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    MOLECULAR MECHANICS and Force Field Calculations

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    Ashish Shekhawat
    Molecular mechanics is a computational method that uses classical mechanics to model molecular systems. It approximates molecules as balls and springs and calculates the potential energy using force fields, which define parameters for atom types. The potential energy is calculated as the sum of bonded and nonbonded terms. Force fields allow modeling of large biomolecules quickly. While computationally efficient, molecular mechanics cannot model chemical reactions and has limited parameter availability. Its main applications are geometry optimization and studying large biomolecular systems.

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    MOLECULAR MECHANICS and Force Field Calculations

    Uploaded by

    Ashish Shekhawat
    84 views23 pages
    Molecular mechanics is a computational method that uses classical mechanics to model molecular systems. It approximates molecules as balls and springs and calculates the potential energy using force fields, which define parameters for atom types. The potential energy is calculated as the sum of bonded and nonbonded terms. Force fields allow modeling of large biomolecules quickly. While computationally efficient, molecular mechanics cannot model chemical reactions and has limited parameter availability. Its main applications are geometry optimization and studying large biomolecular systems.

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    MOLECULAR MECHANICS and force field calculations

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    Molecular mechanics is a computational method that uses classical mechanics to model molecular systems. It approximates molecules as balls and springs and calculates the potential energy using force fields, which define parameters for atom types. The potential energy is calculated as the sum of bonded and nonbonded terms. Force fields allow modeling of large biomolecules quickly. While computationally efficient, molecular mechanics cannot model chemical reactions and has limited parameter availability. Its main applications are geometry optimization and studying large biomolecular systems.

    Copyright:

    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    84 views23 pages

    MOLECULAR MECHANICS and Force Field Calculations

    Uploaded by

    Ashish Shekhawat
    Molecular mechanics is a computational method that uses classical mechanics to model molecular systems. It approximates molecules as balls and springs and calculates the potential energy using force fields, which define parameters for atom types. The potential energy is calculated as the sum of bonded and nonbonded terms. Force fields allow modeling of large biomolecules quickly. While computationally efficient, molecular mechanics cannot model chemical reactions and has limited parameter availability. Its main applications are geometry optimization and studying large biomolecular systems.

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    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    of 23

    1/21/2020

    MOLECULAR MECHANICS
    AND
    FORCE FIELD CALCULATIONS
    BY

    SUSNEHA PATRA

    1
    CONTENTS
     Molecular mechanics
     Force field
     Functional form
     Parametrization
     Types of force fields
     An example
     Areas of application
     Advantages and disadventages
     Refernces

    2
    MOLECULAR MECHANICS

     Molecular mechanics is the application of


    classical mechanics to molecules.
     Molecular mechanics uses Newtonian
    mechanics to model molecular systems.
     Molecular mechanics can be used to study
    small molecules as well as large biological
    systems

    3
    All-atomistic molecular mechanics methods have
    the following properties:
     Each atom is simulated as a single particle

     Each particle is assigned a radius, polarizability


    and a constant net charge.
     Bonded interactions are treated as "springs"
    with an equilibrium distance equal to the
    experimental or calculated bond length

    4
     The potential energy of all systems in
    molecular mechanics is calculated using
    force fields.

    5
    FORCE FIELD
     In the context of molecular modeling, a force field refers
    to the form and parameters of mathematical
    functions used to describe the potential energy of a
    system of particles (typically molecules and atoms).
     2 types:
    "All-atom" force fields
    "united-atom" force fields
    "Coarse-grained" force fields, which are frequently
    used in long-time simulations of proteins, provide even
    more crude representations for increased computational
    efficiency.

    6
    A force field is used
    To minimize the bond
    streching energy of this
    Ethane molecule

    7
    FUNCTIONAL FORM
     Molecular system's potential energy (E) in a given
    conformation is expressed as a sum of individual
    energy terms.
    E = E(covelent) + E(noncovelent)
    where ,

    E(covelent) = E(bond) + E(angle) + E(dihedral)


    E(noncovalent)= E(electrostatic) + E(vanderwaals)

    8
    Some of the energy terms that need to be
    taken into account are:
     (1) Bond stretching (l)

     (2) Bond angle bending

     (3) Dihedral angle rotation

     (4) van der Waals forces

     (5) Hydrogen bonding

     (6) Electrostatic interactions

    9
    The exact functional form of the potential
    function, or force field, depends on the particular
    simulation program being used.
     bond and angle terms are modeled
    as harmonic potentials
     For accurate reproduction of vibrational
    spectra, the Morse potential can be used
    instead
     the van der Waals term falls off rapidly – it is
    typically modeled using a "6–12 Lennard-Jones
    potential“
     Electrostatic term with coulomb potential

    10
    Molecular mechanics
    Potential energy
    function
    with continuum
    Solvent

    11
    PARAMETRIZATION
    A force field defines a set of parameters for
    each type of atom.
    The typical parameter set includes
    values for atomic mass, van der Waals radius,
    and partial charge for individual atoms, and
    equilibrium values ofbond lengths, bond
    angles, and dihedral angles for pairs, triplets,
    and quadruplets of bonded atoms, and values
    corresponding to the effective spring
    constant for each potential.

