CCL: dimensionless reaction coordinate

[Thomas Manz <thomasamanz|*|gmail.com>]

 Sent to CCL by: Thomas Manz [thomasamanz=gmail.com]
 Dear Oscar Odio,
 The error you mentioned arises because Matlab 6 does not support the
 textscan function.
 The program for computing the relative lateness of transition states
 has been updated so that it now works with both MatLab 6 and 7.
 The updated program is found at
 https://sourceforge.net/projects/drcs/files/
 As mentioned previously, this program computes a dimensionless
 reaction coordinate, W,  that varies from 0 to 1 along a minimum
 energy reaction pathway (MERP). The only input required for this
 calculation is a series of optimized geometries along the MERP. A
 minimum of three images (reactant state, transition state, and product
 state) is required, and there is no maximum in the number of images
 that can be used. This method allows one to classify transition states
 as either (a) early (WTS < 0..5) , (b) equidistant (WTS = 0.5), or (c)
 late (WTS > 0.5). An early transition state resembles the reactant
 state more than the product state, and vice versa for a late
 transition state. Application of several postulates in chemistry and
 catalysis requires the classification of transition states as either
 early or late. The most common postulate of this type is the
 Hammond-Leffler postulate which asserts that transition states for
 endothermic reactions are late while transition states for exothermic
 reactions are early. The program mentioned above allows evaluation of
 postulates of this type for specific reactions.
 Sincerely,
 Tom Manz
 On Tue, Nov 24, 2009 at 11:55 AM,  <odio=imre.oc.uh.cu> wrote:
 > Dear T. Manz:
 > Thanks for sharing the program. I think is a nice solution for many
 > problems and controversies.
 > While trying to prove it in a simple case, I got the following error in
 > the Matlab window:
 >
 >>> calculate
 >
 > p =
 >
 >     4
 >
 >
 > m =
 >
 >     2
 >
 >
 > nimages =
 >
 >     3
 >
 > ??? Undefined function or variable 'textscan'.
 >
 > Error in ==>
 > D:\transition_state_lateness_matlab_script_10_07_2009\calculate.m
 > On line 27  ==>     data = textscan(fid1,'%f %f %f',
 n_atoms);
 >
 > How could I overcome this?
 > Thanks again,
 > Oscar Odio
 >
 >
 >>
 >> Sent to CCL by: "Thomas A. Manz" [thomasamanz*gmail.com]
 >> An early transition state resembles the reactants more than the
 products,
 >> while a late transition state resembles the products more than the
 >> reactants. Several postulates in chemistry and catalysis require a
 >> quantitative measure of transition state lateness for their
 application.
 >> These include the Hammond-Leffler postulate, the structure sensitivity
 >> postulate, and the reactant sensitivity postulate. The Hammond-Leffler
 >> postulate is taught in several college textbooks, and Hammonds 1955
 >> article describing it (J. Am. Chem.Soc. 77 (1955) 334-338.) has
 received
 >> more than three thousand citations. However, until now there was no
 >> universal method for quantifying transition state lateness from
 geometries
 >> along a minimum energy reaction pathway.
 >>
 >> A new method published in the Journal of Computational Chemistry
 describes
 >> a dimensionless reaction coordinate, W, that can be used to quantify
 the
 >> relative lateness of transition states. W varies monotonically from 0
 >> (reactant) to 1 (product) along a minimum energy reaction pathway. Let
 WTS
 >> denote the dimensionless reaction coordinate of the transition state.
 When
 >> WTS < 0.5, the transition state is early. When WTS > 0.5, the
 transition
 >> state is late. When WTS = 0.5, the transition state is equidistant
 between
 >> reactants and products. This descriptor can be computed using only a
 >> series of optimized geometries (aka images) along the minimum energy
 >> reaction pathway. A minimum of three images (reactant, transition
 state,
 >> and product) is required, and there is no maximum in the number of
 images
 >> that can be used.
 >>
 >> Once optimized geometries along the minimum energy reaction pathway are
 >> known, the time for computing W is a small fraction of a second. (The
 >> equations for computing W of each image are simple algebraic
 equations.)
 >>
 >> A free program implementing the method is available at
 >>
 >> http://sourceforge.net/projects/drcs/
 >>
 >> This type of analysis should be useful to those performing nudged
 elastic
 >> band (NEB), quadratic synrchronous transit (QST), or intrinsic reaction
 >> coordinate (IRC) calculations. The method is applicable to both
 periodic
 >> and nonperiodic systems and can be used for reactions occuring in the
 >> gas-phase, in liquid-phase, in solids, or on surfaces.
 >>
 >> Link to the published abstract:
 >>
 >> http://www3.interscience.wiley.com/journal/122682417/abstract
 >>
 >> The article describes both the quantification of transition state
 lateness
 >> and its application to several postulates in chemistry and catalysis.
 >>
 >> Tom Manz
 >>
 >> thomasamanz [at] gmail.com
 >>
 >>
 >>
 >> -= This is automatically added to each message by the mailing script
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