The three-dimensional structure of humic substances and soil ...

First, a preliminary 2 D structure of the C-C skeleton
is drawn by hand into the workspace using the drawing
tool and is far from perfect as shown in Fig. 3. In addi-
tion to carbon, the elements oxygen and nitrogen are in-
cluded (Default Element). In this manner 308 carbon-,
90 oxygen- and 5 nitrogen-atoms (403 atoms in total) are
positioned.
Second, hydrogen is attached with accurate bond
lengths and angles to the preliminary structure using the
software (Add Hydrogen) as shown in Fig. 4. Whereas in
the original publication the 2 D HA subunit structure [2]
was incomplete and was supposed to have a wide variety
of different bonding sequences (see :k-- symbols), the mol-
ecule in Fig. 4 represents a defined, intact HA monomer
(738 atoms). Thus, in order to obtain a complete chemi-
cal compound, it had to be supplemented by 7 hydrogen
atoms. The corresponding elemental composition then is
C308H335090N 5 with a molecular mass of 5547.004g
mol -~ and an elemental analysis of 66.69% C, 6.09% H,
25.96% O, and 1.26% N.
Third, building the 3 D structure of the selected HA
molecule (Model BuiM) with accurate bond distances
and bond angles, torsion angles, van der Waals forces,
and hydrogen bonds, is illustrated in Fig. 5. This prelimi-
nary, energetically still unoptimized structure shows
clearly the atomic distances and angles (Sticks) and gives
a first three-dimensional structure information. Even this
rough display indicates already the importance of
aliphatic chains as link between the aromatic moieties
and prerequisite for the formation of gaps and voids in
the HA structure.
Fourth, the (Sticks) structure in Fig. 5 is converted in-
to the 3 D structure (Disks, Perspective) shown in Fig. 6
which better reflects the space requirements of the 738 at-
oms. The white disks are hydrogen atoms, black disks ni-
trogen, the brighter shaded disks are carbons and the
darker ones oxygen. It is evident that even more complex
structures such as naturally occurring organomineral
complexes or trapping of biological and anthropogenic
substances in SOM will be difficult to evaluate in these
Fig. 3. Handdrawn two-dimensional version (2D) of the humic acid
draft structure using the drawing tool in the HyperChem ® workspace
-2
Fig. 4. Hydrogen attachment to the handdrawn humic acid draft struc-
ture performed by HyperChem ® (Add Hydrogen)
black and white plots. As will be illustrated in the follow-
ing fifth step, colourplots can be of great help and allow
a distinct view and facilitated evaluation of the complex,
large macromolecules.
Chemical calculations
After building the molecule from scratch (Fig. 3), the
atomic coordinates in the software files allow a wide
range of quantitative evaluations. Measuring structural
properties includes the determination of bond distances,
bond angles, torsion angles, non-bonded distances, and
hydrogen bonds. For minimizing the total energy of the
molecular system and thus increasing the stability of its
conformation, step-by-step instructions for performing
single point calculations, geometry optimization, and
molecular dynamics are given by HyperChem ®.
When one cycle of a single-point calculation of the
HA 3 D structure in Fig. 6 was performed using the algo-
rithm of Polak-Ribiere (conjugate gradient), the total en-
Fig. 5. Three-dimensional structure (3D) of the draft HA structure
shown in Fig. 4 using HyperChem ® for molecular modelling (Build
Model). Display of the structure in the sticks mode (Rendering; Sticks)
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