Intrinsic Reaction Coordinate (IRC) Keywords in the Jaguar Input File

  • Overview
  • Examples

IRC scans have been implemented using the methods described in Ref. [257]. The implementation includes IRC and minimum energy path (MEP) calculations. The calculations start at a transition state and move downhill in energy along the reaction path toward a minimum of the potential energy surface. They are mainly used to check that the given transition state is indeed the expected transition state for the reaction of interest. The local quadratic approximation (LQA) described in Ref. [276] has also been implemented. This provides a more robust method, as the calculations are not constrained, but it may deviate from the true IRC path if the steps are too large. For checking a transition state you can also use the "three-point IRC" method, in which one IRC step is taken in each direction, then a minimization performed to locate the reactants and products. This method is fast, but does not produce an IRC path. The keywords for IRC and MEP calculations are listed in Table 1. You can also use the keywords listed in Table 1 in Geometry Scan Keywords in the Jaguar Input File.

Table 1. Keywords for IRC calculations

Keyword

Value

Description

irc

0

Do not do IRC calculation

 

1

Do IRC calculation with non-mass-weighted coordinates (minimum energy path scan)

 

2

Do IRC with mass-weighted coordinates

ircmode

forward

Find IRC points in “forward” direction from the transition state

 

reverse

Find IRC points in “reverse” direction from the transition state

 

downhill

Find IRC points by moving downhill from an initial geometry that is not a transition state

 

both

Find IRC points in both “forward” and “reverse” directions from the transition state

three_pt_irc

0

Do not do three-point IRC calculation

 

1

Do three-point IRC calculation. The first point on each side of the transition state is located as usual, then the constraint on the distance from the transition state is relaxed and the points are optimized to find the end points, corresponding to the reactant and product complexes. Requires irc to be set as well.

ircmax

6

Maximum number of IRC points to be found in any direction. Must be a positive integer.

ircmxcyc

30

Maximum number of geometry iterations used to calculate each IRC point. Must be a positive integer.
lqa_step

0

Do not use the local quadratic approximation (LQA) to define the steps for the IRC path.
 

1

Use the local quadratic approximation (LQA) to define the steps for the IRC path.

lqa_arclength

0.1

Step size taken for each LQA point, in bohrs.

ircstep

0.1

Step size taken for each IRC point, in bohrs amu−1/2 or radians amu−1/2.

ircfacinit

1.0

Factor for determining the IRC step size in retries of finding the first IRC point. The step size at each retry is ircstep * fac * gfac, where gfac is a factor involving the gradient, and fac is initially set to the value of ircfacinit, and is increased by irfacramp for each retry.

ircfacramp

0.5

Increment for ramping up the factor determining the IRC step size when attempts to find the first IRC point are retried. This is the amount by which the factor specified by ircfacinit is increased for each retry, i.e. fac = ircfacinit + irfacramp*nretry where nretry is the number of retries (starting at zero).

ircgcut

1.0

Scale factor for the cutoff that is used to determine whether the gradient is too small to locate the next IRC point. Use values that are less than 1.

irc_grad_check

0

Do not perform a gradient check before starting an IRC calculation. This is useful when the job is run to determine the endpoints of the IRC calculation, rather than ensure that the transition state is accurate.
 

1

Perform a gradient check before starting an IRC calculation. The job fails if the gradient at the transition state is too large.

irc_cyc_retry

0

Do not retry to find an IRC point or release constraints when running out of cycles.
 

1

When running out of cycles, try again to find the IRC point.
 

2

When running out of cycles, first try again to find the IRC point, then release constraints.
 

−1

When running out of cycles, release constraints.

irc_init_retries

3

Maximum number of retries permitted to find the first IRC point (in either direction) with an appreciable gradient.

ip472

0

Do not save the IRC structures in the .mae output file.
 

2

Save the IRC structures in the .mae output file and write the reaction coordinate value as a property.

The “forward” and “reverse” directions are defined as follows. The first set of conditions that constitutes a valid definition is used.

1. If two additional geometries are entered in the zmat2 and zmat3 sections, they are assumed to be the geometries for the reactant (in zmat2) and product (in zmat3). The forward direction is defined as moving from reactant to product.
2. If a vector is entered in the tvec section, it defines the forward direction. For example,

&tvec
C2 H3 * 0.5
O1 C2 H3 * -1.0
&

This definition produces a composite coordinate that is the sum of 0.5 times the distance between atoms C2 and H3 and −1.0 times the angle O1-C2-H3.

Coordinates comprising this composite can be any combination of bond stretches (2 atoms listed), angle bends (3 atoms), and dihedral angles or torsions (4 atoms). Atom labels or index numbers for the atoms can be used in specifying atoms. Coordinate coefficients, specified by including an asterisk followed by a value after the last atom are optional. The default coefficient value is 1.0. The forward direction is the direction that makes the composite coordinate defined in this section larger.

3. The Hessian eigenvector for the imaginary frequency mode with the most negative eigenvalue of the Hessian is used to define the forward direction. The phase of the eigenvector is chosen so that the largest coefficient is positive, and the forward direction is the direction that increases the coordinate for the largest coefficient.

IRC calculations can be done in either Cartesian coordinates (specified with intopt=0), or redundant internal coordinates (intopt=1), which is the default.

