This document summarizes a presentation on developing new computational tools to study excited states in biological systems. It discusses how computational studies of excited thymine require extensive quantum mechanical models of nucleobases and nucleotides in solution. New software is being developed to apply hybrid quantum mechanics/molecular mechanics methods to efficiently model larger biological systems involving excited states. Preliminary tests on the implementation show its ability to calculate energy differences during optimization of a test system like thymidine monophosphate. Further studies on more demanding systems are still needed to fully evaluate the new software's performance.

1. IQCC
Science
Slam
November
24
Developing
New
Tools
to
Study
Excited
States
Sílvia
Escayola
Dr.
Lluís
Blancafort

2. Chemistry
of
Electronically
Excited
States
ComputaFonal
studies
of
excited
Thymine1
1.
Improta,
R.;
Santoro,
F.;
Blancafort,
L.
Chem.
Rev.
2016,
116,
3540–3593.
h·∙ν
Conical
intersecFon
S0
S1

3. ComputaFonal
Requirements
of
Biological
Systems
NucleoBdes
in
soluBon
and
DNA
strand
fragments
Isolated
nucleobases
and
nucleoBdes
Simple
model
Extensive
model
(System
>100
atoms)
(System
<100
atoms)
Hybrid
method
(QM:MM)
(ONIOM)
High
level
calculaBon
+
low
level
calculaBon
ComputaBonal
approach
Quantum
Mechanics
(CASSCF,
CASPT2,
TD-­‐DFT)
High
level
calculaBon
ComputaFonal
Requirements
of
biological
systems

4. Ruiz-­‐Barragan,
S.;
Morokuma,
K.;
Blancafort,
L.
J.
Chem.
Theory
Comput.
2015,
11,
1585–1594.
Conical
IntersecBon
Development
of
new
SoZware

5. Preliminary
Tests
of
the
ImplementaFon
Energy
Difference
(S1-­‐S0)
in
hartree
No.
of
MicroiteraBons
cycle
Figure
1.
VariaBon
of
the
energy
difference
during
the
1st
macroiteraBon
cycle
Further
studies
using
more
demanding
systems
are
required
to
evaluate
the
performance
of
the
implementaBon
Thymidine
monophosphate
(TMP)
TEST
SYSTEM