Challenges in Creating Online Exercises and Exams in Organic Chemistry.

e-Learning has become increasingly important in chemical education and online exams can be an attractive alternative to traditional exams written on paper, particularly in classes with a large number of students. Ten years ago, we began to set up an e-course complementing our lecture courses Organic Chemistry I and II within the open-source e-learning environment Moodle. In this article, we retrace a number of decisions we took over time, thereby illustrating the challenges one faces when creating online exercises and exams in (organic) chemistry.

Advanced electron paramagnetic resonance on the catalytic iron-sulfur cluster bound to the CCG domain of heterodisulfide reductase and succinate: quinone reductase.

Heterodisulfide reductase (Hdr) is a key enzyme in the energy metabolism of methanogenic archaea. The enzyme catalyzes the reversible reduction of the heterodisulfide (CoM-S-S-CoB) to the thiol coenzymes M (CoM-SH) and B (CoB-SH). Cleavage of CoM-S-S-CoB at an unusual FeS cluster reveals unique substrate chemistry.

Methyl-coenzyme M reductase from methanogenic archaea: isotope effects on the formation and anaerobic oxidation of methane.

The nickel enzyme methyl-coenzyme M reductase (MCR) catalyzes two important transformations in the global carbon cycle: methane formation and its reverse, the anaerobic oxidation of methane. MCR uses the methyl thioether methyl-coenzyme M (CH3-S-CH2CH2-SO3(-), Me-S-CoM) and the thiol coenzyme B (CoB-SH) as substrates and converts them reversibly to methane and the corresponding heterodisulfide (CoB-S-S-CoM). The catalytic mechanism is still unknown.

Methyl-coenzyme M reductase from methanogenic archaea: isotope effects on label exchange and ethane formation with the homologous substrate ethyl-coenzyme M.

Ethyl-coenzyme M (CH3CH2-S-CH2CH2-SO3(-), Et-S-CoM) serves as a homologous substrate for the enzyme methyl-coenzyme M reductase (MCR) resulting in the product ethane instead of methane. The catalytic reaction proceeds via an intermediate that already contains all six C-H bonds of the product. Because product release occurs after a second, rate-limiting step, many cycles of intermediate formation and reconversion to substrate occur before a substantial amount of ethane is released.

N,N'-Dicyanoquinone diimide-derived donor-acceptor chromophores: conformational analysis and optoelectronic properties.

A formal [2 + 2] cycloaddition-cycloreversion (CA-CR) between N,N'-dicyanoquinone diimides (DCNQIs) and electron-rich alkynes was explored, providing a new class of π-conjugated donor-acceptor chromophores. These DCNQI adducts exist in the solid state as single diastereoisomers, but as two interconverting diastereoisomers in solution. Solid- and solution-state evidence for intramolecular charge transfer (CT) was obtained; additionally, the DCNQI adducts exhibit positive solvatochromism and significant solution-state third-order polarizabilities.

The key nickel enzyme of methanogenesis catalyses the anaerobic oxidation of methane.

Large amounts (estimates range from 70 Tg per year to 300 Tg per year) of the potent greenhouse gas methane are oxidized to carbon dioxide in marine sediments by communities of methanotrophic archaea and sulphate-reducing bacteria, and thus are prevented from escaping into the atmosphere. Indirect evidence indicates that the anaerobic oxidation of methane might proceed as the reverse of archaeal methanogenesis from carbon dioxide with the nickel-containing methyl-coenzyme M reductase (MCR) as the methane-activating enzyme. However, experiments showing that MCR can catalyse the endergonic back reaction have been lacking.

Reaction of Fe3(CO)12 with octreotide--chemical, electrochemical and biological investigations.

In search for peptidic [FeFe] hydrogenase mimics, the cyclic disulfide Sandostatin (octreotide) was allowed to react with Fe(3)(CO)(12). An octreotide-Fe(2)(CO)(6) complex was isolated and characterized spectroscopically as well as by elemental and thermochemical analysis. The complex catalyzes the electrochemical reduction of H(+) to H(2).

Binding of coenzyme B induces a major conformational change in the active site of methyl-coenzyme M reductase.