IRC in any mode but “downhill” requires a Hessian, which must either be entered in the hess section, or calculated analytically with inhess=4 in the gen section. Initial guess Hessians are not useful, as they do not have any imaginary frequencies. If a Hessian is entered in the hess section (whether directly or from a restart file for a calculation that performed a Hessian evaluation) and symmetry is on, the IRC calculation might not produce any points or might not produce points on the actual reaction path if the transition state has higher symmetry than the reaction path. If this is the case, you should turn symmetry off (isymm=0 in the gen section). If you evaluate the Hessian with inhess=4 in the gen section, symmetry is turned off for analytic Hessian calculations, and the subsequent IRC calculations are done without symmetry.

The IRC calculation can fail if the step size is too small. The warning message states that the vector used to determine the step is too small. You can increase the step size by setting ircstep, or you can use irc_init_retry, ircfacinit and ircfacramp to automatically retry the first step with an increasing step size.

The IRC calculation can also fail if the potential energy surface is very flat, and the gradient that is used to find the next IRC point is too small. You can reduce the magnitude of the cutoff for determining when the gradient is too small with the keyword ircgcut, which should be set to a value less than 1.0. If you set this keyword, you should be careful not to set it so small that it does not filter out “noise” in the gradient.

The restart file for an IRC job includes the geometry of the last found IRC point in the zmat section. An ircmode=downhill setting is included in the gen section regardless of the initial setting, as a restart job proceeds downhill from the last found IRC point. If the job has not gone far enough to have found another IRC point, no ircmode=downhill setting is included.

Transition State Geometry Optimization Examples

Note: To get the other side of the reaction path, set ircmode=backward. One could also get the whole path in one job with ircmode=both, but this is inefficient. The transition state should be optimized at the same level of theory as used for the IRC.

Example input file (opt_ts-irc-0001.in):

