+
+
+ );
+};
+
+export default DataTable;
+
diff --git a/frontend/src/pages/About.jsx b/frontend/src/pages/About.jsx
index 6b86077..9247321 100644
--- a/frontend/src/pages/About.jsx
+++ b/frontend/src/pages/About.jsx
@@ -1,42 +1,83 @@
-import Typography from '@mui/material/Typography';
-import Container from '@mui/material/Container';
+import {
+ Container,
+ Typography,
+ List,
+ ListItem,
+ Link
+} from '@mui/material';
+
+import DataTable from '../components/DFTTable';
function About() {
- return (<>
-
-
About
-
-
- Kraken stands for ...Kolossal viRtual dAtabase
- for moleKular dEscriptors of orgaNophosphorus
- ligands.
-
-
-
- With descriptors for 330949 monodentate organophosphorus(III)
- ligands at two levels of theory as well as property estimation
- powered by machine learning, we hope experimentalists,
- theoreticians, and data scientists will find utility in this library
- when designing new ligands for catalysis. This descriptor set
- accounts for conformational flexibility and was created by the authors of "Mapping the Property
- Space of Monodentate Organophosphorus Ligands for Catalysis",
- preprint on ChemRxiv (doi: 10.26434/chemrxiv.12996665).
-
-
-
- This project was originally created as a collaboration between University of Toronto,
- University of Utah, Technische Universität Berlin, Karlsruhe
- Institute of Technology, Vector Institute for Artificial
- Intelligence, Center for Computer Assisted Synthesis, IBM Research,
- and AstraZeneca.
-
+ return (
+
+
+ Library Details
+
+ Conformational Searching
+
+ Initial ligand geometries were generated using SMILES strings and converted to free ligands and [LNi(CO)3] complexes using RDKit, OpenBabel or Molconvert.
+ These guess geometries were optimized at the GFN2-xTB level of theory (xTB v6.2.2).
+ Optimized geometries were subjected to a conformational search using CREST (v2.8) at the GFN2-xTB level with toluene solvation (GBSA model).
+ For ligands containing ferrocene, conformational searches were performed at the GFN-FF level to avoid structural changes.
+ Molecular descriptors at the xTB level for the full conformational ensembles from CREST were collected using MORFEUS.
+
+
+
+
+ Molecular descriptors at the xTB level for the full conformational ensembles from CREST were collected using MORFEUS.
+
+
+ Selection of conformers for DFT computations
+
+ Conformers from both sets (free ligand and Ni complex) were selected based on the following two criteria:
+
+
-
- This project is now maintained by The Molecular Sciences Software Institute.
-
-
- )
+
+ Conformers that minimize or maximize any of the following xTB-level steric properties in any of the two conformer sets:
+ B1, B5, lval, far_vbur, far_vtot, max_delta_qvbur, max_delta_qvtot, near_vbur, near_vtot, ovbur_max, ovbur_min, ovtot_max,
+ ovtot_min, pyr_val, qvbur_max, qvbur_min, qvtot_max, qvtot_min, vbur.
+
+
+
+ Up to 20 conformers within 3 kcal/mol relative energy in the free ligand conformer set.
+ If more than 20 conformers are in that range, the selection was made by RMSD pruning (using PyDP4).
+ This enables structurally diverse selection of conformers in the relevant energy window.
+
+
+
+
+ DFT computations
+
+
+ Prior to DFT computations, the [Ni(CO)3]-fragment was removed from the Ni complex conformer set to obtain free-ligand initial geometries.
+ All DFT optimizations (Gaussian 16, rev C.01) were performed at the PBE-D3(BJ)/6-31+G(d,p) level of theory.
+ The corresponding geometries were used for a series of single-point energy calculations at the PBE0-D3(BJ)/def2-TZVP and PBE0-D3(BJ)/def2-TZVP/SMD(CHCl3) levels of theory.
+ Additional single-points were also run for the radical cations and radical anions from the optimized geometry of the neutral free ligand.
+
+
+
+ From the DFT calculations, steric, electronic, or full molecule/interaction-type descriptors were collected for each conformer.
+ The range of properties across the conformers of a single ligand was treated by using up to five condensed measures for each of the properties.
+
+
+
+
+
+
+ An extended explanation of the computational workflow used to build the monophosphine library, as well as details on the descriptors collected
+ (xTB- and DFT-level) can be found in the original publication supporting information.
+
+
+
+ Gensch, T.; dos Passos Gomes, G.; Friederich, P.; Peters, E.; Gaudin, T.; Pollice, R.; Jorner, K.; Nigam, A.; Lindner-D’Addario, M.; Sigman, M. S.; Aspuru-Guzik, A. A Comprehensive Discovery Platform for Organophosphorus Ligands for Catalysis. J. Am. Chem. Soc. 2022, 144, 3, 1205–1217. DOI: 10.1021/jacs.1c09718
+
+
+
+ )
+
}
-export default About;
+export default About;
\ No newline at end of file
diff --git a/frontend/src/pages/Home.jsx b/frontend/src/pages/Home.jsx
index 7f731d2..c037b43 100644
--- a/frontend/src/pages/Home.jsx
+++ b/frontend/src/pages/Home.jsx
@@ -10,6 +10,7 @@ import SearchIcon from '@mui/icons-material/Search';
import BubbleChartIcon from '@mui/icons-material/BubbleChart';
//import DownloadIcon from '@mui/icons-material/Download';
import AutoStoriesIcon from '@mui/icons-material/AutoStories';
+import InfoIcon from '@mui/icons-material/Info';
import StatCard from '../components/SummaryCard';
import IconLink from '../components/IconLink';
@@ -145,6 +146,9 @@ function Home() {
+
+
+
{/* Hide until we're ready to add