The
recent and publicly available toolkit AutoSolvate37 (link) was run in an Ubuntu 22.04 LTS environment, encompassing
Python 3.7, Openbabel 2.4.0, AmberTools 22, MDTraj 1.9.4, and NGLView
3.0.3. The process involved Antechamber with the AM1-BCC model to
assign point charges, LEaP for Generalized Amber Force Field parameters,
and the B3LYP hybrid exchange-correlation functional for density functional
theory (DFT) calculations. Both water and chloroform at 298 K were
tested as solvents.
Three XYZ files (ESI-01 ) were studied for the structures of DTZ: dithizone_planar.xyz corresponds
to the highly conjugated symmetric form, with the nonaromatic hydrogen
atoms on the outer nitrogen atoms (Figure 1 a); dithizone_thione.xyz differentiates the
azo group at one side of the thiocarbazone chain and two secondary
amino groups at the other side; and dithizone_anion.xyz corresponds
to the deprotonated thiol tautomer of dithizone with ammonium as counterion.
Finally, oxycellobiose.xyz is a proxy for CNFs, simply containing
a cellobiose molecule with regioselective oxidation on carbon 6 in
one of its two glucose units. Bond angles, bond distances, and molecular
surfaces of these three forms were calculated and displayed by Jmol
14.
With the same toolkits (AutoSolvate, AmberTools),
a simulation
of molecular dynamics was run on the basis of molecular mechanical
(MM) energy minimization.38 (link) Then, a solvation
shell considering the most neighboring solvent molecules was modeled
and 10 XYZ files, also included inESI-01 , were extracted. Each file corresponds to every 10 frames, spaced
by a timelapse of 4 ps, of the dynamic simulation.
recent and publicly available toolkit AutoSolvate37 (link) was run in an Ubuntu 22.04 LTS environment, encompassing
Python 3.7, Openbabel 2.4.0, AmberTools 22, MDTraj 1.9.4, and NGLView
3.0.3. The process involved Antechamber with the AM1-BCC model to
assign point charges, LEaP for Generalized Amber Force Field parameters,
and the B3LYP hybrid exchange-correlation functional for density functional
theory (DFT) calculations. Both water and chloroform at 298 K were
tested as solvents.
Three XYZ files (
to the highly conjugated symmetric form, with the nonaromatic hydrogen
atoms on the outer nitrogen atoms (
azo group at one side of the thiocarbazone chain and two secondary
amino groups at the other side; and dithizone_anion.xyz corresponds
to the deprotonated thiol tautomer of dithizone with ammonium as counterion.
Finally, oxycellobiose.xyz is a proxy for CNFs, simply containing
a cellobiose molecule with regioselective oxidation on carbon 6 in
one of its two glucose units. Bond angles, bond distances, and molecular
surfaces of these three forms were calculated and displayed by Jmol
14.
With the same toolkits (AutoSolvate, AmberTools),
a simulation
of molecular dynamics was run on the basis of molecular mechanical
(MM) energy minimization.38 (link) Then, a solvation
shell considering the most neighboring solvent molecules was modeled
and 10 XYZ files, also included in
by a timelapse of 4 ps, of the dynamic simulation.
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