Merge pull request #393 from openforcefield/add-i-hessians

Add i hessians

README.md

@@ -247,6 +247,7 @@ These are currently used to compute properties of a minimum energy conformation
 | `OpenFF Aniline Para Hessian v1.0` | [2024-10-07-OpenFF-Aniline-Para-Hessian-v1.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-10-07-OpenFF-Aniline-Para-Hessian-v1.0) | Hessian single points for the final molecules in the `OpenFF Aniline Para Opt v1.0` [dataset](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2021-04-02-OpenFF-Aniline-Para-Opt-v1.0) | 'O', 'Cl', 'S', 'Br', 'H', 'F', 'N', 'C' ||
 |`OpenFF Gen2 Hessian Dataset Protomers v1.0` | [2024-10-07-OpenFF-Gen2-Hessian-Dataset-Protomers-v1.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-10-07-OpenFF-Gen2-Hessian-Dataset-Protomers-v1.0/) | Hessian single points for the final molecules in the `OpenFF Gen2 Optimization Dataset Protomers v1.0` [dataset](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2021-12-21-OpenFF-Gen2-Optimization-Set-Protomers) | 'H', 'C', 'Cl', 'P', 'F', 'Br', 'O', 'N', 'S'||
 | `MLPepper-RECAP-Optimized-Fragments-Add-Iodines-v1.0` | [2024-10-11-MLPepper-RECAP-Optimized-Fragments-Add-Iodines-v1.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-10-11-MLPepper-RECAP-Optimized-Fragments-Add-Iodines-v1.0)  | Set of diverse iodine containing molecules with a number of calculated electrostatic properties.   | Br, Cl, S, B, O, Si, C, N, I, P, H, F|   |
+| `OpenFF Iodine Chemistry Hessian Dataset v1.0` | [2024-11-11-OpenFF-Iodine-Chemistry-Hessian-Dataset-v1.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-11-11-OpenFF-Iodine-Chemistry-Hessian-Dataset-v1.0) | Hessian single points for the final molecules in the `OpenFF Iodine Chemistry Optimization Dataset v1.0` [dataset](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2022-07-27-OpenFF-iodine-optimization-set) |  I, F, Br, C, Cl, O, S, N, H ||
 
 
 # Optimization Datasets

submissions/2024-11-11-OpenFF-Iodine-Chemistry-Hessian-Dataset-v1.0/README.md

@@ -0,0 +1,50 @@
+# OpenFF Iodine Chemistry Hessian Dataset v1.0 
+
+## Description
+
+Hessian single points for the final molecules in the [OpenFF Iodine Chemistry Optimization Dataset v1.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2022-07-27-OpenFF-iodine-optimization-set) at the B3LYP-D3BJ/DZVP level of theory.
+
+## General information
+
+* Date: 2024-11-11
+* Class: OpenFF Basic Dataset
+* Purpose: Hessian dataset generation for MSM parameters
+* Name: OpenFF Iodine Chemistry Hessian Dataset v1.0 
+* Number of unique molecules: 99
+* Number of conformers: 327
+* Number of conformers (min, mean, max): 1, 3.30, 22
+* Molecular weight (min, mean, max): 221.95 318.54 533.92
+* Charges: -1.0, 0.0, 1.0
+* Dataset submitter: Alexandra McIsaac
+* Dataset generator: Alexandra McIsaac
+
+
+## QCSubmit generation pipeline
+
+* `generate-dataset.ipynb`: This notebook shows how the dataset was prepared from the input files.
+
+
+## QCSubmit Manifest
+
+* `dataset.json.bz2`: Compressed dataset ready for submission
+* `dataset.pdf`: Visualization of dataaset molecules
+* `dataset.smi`: Smiles strings for dataset molecules
+* `generate-dataset.ipynb`: Notebook describing dataset generation and submission
+* `input-environment.yaml`: Environment file used to create Python environment for the notebook
+* `full-environment.yaml`: Fully-resolved environment used to execute the notebook.
+
+
+## Metadata
+
+* elements: I, F, Br, C, Cl, O, S, N, H
+* unique molecules: 99
+* Spec: B3LYP-D3BJ/DZVP
+    * SCF properties:
+        * dipole
+        * quadrupole
+        * wiberg_lowdin_indices
+        * mayer_indices
+    * QC Spec:
+        * name: default
+        * method: B3LYP-D3BJ
+        * basis: DZVP

