Dataset title: 
Data for "Electric Fields Can Drive Prebiotic Reactivity on Hydrogen Cyanide Nanocrystals"

Creators:
Marco Cappelletti and Martin Rahm

Responsible organization:
Chalmers University of Technology, Gothenburg, Sweden

See the Researchdata.se catalogue entry for this dataset for compete metadata, including the dataset description, recommended citation, contact information and information about how to obtain the dataset.

Description: quantum chemical calculations on HCN crystal slabs and linear HCN chains.


Content
-------------------------
README.txt
linear_chains/
    electric_fields/
    HCN-HNC_isomerization/
	deprotonation/
            optscan-n-[n]/
	isolated-species/
	neutral-chain/
	protonation/
            optscan-n-[n]/
bulk_and_slabs/
    HCN-bulk/
    HCN-slabs/
	inputfiles/
	s-[hkl]/
	    kpointsfile/
	    n-[n]/
        electric-field_s-001_n-4
-------------------------


Folder and file descriptions
----------------------------

- linear_chains: it contains Gaussian 16 and ORCA 6.0.1 calculations on HCN linear chains.

- bulk_and_slabs: it contains VASP 6.4.1 periodic calculations on bulk and slabs of the HCN crystal.


linear_chains/ folder
---------------------

electric_fields/
-----
Gaussian 16 calculations on linear HCN chains of various length. 

File nomenclature:
	HCN-chain-n[n]_Vac_Opt_B3LYP-D3BJ.[file ext]

    n - 	    number of HCN units in the chain
    Vac -	    calculation in vacuum
    Opt -	    optimization
    B3LYP-D3BJ -    B3LYP-D3(BJ)/6-31+G(d,p)
    file ext -	    com for input files, log for output files, fchk for formatted checkpoint files.


Pot_Ez_from_fchk.sh: script that calculates the electric field at 2.1 Angstrom from the H-end of the chain.
    Usage: ./Pot_Ez_from_fchk.sh [fchk file]


HCN-HNC_isomerization/
----

deprotonation/: calculations on the deprotonated chains
isolated-species/: calculations on isolated species (HCN, HNC, CN-, HCNH+)
neutral-chain/: calculations on the neutral chains
protonation/: calculations on the protonated chains

optscan-n-[n]: relaxed scan calculations of the proton transfer with a linear chain of [n] HCN units


File nomenclature:
	[system]_Vac_[type of job]_[method].[file ext]

system -	name specific for the system. Examples:
		HCNchain-n[n]: is a neutral HCN linear chain that is n HCN unit long.
		HCNchain-n19-HNC-n1: is a neutral chain composed of 19 units of HCN and one HNC at the N-end of the chain.
		HNC-n1-HCNchain-n19: is a neutral chain composed of 19 units of HCN and one HNC at the H-end of the chain.
		HCNchain-n20-HCNH-end: is a positively charged chain composed of 20 HCN units that is protonated at the N-end of the chain.
		HCNchain-n20-HCNH-in: same as above, except a proton that move and formed an HCNH+ inside the chain, and a terminal HNC.
		HCNchain-n20-CN-TS: the transition state between HCNchain-n20-CN-end and HCNchain-n20-CN-in
type of job -	Opt (optimization), SP (single point on the B3LYP-D3(BJ)/6-31+G(d,p) optimization in vacuum), OptScan (relaxed scan)
method - 	B3LYP-D3BJ for B3LYP-D3(BJ)/6-31+G(d,p)
		DLPNO-CCSDT for DLPNO-CCSD(T)/aug-cc-pVTZ
file ext -	com/inp for input files, log/out for output files, xyz for (optimized) coordinate files


for the relaxed scan (optscan-n-[n] folders):
        step-[n].inp	- ORCA input file for DLPNO-CCSD(T)/aug-cc-pVTZ calculation on step number [n] of the relaxed scan
        step-[n].out	- output file


bulk_and_slabs folder
------------------

HCN_bulk/: calculation (optimization) on bulk HCN
HCN_slabs/: calculations on slab models. 

    s-[hkl]/: calculation on each (h,k,l) plane considered.
        Inside each s-[hkl] folder, are n-[n] folders that contain the calculations on a slab that is n unit cell thick.
    
    electric-field_s-001_n-4/: calculation to extract the LOCPOT for the (0,0,1) slab 4 unit cell thick.
        LOCPOT is not included because it weights 20 GB (we pushed the accuracy to the limit). 
        You may want to decrease NGX, NGY, NGZ, NGFX, NGFY, and NGFZ.


File nomenclature:
    As VASP default: INCAR, POSCAR, KPOINTS, POTCAR, CONTCAR, OUTCAR, vasprun.xml. Except:

        OUTCAR_ISMEAR0: output of a calculation with ISMEAR = 0
        OUTCAR_ISMEAR-5: output of a calculation with ISMEAR = -5

	ISMEAR = 0 was used to reach convergence with respect to SIGMA. ISMEAR = -5 was used to extract the energies.