Methyl-coenzyme M reductase (MCR) is the key enzyme in methane formation by methanogenic Archaea. It converts the thioether methyl-coenzyme M and the thiol coenzyme B into methane and the heterodisulfide of coenzyme M and coenzyme B. The catalytic mechanism of MCR and the role of its prosthetic group, the nickel hydrocorphin coenzyme F(430), is still disputed, and no intermediates have been observed so far by fast spectroscopic techniques when the enzyme was incubated with the natural substrates.

Folding and unfolding of two mixed alpha/beta peptides.

We present a molecular dynamics simulation study of two peptides containing alpha- and beta-amino acid residues. According to experiment, the two peptides differ in the dominant fold when solvated in methanol: one shows a helical fold, the other a beta hairpin. The simulations at 300 and 340 K were done by starting from a NMR spectroscopic model structure and from an extended (denatured) structure.

Interpreting experimental data by using molecular simulation instead of model building.

A proper description of the conformational equilibrium of polypeptides or proteins is essential for a correct description of their function. The conformational ensembles from 16 molecular dynamic simulations of two beta- heptapeptides were used to interpret the primary NMR data, which were also compared to a set of NMR model structures (see graphic).One of the most used spectroscopic techniques for resolving the structure of a biomolecule, such as a protein or peptide, is NMR spectroscopy.

Probing the role of the proximal heme ligand in cytochrome P450cam by recombinant incorporation of selenocysteine.

The unique monooxygenase activity of cytochrome P450cam has been attributed to coordination of a cysteine thiolate to the heme cofactor. To investigate this interaction, we replaced cysteine with the more electron-donating selenocysteine. Good yields of the selenoenzyme were obtained by bacterial expression of an engineered gene containing the requisite UGA codon for selenocysteine and a simplified yet functional selenocysteine insertion sequence (SECIS).

Nickel-alkyl bond formation in the active site of methyl-coenzyme m reductase.

Methyl-coenzyme M reductase (MCR) catalyzes the methane-forming step in methanogenic archaea and most probably also the methane-oxidizing step in methanotrophic archaea. The enzyme contains coenzyme F(430) as prosthetic group. F(430) is a nickel porphinoid that has to be in the reduced Ni(I) state for the enzyme to be active.

The structure of a TNA-TNA complex in solution: NMR study of the octamer duplex derived from alpha-(L)-threofuranosyl-(3'-2')-CGAATTCG.

TNA (alpha-( l)-threofuranosyl-(3'-2') nucleic acid) is a nucleic acid in which the ribofuranose building block of the natural nucleic acid RNA is replaced by the tetrofuranose alpha-( l)-threose. This shortens the repetitive unit of the backbone by one bond as compared to the natural systems. Among the alternative nucleic acid structures studied so far in our laboratories in the etiological context, TNA is the only one that exhibits Watson-Crick pairing not only with itself but also with DNA and, even more strongly, with RNA.

Coordination and binding geometry of methyl-coenzyme M in the red1m state of methyl-coenzyme M reductase.

Methane formation in methanogenic Archaea is catalyzed by methyl-coenzyme M reductase (MCR) and takes place via the reduction of methyl-coenzyme M (CH3-S-CoM) with coenzyme B (HS-CoB) to methane and the heterodisulfide CoM-S-S-CoB. MCR harbors the nickel porphyrinoid coenzyme F430 as a prosthetic group, which has to be in the Ni(I) oxidation state for the enzyme to be active. To date no intermediates in the catalytic cycle of MCRred1 (red for reduced Ni) have been identified.

A nickel hydride complex in the active site of methyl-coenzyme m reductase: implications for the catalytic cycle.

Methanogenic archaea utilize a specific pathway in their metabolism, converting C1 substrates (i.e., CO2) or acetate to methane and thereby providing energy for the cell.

Structure of an F430 variant from archaea associated with anaerobic oxidation of methane.

