Reaction plusPro 2 / Express 2

Mechanism finder of chemical reactions

Reaction plus Pro 2/Express 2 is our original software that supports you to identify chemical reaction pathways automatically just by inputting information of reactants and products. This program was developed to solve the extreme difficulty of optimizing transition state structures during reaction pathways which fully requires experiences and intuitions of experts in the conventional method.
In the latest version of Reaction plus, Pro2/Express2 (meaning version 2), calculations of various reaction systems are additionally able to be performed from the previous version, such as enzyme reactions by the ONIOM method, heterogenous catalytic reactions, and open-shell reactions.

Notable Features

• 01

  Transition states of chemical reactions can be found easily

  In the conventional optimization method of transition states, a structure close to that of the target transition state has to be specified as the initial structure, which requires a craftsmanship level of techniques. This method causes exhaustive cases that the obtained TS had nothing to do with the reaction after vibration analyses, or that IRC calculations did not run well from TS and eventually the reaction pathways could not be obtained.

  

  Reaction plus optimizes the entire reaction path based on the Nudged Elastic Band (NEB) method. This enables us to obtain the transition state structure on the reaction pathway without any difficulty.
  Reaction plus uses the NEB method and String method to optimize the entire rection path.
  If we compare the molecular structure to a single bead, the reaction path can be expressed as a string of beads. When this string rolls on the reaction potential curved surface, the reaction path of the string finally becomes a solution due to the balance between the force that each bead tries to roll in the direction of decreasing energy and the binding force of the string. Converge to this is the basic mechanism for reaction path optimization.

  

  The basic mechanism of Reaction plus

  At first, initial and final states of chemical structures are specified by the users, and beads (chemical structures) will be placed at equal intervals between the two inputs, forming a string of beads.

  

  The shape of the string (positions of the beads) will be optimized according to movements of each bead driven by the forces, which means to be a conversion to the target reaction pathway. At this time, the beads avoid approaching too close together by moving toward orthogonal direction toward the string.

  

  The optimization will be finished when the beads stop their movement. Since the direction of the force against each bead are limited to the direction along the string (the reaction pathway), this implies the pathway is successfully solved.

  

  The molecule structures of initial and final state don’t have to be stable structures necessarily. Therefore, users are also able to solve the reaction pathways by specifying the structures instinctively from their past experiences and intuitions.

  

• 02

  Adapted to ONIOM, heterogeneous, and open-shell reaction systems respectively

  [Adapted to ONIOM method]
  ONIOM method is suitable to ensure both calculation accuracy and speed, which computes minutely to reaction active site but roughly to surroundings. By applying this method, calculations of large-scale molecules such as enzyme reactions are now available.

  

  [Atomic coordinate fixing function for homogeneous reactions]
  Reaction simulation can be performed by fixing coordinates of particular atom. This function enables calculations of homogeneous reaction systems such as catalytic reactions on metal surface.

  

  [Reading function of molecular orbit adapting to open-shell reactions]
  By using Gaussian checkpoint (chk) file, designations of initial orbit to molecular structures on reaction pathways can be done (initial guess). This allows you to handle reactions of complex open-shell systems such as radical dissociations and intersystem crossings.

  

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• 03

  GaussView, AMBER, GROMACS can be used to create inputs

  [Usage with GaussView]
  Able to use in the format of QST2/QST3 calculation of Gaussian.

  

  Input Creating with GaussView

  

  Contents of the input file to be created
  The red part is the original keyword for Reaction plus.
  Three structures are specified: initial state, intermediate state, final state

  [Usage with AMBER / GROMACS]
  ONIOM input-making support tool is attached to enables transforming topology / coordinate file of AMBER and GROMACS to Gaussian format.

  

  In addition, PDB and Mol2 file can be used as input file.

  

  Specification of initial structure from PDB file

• 04

  States of chemical reactions can be seen in animations

  [Adapted to ONIOM method]
  ONIOM method is suitable to ensure both calculation accuracy and speed, which computes minutely to reaction active site but roughly to surroundings. By applying this method, calculations of large-scale molecules such as enzyme reactions are now available.

  

  A Display example of GaussView
  Chemical reaction animations and energy graphs can be shown at a same time.

• 05

  Comes with easy-to-understand tutorial, and support options as well

  A tutorial is collectively attached, explaining how to create an input file in GaussView and how to run the calculation (including Oniom calculation) with examples of organic chemical reactions as well as frequently used techniques.
  We also have a fee-based support service by E-mail in which our staffs respond to various problems about techniques and solving the errors.