Bibliography on Computational Chemistry

University of Missouri at Columbia
Chemistry 433 - Computational Chemistry - WS98

LITERATURE ON
COMPUTATIONAL CHEMISTRY

COMPUTATIONAL CHEMISTRY TODAY Molecular Modeling Software in Use: Publication Trends. Donald B. Boyd, Chapter 5 in Vol. 6 of Reviews of Computational Chemistry Kenny B. Lipkowitz, Donald B. Boyd, Eds.; VCH, Weinheim, Germany, 1995. ISBN 1-56081-667-8. BOOK CHAPTER (Hand-Out) BONDING THEORY The Chemical Bond. Structure and Dynamics. Ahmed Zewail, Ed.; Academic Press, Inc., Boston, 1992. ISBN 1-12-779620-7 (acid-free paper). BOOK Deciphering the Chemical Code. Bonding Across the Periodic Table. Nicolaos D. Epiotis; VCH, Weinheim, Germany, 1994. ISBN 1-56081-946-4 (alk. paper). BOOK The Mechanism of Covalent Bonding. George B. Bacskay, Jeffrey R. Reimers J. Chem. Educ. 1997, 74, 1494-1502. ARTICLE (Hand-Out) This JCE article is available online as a pdf file with the advantage of having color pictures. POTENTIAL ENERGY SURFACES Extending the Diatomic FTIR Experiment: A Computationsl Exercise To Calculate Potential Energy Curves. O. Sorkhabi, W. M. Jackson, I. Daizadeh J. Chem. Educ. 1998, 75, 238-240. ARTICLE (Hand-Out) Morse functions and Hulbert-Hirschfelder functions. Energy Surfaces and Chemical Reactions. Chapter 2 in Theoretical Aspects of Physical Organic Chemistry. The S_N2 Mechanism. Sason S. Shaik, H. Bernhard Schlegel, Saul Wolfe; John Wiley & Sons, Inc., New York, 1992. ISBN 0-471-84041-6. BOOK CHAPTER (Hand-Out) Probably the best current review on the subject written by the pioneer of the methods! Computing Reaction Pathways on Molecular Potential Energy Surfaces. Chapter 2 in Reviews in Computational Chemistry, Kenny B. Lipkowitz, Donlad B. Boyd, Eds.; VCH Publishers, New York, . ISBN 3-527-27620-1. BOOK CHAPTER (Hand-Out) A general method for constructing multidimensional molecular potential energy surfaces from ab initio calculations. T.-S. Ho and H. Rabitz J. Chem. Phys. 1996, 104, 2584-2597. ARTICLE Discusses the general problem of constructing multi-dimensional potential energy surfaces from either gridded or scattered ab initio data. Demonstrates a method based on "reproducing kernel Hilbert spaces" (RKHS). Do not worry so much about the mathematics when you read this, look more for the definition of the problem and see what kinds of applications are being dealt with. Recognize for example that their most difficult case contains only 3 atoms (!) and this is far from anything useful for "real chemistry". Electronic Structuee Makes a Difference: Cytochrome P-450 Mediated Hydroxylations of Hydrocarbons as a Two-State Reactivity Paradigm. Sason S. Shaik, Michael Filatov, Detlef Schroeder, Helmut Schwarz Chem. Eur. J. 1998, 4, 193-199. CONCEPT ARTICLE A timely discussion of potential energy surface crossing and spin inversion in the context of P-450. QM BACKGROUND & SELF-CONSISTENT FIELD THEORY Quantum-Mechanical Background. Chapter 1 inApproximate Molecular Orbital Theory. John A. Pople, David L. Beveridge, McGraw-Hill Book Company, New York, 1970. Lib. of Congress Nr. 70-95820. BOOK CHAPTER (Hand-Out) Self-Consistent Molecular Orbital Theory. Chapter 