Microbial mats collected at cold methane seeps in the Black Sea carry out anaerobic oxidation of methane (AOM) to carbon dioxide using sulfate as the electron acceptor. These mats, which predominantly consist of sulfate-reducing bacteria and archaea of the ANME-1 and ANME-2 type, contain large amounts of proteins very similar to methyl-coenzyme M reductase from methanogenic archaea. Mass spectrometry of mat samples revealed the presence of two nickel-containing cofactors in comparable amounts, one with the same mass as coenzyme F430 from methanogens (m/z = 905) and one with a mass that is 46 Da higher (m/z = 951).

Sodium 2-mercaptoethanesulfonate monohydrate (coenzyme M sodium salt monohydrate).

The 2-thio-ethanesulfonate anion is the smallest known coenzyme in nature (HS-CoM) and plays a key role in methano-genesis by anaerobic archaea, as well as in the oxidation of alkenes by Gram-negative and Gram-positive eubacteria. The title compound, Na(+)·C(2)H(5)O(3)S(2) (-)·H(2)O, is the Na(+) salt of HS-CoM crystallized as the monohydrate. Six O atoms form a distorted octa-hedral coordination geometry around the Na atom, at distances in the range 2.

Solution structure of a DNA duplex containing a biphenyl pair.

Hydrogen-bonding and stacking interactions between nucleobases are considered to be the major noncovalent interactions that stabilize the DNA and RNA double helices. In recent work we found that one or multiple biphenyl pairs, devoid of any potential for hydrogen bond formation, can be introduced into a DNA double helix without loss of duplex stability. We hypothesized that interstrand stacking interactions of the biphenyl residues maintain duplex stability.

Two sub-states of the red2 state of methyl-coenzyme M reductase revealed by high-field EPR spectroscopy.

Methyl-coenzyme M reductase (MCR) catalyzes the formation of methane from methyl-coenzyme M and coenzyme B in methanogenic archaea. The enzyme has two structurally interlinked active sites embedded in an alpha(2)beta(2)gamma(2) subunit structure. Each active site has the nickel porphyrinoid F(430) as a prosthetic group.

Comparison of the NMR spectroscopy solution structures of pyranosyl-rNA and its nucleo-delta-peptide analogue.

The design of polymers that could mimic biomolecules in their ability to form assemblies similar to ribo- and deoxyribonucleic acids has become an attractive field of chemical research, and NMR spectroscopy has played a vital role in the determination of the three-dimensional structure of these newly designed nonnatural polymers. The structure of a self-complementary octamer duplex of pyranosyl-RNA (pRNA) has been determined by using NMR spectroscopy experimental data and an Xplor structure calculation protocol. The structure has been compared with the structure of a duplex formed by a designed nucleo-delta-peptide analogue of pRNA.

Simulation of beta-depsipeptides: the effect of missing hydrogen-bond donors on their folding equilibria.

beta-Depsipeptides are beta-peptides in which one or more peptide linkages are replaced by ester linkages, resulting in a loss of a hydrogen-bond donor (N--H) and weakening of the corresponding carbonyl hydrogen-bond acceptor moiety. The effects of three of such peptide by ester substitutions in a hepta-beta-peptide upon its (un)folding equilibrium in methanol solution are investigated using molecular dynamics simulations and compared to experimental data from NMR spectroscopy. The simulated conformational ensembles largely reproduce the experimentally measured NOE and 3J-coupling constant data for the three different hepta-beta-peptides, and confirm the relative stabilities of the 3(14)-helical conformation, which is most weakened by substitution of the 4th peptide linkage and least by substitution of the 6th peptide linkage.

Simulation of an all-beta 3-icosapeptide containing the 20 proteinogenic side chains: effect of temperature, pH, counterions, solvent, and force field on helix stability.

Simulations of various beta-peptides have in the last years clarified several issues concerning peptide folding equilibria and interpretation of experimental data, especially from NMR and CD spectroscopy. These simulations involved different temperatures, pH-values, ionic strengths, solvents, and force-field parameters, but a variation of these factors for one beta-peptide has not yet been done. To investigate the influence of varying these factors, we analyze the helix stability of an all-beta3-icosapeptide bearing all 20 proteinogenic amino acid side chains, which is experimentally observed to fold into a 3(14)-helix in methanol but not in water.