&gen
irc=1
ircmode=forward
dftname=B3LYP-D3
basis=6-31G**
&
&zmat
C1            0.0692136180      0.2132816644     -0.3879323240 
C2            1.4720844665      0.2296330313      0.1734604239 
O3            2.2428204464      1.1677738906      0.1309430510 
N4            2.1499220058     -1.2437703044      0.0898551824 
C5            3.5627058603     -1.2437951941     -0.3080475774 
H6            4.0343246067     -2.1845128465     -0.0147401167 
H7           -0.4855722193     -0.6754858693     -0.0829860366 
H8           -0.4514113750      1.0974920377     -0.0186382961 
H9            0.1210183915      0.2689320396     -1.4813556128 
H10           1.5855338582     -1.8961919808     -0.4512488016 
H11           3.6665480964     -1.1009168850     -1.3871598360 
H12           4.0480965526     -0.4072652266      0.1955270219 
O13           1.0996672074     -0.3560287728      1.9259912398 
H14           1.8663029436     -1.2303195726      1.2206894514 
H15           1.6407504151      0.2556717461      2.4468241668 
&
&hess
   1
   1  4.985984E-01
   2  1.022192E-02  6.036747E-01
   3 -4.467415E-02 -1.042631E-03  5.443946E-01
   4 -1.847519E-01 -1.236992E-03 -4.896982E-02  7.032186E-01
   5  3.569906E-03 -7.889063E-02  5.341051E-04  3.093762E-01  5.805400E-01
   6 -4.414289E-02  3.075284E-03 -8.099072E-02  1.068053E-01 -1.445122E-02
   7 -2.638700E-02 -3.841405E-02  1.186097E-03 -3.696389E-01 -2.930791E-01
   8 -1.579608E-02 -1.203816E-03  3.307070E-04 -3.135045E-01 -4.418800E-01
   9 -9.846858E-03 -1.116586E-02  1.272042E-02  4.209255E-03  1.031146E-02
  10 -1.256079E-02  2.837095E-02  6.328622E-03 -9.420234E-02 -2.760635E-02
  11  8.074277E-03 -8.180085E-03 -4.246788E-03 -1.403619E-02 -2.511348E-03
  12 -6.141829E-03  8.876670E-03  9.186548E-03  6.449519E-03 -6.634393E-03
  13  1.131178E-03 -4.200063E-04 -1.016255E-05 -1.510764E-02  2.598603E-02
  14  1.070207E-03 -4.879721E-03 -1.405763E-03  2.782561E-02  1.109159E-02
  15 -1.655723E-03  2.936403E-03  1.590250E-03 -3.800617E-03 -5.299978E-03
  16 -5.901058E-04  2.125121E-03  8.436201E-04 -4.377328E-03 -1.041980E-02
  17 -3.846097E-05  1.373446E-04 -5.110873E-05 -1.966200E-03 -1.326630E-03
  18  1.237235E-04 -6.688404E-04 -3.383283E-04  1.998806E-03  9.666394E-04
  19 -1.173074E-01 -1.094637E-01  3.812270E-02 -1.150648E-02 -3.048214E-02
  20 -1.130304E-01 -2.317935E-01  6.339941E-02  1.986910E-03 -2.210707E-03
  21  4.106264E-02  6.657354E-02 -6.890803E-02 -4.891653E-03 -1.331228E-02
  22 -1.084907E-01  1.054392E-01  4.532612E-02 -1.429915E-02  2.798514E-02
  23  1.080574E-01 -2.318369E-01 -7.814281E-02  1.958646E-04 -1.413140E-03
  24  4.718613E-02 -7.944934E-02 -7.820947E-02 -6.806352E-03  1.139206E-02
  25 -5.024001E-02 -1.452310E-03  1.352202E-02  2.649424E-03  5.370487E-05
  26 -1.826418E-03 -4.918181E-02  1.368002E-02  3.639358E-04 -2.231746E-03
  27  1.452739E-02  1.321935E-02 -3.075969E-01  3.084118E-03  4.864820E-04
  28 -2.538287E-04  1.656919E-03 -3.835681E-04  1.146800E-02 -5.379098E-04
  29 -2.614891E-04  1.640485E-03  1.317667E-03 -2.194747E-02 -5.552470E-03
  30 -5.123418E-04 -7.816618E-04  9.256446E-04  4.276077E-03  2.772825E-03
  31  1.135445E-04 -1.452176E-04 -8.656111E-05  2.617790E-04 -3.392604E-03
  32 -1.812774E-05  4.009060E-05 -2.733422E-05 -2.768754E-06  1.079156E-03
  33  1.734414E-04 -2.531512E-04 -1.627890E-04  2.129085E-04  2.837961E-03
  34  1.355931E-04  5.585949E-04  1.242287E-04 -3.382290E-03 -6.716188E-03
  35 -4.872590E-04 -5.381049E-04  8.740019E-05  2.386577E-03  1.169051E-03
  36 -5.601811E-05  5.784216E-05  3.629654E-05 -4.393252E-04 -2.036535E-03
  37  2.436439E-03  9.573235E-04 -1.428457E-02 -4.082285E-02  5.078931E-03
  38 -1.454727E-03  2.951483E-03  6.410734E-03  5.713458E-03 -4.965616E-02
  39  1.897772E-04  1.530101E-03 -2.357119E-02 -1.434384E-02 -2.050847E-02
  40 -1.955888E-03  2.486889E-03  3.253569E-03  1.837701E-02 -2.956220E-03
  41  2.542492E-03 -1.906310E-03 -3.832832E-03 -4.464500E-03 -1.733952E-02
  42  2.717630E-03 -3.728952E-03 -5.891615E-03 -3.269098E-02  4.798331E-02
  43  8.508411E-05 -7.230364E-04 -2.827313E-04  2.127656E-03  3.123252E-03
  44 -6.330762E-04 -4.139792E-05  2.982404E-03  9.251580E-03  9.058447E-03