2 inApproximate Molecular Orbital Theory. John A. Pople, David L. Beveridge, McGraw-Hill Book Company, New York, 1970. Lib. of Congress Nr. 70-95820. BOOK CHAPTER (Hand-Out) Quantum Chemistry Workbook. Jean-Louis Calais; John Wiley & Sons, Inc., 1994. ISBN 0-471-59435-0. WORKBOOK (Hand-Out in part only) Introduction to Quantum Chemistry. C. E. Dykstra; Prentice Hall, Eaglewood Cliffs, New Jersey, 1994. ISBN 0-13-701293-4 (paper). BOOK A successful introduction to the quantum-mechanical theory of vibrational-rotational spectroscopy, electronic structure theory, and NMR theory. Modern Quantum Chemistry: Introduction to Advanced Electronic Structure Theory. Attila Szabo, Neil S. Ostlund; MacMillan Publishing Co., Inc., Prentice Hall, New York, 1982. ISBN 0-02-949710-8. BOOK Perhaps the best quantum chemistry book on the market. We will cover most of what is described in this book but our discussions will be more qualitative. The quantitative aspects are more suitable for QM courses per se. Quantum Chemistry. Ira N. Levine; 3rd ed.; Allyn and Bacon, Inc.; Boston, 1983. ISBN 0-205-07952-0. BOOK Quantum Chemistry. John P. Lowe; 3rd ed.; Academic Press, Inc.; Boston, 1978. ISBN 0-12-457552-8. BOOK HUECKEL THEORY Molecular Orbital Theory for Organic Chemists. A. Streitwieser; John Wiley & Sons, Inc., New York, 1961. Lib. of Cong. Nr. 61-17363. BOOK (Hand-Out) Chapter 5 on "Heteroatoms" will be distributed as a handout. Das HMO-Modell und seine Anwendungen. Grundlagen und Handhabung. E. Heilbronner, H. Bock; 2nd ed.; Verlag Chemie, Weinheim, 1978. ISBN 3-527-25775-6 (paper). BOOK Introduction to Theoretical Organic Chemistry and Molecular Modeling. William B. Smith, Verlag Chemie, Weinheim, 1996. ISBN 1-56081-937-5. BOOK This is essentially a book on Hueckel theory (Chapter 1 - 6) with short additions on extended Hueckel Theory and other electronic structure methods. The Hueckel Molecular Orbital Method and Properties of Hueckel Molecular Orbitals Section 1.2.1 and 1.2.2 in Physical Organic Chemistry. N. S, Isaacs; Longman Scientific and Technical, co-published in the US with John Wiley & Sons, Inc., New York, 1987. ISBN 0-582-00474-8. BOOK (Hand-Out) Hueckel treatment of carbon species with icosahedral symmetry. Tang, A. C.; Huang, F. Q.; Li, Q. S.; Liu, R. Z. Chem. Phys. Lett. 1994, 227, 579-587. ARTICLE EXTENDED HUECKEL THEORY Theory of Polyhedral Molecules. I. Physical Factorizations of the Secular Equation. Hoffmann, R.; Lipscomb, W. N. J. Chem. Phys. 1962, 36, 2179-2189. ARTICLE (Hand-Out) The basic outline of EHMO theory is presented. Valence minimal basis set. Hij = K Sij. Theory of Polyhedral Molecules. III. Population Analyses and Reactivities for the Carboranes. Hoffmann, R.; Lipscomb, W. N. J. Chem. Phys. 1962, 36, 3489-3493. ARTICLE (Hand-Out) Describes the Mulliken population analysis for EHMO. An Extended Hueckel Theory. I. Hydrocarbons. Hoffmann, R. J. Chem. Phys. 1963, 39, 1397-1412. ARTICLE (Hand-Out) EHMO theory for hydrocarbons. MO Theory Made Easy. Mealli, C.; Proserpio, D. M. J. Chem. Educ. 1990, 67, 399-403. PROGRAM DESCRIPTION (Hand-Out) EHMO computations on the PC. The features of the program CACAO are