration within 2 h and pH 7.4, DNA cleavage rate decreased in the order: 1-Cl ≈ 1-ClO4 > 3-ClO4 ≥ 2-ClO4 with cleavage enhancements of up to 23 million. Complexes 4-Cl, 5-Cl, and 6-ClO4 were inactive. In order to elucidate the cleavage mechanism, the cleavage of bis(4-nitrophenyl)phosphate (BNPP) and reactive oxygen species (ROS) quenching studies were conducted. The mechanistic pathway of DNA cleavage depends on the ligand’s skeleton: while an oxidative pathway was preferable for 1-Cl/1-ClO4, DNA cleavage by 2-ClO4 and 3-ClO4 predominantly proceeds via a hydrolytic mechanism. Complexes 1-ClO4, 3-ClO4, and 5-Cl were found to be cytotoxic against A2780 cells (IC50 30–40 µM). In fibroblasts, the IC50 value was much higher for 3-ClO4 with no toxic effect.

Synthesis, structural characterization and catalytic activity of chlororuthenium(II) complexes with substituted Schiff base/phosphine ancillary ligands

2020 ◽  
Vol 75 (9-10) ◽  
pp. 851-857
Author(s):  
Chong Chen ◽  
Fule Wu ◽  
Jiao Ji ◽  
Ai-Quan Jia ◽  
Qian-Feng Zhang
Keyword(s):  
Schiff Base ◽  
Catalytic Activity ◽  
Structural Characterization ◽  
Room Temperature ◽  
Molecular Structures ◽  
Cationic Complex ◽  
Neutral Complex ◽  
Ancillary Ligands ◽  
X Ray ◽  
X Ray Crystallography

AbstractTreatment of [(η6-p-cymene)RuCl2]2 with one equivalent of chlorodiphenylphosphine in tetrahydrofuran at reflux afforded a neutral complex [(η6-p-cymene)RuCl2(κ1-P-PPh2OH)] (1). Similarly, the reaction of [Ru(bpy)2Cl2·2H2O] (bpy = 2,2′-bipyridine) and chlorodiphenylphosphine in methanol gave a cationic complex [Ru(bpy)2Cl(κ1-P-PPh2OCH3)](PF6) (2), while treatment of [RuCl2(PPh3)3] with [2-(C5H4N)CH=N(CH2)2N(CH3)2] (L1) in tetrahydrofuran at room temperature afforded a ruthenium(II) complex [Ru(PPh3)Cl2(κ3-N,N,N-L1)] (3). Interaction of the chloro-bridged complex [Ru(CO)2Cl2]n with one equivalent of [Ph2P(o-C6H4)CH=N(CH2)2N(CH3)2] (L2) led to the isolation of [Ru(CO)Cl2(κ3-P,N,N-L2)] (4). The molecular structures of the ruthenium(II) complexes 1–4 have been determined by single-crystal X-ray crystallography. The properties of the ruthenium(II) complex 4 as a hydrogenation catalyst for acetophenone were also tested.

scholarly journals 4-vinylpyridine derivatives: Protonation, methylation and silver(I) coordination chemistry

2021 ◽  
pp. 174751982198965
Author(s):  
Guoqi Zhang
Keyword(s):  
Mass Spectrometry ◽  
Schiff Base ◽  
Coordination Chemistry ◽  
Elemental Analysis ◽  
Silver Complex ◽  
Spectroscopic Techniques ◽  
X Ray ◽  
X Ray Crystallography ◽  
Pyridine Moiety ◽  
New Compounds

( E)-4-[2-(Pyridin-4-yl)vinyl]benzaldehyde, containing both a 4-vinylpyridine and an aldehyde functionality, is utilized to develop new, highly conjugated chalcone compounds and a bis-Schiff base azine compound. The chalcone-containing compounds are further explored for their protonation, methylation and silver(I) coordination chemistry using the pyridine moiety. In parallel, a cyano-containing analogue, ( E)-4-[2-(pyridin-4-yl)vinyl]benzonitrile is also synthesized and studied for its silver(I) coordination chemistry. These new compounds are fully characterized by mass spectrometry, elemental analysis and spectroscopic techniques. The methylated product of ( E)-1-(9-anthryl)-3-{4-[2-(pyridin-4-yl)vinyl]phenyl}prop-2-en-1-one and a silver complex of ( E)-4-[2-(pyridin-4-yl)vinyl]benzonitrile are structurally determined by X-ray crystallography.

scholarly journals Structural Characterization of Heterodinuclear ZnII-LnIII Complexes (Ln = Pr, Nd) with a Ring-Contracted H2valdien-Derived Schiff Base Ligand

2021 ◽  
Author(s):  
Shabana Noor ◽  
Richard Goddard ◽  
Fehmeeda Khatoon ◽  
Sarvendra Kumar ◽  
Rüdiger W. Seidel
Keyword(s):  
Molecular Structure ◽  
Schiff Base ◽  
Structural Characterization ◽  
Schiff Base Ligand ◽  
Crystal And Molecular Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Imidazoline Ring

AbstractSynthesis and structural characterization of two heterodinuclear ZnII-LnIII complexes with the formula [ZnLn(HL)(µ-OAc)(NO3)2(H2O)x(MeOH)1-x]NO3 · n H2O · n MeOH [Ln = Pr (1), Nd (2)] and the crystal and molecular structure of [ZnNd(HL)(µ-OAc)(NO3)2(H2O)] [ZnNd(HL)(OAc)(NO3)2(H2O)](NO3)2 · n H2O · n MeOH (3) are reported. The asymmetrical compartmental ligand (E)-2-(1-(2-((2-hydroxy-3-methoxybenzylidene)amino)-ethyl)imidazolidin-2-yl)-6-methoxyphenol (H2L) is formed from N1,N3-bis(3-methoxysalicylidene)diethylenetriamine (H2valdien) through intramolecular aminal formation, resulting in a peripheral imidazoline ring. The structures of 1–3 were revealed by X-ray crystallography. The smaller ZnII ion occupies the inner N2O2 compartment of the ligand, whereas the larger and more oxophilic LnIII ions are found in the outer O2O2’ site. Graphic Abstract Synthesis and structural characterization of two heterodinuclear ZnII-LnIII complexes (Ln = Pr, Nd) bearing an asymmetrical compartmental ligand formed in situ from N1,N3-bis(3-methoxysalicylidene)diethylenetriamine (H2valdien) through intramolecular aminal formation are reported.

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