    12
    TYPES OF FORCE FIELDS
    Classical force fields
     AMBER (Assisted Model Building and Energy
    Refinement) - widely used for proteins and DNA.
     CHARMM (Chemistry at HARvard Molecular
    Mechanics) - originally developed at Harvard,
    widely used for both small molecules and
    macromolecules
     CHARMm - commercial version of CHARMM,
    available through Accelrys.

    13
    Second-generation force fields
     CFF - a family of forcefields adapted to a broad
    variety of organic compounds, includes force
    fields for polymers, metals, etc.
     MMFF (Merck Molecular Force Field)-
    developed at Merck, for a broad range of
    molecules.

    14
    Coarse-grained Force fields
     VAMM (Virtual atom molecular mechanics)
    Polarizable force fields based on electronic
    structural theory
     X-Pol: the Explicit Polarization Theory[1]
    Other
     VALBOND - a function for angle bending that
    is based on valence bond theory and works
    for large angular distortions, hypervalent
    molecules, and transition metal complexes

    15
    EXAMPLE
    TABLE V. Computed and experimental fundamentals ~cm21! for various isomers of C2H4

    C2H3D H2CCD2 cis-C2H2D2 trans-C2H2D2 C2HD3 C2D4


    Experiment ~Ref. 27 unless indicated otherwise!

    n1 3028.2m 3017.12n 2299 2284 2281.5m 2261.6q


    n2 1605.5m 1586.05o 1571 1571 1548.0m 1518
    n3 1288.0m 1029.86n 1218 1286 1045 984.6q
    n4 1000 888.71n 988 764 729.95 8~15!r
    n5 3061.6m 2335.02p 3054 3045 2220.2m 2315.4q
    n6 1129 1142.27n 1044 1004 999 '1011, '1000s
    n7 808 750.57n 842 725.2 725 719.770 8~5!r
    n8 943 943.41n 763 864 919 780
    n9 3096.1m 3094.11p 3059 3065 3048.1m 2341.9q
    n10 730 684.64n 662 673 '6 10 593.344 4~9!r
    n11 2274.0m 2230.54n 2254 2273 2333.5m 2201.0q
    n12 1400.0m 1383.93o 1342 1299 1290 1076.9883~6!r

    16
    Calculated
    n1 3031.4a 3014.8c 2294.2 2283.0 2277.4j 2260.3
    n2 1602.1 1582.3 1567.9 1568.5 1544.5 1513.8l
    n3 1286.0 1029.1 1215.8 1283.0g 1041.8 984.1
    n4 999.6 890.4 975.0 988.0 757.4 729.2
    n5 3050.6 2328.0 3050.6d 3040.3h 2217.5 2308.2
    n6 1121.6 1137.5 1035.7 1000.0 996.0 999.6
    n7 803.0 746.7 842.4 724.7 724.0 720.0
    n8 937.5 937.3 754.2 853.0 915.1 768.8
    n9 3089.9 3087.6 3053.9e 3059.3 3041.5k 2337.1
    n10 728.2 680.9 659.5 669.4 625.6 590.0
    n11 2267.5b 2227.9 2255.4f 2270.4j 2327.0 2197.3
    n12 1397.9 1379.8 1338.1 1296.0 1285.6 1075.8

    17
    AREAS OF APPLICATION

     In computational terms, molecular mechanics


    is the least expensive (fastest)method.
     The prototypical molecular mechanics
    application is energy minimization. That is,
    the force field is used as
    an optimization criterion and the (local)
    minimum searched by an appropriate algorithm
    (e.g.steepest descent).

    18
    Global energy optimization can be
    accomplished using simulated annealing,
    the Metropolis algorithm and other Monte
    Carlo methods
     The main aim of optimization methods is
    finding the lowest energy conformation of a
    molecule or identifying a set of low-energy
    conformers that are in equilibrium with each
    other.

    19
    ADVANTAGES

     Perhaps the greatest advantage of molecular


    mechanics is its computational speed.
     As the fastest computational chemistry method,
    this method can be used to study large
    biomolecules.
     The main advantage of molecular mechanics
    with typical computer hardware is in the area of
    geometry optimization – finding the most stable
    conformer of a molecule.

    20
    DISADVANTAGES

     The main disadvantage of molecular mechanics, and


    it is a serious one, is the lack of available parameters
    for many compound types. Approximately 80% of
    known compounds do not have parameters available.
     The other drawback of the method is the inability to
    model certain things of interest to chemists, such as
    chemical reactions.
     The harmonic oscillator approximation allows bonds
    to stretch and compress, but not break and reform
    new bonds. Also, because we do not have electrons
    and orbitals in the model, we also can’t use
    molecular mechanics to predict reactivity.

    21
    REFERENCES
     http://en.wikipedia.org/wiki/Force_field_(ch
    emistry)
     http://chemistry.ncssm.edu/book/Chap6Mo
    lMech.pdf
     evgenii.rudnyi.ru/doc/teaching/md/md7.pdf

     http://theochem.weizmann.ac.il/AIPreprints
    /69.pdf
     linkinghub.elsevier.com/retrieve/pii/002228
    5271900087
    22
    THANK
    YOU

    23

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