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    Historical Background of Computational Chemistry: I. The Ancients

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    Ja'far LK
    The document provides a historical overview of computational chemistry from ancient times to modern applications. It discusses early chemical theories proposed by Empedocles and Democritus in 5th century BC. In the 19th century, opinions differed on using mathematics in chemistry, with some advocating its use and others opposing it. Major developments in the 20th century included Bohr's model of the hydrogen atom in 1913, Schrodinger's wave equation in 1926, and the introduction of quantum chemistry programs in the 1950s-1960s. Since the 1970s, computational chemistry has grown dramatically due to increasing computer power and the ability to study larger molecules. The document outlines common computational chemistry methods and terminology.

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    Historical Background of Computational Chemistry: I. The Ancients

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    Ja'far LK
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    The document provides a historical overview of computational chemistry from ancient times to modern applications. It discusses early chemical theories proposed by Empedocles and Democritus in 5th century BC. In the 19th century, opinions differed on using mathematics in chemistry, with some advocating its use and others opposing it. Major developments in the 20th century included Bohr's model of the hydrogen atom in 1913, Schrodinger's wave equation in 1926, and the introduction of quantum chemistry programs in the 1950s-1960s. Since the 1970s, computational chemistry has grown dramatically due to increasing computer power and the ability to study larger molecules. The document outlines common computational chemistry methods and terminology.

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    The document provides a historical overview of computational chemistry from ancient times to modern applications. It discusses early chemical theories proposed by Empedocles and Democritus in 5th century BC. In the 19th century, opinions differed on using mathematics in chemistry, with some advocating its use and others opposing it. Major developments in the 20th century included Bohr's model of the hydrogen atom in 1913, Schrodinger's wave equation in 1926, and the introduction of quantum chemistry programs in the 1950s-1960s. Since the 1970s, computational chemistry has grown dramatically due to increasing computer power and the ability to study larger molecules. The document outlines common computational chemistry methods and terminology.

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    79 views9 pages

    Historical Background of Computational Chemistry: I. The Ancients

    Uploaded by

    Ja'far LK
    The document provides a historical overview of computational chemistry from ancient times to modern applications. It discusses early chemical theories proposed by Empedocles and Democritus in 5th century BC. In the 19th century, opinions differed on using mathematics in chemistry, with some advocating its use and others opposing it. Major developments in the 20th century included Bohr's model of the hydrogen atom in 1913, Schrodinger's wave equation in 1926, and the introduction of quantum chemistry programs in the 1950s-1960s. Since the 1970s, computational chemistry has grown dramatically due to increasing computer power and the ability to study larger molecules. The document outlines common computational chemistry methods and terminology.

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    of 9

    Historical Background of Computational Chemistry

    I. The Ancients:
    5th Century BC Earliest publication of conflicting chemical theories.
    Empedocles: All matter composed of four infinitely divisible elements, Earth,
    Air, Fire, and Water
    Democritus: All matter composed of indivisible "atoms."
    4th Century BC Early example of the danger of purely theoretical chemistry.
    Aristotle advocates Empedocles's four element model, which dominates chemical
    theory until the 18th century.

    II. Beginnings of Modern Chemistry:


    19th Century: Opinions differ on the value of computational chemistry.
    The more progress physical sciences make, the more they tend to enter the domain of
    mathematics, which is a kind of centre to which they all converge. We may even judge
    the degree of perfection to which a science has arrived by the facility with which it may
    be submitted to calculation.
    -- A. Quetelet, 1828
    Every attempt to employ mathematical methods in the study of chemical questions must
    be considered profoundly irrational and contrary to the spirit of chemistry. If
    mathematical analysis should ever hold a prominent place in chemistry--an aberration
    which is happily almost impossible--it would occasion a rapid and widespread
    degeneration of that science.
    -- A. Compte, 1830

    III. Quantum Mechanics and Quantum Chemistry: (see bibliography for


    references)
    1913: Bohr's quantized model of the hydrogen atom accurately predicts the
    electronic spectra of hydrogen and one-electron ions (He+, Li++, etc).
    1924: de Broglie's hypothesis of wave-particle duality.

