Transcript Computational Modeling of Varying Nucleophile Activity on

Computational Modeling
of Varying Nucleophile
Activity on the RNA
Cleavage Transition State
Jennifer Andre, Aastha Chokshi, Daniel Greenberg, Jay Karandikar, Steven
Kunis, Joshua Loughran, Elena Malloy, David Mazumder, Dushyant Patel,
Jeffrey Wu, Grace Zhang
Advisor: Adam Cassano
Assistant: Zack Vogel
RNA Cleavage
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Role of RNA
RNA Cleavage
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DNA
RNA
Importance & Ubiquity
Change or inhibit gene expression
Understanding the Mechanism
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Potential Applications
 Artificial Nucleases
 Target harmful RNA
 Cure diseases
Protein
Observing the Nucleophile
The strength of a nucleophile depends upon how negative its
charge is.
Transition States
Harris and Cassano, Current Opinion in Chemical Biology, 2008, 12, 626-639
Describing the Transition State
Computational Chemistry
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Life Span of Transition State: 10-13 Seconds
Allows us to visualize structures that cannot
be observed
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Distances
Charges
Angles
Electronic Structure Methods
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Levels of Theory:
DFT, Hartree-Fock,
MP2, MP4,....
Basis Set: Set of
functions to model
molecular orbitals
Larger basis set =
better model, but
more computing
time
Locke, W., Molecular Orbital Theory, 2006
Models
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GaussView
Simplification
Structure
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Variation of the electronegative portion
Effects on nucleophile
Lönnberg, Org. Biomol. Chem., 2011, 9, 1687–1703
Nucleophile
Optimization
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Finding molecular
geometries:
bond lengths
o bond angles
o charges
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Ground state and
transition state
B3LYP/6-31++G(d,p)
Frequency
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Determines if molecule at minimum or transition state
Calculating atomic motion within molecules
o Vibrations within bonds
o Thermochemical data
B3LYP/6-31++G(d,p)
The Ground State
-CH3
P-O
(Nuc)
P-O
(LG)
Charge Charge
(ONuc) (OLG)
4.565
1.664
-0.929
-0.72
-0.9
-0.717
-CFH2 4.56078 1.66327
-CF2H 4.53447 1.64745 -0.897 -0.692
-CF3
4.439
1.661
-0.873
-0.71
Transition States
P-O
P-O P-O(Nuc)
(Nuc) (LG)
+ PO(LG)
-CH3
1.78
2.36
4.14
-CFH2
1.78
2.43
4.21
-CF2H
1.79
2.44
4.23
-CF3
1.78
2.50
4.28
The Phenol Leaving Group
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Structure:
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Methyl group by nucleophile
Phenol leaving group
Different basis set
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B3LYP/6-311++G(d,p)
Test effect of good leaving
group on transition state
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Reactant-like
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P-ONuc Longer (2.31Å vs 1.78Å)
P-OLg Shorter (1.83Å vs 2.36Å)
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Energy Calculations
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Calculating Electronic Energy
Methods
B3LYP
o MPWB1K - more accurate
G = (((Ee +ZPVE) + Evib + Erot + Etrans)+ RT) - TS
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Both the ground state and the transition
state
∆G = Gtransition state - Gground state
k = kB T h-1 e -∆G/RT
Ribeiro A, Ramos M, Fernandes P. Benchmarking of DFT functionals for the hydrolysis of phosphodiester bonds. J. Chem. Theory Comput. 2010; 6: 22812292.
Lopez X, Dejaegere A, Leclerc F, York D, Karplus M. Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic,
monoanionic, and neutral systems. J. Phys. Chem. 2006; 110(23): 11525-11539.
Energy Results - B3LYP
Ground
Transition
State Energy State Energy
(kJ/mol)
(kJ/mol)
ΔG‡
(kJ/mol)
Rate
Constant
-CH3
-2298667.1
-2298564.5
102.6
6.46 X 10-6
-CFH2
-2559250.3
-2559143.3
107.0
1.09 X 10-6
-CF2H
-2819863.0
-2819743.1
119.9
6.08 X 10-9
-CF3
-3081577.4
-3081460.8
129.9
1.06 X 10-10
Energy Results - MPWB1K
Ground
Transition
State Energy State Energy
(kJ/mol)
(kJ/mol)
ΔG‡
(kJ/mol)
Rate
Constant
-CH3
-2298016.3
-2297921.9
94.4
1.76 X 10-4
-CFH2
-2558531.8
-2558431.5
100.2
1.65 X 10-5
-CF2H
-2819084.0
-2818969.5
114.5
5.37 X 10-8
-CF3
-3081577.4
-3081460.8
116.7
2.18 X 10-8
Energy Results - Graph
Brønsted Plot Comparing Acidity of Nucleophile and Reaction
Rate
Conclusions
As pKa decreases (acidity increases):
free energy of activation increases.
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leaving group bond length increases.
nucleophile bond length stays roughly the
same.
TS becomes more dissociative.
nucleophile charge becomes less negative.
As nucleophile charge becomes less negative, ...
leaving group bond length increases.
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Why are our results important?
Showed that RNA cleavage can be manipulated
Methyl group
Distances
Transition states
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Therapies
Ras
VEGF - Vascular Endothelial Growth Factor
EGF - Epidermal Growth Factor
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Future Investigations
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Changing leaving group
Changing nucleophile
Larger basis set
Thank you!
Team 1 Project Advisor:
Assistant:
Dr. Adam Cassano
Zack Vogel
Program Administrators:
Dr. David Miyamoto,
Dr. Steve Surace,
Janet Quinn,
Anna Mae S. Dinio-Bloch
Sponsors,
Without whom NJGSS'12 would not have been possible.
Questions?
Works Cited
Abu-Awwad, Fakhr, Computational & Biophysical Chemistry, 2007
Gaussian 09, Revision A.02, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R.
Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P.
Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J.
Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E.
Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, R. Kobayashi, J.
Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam,
M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev,
A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth,
P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski,
and D. J. Fox, Gaussian, Inc., Wallingford CT, 2009.
Harris and Cassano, Current Opinion in Chemical Biology, 2008, 12, 626-639
Locke, W., Molecular Orbital Theory, 2006
Lönnberg, Org. Biomol. Chem., 2011, 9, 1687–1703
Lopez X, Dejaegere A, Leclerc F, York D, Karplus M. Nucleophilic attack on phosphate diesters: a density
functional study of in-line reactivity in dianionic, monoanionic, and neutral systems. J. Phys. Chem. 2006;
110(23): 11525-11539.
Ribeiro A, Ramos M, Fernandes P. Benchmarking of DFT functionals for the hydrolysis of phosphodiester
bonds. J. Chem. Theory Comput. 2010; 6: 2281-2292.