Bookmarks



Some Books Recommended for Newbies of Theoretical and Computational Chemistry
  1. "AB initio Molecular Orbital Theory" By J. W. Hebre, L. Radom, P.v.R. Schleyer and J. A. Pople, New York: Wiley, 1986. (Available at the XMU Lib.)

  2. "Molecular Modelling -- Principles and Applications" By Andrew R. Leach, Addison Wesley Longman Limited 1996.(Available at the XMU Lib.)

  3. "Quantum Chemistry" By I.N. Levine, Allyn and Bacon, 1975 (Available at the XMU Lib.)

  4. 《物质结构》(第二版)， 徐光宪、王祥云，高等教育出版社(Available at the XMU Lib.)

  5. 《量子化学基本原理和从头计算法》(上、中)， 徐光宪、黎乐民，科学出版社(Available at the XMU Lib.)

  6. 《固体能带理论》， 谢希德、陆栋主编，复旦大学出版社(Available at the XMU Lib.)

  7. 《群论在化学中的应用》，F.A. Cotton著， 刘春万等译，科学出版社(Available at the XMU Lib.)

Local Sources
  1. Theoretical Chemistry--Quo Vadis? (Angew. Chem. 2011) by Walter Thiel (pdf file).

  2. Predicting Molecules, More Realism Please! a paper regarding the general rules and logics to be used in theoretical computations by R. Hoffman et al. (pdf file).

  3. "Challenges in Theoretical Chemistry.", a series of perspective papers published in a special issue of Science, 2008, 321 ( Aug. 8th). Especially, I recommend herein two of these articles, i.e., "Insights into Current Limitations of Density Functional Theory" by W. Yang et al. (Science 2008, 321, 792) and "Challenges in Modeling Materials Properties without Experimental Input" By Carter EA.

  4. "How to write a scientific paper--Advice from Prof. P. v. R. Schleyer" (ppt file)


  5. "Whitesides' Group: Writing a Paper" (Adv. Mater., 2004, 16,1375) by George M. Whitesides (pdf file)

  6. "Assumptions: Taking Chemistry in New Directions" (Angew. Chem. Int Ed. 2004, 43,3632) by George M. Whitesides (pdf file)


  7. "ABC of Scientific Research--A Personal Notes from Prof. M. Poo" (ppt file) and his Booknotes (ms word doc)


  8. Self-cultivation and creative research----Video fragment of "Prof. Y.T. Lee's Lecture on the Zhangzhou Campus of XMU" (mp4 file)


  9. "Chemistry's Essential Tension" -- R. Hoffmann's Lecture at Harvard (video, MP4 file).


  10. R. B. Woodward's Lecture at Harvard. (voice, MP4 file).

  11. General Advices from Xin Lu


Online Databases, Resources, and Freewares for Quantum Chemistry Computations.
  1. NIST Chemistry Webbook: NIST Standard Reference Database on Molecules and Ions (Spectra and thermodynamics data).


  2. EMSL Basis Sets Exchange (Various atomic basis sets preformatted for different quamtum chemical computational packages such as Gaussian, ADF, Molpro etc.)


  3. Molden (click to download), a freeware for visualizing Molecular Structure and Density from the Ab Initio packages.


  4. Molkel (click to download), a freeware for visualizing Molecular Structure and Density from the Ab Initio packages.


  5. Gaussian 09 Online Manual

  6. Gaussian 03 Manual (click to download)


A Personal Selection of Papers on Benchmark Computations. (incomplete list, plz send me your addition!)

Genenral Theory

  1. A Chemistry Guide to Density Functional Theory by W. Koch.

Solvent Model

  1. "Comment on the Correct Use of Continuum Solvent Models" (J. Phys. Chem. A, 2010,114,13442) by M. L. Coote et al.

  2. "On the Performance of Continuum Solvation Methods. A Comment on 'Universal Approaches to Solvation Modeling'” (Acc. Chem. Res., 2009,42,489) by A. Klamt et al.

TD-DFT

  1. "Benchmarks for electronically excited states: Time-dependent density functional theory and density functional theory based multireference configuration interaction" ( J. Chem. Phys., 2008,129,104103) by W. Thiel et al.