    1926: Erwin Schrdinger publishes the wave equation.


    1928: Hylleraas publishes quantum mechanical calculations on He.
    1930: Publication of the Hartree-Fock equations.
    1933: James and Coolidge publish quantum mechanical calculations on H2.
    1950: Boy's introduces the use of Gaussian-type basis functions in quantum
    chemistry programs.
    1951: Roothan publishes matrix version of Hartree-Fock method, that, with
    minor improvements, is still in use today.
    1965: First "black box" quantum chemistry program, POLYATOM, developed by
    M.P. Barnett.
    1970: Schaefer and Bender successfully refute Herzberg's assignment of the
    ground electronic state of methylene (CH2).

    Since 1970 at Dramatic Growth in Computational Chemistry


    A steadily increasing fraction of the articles listed in the Current Journals of the ACS
    database (CJACS) reference a computational chemistry software package.
    Data from Figure 3 of D.B. Boyd, 1995 (see bibliography)
    Workstation Performance at Fixed Cost

    This increase in computer power has led to a concomitant


    increase in the size of molecules that can be studied using ab
    initio quantum chemistry
    Some examples from a quantum chemist's curriculum vitae

    Why do chemistry on Computers?


    Reduced Cost:
    Calculation of pKa's of phosphoramidic acids.

    Increased Safety:
    Comparison of combustion products of sarin and non-toxic simulants.
    Faster Turnaround:
    Pyrolysis rate of sulfur mustard gas.
    Better Accuracy:
    Heats of formation for neutral, first row molecules.
    Improved Understanding:
    Novel metabolic pathway for AIA mutagens.
    Caveat:
    Computational chemistry is far from black box--Care must be taken in
    choice of method and interpretation of results.

    There are wide range of computational chemistry methods with


    different strengths and computational costs

    Reliability of Chemical Properties Calculated With Most Rigorous Computational


    Chemical Methods
    Listed in order of difficulty: (errors given where well characterized)
    Molecular Structures (+/- 1%)
    Reaction Enthalpies (+/- 1 kcal/mole)
    Dipole Moments and Infrared Intensities
    Vibrational Frequencies (+/- 5 %)
    Reaction Free Energies (+/- 2 kcal/mole)
    Relative Acid Constants (+/- 2 pKa units)
    Reaction Rates (for certain types of reactions)

    General Computational Chemistry Terminology


    Potential Energy Surfaces
    The energetics of an N-atom molecule can be described in terms of a 3N-6 dimensional
    (3N-5 for linear molecules) hypersurface known as the Potential Energy
    Surface (PES). Most computational chemical studies involve characterizing key features
    of the PES or integrating the trajectories on this surface.
    The following figure shows a one-dimensional potential energy surface (or a slice of a
    higher-dimensional PES).

    Example: 2-D PES for Water


    The plot below shows a small portion of H2O PES with the H-O-H bond angle and
    symmetric O-H stretch as the independent coordinates. The ab initio energies were
    calculated using the Hartree-Fock Method with a 6-31G** basis set. To generate the
    entire 242-point surface took 16 minutes on a SGI workstation.

    Statics vs. Dynamics


    Thermal motion or (at 0deg. K) quantum mechanical zero-point motion causes
    molecules to constantly move on their PES. How this motion is treated leads to the
    greatest difference in computational chemical methods:
    Statics: The chemical system is characterized by the stationary points on its PES
    (minima, transition states). Quantum chemical zero-point motion is used to correct the
    energies and standard thermodynamic equations are used to include temperaturedependent vibrational, rotational and translational energy terms and to calculate the
    entropy and free energy.
    Dynamics: The molecules' classical equations of motion on the PES are integrated.
    Except for the smallest chemical systems, molecular dynamics simulations involve using
    empirical molecular mechanics potentials. Only the thermal vibrational energies are
    included.
    Monte Carlo: Different configurations of the chemical system are randomly generated
    in such a way to sample the desired thermodynamical ensemble. As in molecular
    dynamics, the computational cost usually prohibits using quantum chemical energies.
    Thermodynamics

