ACDB2.0

The purpose of this database is to compile existing atmospheric cluster structures and thermochemical data under one common methodology.

Please cite:

• J. Elm, ACS Omega, 2019, 4, 10965-10974
• J. Kubecka, ACS Omega 2023, 8, 45115-45128
• and the associated original literature if any of the structures or thermochemical properties from the database are used in your published research.

README content:

• How to download only specific subfolder!
• Subfolders (i.e. methods that were used to obtain the clusters)
• Type of files (i.e. what is saved in each file)
• Using the pickles files (i.e. how to utilize JKQC or manipulate with databases)

DOWNLOADING FROM ACDB

It does not make sense for you to download whole ACDB. If you can use the printed properties, then just copy those values.

If you want to download e.g. pickle (pkl), GitHub does allow to use svn (svn checkout) anymore. But you can still use wget. For instance, find the pickle file you want, click on it, and with right click on theRaw button copoy the link to the address. You can then:

wget https://github.com/elmjonas/ACDB/raw/refs/heads/master/Articles/besel19_sa_am_chrg/database1DFT.pkl

Another option is to just download the pickle file to your computer with by clicking on the Download raw file button.

USING THE PICKLED FILES

In order to use any database, you can:

• use JKQC (see https://jkcs.readthedocs.io/en/latest/) or see below
• use your own python script (see below)

Subfolders

Articles

• This folder contains over 46 articles and molecular clusters/data provided from them.
• The newest folders contain metadata described in greater detail.
• The old articles sometimes lack proper description.

Full_database

• Full database contains 1269055 entries.

SP_energies

• This folder contains SP energies calculated level of theory specified by each subfolder

• See the levels.txt file for more details on program version and method input.

• B97-3c/

  • contains 79738 entries
  • contains 227 different cluster types

• DLPNO-CCSD-T_aug-cc-pVTZ_NormalPNO/

  • contains 6742 entries
  • contains 1833 different cluster types

• DLPNO-CCSD-T_aug-cc-pVTZ_TightPNO/

  • contains 1210 entries
  • contains 383 different cluster types

• G09-wB97X-D_6-31++Gxx/

  • contains 68708 entries
  • contains 1045 different cluster types

• G16-wB97X-D_6-31++Gxx/

  • contains 107389 entries
  • contains 1806 different cluster types

• GFN1-xTB/

  • contains 347819 entries
  • contains 468 different cluster types

• ORCA-wB97X-D_6-311++Gxx/

  • contains 11804 entries
  • contains 102 different cluster types

• r2SCAN-3c/

  • contains 276593 entries
  • contains 382 different cluster types

Equilibrium_TMD

• This folder contains free energy properties for SP_electronic_energy//geom._optim.+TMD

• Some monomers are missing, hence not all binding properties are provided

• For all wB97X-D TMD, we use anharmonicity (-v 0.996) and low-vibrational (-fc 100) treatement

• B97-3c__B97-3c/

  • contains 21350 entries
  • contains 155 different cluster types

• B97-3c__GFB1-xTB/

  • contains 17082 entries
  • contains 91 different cluster types

• DLPNO-CCSD-T_aug-cc-pVTZ_NormalPNO__G09-wB97X-D_6-31++Gxx/

  • contains 1957 entries
  • contains 811 different cluster types

• DLPNO-CCSD-T_aug-cc-pVTZ_NormalPNO__G16-wB97X-D_6-31++Gxx/

  • contains 3316 entries
  • contains 993 different cluster types

• DLPNO-CCSD-T_aug-cc-pVTZ_TightPNO__G09-wB97X-D_6-31++Gxx/

  • contains 118 entries
  • contains 107 different cluster types

• DLPNO-CCSD-T_aug-cc-pVTZ_TightPNO__G16-wB97X-D_6-31++Gxx/

  • contains 972 entries
  • contains 320 different cluster types

• G09-wB97X-D_6-31++Gxx__G09-wB97X-D_6-31++Gxx/

  • contains 44490 entries
  • contains 912 different cluster types

• G16-wB97X-D_6-31++Gxx__G16-wB97X-D_6-31++Gxx/

  • contains 74488 entries
  • contains 1662 different cluster types

• GFN1-xTB__GFB1-xTB/

  • contains 65014 entries
  • contains 91 different cluster types

• r2SCAN-3c__GFB1-xTB/

  • contains 24878 entries
  • contains 91 different cluster types

FORCES

TO BE DONE

Files

• databases:
  • database.pkl
    • all data collected from the given folder
    • database is often split into database_s.pkl files with maximum 10000 entries per file
  • database1DFT.pkl
    • 1 lowest (DFT[geometry+TMD]) Gibbs free energy structure per cluster from database.pkl
  • database1DLPNO.pkl
    • 1 lowest (DLPNO[SP corr]//DFT[geometry+TMD]) Gibbs free energy structure from database.pkl
• structures:
  • structures1DFT.xyzs and structures1DLPNO.xyzs
    • structures from database1DFT.pkl and structures1DLPNO.pkl, respectively
• properties:
  • properties1DFT.txt and properties1DLPNO.txt
    • properties from database1DFT.pkl and structures1DLPNO.pkl, respectively
    • QHA and anharmonicity corrections applied
    • these are in the following format: structure_name | dG(298.15K) | dH(298.15K) | dS(298.15K)
• binding properties:
  • located only in the most outside folder
  • binding_properties3DFT.txt and binding_properties1DLPNO.txt
    • 1 lowest (DFT or DLPNO//DFT) Gibbs free energies of formation from database3DFT.pkl and database1DLPNO.pkl, respectively