  45  1.022238E-03  7.803387E-04 -3.140184E-03 -1.500650E-02 -1.504003E-02
   6
   6  1.891258E-01
   7 -1.215664E-02  3.788865E-01
   8 -5.477972E-03  3.522318E-01  5.287214E-01
   9 -7.781747E-02 -9.765378E-03 -1.866249E-02  5.855060E-02
  10 -9.889992E-03  2.396759E-02 -1.220042E-02 -2.326645E-03  5.719330E-01
  11  2.818519E-02 -1.309695E-02 -6.810470E-02 -4.378007E-03  1.426693E-01
  12 -7.674009E-02 -5.391740E-03 -4.888372E-03  1.843096E-02  2.138924E-02
  13  4.070270E-03 -7.033202E-03 -8.498340E-03 -5.190194E-05 -1.995417E-01
  14 -2.840603E-03 -4.900019E-04 -1.944517E-03  1.739582E-04 -1.953501E-03
  15 -3.667065E-03  7.420796E-04  8.735631E-04  6.980367E-04  4.548669E-02
  16 -1.372223E-03  3.643146E-03  1.342802E-03 -5.934102E-04 -2.550442E-02
  17  5.098645E-04  2.126253E-03  8.719094E-04 -4.502895E-04 -1.889224E-03
  18  8.865701E-04 -8.116343E-05 -7.626028E-05  1.420408E-05  5.665637E-03
  19  1.334386E-02 -6.906796E-03  8.975771E-04 -4.252507E-03  4.914523E-04
  20 -1.590831E-04 -6.971463E-05  2.612244E-03  2.964627E-04  6.419663E-04
  21  2.834154E-03 -4.398264E-03  2.520566E-04  6.041701E-05  4.262514E-04
  22  1.165565E-02  3.241029E-03 -2.258676E-03 -1.202332E-03 -5.242114E-03
  23  1.894415E-04 -8.590803E-04  6.960479E-04  5.511079E-05  3.822324E-04
  24  3.123534E-03  1.491534E-03  2.781627E-04 -2.725460E-04 -3.734763E-03
  25 -3.100032E-02  3.254835E-04  1.023198E-03  3.133684E-03  1.965670E-04
  26  4.697291E-04 -6.581400E-04 -1.149472E-05  3.887231E-04  1.011431E-05
  27 -1.364797E-02 -4.418780E-04 -4.524588E-05  2.314014E-03 -9.033280E-04
  28  5.710707E-03 -1.280890E-04  4.775850E-03 -7.659709E-04 -1.680027E-01
  29 -1.139323E-02  2.806879E-03 -7.685155E-03  1.095925E-03 -1.329562E-01
  30 -6.854407E-04 -1.024416E-04  3.779371E-03  1.886351E-04 -1.162827E-01
  31  2.005472E-03  1.167707E-03  1.322100E-03 -4.103378E-04 -1.358718E-02
  32 -9.255338E-04 -2.058354E-04 -3.552785E-04  1.073493E-03 -6.075124E-04
  33 -8.086579E-04 -8.561612E-04 -1.341512E-03  9.668297E-04  6.813461E-03
  34 -3.866991E-04  3.057775E-03  2.934189E-03  5.583282E-04 -2.477499E-02
  35 -1.363596E-03  1.423101E-03 -3.203031E-03 -1.841376E-04 -2.856143E-03
  36  1.493745E-03  1.712722E-03  1.266629E-04 -1.558178E-03  4.547418E-03
  37 -1.066942E-02  2.756671E-03 -1.106440E-02  1.586406E-02  5.746055E-03
  38 -5.113982E-02 -1.461452E-02 -6.799558E-03  3.087400E-02  2.723057E-02
  39  2.658720E-02  1.815501E-02  2.549021E-02 -9.742119E-03  3.245907E-02
  40 -3.407957E-02 -5.241110E-03  3.237273E-05  5.511014E-03 -5.204521E-02
  41  5.638038E-02  5.203961E-03  1.823917E-03 -8.136735E-03 -2.373028E-02
  42  3.955872E-02  7.390720E-03 -2.579613E-03 -1.055272E-02  5.094914E-03
  43  1.073796E-04 -1.665955E-03 -1.197846E-03  4.358715E-05 -6.852459E-03
  44 -1.017638E-03 -2.251491E-03 -3.495117E-03 -1.321005E-03  4.559514E-03
  45 -9.228660E-03  2.543520E-03  1.939123E-03  5.953171E-03  4.991874E-03
  11
  11  3.932701E-01
  12  1.652254E-01  4.548462E-01
  13 -1.556924E-02  2.117681E-02  4.767899E-01
  14 -9.592103E-02 -8.244157E-03 -6.277825E-03  6.123560E-01
  15 -1.121731E-03 -9.962233E-02  3.212088E-02  6.427710E-03  5.893896E-01
  16  3.498163E-02 -3.645947E-03 -9.065957E-02  9.250206E-02 -3.051712E-02
  17  5.166576E-03 -2.017184E-03  9.761012E-02 -2.537313E-01  6.461120E-02
  18 -1.188736E-02  3.252549E-03 -3.225406E-02  6.780039E-02 -7.309024E-02
  19  1.769291E-03 -2.240635E-04  1.492180E-04 -5.858783E-05  2.770632E-04
  20  1.054983E-04 -7.634075E-04 -3.098770E-04  2.759028E-04  7.940260E-05
  21  2.669748E-04 -3.258095E-04  5.439370E-05 -2.208976E-04 -1.375190E-04
  22  5.028378E-04 -2.916702E-03  2.255912E-04  1.434528E-03 -8.016156E-04
  23  1.003535E-03  5.381508E-05 -1.319391E-04 -1.664722E-04  3.565396E-04
  24  1.070795E-03 -1.297097E-04 -3.301659E-05  9.252162E-04 -6.061892E-04
  25 -2.946594E-04  2.542660E-03  1.358490E-05  8.268202E-05  8.034601E-05
  26  1.874002E-04 -5.698551E-04  2.465401E-05 -7.629418E-05 -1.287487E-04
  27  1.770528E-04  2.002433E-03  4.092991E-05  2.354675E-04 -4.579702E-05
  28 -1.247799E-01 -1.031803E-01 -1.630067E-02 -2.306804E-02 -2.004172E-02
  29 -1.964463E-01 -1.325790E-01  4.878414E-03  3.082449E-03  1.988089E-03
