Students undertaking courses in the
field of chemistry need to
integrate their spatial skills and conceptual knowledge. However,
model perception along with the understanding of spatial processes
and spatial structures of molecules has been a cause of difficulty
for students as conventional teaching methods cannot fully aid student
comprehension. In this research, we propose a technological solution
to aid the spatial learning process by automatically creating a link
between two-dimensional (2D) representations of chemical structures
and three-dimensional (3D) molecular visualization. The image of a
chemical structure is acquired and processed on-the-fly for structure
identification and 3D model generation. The 3D molecular model is
simplified for real-time interactive rendering. The efficacy of the
proposed solution in enhancing spatial ability of individuals is evaluated
through an experiment on first year undergraduate students. Our analysis
of the results suggests that virtual models and mobile applications
are capable of narrowing the performance gap between students with
different levels of spatial ability.
Acetylene hydratase
(AH) of
Pelobacter acetylenicus
is
a tungsten (W)-containing iron–sulfur enzyme that catalyzes
the transformation of acetylene to acetaldehyde, the exact/true reaction
mechanism of which is still in question. Scientists utilized different
computational approaches to understand the reaction mechanism of acetylene
hydration. Some identified it as a multistep (4–16) process
that starts with the displacement of a water molecule present at the
active site of AH with acetylene. However, some said that there is
no need to displace water with acetylene at the active site of AH.
As the reaction mechanism for the conversion of acetylene to acetaldehyde
is still controversial and needs to be investigated further, DFT studies
were performed on the model complexes derived from the native protein
X-ray crystal structure of AH. Based on the computational results,
here we are proposing the nucleophilic reaction mechanism where the
water (Wat1424) molecule is coordinated to the W center and Asp13
is assumed to be in an anionic form. The Wat1424 molecule is activated
by W and then donates one of its protons to the anionic Asp13, forming
the W-bound hydroxide and protonated Asp13. The W-bound hydroxide
then attacks the C1 atom of acetylene together with the transfer of
a proton from Asp13 to its C2 atom, resulting in the formation of
a vinyl alcohol intermediate complex. The energy barrier associated
with this step is 14.4 kcal/mol. The final, rate-limiting, step corresponds
to the tautomerization of the vinyl alcohol intermediate to acetaldehyde
via intermolecular assistance of two water molecules, associated with
an energy barrier of 18.9 kcal/mol. Also, the influence of the metal
on the hydration of acetylene is studied when W is replaced with Mo.
The molybdenum and tungsten active site model complexes, derived from the protein X-ray crystal structure of the first W-containing nitrate reductase isolated from Pyrobaculum aerophilum, were computed for nitrate reduction at the COSMO-B3LYP/SDDp//B3LYP/Lanl2DZ(p) energy level of density functional theory. The molybdenum containing active site model complex (Mo–Nar) has the largest activation energy (34.4 kcal/mol) for the oxygen atom transfer from the nitrate to the metal center as compared to the tungsten containing active site model complex (W–Nar) (12.0 kcal/mol). Oxidation of the educt complex is close to thermoneutral (−1.9 kcal/mol) for the Mo active site model complex but strongly exothermic (−34.7 kcal/mol) for the W containing active site model complex, however, the MVI to MIV reduction requires equal amount of reductive power for both metal complexes, Mo–Nar or W–Nar.Electronic supplementary materialThe online version of this article (doi:10.1186/s13065-017-0263-7) contains supplementary material, which is available to authorized users.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.