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    NWChem Tutorial Transition State

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    michal_lysy
    This document discusses finding transition states for chemical reactions using ab initio methods in NWChem. There are three stages: 1) constructing a geometry near the transition state, 2) refining the transition state using saddle point optimization, and 3) characterizing the transition state by following the reaction path from it to reactants and products. An example is provided of using constrained optimization to find the transition state for a Diels-Alder reaction by first constraining bond distances and then performing an unconstrained saddle point search.

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    NWChem Tutorial Transition State

    Uploaded by

    michal_lysy
    200 views4 pages
    This document discusses finding transition states for chemical reactions using ab initio methods in NWChem. There are three stages: 1) constructing a geometry near the transition state, 2) refining the transition state using saddle point optimization, and 3) characterizing the transition state by following the reaction path from it to reactants and products. An example is provided of using constrained optimization to find the transition state for a Diels-Alder reaction by first constraining bond distances and then performing an unconstrained saddle point search.

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    NWChem tutorial guideline for finding saddle point, transition state example

    Original Title

    NWChem tutorial Transition state

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    This document discusses finding transition states for chemical reactions using ab initio methods in NWChem. There are three stages: 1) constructing a geometry near the transition state, 2) refining the transition state using saddle point optimization, and 3) characterizing the transition state by following the reaction path from it to reactants and products. An example is provided of using constrained optimization to find the transition state for a Diels-Alder reaction by first constraining bond distances and then performing an unconstrained saddle point search.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    200 views4 pages

    NWChem Tutorial Transition State

    Uploaded by

    michal_lysy
    This document discusses finding transition states for chemical reactions using ab initio methods in NWChem. There are three stages: 1) constructing a geometry near the transition state, 2) refining the transition state using saddle point optimization, and 3) characterizing the transition state by following the reaction path from it to reactants and products. An example is provided of using constrained optimization to find the transition state for a Diels-Alder reaction by first constraining bond distances and then performing an unconstrained saddle point search.

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    © All Rights Reserved
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    Download as pdf or txt
    of 4

    Transition-State Searching with NWChem

    One of the most exciting uses of ab initio methods is to use them to map out chemical
    reaction pathways. Mapping chemical reaction pathways involves characterizing the
    reactants, products, intermediates, and transition states. This is followed by the
    calculation of a minimum energy path from the transition states to the reactants and
    products. At first glance this seems like a relatively simple process, however, locating
    transition states can be an arduous task.

    There are three stages involved in locating transition states:

    1. Construct a geometry that is near the transition state


    2. Refine the transition state by using saddle point optimizer
    3. Characterize the transition state (i.e. following the reaction path from the
    transition state to the reactant and product)

    Stage 1 is crucial because saddle point optimizers will not work well unless the gradient
    points roughly in the direction of the saddle point. The following examples show how to
    use constrained optimization and constrained the ab initio molecular dynamics methods
    in NWChem to deteremine geometries that are close to transition states.
    Example: dielsalder.nw

    This example finds the transition state for the following dielsalder reaction:

    1,3-cyclopentadiene + ethene bicyclo[2.1.2]hept-2-ene

    Transition State Product State

    The initial constrained geometry optimization is used to construct a geometry that is near
    the transition state. After which the constraints are released and a saddle point
    optimization is run. In general, a series of constrained geometry optimization will need
    to be run, because the transition state distance is not known a priori (see Example:
    session6/disilane.constrained-opt.nw for an example of how to do this).

