Chemistry
164, Spring, 2008
Molecular
Structure and Modeling
Reading List
Code to frequently used sources of
required reading
1) Leach: A. R. Leach, Molecular Modelling,
Principles and Applications, 2nd. ed. Prentice-Hall,
2) Lide:
D. R. Lide, Jr., and M. A. Paul, Critical Evaluation of Chemical and
Physical Structural Information,
3) Hehre:
W. J. Hehre, A Guide to Molecular Mechanics and Quantum Chemical
Calculations, Wavefunction, Inc.,
4) Spartan ’06,
Tutorial and User’s Guide, Wavefunction,
Required
material is provided in class or is available on the WWW.
Topics
Covered by Date and the Associated
I) Introduction. Does a molecule have a well defined geometry? [24 Jan.]
A) required reading
1) Leach, Chapter 1
2) Lide, section by V. L. Laurie, “Definitions and General Theory of
Interatomic Distances”, pp. 67-76
B) other resources
1) Jan Labanowsi, the director of CCL at OSU, has drafted an instructive overview of molecular modeling.
2) Peter Steinbach at the NIH has written "Introduction to Macromolecular Simulation" which surveys applications of molecular modeling from the perspective of classical mechanics. Browse this as a general introduction to molecular modeling.
3) G. Herzberg, Molecular
Spectra and Molecular Structure, (Volumes I, II, III), D. van Nostrand,
4) W. H.
Flygare, Molecular Structure and Dynamics, Prentice-Hall,
C) case studies covered in class
1) malonaldehyde: W. F. Rowe, Jr., R. W. Duerst,
& E. B.Wilson, “The
intramolecular hydrogen bond in malonaldehyde”, J. Am. Chem. Soc., 98, 4021-4023 (1976) and S. L. Baughcum, R. W. Duerst, W. F. Rowe,
Z. Smith, & E. B. Wilson, “Microwave spectroscopic study of
malonaldehyde (3-hydroxy-2-propenal).
2. Structure, dipole moment, and
tunneling”, J. Am. Chem. Soc., 103, 6296-6303 (1981).
II) Structures derived from Microwave Spectroscopy. [31 Jan.]
A) required reading
1) E. B. Wilson, “Microwave Spectroscopy in Chemistry”, Science, 162, 59 (1968)
2) Lide, section by R. H. Schwendeman , “Structural Parameters from Rotational Spectra”,
pp. 94-115
B) other resources
1) C. H. Townes
and A. L. Schawlow, Microwave Spectroscopy,
2) J. E.
Wollrab, Rotational Spectra and Molecular Structure, Academic Press,
3) N. C. Craig, O. P. Abiog, B. Hu, S. C. Stone, W. J. Lafferty, & L.-H. Xu, “Complete Structure of trans-1,2-Difluoroethylene from the Analysis of High-Resolution Infrared Spectra”, J. Phys. Chem., 100, 5310-5317 (1996)..
4) D. C. McKean, N. C. Craig, & Y. Panchenko, “s-trans-1,3-Butadiene and Isotopomers: Vibrational Spectra, Scaled Quantum-Chemical Force Fields, Fermi Resonances, and C-H Bond Properties”, J. Phys. Chem. A, 110, 8044-8059 (2006).
5) W. J. Lafferty, “Determination of Potential Functions and Barriers to Planarity for the Ring-Puckering Vibrations of Four Membered Ring Molecules”, pp. 386-411 in Lide.
C) case studies discussed in class
1) chloroethanol: R. G. Azrak & E. B. Wilson, Edgar
Bright, “Microwave
spectra and intramolecular hydrogen bonding in the 2-haloethanols: molecular structure and quadrupole coupling
constants for 2-chloroethanol and 2-bromoethanol”, J. Chem. Phys.,
52, 5299-5316 (1970). [A detailed discussion can be found with the Molecular Zoo entry for 2‑chloroethanol.]
