Paper Analysis

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Paper Analysis
Computational Chemistry 5510 Spring 2006 Hai Lin
2
Questions to Ask

• What is the objective of the paper?
• What are the most significant conclusions in the
  paper?
• Which levels of theory were employed? Were the
  selected levels of theory appropriate to the
  research?
• Have the authors employed any explicit or
  implicit assumptions/simplications/approximations
  ?
• How reliable the calculations seem to be? Does
  the computation support the authors conclusions?
  
• Are there any comparisons made with experiment?
  Are the comparisons fair and meaningful?
• Could you improve the study in terms of accuracy
  and efficiency?

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The Objective

• A systematic study of the molecular properties,
  in particular, the electron affinities (EA), for
  C6H5X (X N, S, NH, PH, CH2, and SiH2) and their
  corresponding anions. More specifically,
• Comparisons of three kinds of calculated EA with
  experimental EA
• Prediction of vibrational frequencies
• Comparisons of various DFT methods

W. Xu, A. Gao, Structures, electron affinities,
and harmonic vibrational frequencies of
C6H5X/C6H5X- (X N, S, NH, PH, CH2, and SiH2,
J. Phys. Chem. A 2006, 110, 997.
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EA Calculations

• Comparisons of three kinds of calculated EA with
  experimental EA

E 0
Unoccupied Occupied
Vertical EA Adiabatic EA
Vertical Detachment Energy
5
Zero-point Energy Corrections
E
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Most Significant Conclusions

• Geometries
• Geometries are similar for a neutral specie and
  its anion.
• Most DFT models gives similar geometries BHLYP
  gives usually somewhat shorter bond lengths.
• (How similar? Can you express the similarity in
  terms of averaged and/or maximal discrepancies
  for certain quantities such as bond lengths and
  angles?)
• Mean unsigned errors (MUE) Mean absolute
  differences (MAD)
• Mean signed errors (MSE)

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Most Significant Conclusions (2)

• Electron Affinities
• EAs calculated by three kinds of schemes are
  close to each other. (Why?)
• ZPE-corrected EA agrees with experimental data
  reasonably well. (How well?)
• BHLYP underestimates EA, B3P86 overestimate EA,
  while the other DFT models gives reliable
  predictions. (How seriously the errors are?)
• Can you express the qualitative assessment in
  terms of MUE, MSE, or RMS?

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Most Significant Conclusions (3)

• Vibrational Frequencies
• Vibrational frequencies for a neutral specie are
  normally higher than those for the corresponding
  anion. (Any justification?)
• Calculated and measured frequencies agrees with
  each other reasonably well. (How well?)
• BHLYP overestimate the frequencies. (How large is
  the overestimation? Why BHLYP is so bad?)

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Level of Theory

• Which level of theory? Are they appropriate?
• DFT (Any difficulty? Any justification? Any
  pre-calibration?)
• DZP basis set (Why double Zeta? Why ?)
• RHF for closed shell and UHF for open-shell
  calculations. (Did the authors tell you about
  the spin contaminations?)
• In total, 7 DFT models (B3LYP, BLYP, BHLYP,
  B3P86, BP86, B3PW91, BPW91) are tested. (Why did
  the author make such a selection? Did the authors
  optimized the geometry for all DFT models?)

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Explicit or Implicit Assumptions

• Koopmans Theorem
• EA (How well does this approximation work?)
• Harmonic Approximation
• Vibration analysis and zero-point energy (Do you
  think this approximation a good one? Why?)
• (Of course, we know that the authors were using
  Born-Oppenheimer approximation, HF approximation,
  and LCAO approximation, which we usually accepted
  without questioning except for special cases.)

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Results and Conclusions

• How reliable the calculations seem to be? Does
  the computation support the authors conclusions?
  
• Yes!
• No! (Give me an example!)
• Are there any comparisons made with experiment?
  Are the comparisons fair and meaningful?
• Geometry (What to do if no experimental data are
  available?)
• EA (Which EA is most suitable for comparison?)
• Vibrational frequencies (Harmonic frequencies vs.
  fundamentals? Any scaling factors?)

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Suggestions for Improvement

• Higher level of theory and larger basis sets
• DFT or wave function theory?
• Complete basis set limit?
• How expensive the calculations will be?
• Including anharmonicty in vibrational analysis
• Is that feasible? How about using scaling
  factors?
• IR spectra
• How reliable will they be?
• Any experimental data available?

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Select a Paper to Analysis

• Every student is required to analyze a
  computational paper within the students area of
  interest due on the date of the final and submit
  a short report.
• The paper you selected should be approved by me.
  I am happy to help you in finding a paper, if you
  wish.
• The deadline for choosing a paper is April 5.
• The report of your analysis is expected to be 2
  to 4 pages long excluding excluding references.
  The format requirement is double-spaced, 10 12
  point fonts.
• Try to address the questions outlined in the
  slide.

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Select a Paper to Analysis (2)

• If you want, you can perform calculations to
  verify your own idea about the problem that you
  are analyzing.
• The report of analysis is due on the last class
  (May 11) when you give a presentation of your
  project.
• Grading will be based on
• Clarity (10 points) Did you write the report in
  a clear and professioal manner?
• Accuracy (12 points) Did you make the analysis
  correctly?
• Creativity (3 points) Did you think creatively
  during the analysis?
• Come to me if you have any questions or concerns.
  I will be happy to help you out or make
  suggestions.

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List of Papers

• If you want, you can select one of the papers
  listed here for your analysis. These papers
  should be available from the library or be
  downloaded via internet using a campus computer.
  You can also come to me for a hard copy.
• S. Vemparala, I. Ivanov, V. Pophristic, K.
  Spiegel, M. L. Klein, Ab initio calculations of
  intramolecular parameters for a class of
  arylamide polymers, J. Comput. Chem. 2006, 27,
  693.
• P. R. Schreiner, S.-J. Kim, H. F. Scaefer III, P.
  v. R. Schleyer, CH5 The never-ending story or
  the final world?, J. Chem. Phys. 1993, 99, 3716.
• R. Damrauer, A. J. Crowell, C. F. Craig,
  Electron, hydride, and fluoride affinities of
  silicon-containing species Computational
  studies, J. Am. Chem. Soc. 2003, 125, 10759.

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List of Papers (2)

• Z. Chen, K. Ma, Y. Pan, X. Zhao, A. Tang, J.
  Feng, Calculations on all possible isomers of
  the substituted fullerenes C58X2 (X N, B) using
  semi-empirical methods, J. Chem. Soc. Faraday
  Trans. 1998, 94, 2269.
• M. L. Gupta, M. P. McGrath, R. J. Cicerone, F. S.
  Rowland, M. Wolfsberg, 12C/13C kinetic isotope
  effects in the reaction of CH4 with OH and Cl,
  Geophys. Res. Lett. 1997, 24, 2761.
• H. Park, S. Lee, J. Suh, Structural and
  dynamical basis of broad substrate specificity,
  catalytic mechanism, and inhibition of cytochrome
  P450 3A4, J. Am. Chem. Soc. 2005, 127, 13634.
• C. Sporea, F. Rabilloud, A. R. Allouche, M.
  Frécon, Ab initio study of neutral and charged
  SinNap() (n ? 6, p ? 2) clusters, J. Phys.
  Chem. A 2006, 110, 1046.