described in detail in this article. CACAO is a user-friendly approach to the techniques of EHMO. CACAO comes with a graphical user interface and allows form the computation and display of Walsh diagrams and of molecular orbitals in both the delocalized or contracted modes. Non-Least-Motion Potential Surfaces. The Dimerization of Methylenes and Nitroso Compounds. Hoffmann, R.; Gleiter, R.; Mallory, F. B. J. Am. Chem. Soc. 1970, 92, 1460-1466. ARTICLE (Hand-Out) Counterintuitive Orbital Mixing in Semiempiriacl and ab Initio Molecular Orbaital Calculations. Ammeter, J. H.; BŸrgi, H.-B.; Thibeault, J. C.; Hoffmann, R. J. Am. Chem. Soc. 1978, 100, 3686. ARTICLE (Hand-Out) The Rearrangement Pathway in [Cp₂Mo₂(CO)₄(RCC-CR₂)]⁺ Cations: An Extended Hueckel Molecular Orbital and Buergi-Dunitz Trajectory Study. Girard, L.; Lock, P. E.; Amouri, H. E.; McGlinchey, M. J. J. Organomet. Chem. 1994, 478, 189-196. ARTICLE (Hand-Out) Nice review of the Buergi-Dunitz trajectory approach. Very clearly written. Hueckel treatment of carbon species with icosahedral symmetry. Tang, A. C.; Huang, F. Q.; Li, Q. S.; Liu, R. Z. Chem. Phys. Lett. 1994, 227, 579-587. ARTICLE Use of Hueckel Methodology with ab Initio Molecular Orbitals: Polarizabilities and Prediction of Organic Reactions. Zimmerman, H. E.; Weinhold, F. J. Am. Chem. Soc. 1994, 116, 1579-1580. ARTICLE Choice of Hamiltonian Matrix Elements for SCC-IEH Calculations on Transition-Metal Complexes. Blomquist, J. Kjaell, P. J. Phys. Chem. 1994, 98, 10098. ARTICLE Planar Tetracoordinate Carbons in Dimetallic Complexes: Quantum Chemical Investigations. Poumbga, C. N.; BŽnard, M.; Hyla-Kryspin, I. J. Am. Chem. Soc. 1994, 116, 8259. ARTICLE Moleculare Structure, Dynamics, and Crystal Organization of [{Cl₃(arene)Ru}₂[[BF₄] and a Bonding Study by Extended Hueckel Calculations. F. Grepioni, D. Braga, P. J. Dyson, B. F. G. Johnson, F. M. Sanderson, M. J. Calhorda, and L. F. Veiros Organometallics 1995, 14, 121-130. ARTICLE SEMI-EMPIRICAL THEORY Approximate Molecular Orbital Theories. Chapter 3 in Approximate Molecular Orbital Theory. J. A. Pople, D. L. Beveridge McGraw-Hill Book Company, New York, 1970. Lib. of Cong. Nr. 07-050512-8. BOOK CHAPTER (Hand-Out) This chapter will be used to discuss CNDO, INDO and NDDO. Approximate Self-Consistent Molecular Orbital Theory. I. Invariant Procedures. J. A. Pople, D. P. Santry, G. A. Segal J. Chem. Phys. 1965, 43, S129-S135. ARTICLE CNDO and NDDO Approximations. Approximate Self-Consistent Molecular Orbital Theory. II. Calculations with Complete Neglect of Differential Overlab. J. A. Pople and G. A. Segal J. Chem. Phys. 1965, 43, S136-S151. ARTICLE CNDO calculations of diatomic molecules and small polyatomic molecules (water, ammonia, ethane). Populations, charge densities, dipole moments are OK. Energy changes due to angle changes also are OK. (Students: Try to reproduce some of the calculations by yourself!) Approximate Self-Consistent Molecular Orbital Theory. III. CNDO Results for AB₂ and AB₃ Systems. J. A. Pople and G. A. Segal J. Chem. Phys. 1966, 44, 3289-3296. ARTICLE CNDO/2 is described. Gives good equlibrium angles, dipole moments, and bending force