Merge pull request #50 from janash/feature/about

adds library details page

frontend/src/App.jsx

@@ -10,11 +10,13 @@ import Home from './pages/Home';
 
 const Search = lazy(() => import('./pages/SearchHook'));
 const NeighborSearch = lazy(() => import('./pages/Neighbors'));
+const About = lazy(() => import('./pages/About'))
 
 const pages = {
   'Home': <Home />, 
   'Search': <Search />,
   'Neighbors': <NeighborSearch/>, 
+  'About': <About/>,
 };
 
 function Content() {

frontend/src/components/DFTTable.jsx

@@ -0,0 +1,60 @@
+import {
+    Container, 
+    Table,
+    TableHead,
+    TableContainer,
+    TableRow,
+    TableBody,
+    TableCell,
+    Paper,
+} from '@mui/material';
+
+function createData(
+    name,
+    description,
+    forXTB,
+    forDFT
+) {
+    return { name, description, forXTB, forDFT }
+};
+
+const rows = [
+    createData("boltz", "Boltzmann-weighted average of all conformers' properties (T=298.15 K", true, true),
+    createData("max", "highest value of a property of any conformer", true, true),
+    createData("min", "lowest value of a property of any conformer", true, true),
+    createData("std", "standard deviation of the value across all conformers", true, false),
+    createData("vburminconf", "property value of the conformer with the smallest buried volume", false, true),
+    createData("delta", "difference between the maximum and minimum property values", false, true),
+];
+
+function DataTable() {
+    return (
+        <Container sx={{marginTop: "20px", marginBottom: "20px"}}>
+            <TableContainer component={Paper}>
+                <Table>
+                    <TableHead>
+                        <TableRow>
+                            <TableCell>Condensed Properties</TableCell>
+                            <TableCell>Description</TableCell>
+                            <TableCell>For XTB</TableCell>
+                            <TableCell>For DFT</TableCell>
+                        </TableRow>
+                    </TableHead>
+                    <TableBody>
+                        {rows.map((row) => (
+                            <TableRow key={row.name}>
+                                <TableCell>{row.name}</TableCell>
+                                <TableCell>{row.description}</TableCell>
+                                <TableCell>{row.forXTB ? '✔️' : ''}</TableCell>
+                                <TableCell>{row.forDFT ? '✔️' : ''}</TableCell>
+                            </TableRow>
+                        ))}
+                    </TableBody>
+                </Table>
+            </TableContainer>
+        </Container>
+    );
+};
+
+export default DataTable;
+

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 (<>
-        <Container maxWidth="lg">
-            <h2>About</h2>
-
-            <Typography variant="subtitle1" sx={{mb:3}}>
-                Kraken stands for ...<b>K</b>olossal vi<b>R</b>tual d<b>A</b>tabase
-                for mole<b>K</b>ular d<b>E</b>scriptors of orga<b>N</b>ophosphorus
-                ligands.
-            </Typography>
-
-            <Typography variant="body1" align="justify" paragraph={true}> 
-                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).
-            </Typography>
-
-            <Typography variant="body1" align="justify" paragraph={true}>
-                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.
-            </Typography>
+    return  (
+    <Container maxWidth="xl" sx={{marginBottom: "30px"}}>
+
+        <Typography variant="h2" component="h1" textAlign="center">Library Details</Typography>
+
+        <Typography variant="h5" component="h2"  sx={{fontStyle:"oblique",  marginBottom:"15px"}} >Conformational Searching</Typography>
+        <Typography variant="body1" paragraph>
+        Initial ligand geometries were generated using SMILES strings and converted to free ligands and [LNi(CO)<sub>3</sub>] 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.
+        </Typography>
+
+        <Typography variant="body1" paragraph></Typography>
 
+        <Typography variant="body1" paragraph>
+            Molecular descriptors at the xTB level for the full conformational ensembles from CREST were collected using MORFEUS.
+        </Typography>
+
+        <Typography variant="h5" component="h2"  sx={{fontStyle:"oblique", marginTop:"30px", marginBottom:"15px"}}>Selection of conformers for DFT computations</Typography>
+        <Typography variant="body1" paragraph>
+            Conformers from both sets (free ligand and Ni complex) were selected based on the following two criteria:
+
+            <List sx = {{listStyleType: 'disc', pl: 2,'& .MuiListItem-root': {display: 'list-item',},}}>
 
-            <Typography variant="body1" align="justify" paragraph={true}>
-                This project is now maintained by The Molecular Sciences Software Institute.
-            </Typography>
-        </Container>
-    </>) 
+                <ListItem>
+                    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.
+                </ListItem>
+
+                <ListItem>
+                Up to 20 conformers within 3 kcal/mol relative energy in the <i>free ligand conformer set.</i> 
+                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.
+                </ListItem>
+            </List>
+        </Typography>
+
+        <Typography variant="h5" component="h2"  sx={{fontStyle:"oblique", marginTop:"30px", marginBottom:"15px"}}>DFT computations</Typography>
+
+        <Typography variant="body1" paragraph>
+                Prior to DFT computations, the [Ni(CO)<sub>3</sub>]-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.
+        </Typography>
+
+        <Typography variant="body1" paragraph>
+            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.
+        </Typography>
+
+
+        <DataTable></DataTable>
+
+        <Typography variant="body1" paragraph>
+            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 <Link target="_blank" href="https://pubs.acs.org/doi/10.1021/jacs.1c09718">original publication supporting information.</Link>
+        </Typography>
+
+        <Typography variant="body1" paragraph>
+            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
+        </Typography>
+
+    </Container>
+    )
+
 }
 
-export default About;
+export default About;

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() {
           <Grid item>
             <IconLink IconElement={BubbleChartIcon} text="Neighbor Search" link='/neighbors'></IconLink>
           </Grid>
+          <Grid item>
+            <IconLink IconElement={InfoIcon} text="Library Details" link="/about"></IconLink>
+          </Grid>
           {/* Hide until we're ready to add
             <Grid item>
               <IconLink IconElement={DownloadIcon} text="Download" link="/download"></IconLink>