CCL: dimensionless reaction coordinate
- From: Thomas Manz <thomasamanz|*|gmail.com>
- Subject: CCL: dimensionless reaction coordinate
- Date: Mon, 14 Dec 2009 19:47:41 -0500
Sent to CCL by: Thomas Manz [thomasamanz=gmail.com]
Dear Oscar Odio,
The error you mentioned arises because Matlab 6 does not support the
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
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.
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:
> p =
> m =
> nimages =
> ??? Undefined function or variable 'textscan'.
> Error in ==>
> On line 27 ==> data = textscan(fid1,'%f %f %f',
> 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
>> 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
>> 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
>> more than three thousand citations. However, until now there was no
>> universal method for quantifying transition state lateness from
>> along a minimum energy reaction pathway.
>> A new method published in the Journal of Computational Chemistry
>> a dimensionless reaction coordinate, W, that can be used to quantify
>> relative lateness of transition states. W varies monotonically from 0
>> (reactant) to 1 (product) along a minimum energy reaction pathway. Let
>> denote the dimensionless reaction coordinate of the transition state.
>> WTS < 0.5, the transition state is early. When WTS > 0.5, the
>> state is late. When WTS = 0.5, the transition state is equidistant
>> 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
>> and product) is required, and there is no maximum in the number of
>> 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
>> A free program implementing the method is available at
>> This type of analysis should be useful to those performing nudged
>> band (NEB), quadratic synrchronous transit (QST), or intrinsic reaction
>> coordinate (IRC) calculations. The method is applicable to both
>> 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:
>> The article describes both the quantification of transition state
>> and its application to several postulates in chemistry and catalysis.
>> Tom Manz
>> thomasamanz [at] gmail.com
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