constants. Approximate Self-Consistent Molecular Orbital Theory. IV. Calculations on Molecules Including the Elements Sodium through Chlorine. D. P. Santry and G. A. Segal J. Chem. Phys. 1967, 47, 158-174. ARTICLE CNDO/2 for second-row molecules. Gives good equilibrium angles, dipole moments, and bending force constants. Parameterization of NDDO wavefunctions using genetic algorithms. An evolutionary approach to parameterizing potential energy surfaces and direct dynamics calculations for organic molecules. I. Rossi and Donald G. Truhlar Chem. Phys. Lett. 1995, 233, 231-236. ARTICLE NDDO-SRF. NDDO is parameterized with specific reaction parameters (SRF) such that the NDDO data can be used to give highly accurate potential energy surfaces for the reactions for which they are parameterized. Neglect of Diatomic Differntial Overlap" in Nonempirical Quantum Chemical Orbital Theories. I. On the Justification of the Neglect of Diatomic Differential Overlap Approximation. K. Neymeyr and Friedrich Franz Seelig Int. J. Qunatum. Chem. 1995, 53, 515-518. ARTICLE A brief review of NDDO justifications. Heavy on math. Ground States of Molecules. 38. The MNDO Method. Approximations and Parameters. Michael J. S. Dewar and Walter Thiel J. Am. Chem. Soc. 1977, 99, 4899-4907. ARTICLE (Hand-Out) Ground States of Molecules. 39. MNDO Results for Molecules Containing Hydrogen, Carbon, Nitrogen, and Oxygen. Michael J. S. Dewar and Walter Thiel J. Am. Chem. Soc. 1977, 99, 4907-4916. ARTICLE (Hand-Out) Calculations of Electron Affinities Using the MNDO Semiempirical SCF-MO Method. Michael J. S. Dewar and Henry S. Rzepa J. Am. Chem. Soc. 1978, 100, 784-790. ARTICLE Semiempirical Molecular Orbital Methods James J. P. Stewart, Chapter 2 in Reviews of Computational Chemistry, Kenny B. Lipkowitz, Donald B. Boyd, Eds.; VCH, Weinheim, Germany, 1990. ISBN 3-527-27845-1. BOOK CHAPTER (Hand-Out) AM1 and PM3. Semiempirical Methods: Current Status and Perspectives Walter Thiel Tetrahedron, 1988, 44, 7393-7408. REVIEW ARTICLE Review of MNDO methods. Semiempirical Molecular Orbital Methods Michael C. Zerner, Chapter 8 in Reviews of Computational Chemistry, Volume 2, Kenny B. Lipkowitz, Donald B. Boyd, Eds.; VCH, Weinheim, Germany, 1991. ISBN 3-527-28338-2. BOOK CHAPTER Review of MNDO methods. HARTREE FOCK THEORY Ab Initio Molecular Orbital Theory. Warren J. Hehre, Leo Radom, Paul v. R. Schleyer, and John A. Pople, John Wiley & Sons, New York, 1986. ISBN 0-471-81241-2. BOOK (Recommended Text) Exploring Chemistry with Electronic Structure Methods., James B. Foresman, AEleen Frisch, 2nd ed.; Gaussian Inc.; Pittsburgh, PA, 1996. BOOK (Recommended Text) Basis Sets Basis Sets for Ab Initio Molecular Orbital Calculations and Intermolecular Interactions. David Feller and Ernest R. Davidson, Chapter 1 in Vol. 1 of Reviews of Computational Chemistry Kenny B. Lipkowitz, Donald B. Boyd, Eds.; VCH, Weinheim, Germany, 1989. ISBN 3-527-27845-1. BOOK CHAPTER (Hand-Out) Atomic Basis Sets of Gaussian Functions. Chapter 4.3 in Ab Initio Molecular Orbital Theory. Warren J. Hehre, Leo Radom, Paul v. R. Schleyer, and John A. Pople, John Wiley & Sons, New York, 1986. ISBN 0-471-81241-2. BOOK