2) sulfur dioxide: Y. Morino, Y. Kikuchi, S. Saito, &
E. Hirota, “Equilibrium structure
and potential function of sulfur dioxide from the microwave
spectrum in the excited vibrational state”, J. Mol. Spectrosc.,
13, 95-118 (1964)
3) sulfur dioxide: F. J. Lovas, “Microwave spectra of molecules of astrophysical interest. XXII. Sulfur dioxide (SO2)”, J. Phys. Chem. Ref. Data, 14, 395-488 (1985). [a critical review of the entire microwave literature on sulfur dioxide]
III) Structures derived from electron diffraction. [7 Feb.]
A) required reading
1) D. W. H.
Rankin, “Electron Diffraction and Molecular Structure”, Chem. in
2) Lide, section by K. Hedberg, “Critical Evaluation of Structural Information from Gaseous Electron Diffraction”, pp. 77-93
3) H. Ihee, V. A. Lobastov, U. M. Gomez, B. M. Goodson, R. Srinivasan, C.-Y. Ruan, and A. H. Zewail, “Direct Imaging of Transient Molecular Structures with Ultrafast Diffraction”, Science, 291, 458-462 (2001).
B) other resources
1) L. S. Bartell, “Electron Diffraction by Gases”, Chapter 11 in Physical Methods of Chemistry, A. Weissberger, ed.,
Wiley,
2) S. H. Bauer, “Diffraction of
Electrons by Gases”, Chapter 14 in Physical Chemistry, An Advanced Treatise,
D.
3) I.
4) Douglas Cameron has written GPED which simulates gas-phase electron diffraction data for a select number of molecules and calculates the radial distribution function. An astute user can write his/her own coordinate files which use xyz Cartesian format.
5) D. van Hemelrijk, L. van den Enden, H. J. Geise, H. L. Sellers, & L. Schäfer, “Structure Determination of 1-Butene by Gas Electron Diffraction, Microwave Spectroscopy, Molecular Mechanics, and Molecular Orbital Constrained Electron Diffraction”, J. Am. Chem. Soc., 102, 2189-2195 (1980).
C) case studies discussed in class
1) silicon tetrafluoride: K. Hagen & K. Hedberg, “Interatomic distances and rms (root-mean square) amplitudes of vibration of gaseous silicon tetrafluoride from electron diffraction”, J. Chem. Phys., 59, 1549-1550 (1973)
2) 2-chloroethanol: K. Almenningen, L. Fernholt, and K.
Kveseth, "An Electron Diffraction Study of the anti-gauche Ratio as
a Function of Temperature for Ethylene Chlorohydrin, 2-Chloroethanol", Acta
Chem. Scand., Part A, 31, 297-305 (1977). [A detailed discussion can be found with the Molecular Zoo entry for 2‑chloroethanol.]
IV) Molecular Mechanics [14 Feb.]
A) required reading
1)
2) Spartan ’06 [Use as needed.]
B) other resources
1) EBI (European Bioinformatics Institute) provides an annotated bibliography of the literature on force fields and evaluations of force fields.
2) Section II of Hehre contains extensive data on the validation of the Tripos and MMFF force fields.
3) F. Jensen, Chapter 2 in Introduction to Computational Chemistry, Wiley, NY (1999)
4) C. J. Cramer, Chapter 2 in Essentials of Computational Chemistry, Wiley, NY (2002)
5) J. Gao, “Hybrid Quantum and Molecular Mechanical Simulations”,
Acc. Chem. Res., 29, 298-305 (1996)
6) G. Monard and K. M.Merz, Jr., “Combined Quantum Mechanical/Molecular Mechanical Methodologies
Applied to Biomolecular Systems”, Acc. Chem. Res., 32, 904-911 (1999)
7) The online and printed manuals for SYBYL contain an extensive discussion of force fields.
8) P. Comba and T. W. Hambley, Molecular Modeling of Inorganic Compounds, Wiley-VCH, Weinheim (2001)
9) A. Holt, Polarizable Force
Fields for Flexible Molecules, Masters Thesis,
C) case studies presented in class
1) W. E. Steinmetz, P. J.
Robustelli,
V) Searching Conformational Space [21 Feb.]
