3 research outputs found
Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases
Aromatic molecules with π electrons
are commonly involved
in chemical and biological recognitions. For example, nucleobases
play central roles in DNA/RNA structure and their interactions with
proteins. The delocalization of the π electrons is responsible
for the high polarizability of aromatic molecules. In this work, the
AMOEBA force field has been developed and applied to 5 regular nucleobases
and 12 aromatic molecules. The permanent electrostatic energy is expressed
as atomic multipole interactions between atom pairs, and many-body
polarization is accounted for by mutually induced atomic dipoles.
We have systematically investigated aromatic ring stacking and aromatic-water
interactions for nucleobases and aromatic molecules, as well as base–base
hydrogen-bonding pair interactions, all at various distances and orientations.
van der Waals parameters were determined by comparison to the quantum
mechanical interaction energy of these dimers and fine-tuned using
condensed phase simulation. By comparing to quantum mechanical calculations,
we show that the resulting classical potential is able to accurately
describe molecular polarizability, molecular vibrational frequency,
and dimer interaction energy of these aromatic systems. Condensed
phase properties, including hydration free energy, liquid density,
and heat of vaporization, are also in good overall agreement with
experimental values. The structures of benzene liquid phase and benzene-water
solution were also investigated by simulation and compared with experimental
and PDB structure derived statistical results
Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases
Aromatic molecules with π electrons
are commonly involved
in chemical and biological recognitions. For example, nucleobases
play central roles in DNA/RNA structure and their interactions with
proteins. The delocalization of the π electrons is responsible
for the high polarizability of aromatic molecules. In this work, the
AMOEBA force field has been developed and applied to 5 regular nucleobases
and 12 aromatic molecules. The permanent electrostatic energy is expressed
as atomic multipole interactions between atom pairs, and many-body
polarization is accounted for by mutually induced atomic dipoles.
We have systematically investigated aromatic ring stacking and aromatic-water
interactions for nucleobases and aromatic molecules, as well as base–base
hydrogen-bonding pair interactions, all at various distances and orientations.
van der Waals parameters were determined by comparison to the quantum
mechanical interaction energy of these dimers and fine-tuned using
condensed phase simulation. By comparing to quantum mechanical calculations,
we show that the resulting classical potential is able to accurately
describe molecular polarizability, molecular vibrational frequency,
and dimer interaction energy of these aromatic systems. Condensed
phase properties, including hydration free energy, liquid density,
and heat of vaporization, are also in good overall agreement with
experimental values. The structures of benzene liquid phase and benzene-water
solution were also investigated by simulation and compared with experimental
and PDB structure derived statistical results
Expanding the Product Profile of a Microbial Alkane Biosynthetic Pathway
Microbially produced alkanes are a new class of biofuels
that closely match the chemical composition of petroleum-based fuels.
Alkanes can be generated from the fatty acid biosynthetic pathway
by the reduction of acyl-ACPs followed by decarbonylation of the resulting
aldehydes. A current limitation of this pathway is the restricted
product profile, which consists of <i>n</i>-alkanes of 13,
15, and 17 carbons in length. To expand the product profile, we incorporated
a new part, FabH2 from <i>Bacillus subtilis</i>, an enzyme known to have a broader specificity profile
for fatty acid initiation than the native FabH of <i>Escherichia coli</i>. When provided with the
appropriate substrate, the addition of FabH2 resulted in an altered
alkane product profile in which significant levels of <i>n</i>-alkanes of 14 and 16 carbons in length are produced. The production
of even chain length alkanes represents initial steps toward the expansion
of this recently discovered microbial alkane production pathway to
synthesize complex fuels. This work was conceived and performed as
part of the 2011 University of Washington international Genetically
Engineered Machines (iGEM) project