  2. "Dependence of Spurious Charge-Transfer Excited States on Orbital Exchange in TDDFT: Large Molecules and Clusters" ( J. Chem. Theory Comput., 2007,3,976-987) by S. Tretiak et al.

  3. "TD-DFT Performance for the Visible Absorption Spectra of Organic Dyes: Conventional versus Long-Range Hybrids" (J. Chem. Theory Comput., 2008,4(1),123-135) by D. Jacquemin et al.

  4. "Extensive TD-DFT Benchmark: Singlet-Excited States of Organic Molecules" (J. Chem. Theory Comput., 2009,5,2420-2435) by D. Jacquemin et al.

  5. "Accurate Simulation of Optical Properties in Dyes" (Acc. Chem. Res., 2009,42,326-334) by D. Jacquemin et al.

  6. "Excited States of DNA Base Pairs Using Long-Range Corrected Time-Dependent Density Functional Theory" (J. Phys. Chem. A., 2009,113,9761) by L. Jensen and N. Govind. This work revealed the difficulties to obtain a good description of both groundstate and excited-state properties using the long-range correction model of Hirao and co-workers.

  7. "Ab Initio Modeling of Donor-Acceptor Interactions and Charge-Transfer Excitations in Molecular Complexes: The Case of Terthiophene-Tetracyanoquinodimethane" (J. Chem. Theory Comput., 2011,7,2068-2077) by D. Jacquemin et al..

  8. "TD-DFT Vibronic Couplings in Anthraquinones: From Basis Set and Functional Benchmarks to Applications for Industrial Dyes" (J. Chem. Theory Comput., 2011,7,1882-1892) by D. Jacquemin et al..

  9. "Excitation energies in density functional theory: An evaluation and a diagnostic test" ( J. Chem. Phys., 2008,128,044118) by D.J. Tozer et al.

  10. "The Vibronic Structure of Electronic Absorption Spectra of Large Molecules: A Time-Dependent Density Functional Study on the Influence of “Exact” Hartree-Fock Exchange" (J. Phys. Chem. A, 2004,108,10225-10237) by S. Grimme et al.

  11. For a TDDFT study on the geometry and emission spectra of long-range charge-transfer excited states, plz refer to "Long-range corrected time-dependent density functional study on fluorescence of 4,4'-dimethylaminobenzonitrile" ( J. Chem. Phys., 2007,126,034504) by K. Hirao et al.

Applications of DFT in Transitional Metal Complexes and Catalysis

  1. "Performance of density functional theory on homogeneous gold catalysis" (Theor. Chem. Acc., 2011, 128,647) by O.N. Faza et al.

  2. On the nature of homo- and hetero-dinuclear metal–metal quadruple bonds — Analysis of the bonding situation and benchmarking DFT against wave function methods (Can. J. Chem. 2010, 88, 1079) by G. Frenking et al.

  3. The Physical and Electronic Structure of M2 Quadruply Bonded Complexes: A Density Functional Theory Study (J. Cluster Sci., 2007,18,27) by M.H. Chisholm et al.

  4. Databases for Transition Element Bonding: Metal-Metal Bond Energies and Bond Lengths and Their Use To Test Hybrid, Hybrid Meta, and Meta Density Functionals and Generalized Gradient Approximations (J. Phys. Chem. A, 2005,109,4388) by D. Truhlar et al.


Some words from Xin Lu to graduate students in my lab.


A) The Art of The Life is Also the Art of Science (生活的准则也是科学的准则）

  • Mile journey starts with the first step! (千里之行，始于足下! -- 白话： 踏踏实实做事，老老实实做人，成功没有捷径！)
  • Once started, end at Perfection! (止于至善! -- 白话：做事情/学问要善始善终！)
  • Stay high and you can see more, experience more and know deeper. (站得高，才能看得远；积蓄经验，才能看得透切)

B) Tips for you to be expertized in applied quantum chemistry?

  • Grasp the basic knowledge of quantum chemistry (QM) as well as the applicability of various QM methods available in those widely used QM packages such as Gaussian, GAMES, ADF, Material Studio, and VASP etc.
  • Understand as much as possible the background of the chemical/physical systems that are closely related to the chemical problems to be solved.
  • Make full use of your computing facilities.