A) required reading
1)
B) other resources
1) The online and printed manuals for SYBYL contain an extensive discussion of
its broad repertoire for tools for searching conformational space.
2) G. M. Crippen, Distance Geometry and Conformational Calculations, Research
Studies Press, Wiley, NY (1981) [the classic monograph on distance geometry]
3) D. G. Crippen & T. F. Havel, Distance Geometry and Molecular Conformation, Wiley, NY (1988)
4) D. C. Spellmeyer, A. K. Wong, M. J. Bower, & J. M. Blaney, “Conformational Analysis Using Distance Geometry Methods”, J. Mol. Graphics Model., 15, 18-36 (1997).
5) M. Saunders, “Stochastic exploration of molecular mechanics energy surfaces.
Hunting for the global minimum”, J. Am. Chem. Soc., 109, 3150-3152 (1987) [the
basis for random searching in torsional space]
6) W. J.
Fairbrother, R. S. McDowell, & B. C. Cunningham, “Solution conformation of
an atrial natriuretic peptide variant selective for the type A
receptor.”, Biochemistry, 33,
8897-8904 (1994).
7) V. Villani
& A. M. Tamburro, “Conformational
modeling of elastin tetrapeptide Boc-Gly-Leu-Gly-Gly-NMe by molecular
dynamics simulations with
improvements to the thermalization procedur”, J. Biomol. Struct. Dynamics,
12, 1173-1202 (1995)
8) T. Schlink,
9) M. Saunders, K.
N. Houk, Y.-D. Wu, W. C. Still, M. Lipton, G. Chang, & W. C. Guida,
“Conformations of Cycloheptadecane. A
Comparison of Methods for Conformational Searching”, J. Am. Chem. Soc., 112,
1419-1427 (1990).
C) case
studies discussed in class
1) calix[4]arene: C. D. Gutsche & L. J. Bauer, “Calixarenes. 13. The conformational properties of calix[4]arenes, calix[6]arenes, calix[8]arenes, and oxacalixarenes”, J. Am. Chem. Soc., 107, 6052-6059 (1985), 107(21), 6052-9.
VI) Determination of 3D Structures from NMR [28 Feb.]
A) required reading
1)
2) Nobel lecture of Kurt Wüthrich
3) brief discussion of PISEMA from the Physics Today online site
B) other resources
1) K. Wüthrich, NMR of Proteins and Nucleic Acids, Wiley, NY (1986) [the classic!]
2) D. Neuhaus and M. Williamson, The Nuclear Overhauser Effect, VCH, Weinheim (1989)
3) M. J. Duer, Introduction to
Solid-State NMR Spectroscopy, Blackwell,
4) Lide, section by L. C. Snyder & S. Meiboom, “Molecular Structure from NMR
in Liquid Crystalline Solvents”, pp. 143-156
5) P. Permi, Applications for Measuring Scalar and Residual Dipolar Couplings in Proteins, University of Oulu, Oulu, Finland (2000) [doctoral dissertation of P. Permi, hence more details than found in most papers]
6) S. Achuthan, Analysis
of Orientational Restraints in Solid-State Nuclear Magnetic Resonance
with Applications to Protein Structure
Determination,
7) A. A. Nevzorov & S. J. Opella, “Structural fitting of PISEMA spectra of aligned proteins”, J. Magn. Reson., 160, 33-39 (2003)
8) G. Cornilescu, F. Delagio, & A. Bax, “Protein backbone angle restraints from searching a database
for chemical shift and sequence homology”, J. Biomol. NMR, 13, 289-302 (1999)
9) A. Cavalli, X. Salvatella, C. M. Dobson, & M. Vendruscolo, Proc. Natl. Acad. Sci. USA,
104, 9615-9620 (2007)
10) V. F. Bystrov, “Spin-Spin Coupling between Geminal and Vicinal Protons“, Russ. Chem. Rev., 41, 281-304 (1972).