    From the NWChem Users Manual


    6.5 ZCOORD -- Forcing internal coordinates
    By default redundant internal coordinates are generated for use in geometry
    optimizations. Connectivity is inferred by comparing inter-atomic distances with the sum
    of the van der Waals radii of the two atoms involved in a possible bond, times a scaling
    factor. The scaling factor is an input parameter of ZCOORD which maybe changed from its
    default value of 1.3. Under some circumstances (unusual bonding, bond dissociation, ...)
    it will be necessary to augment the automatically generated list of internal coordinates to
    force some specific internal coordinates to be included in among the internal coordinates.
    This is accomplished by including the optional directive ZCOORD within the geometry
    directive. The general form of the ZCOORD directive is as follows:

    ZCOORD
    CVR_SCALING <real value>
    BOND <integer i> <integer j> \
    [<real value>] [<string name>] [constant]
    ANGLE <integer i> <integer j> <integer k> \
    [<real value>] [<string name>] [constant]
    TORSION <integer i> <integer j> <integer k> <integer l> \
    [<real value>] [<string name>] [constant]
    END

    The centers i, j, k and l must be specified using the numbers of the centers, as supplied
    in the input for the Cartesian coordinates. The ZCOORD input parameters are defined as
    follows:

    cvr_scaling -- scaling factor applied to van der Waals radii.


    bond -- a bond between the two centers.

    angle -- a bond angle .


    torsion -- a torsion (or dihedral) angle. The angle between the planes i-j-k and
    j-k-l.

    A value may be specified for a user-defined internal coordinate, in which case it is forced
    upon the input Cartesian coordinates while attempting to make only small changes in the
    other internal coordinates. If no value is provided the value implicit in the input
    coordinates is kept. If the keyword constant is specified, then that internal variable is
    not modified during a geometry optimization with DRIVER (Section 21). Each internal
    coordinate may also be named either for easy identification in the output, or for the
    application of constraints (Section 6.6).

    If the keyword adjust is specified on the main GEOMETRY directive, only ZCOORD data
    may be specified and it can be used to change the user-defined internal coordinates,
    including adding/removing constraints and changing their values.

    The following input example use the DFT module, for finding the transition state for the
    dielsalder reaction:

    1,3-cyclopentadiene + ethene bicyclo[2.1.2]hept-2-ene

    This example is simple enough so that other ab initio theories can also be used, such as
    the HF, PSPW, and MP2 modules.
    NWChem Input Deck
    title "parent diels-alder - constrained geometry optimization + saddle search"
    #dielsalder.nw input deck

    permanent_dir ./perm
    scratch_dir ./perm

    echo
    start

    # tests constrained optimization, saddle search,


    # use of constraints with symmetry

    # norbornene = -45.69811295 au r = 1.539 Angstroms

    geometry autosym # Equil nonbornene geometry


    C 0.48438728 -1.26420666 0.66379632
    C 0.48438728 -1.26420666 -0.66379632
    C -0.32763055 -0.09123377 1.11105174
    C -0.32763055 -0.09123377 -1.11105174
    C -1.36089042 -0.02893165 0.00000000
    C 0.50866739 1.15402721 0.76530727
    C 0.50866739 1.15402721 -0.76530727
    H -0.69016477 -0.11291256 -2.13538649
    H -0.69016477 -0.11291256 2.13538649
    H -1.93888714 0.89733827 0.00000000
    H 1.50914212 1.10998500 -1.19387233
    H 1.50914212 1.10998500 1.19387233
    H 1.09450829 -1.87707752 -1.31279758
    H 1.09450829 -1.87707752 1.31279758
    H -2.02362675 -0.89310262 0.00000000
    H 0.02217904 2.04804733 1.15788544
    H 0.02217904 2.04804733 -1.15788544
    end
    driver
    maxiter 101
    end

    basis
    * library 6-31G*
    end

    dft
    xc b3lyp
    end

    geometry adjust # move to guess geometry & apply constraints


    zcoord The following input is used to apply constraints
    bond 6 3 2.267 r constant to the input geometry. In this example the bond
    bond 7 4 2.267 r constant
    end distances between carbon atoms in 1,3-
    end cyclopentadiene and ethane are constrained to be
    task dft optimize # relax with constraints
    2.267 .

    geometry adjust # release constraints


    zcoord
    bond 6 3 2.267 r The following input releases the
    bond 7 4 2.267 r constraints and then runs a saddle
    end
    end point search
    task dft saddle # go for the transition state

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