USING JKQC

First, donwload JKCS:

cd <App_dir>

git clone https://github.com/kubeckaj/JKCS2.1.git

1. Then, setup JKCS and python environment for JKQC with correct python (see the online manual):

 sh setup.sh -help

 sh setup.sh -python python3.9 -module "module load python3.9" -r

3. It will add one line to your ~/.bashrc file, therefore source it

source ~/.bashrc

4. Now you should be able to use JKQC, e.g.:

JKQC -help

JKQC DATABASE.PKL -b -el

JKQC DATABASE.PKL -xyz

(see other functionalities: https://jkcs.readthedocs.io/en/latest/)

USING YOUR OWN PYTHON SCRIPT

Theoretically, you can use only your own python but I really recommend to setup your python environment via JKCS (step 1-3 above). Then run:

JKpython

After activating the correct python environment, use python to analyse/use the data:

$USER/: python

import pandas as pd

clusters_dataframe = pd.read_pickle("DATABASE.PKL")

STUCTURES NAMES

Water:

• w=water

Positive charges:

• 1p=proton (+)
• 1am1p=ammonium cat (+)
• 1dma1p=dimethylammonium cat. (+)
• 1gly1p=glycinium cat. (+)
• 1gd1p=guanidium cat. (+)
• na=sodium cat. (+)

Bases:

• am=ammonia
• bda=butane-1,4-diamine
• buta=butamine
• dbma=dibuthylmethylamine
• dea=diethylmine
• dma=dimethylamine
• dmea=dimethylethylamine
• dpenta=dipentamine
• dpropa=dipropamine
• eda=ethylendiamine
• gd=guanidine
• dhexa=dihexamine
• ibuta=isobutylamine
• ipropa=iso-propylamine
• ipropea=iso-propylethylamine
• ma=methylamine
• mda=methylethylendiamine
• mea=monoethylamine
• nona=nonamine
• pda=propan-1,3-diamine
• propa=propamine
• put=putrescine
• pz=piperazine
• sbuta=sec-butamine
• tbuta=tributylamine
• tibuta=triisobutylamine
• tea=triethylamine
• tma=trimethylamine
• tpropa=tripropamine
• diAAmda=N,N-dimethylethylendiamine
• diABmda=N,N-dimethylethylendiamine
• triAABmda=trimethylethylendiamine
• teAABBmda=tetramethylethylendiamine
• IIebuta=2-ethylbutylamine

Anorganic acids:

• sa=sulfuric acid
• cba=carboxylic acid
• cbt=carboxylate (-)
• cna=cabonic acid
• cnt=carbonate (-)
• b=bisulphate (-)
• brd=bromide (-)
• id=iodide (-)
• pha=phosforic acid
• msa=methanesulfonic acid
• mb=methanebisulfate (-)
• hcl=hydrogenchloride
• cl=chloride (-)
• cla=chloric acid
• pcla=perchloric acid
• nta=nitric acid
• nt=nitrate (-)

Iodine-containing:

• it=iodine tatraoxide
• ip=iodine pentoxide
• ica=iodic acid
• isa=iodous acid

Organics:

• gly=glycine
• glyt=glycinate an. (-)
• homF=C6H8O7
• homJ=C10H16O8
• fd=formaldehyde
• ml=methanol
• pxml=methanolperoxide/methyl hydroperoxide
• mf=methyl formate
• etox=ethylene oxide
• acal=acetaldehyde
• acan=acetic anhydride
• dme=dimethylether
• acon=acetone

Organic acids:

• ABisopooh = 1,2-isoprene hydroxy hydroperoxide
• aca=acetic acid
• acc=acetic an. (-)
• bza=benzoic acid
• bzc=benzoic an. (-)
• ca=caric acid
• cc=caric an. (-)
• dhppa=2,2-dihydroxypropanoic acid
• fa=formic acid
• fc=formic an. (-)
• hgta=3-hydroxy-glutaric acid
• hptmf=hydroperoxymethyl thioformate
• lca=lactic acid
• maa=maleic acid
• mbtca=3-methyl-1,2,3-butanetricarboxylic acid
• mbtcc=3-methyl-1,2,3-butanetricarboxylic an. (-)
• mca=malic acid
• moa=malonic acid
• oa=oxalic acid
• oc=oxalic an. (-)
• pa=pinic acid
• poa=pinonic acid
• paca=phenylacetic acid
• pc=pinic an. (-)
• ppa=propionic acid
• pta=phtalic acid
• pua=pyruvic acid
• pue=pyruvate an. (-)
• pxfa=peroxyformic acid
• pxaca=peroxyacetic acid
• sua=succinic acid
• suc=succinic an. (-)
• tba=terebic acid
• tbc=terebic an. (-)
• tpa=terpenylic acid
• tpc=terpenylic an. (-)
• tta=tartaric acid
• ttc=tartaric an. (-)