11) M. Barfield, “Structural Dependencies of Interresidue Scalar Coupling h3JNC’ and Donor 1H Chemical Shifts in the Hydrogen Bonding Regions of Proteins”, J. Am. Chem. Soc., 124, 4158-4168 (2002)
12) W. E. Steinmetz, J. D. Sadowsky, J. S. Rice, J. J. Roberts, & Y. K. Bui, “Determination of the aqueous-phase structure of 6-O-methylerythromycin from NMR constraints”, Magn. Reson. Chem., 39, 163-172 (2001) [This paper discusses the application of the Wüthrich approach to small molecules.]
VII) Hartree-Fock Ab Initio Quantum Mechanics and Basis Functions [6 Mar.]
A) required reading
1) Leach,
pp. 27-74 in
2)
3) Spartan ’06 [Use as needed.]
4) We all get lost in the maze of acronyms and methods. This item is here as a reference. A Quick Reference Guide to methods and acronyms was provided by Chamot Labs, Inc. and is available at the CCL site.
B) other resources
1)
A. Szabo and N. S. Ostlund, Modern Quantum Chemistry,
2) J. B. Foresman and A. Frisch, Exploring Chemistry with Electronic Structure Methods,
2nd.
ed., Gaussian, Inc.,
3) F. Jensen, Chapters 3 & 6 in Introduction to Computational Chemistry, Wiley, NY (1999)
4) C. J. Cramer, Chapters 4-6 in Essentials of Computational Chemistry, Wiley, NY (2002)
5) J. Kong et al., “Q-Chem 2.0: A High Performance Ab Initio Electronic Structure
Program Package”, J. Comput. Chem., 21, 1532-1548 (2000). [This paper describes
the kernel of Spartan.]
6) J. Simons, “An Experimental Chemist’s Guide to ab Initio Chemistry”, J. Phys. Chem., 95,
1017-1029 (1991) [A landmark paper that discusses the strengths and weaknesses
of ab initio quantum mechanics as well as the tricks crucial for its success.]
7) J. J. Stewart, “MOPAC: A semiempirical molecular orbital program”, J. Comp.-Aided Mol. Design,
4, 1-105 (1990) [This landmark paper describes semi-empirical approaches in detail.]
8) J. Pople, “Nobel Lecture: Quantum chemical models”, Rev. Mod. Phys., 71, 1267-1274 (1999)
9) H. M. James & A. S. Coolidge, “The Ground State of the Hydrogen Molecule”, J. Chem. Phys., 1,
825-835 (1933). [Note the year. In this crucial paper, James and Coolidge calculated the
properties of hydrogen to experimental accuracy and demonstrated that quantum mechanics
provided the explanation for the nature of the covalent chemical bond.]
VIII) Validation of Ab initio Quantum Mechanics and Advanced Hartree-Fock Methods [13 Mar.]
A) required reading
1) Leach, pp. 86-104 and 108-126
B) other resources
1) Much of Hehre is devoted to validation of various computational methods.
2) F. Jensen, Chapter 4 in Introduction to Computational Chemistry, Wiley, NY (1999)
3) C. J. Cramer, Chapter 7 in Essentials of Computational Chemistry, Wiley, NY (2002)
4) A. Szabo
and N. S. Ostlund, Modern Quantum Chemistry,
5) NIST’s Computational Chemistry Comparison and Benchmark Database provides a very
comprehensive comparison of the results of ab initio calculations of properties via a wide array
of methods.
IX) Properties Obtained from Quantum Mechanics and Molecular Mechanics [27 Mar.]
A) required reading
1) Leach, pp. 74-85
2) Spartan ’06 [use as needed]
B) other resources
1)
2) W. J.
Hehre, A. J. Shusterman, & J. E. Nelson, The Molecular Modeling Workbook
for
Organic
Chemistry, Wavefunction,
3) J. B. Foresman and A. Frisch, Exploring Chemistry with Electronic Structure Methods,
2nd.
ed., Gaussian, Inc.,
4) F. Jensen, Chapters 10-11 in Introduction to Computational Chemistry, Wiley, NY (1999)
[Table 1.1 provides an instructive summary of properties and their relationship to derivatives of the energy.]