  30 -1.421179E-01 -1.569486E-01  9.117665E-03  9.934487E-03  6.346716E-03
  31 -4.178662E-03  4.379810E-02 -5.012478E-02 -1.222554E-03  1.013150E-02
  32  7.420825E-04 -6.740050E-04 -1.734963E-03 -5.636709E-02  3.455484E-02
  33 -4.074989E-04 -5.749680E-03  1.709728E-02  3.394346E-02 -3.117748E-01
  34 -2.708786E-02 -1.563336E-02 -9.808763E-02 -8.692238E-02 -5.259622E-02
  35  2.467071E-03  1.883205E-03 -9.649032E-02 -2.118278E-01 -1.009351E-01
  36  1.022426E-02  6.514031E-03 -5.859540E-02 -1.011931E-01 -1.141312E-01
  37  2.019490E-02  5.136301E-02  4.424459E-03 -8.919199E-04 -1.616828E-04
  38  5.127094E-03 -6.180091E-02 -5.483989E-03  1.197293E-03 -6.910807E-03
  39 -2.990125E-02 -5.190536E-02 -3.770037E-03 -1.309653E-03 -5.549287E-03
  40 -9.471339E-03 -1.659741E-02 -6.025108E-03 -2.361953E-03  1.910023E-02
  41 -3.792448E-02  4.577650E-02  6.855361E-03 -3.560017E-03  3.809640E-03
  42 -1.048307E-02 -1.017400E-01  1.082948E-02 -3.707784E-03  1.183190E-02
  43  3.373073E-04  7.055651E-03  2.234615E-04  3.067496E-04  1.605956E-03
  44  1.008981E-03 -3.680737E-03 -4.426161E-04  4.441281E-04 -1.208449E-03
  45 -6.154931E-04 -1.147187E-03  1.772656E-04 -4.999787E-04 -1.235412E-03
  16
  16  1.075992E-01
  17 -1.070166E-01  2.684403E-01
  18  3.016255E-02 -7.089293E-02  7.110972E-02
  19  1.418016E-04  1.909962E-05 -2.150361E-05  1.268958E-01
  20 -2.797843E-05  2.604594E-05  4.040160E-05  1.213239E-01  2.478250E-01
  21  5.227808E-05  2.770226E-05  2.173845E-05 -4.164134E-02 -7.039853E-02
  22 -6.130178E-04 -2.755726E-05  2.187754E-04  9.355780E-03 -1.405384E-02
  23  9.939420E-05  6.664764E-05 -7.363411E-06  1.284335E-02 -1.870518E-02
  24 -3.825313E-04  1.733181E-05  1.127314E-04 -5.652362E-03  8.034981E-03
  25  1.884628E-05 -1.468898E-06  4.274247E-05 -9.005034E-04  1.572579E-03
  26  7.787341E-08  1.646921E-05 -3.428845E-06  8.624670E-04  5.596892E-04
  27 -6.342751E-05 -2.993512E-06  3.976158E-05  1.087070E-04 -6.106426E-04
  28 -3.176739E-04  4.731388E-04 -4.897923E-04 -1.590919E-03  5.246652E-04
  29  2.903784E-04  6.148007E-05  2.822240E-04  1.259631E-03  2.403863E-04
  30 -6.196470E-04 -2.566991E-04 -2.349741E-06  5.014511E-04  1.440014E-04
  31  1.784206E-03 -1.019820E-04 -1.345455E-02  6.851997E-05  8.642558E-06
  32 -2.235923E-03 -1.901817E-03  2.825521E-02 -4.559269E-05 -1.552044E-05
  33 -5.501677E-04 -1.144464E-04 -6.556511E-03 -5.339664E-05  9.683820E-07
  34  7.927221E-03  1.038772E-02  8.104638E-03  3.307318E-04  1.226459E-04
  35 -1.168530E-02 -1.771877E-02 -1.326967E-02 -2.866873E-04  6.861106E-05
  36  6.086662E-03  8.597933E-03  5.079666E-03 -2.609755E-05  5.693284E-05
  37 -1.067612E-04  2.033685E-04 -1.640549E-04  7.905363E-04  1.120191E-03
  38 -7.100420E-06 -1.241439E-04  4.393433E-04  1.556122E-03  1.079212E-03
  39  6.737798E-04 -5.661613E-04 -4.713464E-04 -6.847797E-04 -5.324952E-04
  40  1.092119E-03  1.917843E-04  1.270631E-04 -4.314129E-04 -1.414907E-04
  41  1.170476E-04  8.160579E-05 -9.803293E-04 -1.768751E-04  3.376626E-05
  42 -6.716504E-05  4.848445E-04 -7.297572E-05 -3.449237E-04  1.905529E-04
  43 -3.449908E-05  3.662602E-05  2.463782E-05  4.436057E-04  3.549487E-04
  44 -6.806719E-05 -6.466007E-05 -4.080512E-06 -1.761206E-05 -9.826663E-05
  45 -4.057671E-06  9.670880E-05  1.620943E-05  5.843616E-04  2.636593E-04
  21
  21  7.084206E-02
  22 -6.802053E-03  1.166318E-01
  23 -9.027352E-03 -1.168997E-01  2.461293E-01
  24  2.712649E-03 -4.804512E-02  8.523205E-02  8.131038E-02
  25  1.612735E-02 -7.471322E-04 -2.550863E-03  1.556577E-02  4.976099E-02
  26  2.607209E-02 -1.757125E-04  3.002162E-03 -2.651102E-02  8.088077E-04
  27 -6.137251E-03  1.482188E-04  1.451963E-03 -9.323726E-03 -1.425659E-02
  28  4.918087E-04 -2.069955E-04 -4.301813E-04 -3.070037E-05 -9.151932E-05
  29 -3.323884E-04 -5.794746E-04  6.056002E-04 -2.233866E-04  4.493986E-04
  30  1.020200E-04  1.922663E-04  1.590578E-04 -2.168984E-04  4.145534E-06
  31  1.151370E-05  2.387484E-05 -1.092654E-05 -3.400492E-05 -1.441239E-04
  32  3.339002E-05 -3.864463E-05 -1.941527E-05 -7.077499E-06  3.578851E-05
  33  1.101718E-05  8.004633E-05 -2.894326E-05  4.541160E-05  5.963509E-05
  34  1.493342E-05 -8.057138E-05  1.176920E-04 -3.401678E-05  8.050898E-05