C) How to write your report (including research plan, research progress or even manuscript)?



Before reading the following words, PLEASE MAKE SURE you have read Prof. G.M. Whitesides' essay "Whitesides' Group: Writing a Paper" (Adv. Mater., 2004, 16,1375) and have learnt how to make an outline. In his essay, Prof. G.M. Whitesides emphasized the importance of an outline to the efficient composition of a scientific article. Hereby, I would like to emphasize that an outline that is prepared without any available experimental/computation data also serves as a plan for an ongoing specific research topic. That means, after comprehensive literature search/reading with critical thinking, you have figured out a specific topic to do a systematic computational work. At this stage, you must make an outline (or research plan) which includes the following aspects,

  1. General background of the topic, the problem(s) pertaining to this topic that you are going to solve, the importance/significance of this topic. (This part can be extended and will eventually serve as the introduction of your final article)

  2. Which computational methods you are going to use and justifying your choice by their reliability/credibility. You always need to do a survey of literatures or, sometimes, deliberate benchmark computations in order to figure out the computational method(s) that is(are) the most reliable for the chemical systems concerned. (This part can be extended and will be eventually serves as the "computational details" part of your final article)

  3. All possible individual models/molecules/complexes/stationary points(e.g., intermediates and transition states for reaction mechanism, isomers for compounds etc. ) to be computed, the types of computational data to be extracted from these computations, possible key points to be extracted from the computations, the most eye-catching/informative ways to illustrate each type of computational data. (This part can be extended and will eventually serves as the "results and discussion" part of your final article.)

Please discuss with me about your outline. Sometimes you may need to do some computations on key structures/molecules/intermediates to confirm and to convice me of the plausibility of your plan!


While doing your computations, please WELL Schedule your computational jobs in order to MAKE FULL USE of the computational resources and launch as MANY jobs as possible SIMULTANEOUSLY. Meanwhile, please collect your computational data and add the data into the outline TIMELY. In case some data were out of your expectations, figure out the reasons underlying IN TIME and modify your plan accordingly and timely. REPORT to me and Discuss with me about your computational data TIMELY (at least once a week!).


By adding computational results into the aformentioned outline timely, this file becomes the requested biweekly report to me. To make this report more readable/informative to me, you should always add the following data as supporting information,

  1. Cartesian Coordinates, total energies( various thermal correction forms of energy, e.g., entropy, enthalpy, free energy etc if necessary), values with/without spin anilation(essential for open-shell systems) of each stationary points.
  2. MO analysis (especially frontier MOs), NBO data and spin density (essential for open-shell systems) etc for key structures in case your topic is regarding electronic structures and chemical bonding.
  3. Detailed output of excited states from TDDFT computations if your topic is regarding excited states.
  4. For systems having a open-shell singlet (OS) ground state, the stability of such OS ground-state wavefunctions from UDFT/UHF calculations should be confirmed by single-point calculations with use of the keyword "stable" in G09/G03. The computational data of such a stability checking should be included in the supporting information file!
  5. Any background data highly related to the key point of your investigation.


More words, if a cooperation is requested by a colleague (normally experimentalists), please get my permission first. Meanwhile, you should also make an outline regarding the computations to be conducted. ONLY after I agree on your plan can you begin with such a cooperational job. In any case, you MUST know the research history of my laboratory by reading all our publications AS EARLIER AS POSSIBLE!

Finally, Please read the article "Predicting Molecules, More Realism Please!" written by R. Hoffmann et al. to get the general rules and logics for data mining and presentation.


D) Other routine jobs you need to do

  1. Tracking the latest literatures related to your project by browsing relevant journals (SCIENCE,NATURE,JACS,ACIE,JPC,JCP,CPL,CPC,PCCP and so on) day-by-day. Normally, all these online journals have a special part, e.g., ASAP articles in JACS, to release newly accepted ariticles.
  2. Based on your readings, updating your research plan accordingly.
  3. In case "new" tools or "new" theories (herein the term "new" means "not available in your knowledge") are needed in your research, check out and read the relevant books/literatures to improve your knowledge.
  4. Whenever you have a good idea, please discuss it with me ASAP.


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Updated on May 6, 2011!