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Jessica A. Thomas Department of Biology and Chemistry Purdue University North Central
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Gloaguen, et al, J. Phys. Chem. B. (2013) 117, 4945 - 4955. FF_A FF_B FF_C
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C5 C7 C10 T- or L-shaped V-shaped (approaching parallel)
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Dispersion correcting potentials are appended to Gaussian09 input files Torres and DiLabio, J. Phys. Chem. Lett. (2012) 3, 1738 – 1744. Revised values for carbon: DiLabio, Koleini, and Torres, Theor. Chem. Acc. (2013) 132, 1389. Gaussian Potentials applied to atoms:
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FF: Three experimentally assigned conformersWY: One experimentally observed conformer Analogous to FF_C FF_A FF_B FF_C WY_A
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C10 C7 (terminal) C7/C7 C7 (mid) C7/C10C5/C7 C5 g+g+ All three have same low energy structure. Agrees with FF_A
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FY YFFF FF, FY, and YF overlaid g+ C10
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C7 (terminal) C7/C7 C7 (mid) C7/C10C5/C7 C5 g+g+ FF_B is identified FY has an analogous structure FF_A FF_B
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FY FF FF_B and FF overlaid FF and FY overlaid
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C10 C7 (terminal) C7/C7 C7 (mid) C7/C10C5/C7 C5 g+g+ FF_A FF_B Two versions of C5/C7: ag- = T/L-shaped ag+ = V-shaped g+g+ ag- ag+
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Almost parallel rings ag- T/L-shaped rings C5 C7 FF_C and WY_A have ag+ configuration
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C10 C7 (terminal) C7/C7 C7 (mid) C7/C10C5/C7 C5 g+g+ FF_A FF_B ag- ag+ FF_C (and WY_A) g-g- g+g- g-g+ g+g+ g+g- g+g+ g+g- ag+ g+g+ and g+g- g-g+, ag-, and ag+
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C10 C7 (terminal) C7/C7 C7 (mid) C7/C10 C5/C7 C5 g+g+ FF_A FF_B ag- ag+ FF_C (and WY_A) g-g- g+g- g-g+ g+g+ g+g- g+g+ g+g- ag+ T/L NI V Ring Interactions: T/L = T- or L-shaped V = V-shaped NI = No Interaction V T/L V
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The B3LYP-DCP method is significantly faster than other methods while still identifying experimentally observed conformers among the lowest energy results Easily implemented in Gaussian without programming experience Computational results for FY and YF: FY: Three lowest energy structures are analogous to experimental results for FF (and WY) YF: Two lowest energy structures analogous to FF_A and FF_C/WY_A
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Undergraduate Research Assistants: Purdue North Central College of Science and Department of Biology/Chemistry Rosen Center for Advanced Computing Funding from Louis Stokes Alliance for Minority Participation Student support from PNC Honors Program Melanie Shebel Jasmine Moore
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Minimum of 5 starting structures Revising protocol to use more Molecule dynamics simulation Amber, ff14SB force field 150 ns for each starting structure Select low energy structures B3LYP-DCP
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