submissions/2024-11-11-OpenFF-Iodine-Chemistry-Hessian-Dataset-v1.0/dataset.smi

@@ -0,0 +1,99 @@
+c1cc2c(cc(c(c2nc1)O)I)Cl
+c1cc2c(cc(c(c2nc1)[O-])I)Cl
+c1ccc2c(c1)ccc(n2)/C=N/c3ccccc3I
+c1ccc2c(c1)c(cc(n2)/C=N/c3ccccc3I)C(=O)O
+c1cc(c(c(c1Br)C=O)F)I
+c1cc(c(c(c1)Br)I)[N+](=O)[O-]
+c1cc(c(cc1Br)I)[N+](=O)[O-]
+c1ccc(c(c1)[C@@H]2CCN2)I
+c1cc(c(cc1Cl)Cl)NC(=O)c2cc(cc(c2O)I)I
+c1cc(c(c(c1Cl)C=O)F)I
+c1c(cc(c(c1Cl)I)Cl)OC(F)(F)F
+c1ccc(c(c1)/C=N/NC2=Nc3ccccc3S2)I
+c1ccc(c(c1)/C=N/NC2=NCCCCC2)I
+c1cc(ccc1C(=O)CC#N)I
+c1ccc(c(c1)C(=O)NN=C2CCCC2)I
+c1ccc(c(c1)C(=O)NN=C2CCCCC2)I
+c1c(cc(c(c1C(=O)N)N)I)I
+c1cc(c(c(c1C(=O)O)F)F)I
+c1c(cc(c(c1C(=O)O)O)C(F)(F)F)I
+c1cc(c(cc1I)Br)C(=O)O
+c1cc(c(cc1I)C(F)(F)F)F
+c1cc(cc(c1)I)[C@@H]2CCN2
+c1cc(c(c(c1)I)Cl)C(=O)O
+c1c(c(cc(c1I)Cl)F)C(=O)O
+c1cc(c(cc1I)C(=O)O)C#N
+c1cc(c(cc1I)C(=O)O)N2C=NN=N2
+c1c(c(cc(c1I)F)Br)[N+](=O)[O-]
+c1c(c(cc(c1I)F)Cl)C(=O)O
+c1cc(c(c(c1)I)[N+](=O)[O-])N
+c1cc(c(c(c1)I)O)C(=O)O
+c1cc(ccc1N2CC(=O)N(CC2=O)N)I
+c1cc(ccc1N/N=C(/C#N)\C2=NN=C3N2CCCCC3)I
+c1cc(ccc1/N=N\C(C#N)C#N)I
+c1c(cc(c(c1[N+](=O)[O-])N)I)Cl
+c1c(cc(c(c1[N+](=O)[O-])O)I)C#N
+c1cc(ccc1OC2CC2)I
+c1cc(c(cc1OC(F)(F)F)N)I
+c1cc(ccc1S(=O)(=O)NN)I
+c1c(c(cnc1Cl)C(=O)O)I
+C1CCC(=NNC(=O)C2=C(C=NN2)I)C1
+c1c(cnc(c1C(=O)O)Br)I
+c1cc(nc(c1)I)SC(F)(F)F
+C1=C(C(=NN1CC(=O)O)C(=O)O)I
+C1=C(SC(=C1)I)C(=O)CC#N
+CC1(c2ccccc2[N@@]([C@@]13C=Cc4cc(ccc4O3)I)C)C
+Cc1cccc2c1N=C(S2)NS(=O)(=O)c3ccc(cc3)I
+Cc1c(cc(c(c1Br)I)Br)[N+](=O)[O-]
+Cc1ccc(cc1C)C(=O)Nc2ccc(c(c2)I)C
+Cc1ccc(cc1Cl)C(=O)Nc2c(cc(cn2)I)C
+Cc1c(cc(c(c1Cl)I)Cl)[N+](=O)[O-]
+Cc1c(cc(cc1I)Cl)/N=N\OC(=O)C
+Cc1ccc(c(c1)I)NC(=O)C(C)(C)C
+Cc1c(c(ccc1OC)I)C
+CC1=CC(=C(C(=O)O1)/C=N/c2ccc(cc2)I)O
+Cc1cc(cnc1NC(=O)c2ccc(cc2)F)I
+Cc1ccc(nc1)NC(=O)c2cccc(c2)I
+CC1CCC(=NNC(=O)c2ccccc2I)CC1
+Cc1c(cnc(c1Br)I)[N+](=O)[O-]
+Cc1cc(nc(n1)N/N=C/C2=CC=C(O2)I)C
+Cc1cc(nc(n1)N/N=C/C2=C(N=C3N2C=C(C=C3)I)C)C
+CC1=C(C=NN1CC(=O)C)I
+CC1=C(N2C=C(C=CC2=N1)I)/C=N/Nc3ccc4ccccc4c3
+CC1=NN(C=C1I)CC(=O)C
+CC(C)(C#N)C(=O)Nc1cc(ccc1Cl)I
+C=C(C(F)(F)F)I
+CC(C)N1C=C(C(=N1)C(=O)OC)I
+CCN1C=C(C(=N1)C(=O)OC)I
+CCOc1cccc(c1I)Br
+CC(=O)C1=NN(C=C1I)C
+CCOC(=O)c1cc(cc(c1C)I)Br
+CCOC(=O)C1=C(SC(=N1)N)I
+CCOC(=O)C1=NN(C=C1I)C
+CC(=O)N1CCCc2c1cc(cc2)I
+CC(=O)Oc1cccc(c1)I
+CN1C(=c2cccc(c2=N1)C(=O)OC)I
+CN1C=C(C(=N1)C(=O)N2CCCc3c2cccc3)I
+CN1C=C(C(=N1)C(=O)OC)I
+CN1C(=C(C(=N1)C(=O)OC)I)[N+](=O)[O-]
+CN1C=C(C(=O)N(C1=O)CC(=O)N2CC(=O)Nc3c2cccc3)I
+CN(c1ccccc1)C(=O)c2ccc(cc2)I
+CNc1c(nc2=NON=c2n1)Nc3ccc(cc3)I
+CN(C1=Nc2ccccc2S1)C(=O)c3ccc(cc3)I
+CN(C)C(=O)Cc1cccc(c1)I
+COc1ccc(c2c1NN=C2N)I
+COc1c(cc(cc1F)I)F
+COc1ccccc1I
+COc1ccc(cc1I)Cl
+COc1ccc(cc1I)C=O
+COc1cccc(c1I)F
+COc1cc(ccc1I)[N+](=O)[O-]
+COc1ccc(cc1I)[N+](=O)[O-]
+COc1cc(c(cc1I)O)F
+COc1cccc(c1[N+](=O)[O-])I
+COc1cc(cc(c1O)I)C#N
+COc1ccc(c(c1O)I)C=O
+COc1ccnc2c1cc(cc2)I
+COC(=O)c1cc(cc(c1O)I)C#N
+COC(=O)C1=C(SC(=N1)N)I
+COC(=O)[C@@H]1[C@H]2CC[C@H]([N@@H+]2CCCF)C[C@@H]1c3ccc(cc3)I