4 research outputs found
Molecular Dynamics Simulation of a RNA Aptasensor
Single-stranded RNA
aptamers have emerged as novel biosensor tools.
However, the immobilization procedure of the aptamer onto a surface
generally induces a loss of affinity. To understand this molecular
process, we conducted a complete simulation study for the Flavin mononucleotide
aptamer for which experimental data are available. Several molecular
dynamics simulations (MD) of the Flavin in complex with its RNA aptamer
were conducted in solution, linked with six thymidines (T6) and, finally,
immobilized on an hexanol-thiol-functionalized gold surface. First,
we demonstrated that our MD computations were able to reproduce the
experimental solution structure and to provide a meaningful estimation
of the Flavin free energy of binding. We also demonstrated that the
T6 linkage, by itself, does not generate a perturbation of the Flavin
recognition process. From the simulation of the complete biosensor
system, we observed that the aptamer stays oriented parallel to the
surface at a distance around 36 Ć
avoiding, this way, interaction
with the surface. We evidenced a structural reorganization of the
Flavin aptamer binding mode related to the loss of affinity and induced
by an anisotropic distribution of sodium cationic densities. This
means that ionic diffusion is different between the surface and the
aptamer than above this last one. We suggest that these findings might
be extrapolated to other nucleic acids systems for the future design
of biosensors with higher efficiency and selectivity
CO<sub>2</sub> Capture by Diamines in Dry and Humid Conditions: A Theoretical Approach
This work is a mechanistic study of the CO2 reaction
with diamines under both dry and wet conditions. All protic Ī±,Ļ-diamines
R1H1N1-(CH2)n-N2H2R2, with n = 1ā5 and R1 and R2 = H and/or CH3,
were investigated. Depending on the nature of the diamine, the reaction
was found to follow one of two concerted asynchronous reaction mechanisms
with a zwitterion hidden intermediate. Both mechanisms involved two
processes. The first process consisted of a nucleophilic attack of
the nitrogen N1 of the first amine group on the carbon of CO2, accompanied by the transfer of a hydrogen atom H1 from N1 to the
nitrogen N2 of the second amine group, leading to the formation of
a carbamate zwitterion. The subsequent process corresponds to the
transfer of a hydrogen atom H2 from the second amine group N2 to an
oxygen atom of CO2, thus ending the reaction by the formation
of carbamic acid. The structure of the zwitterion hidden intermediate
was determined using the reactive internal reaction coordinates (RIRC),
a reaction pathway visualization tool, consisting of a 3D representation
of the potential energy versus the internuclear distances N2āH1
and N2āH2, which correspond to the bond being formed and the
bond being broken, respectively. The life span of the transitory species,
i.e., the zwitterion, was found to depend on the nature of the second
amine group. For primary amines, the life span of the zwitterion was
āshortā, whereas for secondary amines, it was ālongā.
The corresponding mechanisms were termed the āearlyā
and ālateā asynchronous mechanism, respectively. Regardless
of the mechanism, the activation barriers were found to decrease with
the length of the carbon chain linking the two amine groups, with
an asymptotic behavior from n = 4. Involvement of
a water molecule generates a significant catalytic effect for diamines
with short carbon chains (n < 4), whereas for
longer chain diamines, water has a slightly adverse effect
Some Theoretical and Experimental Insights on the Mechanistic Routes Leading to the Spontaneous Grafting of Gold Surfaces by Diazonium Salts
The
spontaneous grafting of diazonium salts on gold may involve
the carbocation obtained by heterolytic dediazonation and not necessarily
the radical, as usually observed on reducing surfaces. The mechanism
is addressed on the basis of DFT calculations and experiments carried
out under conditions where the carbocation and the radical are produced
selectively. The calculations indicate that the driving force of the
reaction leading from a gold cluster, used as a gold model surface,
and the carbocation to the modified cluster is higher than that of
the analogous reaction starting from the radical. The experiments
performed under conditions of heterolytic dediazonation show the formation
of thin films on the surface of gold. The grafting of a carbocation
is therefore possible, but a mechanism where the cleavage of the ArāN
bond is catalyzed by the surface of gold cannot be excluded
Efficient Covalent Modification of Multiwalled Carbon Nanotubes with Diazotized Dyes in Water at Room Temperature
Tetrafluoroborate
salts of diazotized Azure A (AA-N<sub>2</sub><sup>+</sup>), Neutral
Red (NR-N<sub>2</sub><sup>+</sup>) and Congo
Red (CR-N<sub>2</sub><sup>+</sup>) dyes were prepared and reacted
with multiwalled carbon nanotubes (MWCNTs) at room temperature, in
water without any reducing agent. The as-modified MWCNTs were examined
by IRATR, Raman spectroscopy, XPS, TGA, TEM, and cyclic voltammetry.
The diazonium band located at ā¼2350 cm<sup>ā1</sup> in
the diazotized dye IR spectra vanished after attachment to the nanotubes
whereas the Raman D/G peak ratio slightly increased after dye covalent
attachment at a high initial diazonium/CNT mass ratio. XPS measurements
show the loss of F 1s from the BF<sub>4</sub><sup>ā</sup> anion
together with a clear change in the high-resolution C 1s region from
the modified nanotubes. Thermogravimetric analyses proved substantial
mass loadings of the organic grafts leveling off at 40.5, 34.3, and
50.7 wt % for AA, NR, and CR, respectively. High-resolution TEM pictures
confirmed the presence of 1.5ā7-nm-thick continuous amorphous
layers on the nanotubes assigned to the aryl layers from the dyes.
Cyclic voltammetry studies in acetonitrile (ACN) confirmed the grafting
of the dyes; the latter retain their electrochemical behavior in the
grafted state. The experimental results correlate remarkably well
with quantum chemical calculations that indicate high binding energies
between the dyes and the CNTs accounting for true covalent bonding
(140ā185 kJ/mol with the CNT-aryl distance <1.6 nm), though
attachment by Ļ stacking also contributes to obtaining stable
hybrids. Finally, the pH-responsive character of the robust hybrids
was demonstrated by a higher degree of protonation of Neutral Red-grafted
CNTs at pH 2 compared to that of the neutral aqueous medium. This
work demonstrates that diazotized dyes can be employed for the surface
modification of MWCNTs in a very simple and efficient manner in water
and at room temperature. The hybrids could be employed for many purposes
such as optically pH-responsive materials, biosensors, and optothermal
composite actuators to name a few