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 a specific file!
• 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

If you want to download just one file, e.g.:

https://github.com/elmjonas/ACDB/blob/master/Articles/clusteromics_V_sa_msa_nta_fa_multibase/database1DLPNO_DFT.pkl

then use wget (note: svn is not supported anymore) but you must modify "github" -> "raw.githubusercontent" and remove "blob/"

wget https://raw.githubusercontent.com/elmjonas/ACDB/master/Articles/clusteromics_V_sa_msa_nta_fa_multibase/database1DLPNO_DFT.pkl

Subfolders

Articles

• This folder contains over 37 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 1116728 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 28270 entries
  • contains 108 different cluster types

• DLPNO-CCSD-T_aug-cc-pVTZ_NormalPNO/

  • contains 5096 entries
  • contains 1509 different cluster types

• DLPNO-CCSD-T_aug-cc-pVTZ_TightPNO/

  • contains 1073 entries
  • contains 292 different cluster types

• G09-wB97X-D_6-31++Gxx/

  • contains 68695 entries
  • contains 1045 different cluster types

• G16-wB97X-D_6-31++Gxx/

  • contains 40135 entries
  • contains 1210 different cluster types

• GFN1-xTB/

  • contains 325137 entries
  • contains 382 different cluster types

• ORCA-wB97X-D_6-311++Gxx/

  • contains 11350 entries
  • contains 50 different cluster types

• r2SCAN-3c/

  • contains 276538 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 2233 entries
  • contains 34 different cluster types

• B97-3c__GFB1-xTB/

  • contains 17079 entries
  • contains 91 different cluster types

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

  • contains 1957 entries
  • contains 782 different cluster types

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

  • contains 3309 entries
  • contains 988 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 835 entries
  • contains 228 different cluster types

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

  • contains 44482 entries
  • contains 882 different cluster types

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

  • contains 60255 entries
  • contains 1282 different cluster types

• GFN1-xTB__GFB1-xTB/

  • contains 65001 entries
  • contains 91 different cluster types

• r2SCAN-3c__GFB1-xTB/

  • contains 24874 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 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)

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. (+)

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
• b=bisulphate (-)
• pha=phosforic acid
• msa=methanesulfonic acid
• mb=methanebisulfate (-)
• hcl=hydrogenchloride
• cl=chloride (-)
• cla=chloric acid
• pcla=perchloric acid
• nta=nitric acid

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=folrmaldehyde
• ml=methanol
• pxml=methanolperoxide/methyl hydroperoxide
• mf=methyl formate
• etox=ethylene oxide
• acal=acetaldehyde
• acan=acetic anhydride
• dme=dimethylether
• acon=acetone

Organic acids:

• aca=acetic acid
• acc=acetic an. (-)
• bza=benzoic acid
• bzc=benzoic an. (-)
• ca=caric acid
• cc=caric an. (-)
• fa=formic acid
• fc=formic an. (-)
• hgta=3-hydroxy-glutaric 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
• paca=phenylacetic acid
• pc=pinic an. (-)
• pta=phtalic acid
• pua=pyruvic acid
• 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. (-)