  35 -8.120052E-05  6.417058E-05 -9.709983E-07  2.283781E-05 -3.794701E-05
  36  3.078137E-05 -5.455369E-06 -7.459942E-06  1.753289E-05  1.402053E-05
  37 -2.308452E-04  1.322235E-03 -1.086106E-03  8.344684E-04 -2.026223E-03
  38 -3.601565E-04 -2.373268E-03  1.076191E-03 -1.089129E-03  8.332152E-04
  39 -1.747924E-03  4.112410E-04  6.057099E-04  2.329377E-04 -3.849488E-03
  40 -5.457913E-04 -9.666260E-04  2.016678E-04 -1.907185E-04  1.071373E-03
  41  3.033270E-04  8.585903E-04 -4.216932E-04  2.534718E-04 -1.468491E-03
  42  6.385082E-04  1.928871E-03 -9.543450E-04  1.194677E-03 -1.371073E-03
  43  2.690804E-04 -1.464908E-04  6.568445E-05 -1.339642E-04  4.309044E-05
  44  2.029894E-04  1.191700E-04 -7.605648E-06  5.047541E-05  9.482964E-04
  45  6.617638E-06 -1.815225E-04  5.759636E-05  1.096916E-05 -6.096135E-04
  26
  26  4.647496E-02
  27 -1.520900E-02  3.348778E-01
  28  3.705613E-05 -9.735934E-05  1.799337E-01
  29 -3.948055E-04  4.368426E-04  1.374420E-01  2.019524E-01
  30  3.316152E-04 -3.593068E-04  1.128006E-01  1.418798E-01  1.533453E-01
  31  7.412041E-05 -1.814099E-04  1.501233E-03 -6.619068E-05  2.618818E-04
  32  2.132794E-05  1.399465E-05 -2.608747E-04 -2.758973E-05  8.706471E-04
  33 -2.204672E-05  4.447182E-05  6.050874E-04 -2.191762E-04  8.559955E-04
  34 -2.758119E-05  3.727888E-05 -6.208251E-03  1.044480E-03  2.837404E-03
  35 -1.586116E-06 -1.553492E-05  1.580593E-03 -4.651862E-04  7.125004E-04
  36  2.305705E-06 -6.225054E-06  2.583567E-03 -2.678296E-04  6.908384E-05
  37  7.253214E-04 -2.806103E-03 -3.790065E-03 -2.089409E-04  8.028176E-03
  38  1.744091E-03  8.960351E-05  2.949641E-04  2.182384E-03 -2.909722E-03
  39  7.389532E-04 -4.903622E-05  3.381858E-03 -2.033013E-03 -3.199405E-03
  40 -5.732334E-04  1.030120E-03  3.880135E-03  7.633651E-03 -2.016076E-02
  41  3.764893E-04 -9.026863E-04  2.498825E-03  9.670412E-04 -1.524159E-02
  42  2.041696E-04 -1.642086E-03 -8.972752E-05 -1.634360E-04 -5.927559E-04
  43  3.620831E-04 -2.274561E-04  1.151538E-04  2.182054E-04 -3.459445E-04
  44 -4.792174E-04  6.808451E-04 -2.154003E-04 -1.544890E-04  7.222227E-04
  45  5.653608E-04 -4.808099E-04 -4.975019E-04  2.109566E-04  1.775205E-04
  31
  31  6.033084E-02
  32  2.627628E-03  5.121953E-02
  33 -2.383043E-02 -3.802609E-02  3.338761E-01
  34  1.952740E-03  2.553888E-03  4.783205E-04  1.183110E-01
  35  3.934925E-03  5.423986E-03  3.466954E-03  1.032753E-01  2.247849E-01
  36 -1.391844E-02 -2.498239E-02 -1.338911E-02  5.819228E-02  1.086569E-01
  37 -1.263882E-03 -1.479128E-04  3.334609E-04  1.675174E-05 -2.684526E-06
  38  3.896823E-03 -1.447230E-05 -1.317196E-03  1.190661E-03 -8.042051E-04
  39  2.372182E-03  1.465592E-04 -6.218236E-04 -5.707047E-04  9.574717E-04
  40 -1.454351E-03  1.735561E-04 -7.050432E-04  8.852110E-04 -7.469779E-04
  41 -3.247798E-03  1.351053E-04  1.500980E-03 -1.614742E-03  4.940132E-04
  42 -6.976245E-03 -2.837144E-04  3.292562E-03 -1.430189E-03  1.817977E-04
  43 -6.267468E-04 -8.645682E-05  1.513497E-04 -1.457447E-04 -5.908799E-05
  44  5.023319E-04  3.822368E-05 -3.344543E-05  1.718977E-04  1.384160E-04
  45  3.112351E-04 -2.276136E-05 -2.803434E-05  2.977890E-04 -1.284507E-04
  36
  36  1.162906E-01
  37 -6.326879E-04  2.325917E-01
  38  3.463852E-04  1.730041E-01  2.702908E-01
  39 -3.255435E-04  1.216728E-01  2.033675E-01  2.413789E-01
  40  3.170309E-04 -3.074214E-02 -6.647616E-03  1.344136E-03  6.357577E-02
  41  5.145588E-04 -1.287865E-02 -3.733365E-03 -9.676562E-03  2.646651E-02
  42 -3.825672E-05 -2.785311E-02  4.176285E-02 -1.626648E-02  4.401337E-02
  43  2.216563E-04 -1.713310E-01 -1.831696E-01 -1.573437E-01  9.979555E-03
  44 -1.006902E-04 -1.750219E-01 -2.244648E-01 -1.682154E-01 -1.428958E-02
  45 -8.076661E-05 -1.412104E-01 -1.576788E-01 -1.548879E-01 -2.413239E-03
  41
  41  6.428960E-02
  42 -6.887696E-02  8.438787E-02
  43  3.043791E-03 -1.150293E-03  1.677703E-01
  44 -3.318060E-03 -2.087719E-05  1.773877E-01  2.214424E-01
  45 -8.924798E-04 -4.119387E-03  1.499941E-01  1.709621E-01  1.681916E-01
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_ts_irc_0001 opt_ts-irc-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt_ts-irc-0001.in
Output files