5) C. J. Cramer, Chapters 9 & 10 in Essentials of Computational Chemistry, Wiley, NY (2002)
6) A. P. Scott & L. Radom, “Harmonic Vibrational Frequencies: An Evaluation of
Hartree-Fock, Møller-Plesset, Quadratic Configuration Interaction, Density Functional
Theory, and Semiempirical Scale Factors”, J. Phys. Chem., 100, 16502-16513 (1996).
7) O. L. Polyansky, A. G. Császár, S. V. Shirin, N. F. Zobov, P. Baletta, J. Tennyson, D. W.
Schwenke, & P. J. Knowles, “High-Accuracy ab Initio Rotation-Vibration Transitions for
Water”, Science, 299, 539-542 (2003).
8) C. A. Lipinski, F. Lombardo, B. W. Dominy, & P. J. Feeney, “Experimental and computational
approaches to estimate solubility and permeability in drug discovery and development settings”,
Advanced Drug Delivery Review, 46, 3-26 (2001) [the article that proposes Lipinski’s rules]
9) Y. C. Martin, “A Bioavailability Score”, J. Med. Chem., 48, 3164-3170 (2005) [a more recent study of the search for the characteristics of druglike molecules]
10) Y. C. Martin, “Overview of Concepts and Methods in Computer-Assisted Rational Drug Design” in Volume 203 of Methods in Enzymology, J. Lagone, ed., Academic, NY (1991)
11) C. Hansch & A. Leo, Exploring
QSAR, ACS,
12) K.-C.
Lau & C.Y. Ng, “Benchmarking State-of-the-Art ab
Initio Thermochemical Predictions with
Accurate Pulsed-Field
Ionization Photoion-Photoelectron Measurements”, Acc. Chem. Res.,
41, 823-829 (2006)
13) Michal Jaszunski , Antonio Rizzo, and Kenneth Ruud provide at a Web site at the University of Oslo the document “Electric, magnetic and optical properties and their ab initio calculation in the DALTON program” which discusses calculable properties.
14) P. Mezey, “Molecular
Surfaces”,
15) R. Bader, Atoms in
Molecules,
X) Density Functional Theory (DFT) [3 Apr.]
A) required reading
1) Leach, pp. 126-137
2) W. Kohn, “Nobel Lecture: Electronic structure of matter-wave functions
And density functionals”, Rev. Mod. Phys., 71, 1253-1266 (1999)
B) other resources
1) F. Jensen, Chapter 6 in Introduction to Computational Chemistry, Wiley, NY (1999)
2) C. J. Cramer, Chapter 8 in Essentials of Computational Chemistry, Wiley, NY (2002)
3) R. G.
Parr & W. Yang, Density Functional Theory,
4) Kieron Burke, an expert on DFT at UC-Irvine, is provided the draft of his book devoted to
DFT on his Web site.
5) P. Elliott, K. Burke, & F. Furche, “Excited states from time-dependent density
Functional theory”, Los Alamos National Laboratory, Preprint Archive, Condensed Matter (2007), 1-38,
arXiv:cond-mat/0703590. [link to Burke’s Web site]
6) Mark
Casida at the
Vast array of DFT functionals. This is your guide to DFT alphabet soup.
7) R. O. Jones, “Introduction to Density Functional Theory and Exchange-Correlation Energy Functionals”, Johnny von Neumann Institute for Computing (2006)
8) Hehre provides extensive validation data for DFT as does NIST’s Computational Chemistry Comparison and Benchmark Database .
9) F. Furche & J. P. Perdew, “The performance of semilocal and hybrid density functionals in 3d transition-metal chemistry”, J. Chem.Phys., 124, 044103-044129 (2006) [application of DFT to transition metal species and validation of the method]
10) J. P. Perdew, A. Ruzsinszky, J. Tao, V. N. Staroverov, G. E. Scuseria, & G. I. Csonka, “Prescription for the design and selection of density functional approximations: More constaint satisfaction with fewer fits”, J. Chem.Phys., 123, 062201 (2005) [Perdew and his colleagues describe in a frank manner the art of designing functionals from first principles.]