    Both ab initio methods and empirical molecular mechanics potentials calculate the
    electronic energy, which can be related to the thermodynamic enthalpy by including
    several additional energy terms:
    For gas-phase reactions the rotational, translational and PV terms can approximated
    using expressions for ideal gases (see McQuarrie, 1977, chapter 8 for higher-order
    corrections to these terms):
    The zero-point and temperature-dependent vibrational terms are functions of the
    molecule's 3N-6 vibrational modes:
    The direction of chemical reactions is determined by the sign of the change in the Gibb's
    free energy (G) which can be related to enthalpy by including the entropy.
    Entropy can usually be reliably determined from standard expressions (see Hout, et al.,
    1982):

    Pauling Points
    Computational chemists sometimes describe a local minimum on the Error/Effort curve
    as a Pauling point. (I.e. a place were good results are achieved at a minimal amount of
    effort.) Note that this term is not pejorative, since all computational chemical methods
    are based on judicious cancellation of errors.

    Atomic Units
    Most quantum chemical software is written using atomic units (a.u.) which simplify the
    equations. Atomic units are derived from fundamental quantities in chemical physics:
    Quantity

    Name

    Physical Significance

    Value in SI units*

    Energy

    Hartree

    2x ionization energy of H

    4.3597482 x10-18J

    Length

    Bohr

    Bohr radius of H 1s orbital

    0.529177249 x10-10m

    Charge

    Electron's charge

    1.60217733 x10-19C

    Mass

    Electon's mass

    9.1093898 x10-31kg

    Velocity

    Electron velocity in first Bohr orbit

    2.1876914 x10-6m/s

    Time

    Time required for electron in first Bohr orbit to travel 1


    Bohr radius

    2.4188843 x10-17s

    *1986 CODATA recommended values: E.C. Cohen and B.N. Taylor, Journal of
    Research of the National Bureau of Standards, 92, 82, (1987).
    Units
    A very wide variety of units are used in the computational chemical literature and in the
    inputs and outputs of chemical software, so it's important to be always confirm that
    results are physically reasonable.
    Bond distances are usually in angstroms () or Bohr. 1 = 0.529177 Bohr.
    The most common energy units and their interconversion factors are:
    Units
    1 Hartree=

    Hartree

    kcal/mole

    e.v.

    cm-1

    kJ/mole*

    Hz

    1.00000E+ 6.27510E+ 2.72114E+


    3.15773E+ 2.62550E+
    2.19475+05
    6.57968E+15
    00
    02
    01
    05
    03

    1
    1.59360E- 1.00000E+ 4.33641E- 3.49755E+ 5.03217E+ 4.18400E+
    1.04854E+13
    kcal/mole=
    03
    00
    02
    02
    02
    00
    1 e.v.=

    3.67493E- 2.30605E+ 1.00000E+ 8.06554E+ 1.16045E+ 9.64853E+


    2.41799E+14
    02
    01
    00
    03
    04
    01

    1 cm-1=

    4.55634E- 2.85914E- 1.23984E- 1.00000E+ 1.43877E+ 1.19627E2.99792E+10


    06
    03
    04
    00
    00
    02

    1 K=

    3.16683E- 1.98722E- 8.61738E- 6.95039E- 1.00000E+ 8.31451E2.08367E+10


    06
    03
    05
    01
    00
    03

    1 Kilo J=

    3.80880E- 2.39006E- 1.03643E- 8.35935E+ 1.20272E+ 1.00000E+


    2.50607E+12
    04
    01
    02
    01
    02
    00

    1 Hz=

    1.51983E- 9.53708E- 4.13567E- 3.33564E- 4.79922E- 3.99031E- 1.00000E+00

    16

    14

    15

    11

    11

    13

    *Based on 1986 CODATA values and using 1 kcal = 4.184 J.