Note: To get the other side of the reaction path, set ircmode=backward. One could also get the whole path in one job with ircmode=both, but this is inefficient. The transition state should be optimized at the same level of theory as used for the IRC.

Example input file (opt_ts-irc-0002.in):

&gen
irc=1
ircmode=forward       
ircmax=8             
ircmxcyc=30           
ircstep=0.1           
dftname=B3LYP-D3
basis=6-31G**
&
&zmat
C1            0.0692136180      0.2132816644     -0.3879323240 
C2            1.4720844665      0.2296330313      0.1734604239 
O3            2.2428204464      1.1677738906      0.1309430510 
N4            2.1499220058     -1.2437703044      0.0898551824 
C5            3.5627058603     -1.2437951941     -0.3080475774 
H6            4.0343246067     -2.1845128465     -0.0147401167 
H7           -0.4855722193     -0.6754858693     -0.0829860366 
H8           -0.4514113750      1.0974920377     -0.0186382961 
H9            0.1210183915      0.2689320396     -1.4813556128 
H10           1.5855338582     -1.8961919808     -0.4512488016 
H11           3.6665480964     -1.1009168850     -1.3871598360 
H12           4.0480965526     -0.4072652266      0.1955270219 
O13           1.0996672074     -0.3560287728      1.9259912398 
H14           1.8663029436     -1.2303195726      1.2206894514 
H15           1.6407504151      0.2556717461      2.4468241668 
&
&hess
   1
   1  4.985984E-01
   2  1.022192E-02  6.036747E-01
   3 -4.467415E-02 -1.042631E-03  5.443946E-01
   4 -1.847519E-01 -1.236992E-03 -4.896982E-02  7.032186E-01
   5  3.569906E-03 -7.889063E-02  5.341051E-04  3.093762E-01  5.805400E-01
   6 -4.414289E-02  3.075284E-03 -8.099072E-02  1.068053E-01 -1.445122E-02
   7 -2.638700E-02 -3.841405E-02  1.186097E-03 -3.696389E-01 -2.930791E-01
   8 -1.579608E-02 -1.203816E-03  3.307070E-04 -3.135045E-01 -4.418800E-01
   9 -9.846858E-03 -1.116586E-02  1.272042E-02  4.209255E-03  1.031146E-02
  10 -1.256079E-02  2.837095E-02  6.328622E-03 -9.420234E-02 -2.760635E-02
  11  8.074277E-03 -8.180085E-03 -4.246788E-03 -1.403619E-02 -2.511348E-03
  12 -6.141829E-03  8.876670E-03  9.186548E-03  6.449519E-03 -6.634393E-03
  13  1.131178E-03 -4.200063E-04 -1.016255E-05 -1.510764E-02  2.598603E-02
  14  1.070207E-03 -4.879721E-03 -1.405763E-03  2.782561E-02  1.109159E-02
  15 -1.655723E-03  2.936403E-03  1.590250E-03 -3.800617E-03 -5.299978E-03
  16 -5.901058E-04  2.125121E-03  8.436201E-04 -4.377328E-03 -1.041980E-02
  17 -3.846097E-05  1.373446E-04 -5.110873E-05 -1.966200E-03 -1.326630E-03
  18  1.237235E-04 -6.688404E-04 -3.383283E-04  1.998806E-03  9.666394E-04
  19 -1.173074E-01 -1.094637E-01  3.812270E-02 -1.150648E-02 -3.048214E-02
  20 -1.130304E-01 -2.317935E-01  6.339941E-02  1.986910E-03 -2.210707E-03
  21  4.106264E-02  6.657354E-02 -6.890803E-02 -4.891653E-03 -1.331228E-02
  22 -1.084907E-01  1.054392E-01  4.532612E-02 -1.429915E-02  2.798514E-02
  23  1.080574E-01 -2.318369E-01 -7.814281E-02  1.958646E-04 -1.413140E-03
  24  4.718613E-02 -7.944934E-02 -7.820947E-02 -6.806352E-03  1.139206E-02
  25 -5.024001E-02 -1.452310E-03  1.352202E-02  2.649424E-03  5.370487E-05
  26 -1.826418E-03 -4.918181E-02  1.368002E-02  3.639358E-04 -2.231746E-03
  27  1.452739E-02  1.321935E-02 -3.075969E-01  3.084118E-03  4.864820E-04
  28 -2.538287E-04  1.656919E-03 -3.835681E-04  1.146800E-02 -5.379098E-04
  29 -2.614891E-04  1.640485E-03  1.317667E-03 -2.194747E-02 -5.552470E-03
