Specifying Bonds for Internal Coordinates with a connect Section
- Overview
- Examples
You can use a connect section to specify the bonds used by Jaguar in its generation of internal coordinates. This is particularly important for transition state searches, where bonds are broken and formed. Each line of a connect section should list two atoms by either their atom labels (such as H2 for a hydrogen) or their atom numbers (such as 3 for the third atom listed in the zmat section input). Here is a sample connect section:
&connect C1 C2 C2 C3 &
The two atoms on each line of the connect section are then treated as nearest neighbors by the program when it generates redundant internal coordinates for the optimization. Consequently, the internal coordinates generated by Jaguar include the bond between those two atoms and angles between those two atoms and any other atoms that are nearest neighbors to either of them. For the sample connect section above, for instance, the redundant internal coordinates would include the C1–C2 bond, the C2–C3 bond, and the C1–C2–C3 angle in addition to whatever internal coordinates would be generated without the connect section.
Transition State Geometry Optimization Examples
Example: B3LYP-D3/6-31G** TS optimization for amide hydrolysis. Apply the quadratic synchronous transit (QST) search algorithm that uses the reactant, product, and transition state structure as a guess
&gen igeopt=2 iqst=1 itrvec=-5 dftname=B3LYP-D3 basis=6-31G** & &zmat C1 0.0495980000000 0.2533700000000 -0.3607110000000 C2 1.4197410000000 0.2878870000000 0.2842060000000 O3 2.2207240000000 1.2032400000000 0.2164680000000 N4 2.1467540000000 -1.3358890000000 0.0333660000000 C5 3.5632580000000 -1.2838090000000 -0.3163310000000 H6 4.1158520000000 -2.1250250000000 0.1140940000000 H7 -0.4763550000000 -0.6831700000000 -0.1651180000000 H8 -0.5415720000000 1.0753480000000 0.0506750000000 H9 0.1518600000000 0.4065490000000 -1.4388620000000 H10 1.6081090000000 -1.9865110000000 -0.5310510000000 H11 3.6993010000000 -1.2866820000000 -1.4018320000000 H12 3.9603300000000 -0.3414190000000 0.0702700000000 O13 1.1762500000000 -0.3300010000000 1.7855610000000 H14 1.8708550000000 -1.2482310000000 1.1298150000000 H15 1.6182900000000 0.3172350000000 2.3567090000000 & entry_name2: reactant &zmat2 C1 0.2183000000000 0.2197920000000 -0.5170720000000 C2 1.6171140000000 0.1603480000000 0.0649390000000 O3 2.2489110000000 1.1546850000000 0.3754610000000 N4 2.2587850000000 -1.1023090000000 0.0211870000000 C5 3.5667470000000 -1.1818210000000 -0.6303440000000 H6 4.0512400000000 -2.1268260000000 -0.3715750000000 H7 -0.4157050000000 -0.5937250000000 -0.1597090000000 H8 -0.2405490000000 1.1723010000000 -0.2511220000000 H9 0.2987020000000 0.1576110000000 -1.6096780000000 H10 1.6244180000000 -1.8506820000000 -0.2376340000000 H11 3.5025230000000 -1.1047410000000 -1.7246620000000 H12 4.1807810000000 -0.3612210000000 -0.2579850000000 O13 0.7738580000000 -0.4704350000000 2.1755670000000 H14 1.6301480000000 -0.9058390000000 1.8977370000000 H15 1.0664630000000 0.3258540000000 2.6385140000000 & entry_name3: product &zmat3 C1 0.0728300000000 0.3145440000000 -0.4134690000000 C2 1.2539580000000 0.4686730000000 0.5052290000000 O3 2.1169230000000 1.3158960000000 0.4126330000000 N4 2.3144340000000 -1.5775530000000 0.0007060000000 C5 3.6689680000000 -1.4275930000000 -0.5002000000000 H6 4.3859260000000 -2.1895890000000 -0.1509490000000 H7 -0.4034160000000 -0.6586410000000 -0.2985600000000 H8 -0.6564980000000 1.0912100000000 -0.1489020000000 H9 0.3857450000000 0.4691010000000 -1.4452860000000 H10 1.8719330000000 -2.4265180000000 -0.3320280000000 H11 3.6591630000000 -1.4676670000000 -1.5951720000000 H12 4.0472370000000 -0.4425370000000 -0.2089700000000 O13 1.1199000000000 -0.2596670000000 1.6884280000000 H14 2.1162020000000 -1.3719070000000 0.9864270000000 H15 1.5415760000000 0.2825940000000 2.3744100000000 & &connect C2 O13 N4 H14 C2 N4 O13 H14 &
$SCHRODINGER/jaguar run -jobname=opt_ts_qst_0001 opt_ts-qst-0001.in