computational modeling of varying nucleophile activity on the rna cleavage transition state jennifer...
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![Page 1: Computational Modeling of Varying Nucleophile Activity on the RNA Cleavage Transition State Jennifer Andre, Aastha Chokshi, Daniel Greenberg, Jay Karandikar,](https://reader035.vdocument.in/reader035/viewer/2022081504/56649ea05503460f94ba30ba/html5/thumbnails/1.jpg)
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 CassanoAssistant: Zack Vogel
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RNA Cleavage
• Role of RNA
• RNA Cleavageo Importance & Ubiquityo Change or inhibit gene expression
• Understanding the Mechanismo Potential Applications
Artificial Nucleases Target harmful RNA Cure diseases
DNA RNA Protein
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Observing the Nucleophile
The strength of a nucleophile depends upon how negative its charge is.
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Transition States
Harris and Cassano, Current Opinion in Chemical Biology, 2008, 12, 626-639
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Describing the Transition State
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Computational Chemistry
• Life Span of Transition State: 10-13 Seconds
• Allows us to visualize structures that cannot be observedo Distanceso Chargeso Angles
Abu-Awwad, Fakhr, Computational & Biophysical Chemistry, 2007
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Electronic Structure Methods
Locke, W., Molecular Orbital Theory, 2006
• 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
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Models
• GaussView
• Simplification
• Structureo Variation of the electronegative portiono Effects on nucleophile
Lönnberg, Org. Biomol. Chem., 2011, 9, 1687–1703
Nucleophile
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Optimization
• Finding molecular geometries:o bond lengthso bond angleso charges
• Ground state and transition state
• B3LYP/6-31++G(d,p)
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Frequency
• Determines if molecule at minimum or transition state
• Calculating atomic motion within moleculeso Vibrations within bondso Thermochemical data
• B3LYP/6-31++G(d,p)
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The Ground State
P-O (Nuc)
P-O (LG)
Charge (ONuc)
Charge (OLG)
-CH3 4.565 1.664 -0.929 -0.72
-CFH2 4.56078 1.66327 -0.9 -0.717
-CF2H 4.53447 1.64745 -0.897 -0.692
-CF3 4.439 1.661 -0.873 -0.71
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Transition StatesP-O
(Nuc)P-O(LG)
P-O(Nuc) + P-
O(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
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The Phenol Leaving Group
• Structure:o Methyl group by nucleophileo Phenol leaving group
• Different basis seto B3LYP/6-311++G(d,p)
• Test effect of good leaving group on transition state
o Reactant-likeo P-ONuc Longer (2.31Å vs 1.78Å)
o P-OLg Shorter (1.83Å vs 2.36Å)
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Energy Calculations
• Calculating Electronic Energy
• Methodso B3LYPo MPWB1K - more accurate
G = (((Ee +ZPVE) + Evib + Erot + Etrans)+ RT) - TS
• 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: 2281-2292.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.
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Energy Results - B3LYP
Ground State Energy (kJ/mol)
Transition State Energy (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
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Energy Results - MPWB1K
Ground State Energy (kJ/mol)
Transition State Energy (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
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Energy Results - GraphBrønsted Plot Comparing Acidity of Nucleophile and
Reaction Rate
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Conclusions
As pKa decreases (acidity increases):
• free energy of activation increases.
• 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
Therapies
• Ras
• VEGF - Vascular Endothelial Growth Factor
• EGF - Epidermal Growth Factor
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Future Investigations
• Changing leaving group
• Changing nucleophile
• Larger basis set
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Thank you!Team 1 Project Advisor: Dr. Adam Cassano
Assistant: 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.
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Questions?
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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.