    Some Experimental Bond Lengths and Energies*


    (Always compare computed values with some standard.)
    Bond Lengths
    H-C
    H-N
    H-O
    C-C
    C-N
    C-O
    C-Cl
    P-O
    C=C
    C=N
    C=O
    P=O

    1.09
    1.00
    0.96
    1.54
    1.47
    1.43
    1.76
    1.57
    1.35
    1.30
    1.22
    1.47

    Diatomic Bonds
    (kcal/mole)
    H-H
    104
    O=O
    119
    N=N
    226
    H-F
    135
    H-Cl
    103
    H-Br
    88
    H-I
    71
    F-F
    37
    Cl-Cl
    58
    Br-Br
    46
    I-I
    36

    H-C
    H-N
    H-O
    C-C
    C-N
    C-O
    C-Cl
    C-F
    C=C
    C=N
    C=O
    C%C

    Polyatomic Bonds
    (kcal/mole)
    99
    93
    111
    83
    73
    86
    81
    116
    146
    147
    179
    200

    *From J.B. Hendrickson, D.J. Cram, and G.S. Hammond, Organic Chemistry, New
    York: McGraw-Hill (1970). For a comprehensive listing of bond lengths see: F.H. Allen,
    et al. Journal of the Chemical Society Perkins Transactions II (1987): S1-S19.

    The Computational Chemistry Literature


    I. Books.
    Quantum Chemistry
    W.J. Hehre, L. Radom, P.v.R. Schleyer, J.A. Pople, Ab Initio Molecular Orbital
    Theory. New York: Wiley-Interscience (1986).
    Best available reference on accuracy of ab initio methods--hundreds of
    tables and graphs. Unfortunately, somewhat out of date and hence
    limited to relatively small molecules.
    A. Szabo and N.S. Ostlund, Modern Quantum Chemistry Introduction to
    Advanced Electronic Structure Theory. New York: McGraw-Hill Publishing Co.
    (1989).
    Excellent introduction to the Hartree Fock theory, also contains good

    overviews of the CI, CC and MPPT.


    T. Clark, A Handbook of Computational Chemistry. New York: WileyInterscience (1985).
    Describes usage of common semiempirical programs and Gaussian 82.
    Contains good bibliography of published MNDO and MINDO/3
    calculations listed by molecule..
    J.B. Foresman and . Frisch, Exploring Chemistry with Electronic Structure
    Methods. Pittsburgh: Gaussian Inc. (1993).
    Tutorial on doing quantum chemistry with the Gaussian quantum
    chemistry program. Contains numerous computational examples and
    exercises, and includes a brief appendix summarizing the theoretical
    background of the quantum chemical methods.
    Molecular Mechanics and Dynamics
    J.M. Haile, Molecular Dynamics Simulation: Elementary Methods. New York:
    John Wiley & Sons (1992).
    Good introduction to the theory and methods of molecular dynamics
    simulations. Contains source for 2-d and 3-d hard sphere MD programs.
    M.P. Allen and D.J. Tildesley, Computer Simulation of Liquids. Oxford:
    Clarendon (1991).
    Detailed treatment of the theoretical underpinnings and statistical
    mechanics of molecular dynamics and Monte Carlo simulations.
    C.L. Brooks, M. Karplus, and B.M. Pettitt Proteins: A Theoretical Perspective of
    Dynamics, Structure, and Thermodynamics. New York: Wiley Interscience
    (1991).
    Good introduction to the methods and potential energy functions used in
    protein simulations.
    J.A. McCammon and S.C. Harvey, Dynamics of Proteins and Nucleic Acids.
    New York: Cambridge University Press (1987).
    General overview of biochemical MD simulations.
    II. Journals:
    An increasing fraction of Computational Chemical results are being published in the

    "non-computational chemical" literature, e.g. J. Amer. Chem. Soc., J. Medicinal


    Chemistry, etc. The following are the primary journals publishing new computational
    chemical methods and novel applications, listed roughly in order of mostly method
    oriented to mostly applications oriented.
    Theoretica Chimica Acta
    Chemical Physics
    Chemical Physics Letters
    Journal of Chemical Physics
    Journal of Computational Chemistry
    International Journal of Quantum Chemistry
    J. Molecular Structure/Theochem
    Journal of Physical Chemistry
    Proteins: Structure, Function, Genetics

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