CHAPTER (Hand-Out) Self-Consistent Molecular-Orbital Methods. III. Comparison of Gaussian Expansions and PDDO Methods Using Minimal STO Basis Sets. Marshal D. Newton; W. A. Lathan; W. J. Hehre; J. A. Pople J. Chem. Phys. 1969, 51, 3927-3932. ARTICLE Describes peformance of the basis sets STO-KG. The Influence of Polarization Functions on Molecular Orbital Hydrogenation Energies. P. C. Hariharan; J. A. Pople Theoret. Chim. Acta 1973, 28, 213-222. ARTICLE Describes basis set augmentation by d-functions with exponent 0.8 for C, N, O and F (6-31G*) and p-functions with exponent 1.1 for H (6-31G**). Self-Consistent molecular orbital methods. XXIII. A polarization-type basis set for second-row elements. Michelle M. Francl; William J. Pietro; Warren J. Hehre; J. Stephen Binkley; Douglas J. DeFrees; John A. Pople J. Chem. Phys. 1982, 77, 3654-3665. ARTICLE Describes basis sets 6-31G* and 6-31G** for the elements of the second row, Na - Ar. Self-Consistent Molecular Orbital Methods. 21. Small Split-Valence Basis Sets for First-Row Elements. J. Stephen Binkley; J. A. Pople and Warren J. Hehre J. Am. Chem. Soc. 1980, 102, 939-947. ARTICLE (Hand-Out) Describes basis sets 6-21G and 3-21G for H and He (Table 1) and for Li - Ne (Tables 2 and 3) POST-HARTREE-FOCK METHODS Applications of Post-Hartree-Fock Methods: A Tutorial Rodney J. Bartlett and John F. Stanton Chapter 2 in Volume 5 of Reviews in Computational Chemistry Kenny B. Lipkowitz and Donald B. Boyd, Eds.; VCH Publishers, New York, 1994. ISBN 3-527-89658-9. BOOK CHAPTER (Hand-Out) PERTURBATION THEORY MODERN CI METHODS MODEL THEORIES (G1, G2 et al.) Gaussian-1 theory: A general procedure for prediction of molecular energies John A. Pople, Martin Head-Gordon, Douglas J. Fox, Krishnan Raghavachari, and Larry A. Curtiss J. Chem. Phys. 1989, 90, 5622-5629. ARTICLE (Hand-Out) Gaussian-2 theory for molecular energies of first- and second-row compounds Larry A. Curtiss, Krishnan Raghavachari, Gary W. Trucks, and John A. Pople J. Chem. Phys. 1991, 94, 7221-7230. ARTICLE (Hand-Out) Gaussian-2 theory using reduced Moeller-Plesset orders Larry A. Curtiss, Krishnan Raghavachari, and John A. Pople J. Chem. Phys. 1993, 98, 1293-1298. ARTICLE (Hand-Out) A complete basis set model chemistry. V. Extensions to six and more heavy atoms Joseph W. Ochterski, G. A. Petersson, and J. A. Montomery, Jr. J. Chem. Phys. 1996, 104, 2598-2619. ARTICLE (Hand-Out) PROPERTIES Computational Quantum Chemistry. Alan Hinchcliffe, John Wiley & Sons, New York, 1988. ISBN 0-471-91716-8. BOOK (Hand-Out of selected pages) Natural Bond Orbital (NBO) Method Natural Resonance Theory: I. General Formalism E. D. Glendening, F. Weinhold J. Comput. Chem. 1998, 19, 593-609. ARTICLE Natural Resonance Theory: II. Natural Bond Order and Valency E. D. Glendening, F. Weinhold J. Comput. Chem. 1998, 19, 610-627. ARTICLE Natural Resonance Theory: III. Chemical Applications E. D. Glendening, F. Weinhold J. Comput. Chem. 1998, 19, 628-646. ARTICLE Atoms in Molecules Atoms in Molecules - A Quantum Theory. Richard F. W. Bader, Oxford Science Publications, Clarendon Press, Oxford, 1990. ISBN 0-19-855168-1. BOOK Charges Fitted to the