  30 -5.123418E-04 -7.816618E-04  9.256446E-04  4.276077E-03  2.772825E-03
  31  1.135445E-04 -1.452176E-04 -8.656111E-05  2.617790E-04 -3.392604E-03
  32 -1.812774E-05  4.009060E-05 -2.733422E-05 -2.768754E-06  1.079156E-03
  33  1.734414E-04 -2.531512E-04 -1.627890E-04  2.129085E-04  2.837961E-03
  34  1.355931E-04  5.585949E-04  1.242287E-04 -3.382290E-03 -6.716188E-03
  35 -4.872590E-04 -5.381049E-04  8.740019E-05  2.386577E-03  1.169051E-03
  36 -5.601811E-05  5.784216E-05  3.629654E-05 -4.393252E-04 -2.036535E-03
  37  2.436439E-03  9.573235E-04 -1.428457E-02 -4.082285E-02  5.078931E-03
  38 -1.454727E-03  2.951483E-03  6.410734E-03  5.713458E-03 -4.965616E-02
  39  1.897772E-04  1.530101E-03 -2.357119E-02 -1.434384E-02 -2.050847E-02
  40 -1.955888E-03  2.486889E-03  3.253569E-03  1.837701E-02 -2.956220E-03
  41  2.542492E-03 -1.906310E-03 -3.832832E-03 -4.464500E-03 -1.733952E-02
  42  2.717630E-03 -3.728952E-03 -5.891615E-03 -3.269098E-02  4.798331E-02
  43  8.508411E-05 -7.230364E-04 -2.827313E-04  2.127656E-03  3.123252E-03
  44 -6.330762E-04 -4.139792E-05  2.982404E-03  9.251580E-03  9.058447E-03
  45  1.022238E-03  7.803387E-04 -3.140184E-03 -1.500650E-02 -1.504003E-02
   6
   6  1.891258E-01
   7 -1.215664E-02  3.788865E-01
   8 -5.477972E-03  3.522318E-01  5.287214E-01
   9 -7.781747E-02 -9.765378E-03 -1.866249E-02  5.855060E-02
  10 -9.889992E-03  2.396759E-02 -1.220042E-02 -2.326645E-03  5.719330E-01
  11  2.818519E-02 -1.309695E-02 -6.810470E-02 -4.378007E-03  1.426693E-01
  12 -7.674009E-02 -5.391740E-03 -4.888372E-03  1.843096E-02  2.138924E-02
  13  4.070270E-03 -7.033202E-03 -8.498340E-03 -5.190194E-05 -1.995417E-01
  14 -2.840603E-03 -4.900019E-04 -1.944517E-03  1.739582E-04 -1.953501E-03
  15 -3.667065E-03  7.420796E-04  8.735631E-04  6.980367E-04  4.548669E-02
  16 -1.372223E-03  3.643146E-03  1.342802E-03 -5.934102E-04 -2.550442E-02
  17  5.098645E-04  2.126253E-03  8.719094E-04 -4.502895E-04 -1.889224E-03
  18  8.865701E-04 -8.116343E-05 -7.626028E-05  1.420408E-05  5.665637E-03
  19  1.334386E-02 -6.906796E-03  8.975771E-04 -4.252507E-03  4.914523E-04
  20 -1.590831E-04 -6.971463E-05  2.612244E-03  2.964627E-04  6.419663E-04
  21  2.834154E-03 -4.398264E-03  2.520566E-04  6.041701E-05  4.262514E-04
  22  1.165565E-02  3.241029E-03 -2.258676E-03 -1.202332E-03 -5.242114E-03
  23  1.894415E-04 -8.590803E-04  6.960479E-04  5.511079E-05  3.822324E-04
  24  3.123534E-03  1.491534E-03  2.781627E-04 -2.725460E-04 -3.734763E-03
  25 -3.100032E-02  3.254835E-04  1.023198E-03  3.133684E-03  1.965670E-04
  26  4.697291E-04 -6.581400E-04 -1.149472E-05  3.887231E-04  1.011431E-05
  27 -1.364797E-02 -4.418780E-04 -4.524588E-05  2.314014E-03 -9.033280E-04
  28  5.710707E-03 -1.280890E-04  4.775850E-03 -7.659709E-04 -1.680027E-01
  29 -1.139323E-02  2.806879E-03 -7.685155E-03  1.095925E-03 -1.329562E-01
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  41
  41  6.428960E-02
  42 -6.887696E-02  8.438787E-02
  43  3.043791E-03 -1.150293E-03  1.677703E-01
  44 -3.318060E-03 -2.087719E-05  1.773877E-01  2.214424E-01
  45 -8.924798E-04 -4.119387E-03  1.499941E-01  1.709621E-01  1.681916E-01
&

To submit the job from the command line, download the input file (below) and enter the following command:

$SCHRODINGER/jaguar run -jobname=opt_ts_irc_0002 opt_ts-irc-0002.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: opt_ts-irc-0002.in
Output files