11) Y. Zhaoi & D. G. Truhlar, “Density Functionals with Broad Applicability in Chemistry”, Acc. Chem. Res., 41, 157-161 (2008). [The authors describe the next step on climbing Jacob’s Ladder.]
12) K. E. Riley, B. T. O. Holt, & K. M. Merz, “Critical Assessment of the Performance of Density Functional Methods for Several Atomic and Molecular Properties”, J. Chem. Theory Comput., 3, 407-433 (2007). [A critical comparison of functionals and basis sets through the fourth rung of Jacob’s Ladder.]
XI) Molecular Dynamics (MD) [10 Apr.]
A) required reading
1)
2) F. Ercolesi, A Molecular Dynamics Primer,
B) other resources
1) The June, 2002 issue of Accounts of Chemical Research with Martin Karplus as the
issue editor is devoted entirely to molecular dynamics.
2) F. Jensen, Chapter 16 in Introduction to Computational Chemistry, Wiley, NY (1999)
3) C. J. Cramer, Chapter 3 in Essentials of Computational Chemistry, Wiley, NY (2002)
4) T. Schlink, Molecular Modeling and Simulation, Springer Verlag, NY (2002)
C) case studies discussed in class
1) boiling points of branched versus straight-chain alkanes
2) physical properties of benzene
XII) Modeling of Chemical Kinetics (17 Apr.)
A) required reading
1) Leach, pp. 279-295, 5.9, 5.9.1, 5.9.2, 5.9.3, 5.9.4
B) other resources
1) F. Jensen, Chapter 12 in Introduction to Computational Chemistry, Wiley, NY (1999)
3) C. J. Cramer, Chapter 15 in Essentials of Computational Chemistry, Wiley, NY (2002)
C) case studies discussed in class
1) mechanism of the SN2 reaction: J. Mikosh, S. trippel, C. Eichhorn, R. Otto, U. Lourderaj, J. X. Zhang, W. L. Hase, M. Weidemüller, & R. Wester, “Imaging Nucleophilic Substitution Dynamics”, Science, 319, 183-186 (2008) et op. cit.
2) trajectory of a unimolecular process: S. C. Ammal, H. Yamataka, M. Aida, & M.Dupuis, “Dynamics-Driven Reaction Pathway in an Intramolecular Rearrangment”, Science, 299, 1555-1557 (2003)
3) protonated C60: L. J. Mueller, D. W. Elliott, K.-C. Kim, C. A. Reed, & P. D. W. Boyd, “Establishing Through-Bond Connectivity in Solids with NMR: Structure and Dynamics in HC60+”, J. Am. Chem. Soc., 124, 9360-9361 (2002)
XIII) Crystallography [24 Apr.]
A) required reading
1) Lide, section by D. P. Shoemaker, “Well-Behaved Crystal Structure Determinations”, pp. 157-185
2) Lide,
section by J. A, Ibers, “Problem
B) other resources
1) F. A. Cotton,
Wiley, NY (1990)
2) T. Hahn, ed., International
Tables for Crystallography, Volume A Space-Group Symmetry, D. Reidel,
3) Pomona Chemistry has a site license for the CCDC database which covers the crystal structures of
organic molecules and for the
IUCr database which covers all inorganic compounds. The software is installed on one of the PC’s
in Seaver North 205. The structures of
proteins, peptides, DNA, and RNA can be downloaded from the Protein Data Bank maintained at
4) Berhard Rupp maintains Crystallography 101 which covers all aspects of the subject. In scope and quality, the site is very impressive.
5) Michael Sweha at UCLA maintains the Crystallographer’s Companion, a collection of tutorials on crystallography.
6) The International Union of Crystallography (IUCr) provides in its Web site an annotated bibliography of sites devoted to crystallography.
7) J. D. Dunitz, X-Ray Analysis and the Structure of Organic Molecules, 2nd. ed. ,Wiley-VCH, Weinheim (1996)
last updated, 4 May 2008