Electric Potential Charges Fit to Electric Potentials. II. Can Atomic Charges Be Unambigiously Fit to Electrostatic Potentials? M. Miller Francl, C. Carey, L. E. Chirlian, D. M. Gange J. Comput. Chem. 1996, 17, 367-383. ARTICLE DENSITY FUNCTIONAL METHODS An Introduction to Density Functional Theory. Libero J. Bartoletti, Ken Flurchick, Chapter 4 in Vol. 7 of Reviews od Computational Chemistry Kenny B. Lipkowitz, Donald B. Boyd, Eds.; VCH, Weinheim, Germany, 1996. ISBN 1-56081-915-4. BOOK CHAPTER (Hand-out) Density Functional Methods in Biomolecular Modeling. Alain St-Amant, Chapter 5 in Vol. 7 of Reviews of Computational Chemistry Kenny B. Lipkowitz, Donald B. Boyd, Eds.; VCH, Weinheim, Germany, 1996. ISBN 1-56081-915-4. BOOK CHAPTER Kohn-Sham density-functional theory within a finite basis set John A. Pople, Peter M. W. Gill, Benny M. W. Gill Chem. Phys. Lett. 1992, 197, 557-560. ARTICLE The performance of the Becke-Lee-Yang-Parr (B-LYP) density functional theory with various basis sets Peter M. W. Gill, Benny M. W. Gill, John A. Pople, and Michael J. Frisch Chem. Phys. Lett. 1992, 197, 499-505. ARTICLE The performance of a family of density functional methods Benny G. Johnson, Peter M. W. Gill, John A. Pople J. Chem. Phys. 1993, 98, 5612-5626. ARTICLE (Hand-out) Approximate Density Functional Theory as a Practical Tool in Molecular Energetics and Dynamics. Tom Ziegler Chem. Rev. 1991, 91, 651-667. REVIEW MOLECULAR MECHANICS Molecular Mechanics. U. Burkert, N. L. Allinger; ACS Monograph 177, American Chemical Society, Washington, D.C., 1982. ISBN 0-8412-0584-1. BOOK MOLECULAR MODELING Exploring QSAR. Fundamentals and Applications in Chemistry and Biology. Corwin Hansch, Albert Leo; ACS Professional Reference Book Series S. R. Heller, Cons. Ed.; American Chemical Society, Washington, D.C., 1995. ISBN 0-8412-2993-7 (set with Tables). BOOK Exploring QSAR. Hhydrophobic, Electronic, and Steric Constants. Corwin Hansch, Albert Leo, David Hoekman ACS Professional Reference Book Series S. R. Heller, Cons. Ed.; American Chemical Society, Washington, D.C., 1995. ISBN 0-8412-2993-7 (set with textbook). TABLES QSAR: Hansch Analysis and Related Approaches. Hugo Kubinyi; Vol. 1 of Methods and Principles in Medicinal Chemistry R. Mannhold, H. Kubinyi, H. Timmerman, Eds.; VCH, Weinheim, Germany, 1993. ISBN 3-527-30035-X. BOOK Molecular Modeling. Basic Principles and Applications. H.-D. Hoeltje, H. Folkers; Vol. 5 of Methods and Principles in Medicinal Chemistry R. Mannhold, H. Kubinyi, H. Timmerman, Eds.; VCH, Weinheim, Germany, 1996. ISBN 3-527-29384-1. BOOK This book was recently reviewed, see Angew. Chem. Int. Ed. Engl. 1997, 36, 2020-2021. Molecular Modelling. Principles and Applications. A. R. Leach; Addison Wesley Longman, Singapore, 1996. ISBN 0-582-23933-8. BOOK This book was recently reviewed, see Angew. Chem. Int. Ed. Engl. 1997, 36, 2020-2021. COMBINATION THEORIES Methods and Applications of Combined Quantum Mechanical and Molecular Mechanics Potentials. Jiali Gao, Chapter 3 in Vol. 7 of Reviews od Computational Chemistry Kenny B. Lipkowitz, Donald B. Boyd, Eds.; VCH, Weinheim, Germany, 1996. ISBN 1-56081-915-4. BOOK CHAPTER