Guanosine Dianions Hydrated by One to Four Water Molecules - Computational Data
Creators: name: Makurat Samanta
name: Yuan Qinqin
name: Czub Jacek
name: Chomicz-Mańka Lidia
name: Cao Wenjin
name: Wang Xue-Bin
name: Rak Janusz
Publisher: name: Zenodo
Year: 2022
Subjects: Molecular Dynamics, Gromacs, Quantum Chemistry, Gaussian, input/output files, guanosine dianions, water clusters

description: The upload contains Molecular Dynamics input and output files, as well as the Gaussian output files containing CAM-B3LYP optimized dianions’ and their corresponding anion radicals data for: "Guanosine Dianions Hydrated by One to Four Water Molecules" by S. Makurat, Q. Yuan, J. Czub, L. Chomicz-Mańka, W. Cao, X.-B. Wang, J. Rak, Janusz, published in Journal of Physical Chemistry Letters, DOI: https://doi.org/10.1021/acs.jpclett.2c00512.
ABSTRACT:
Intermolecular interactions as those present in molecule…water complexes may profoundly influence the physico-chemical properties of molecules. Here, we carried out an experimentally-computational study on the doubly-deprotonated guanosine monophosphate…water clusters, [dGMP-2H]2−•nH2O (n=1–4), using a combination of negative anion photoelectron spectroscopy (NIPES) with molecular dynamics (MD) and quantum chemical (QM) calculations. Successive addition of water molecules to [dGMP-2H]2− increases the experimental adiabatic detachment (ADE) and vertical detachment energy (VDE) by 0.5 to 0.1 eV, depending on the cluster size. In order to choose the representative conformations, we combined MD simulations with a clustering procedure to identify low energy geometries for which ADEs and VDEs were computed at the CAM-B3LYP/6-31++G(d,p) level. Our results demonstrate that the assumed approach lead to the sound geometries and energetics of the studied micro-solvates since the calculated ADEs and VDEs are in pretty good agreement with the experimental characteristics. The evolution of hydrogen bonding with cluster size indicates possibility of the occurrence of proton transfer for clusters comprising a larger number of water molecules.
description: The files are organized in .zip archives as follows:
 
1. For the Molecular Dynamics/Gromacs

1.1. SOLVATED_FILES.zip contains starting structures (solvatedN-boxR.gro) and topology files (solvatedN.top) for the systems containing N=1-4 waters in 3 replicas (R=1-3), along with .mdp files used for minimization (em.mdp) and nvt runs (nvt-TEMP.mdp, where TEMP=20, 50, 100, 200 and 300K for which simulations were run).

1.2. SOLVATEDX.zip (X=1-4, for number of waters) contains, in seperate folder for each replica, respective simulation output files, including em.* and nvtTEMP* files (where TEMP=20, 50, 100, 200 and 300K for which simulations were run).

1.3. CLUSTERS.zip, containing folders N-TEMP (N=1-4 waters, TEMP=200, 300 K, since only these simulations were clustered, for all replicas in given temperature joined together) with the clustering results data.

2. For Quantum Chemistry/Gaussian each *.zip file contains optimized (frequencies analysis included) Gaussian output files for double deprotonated guanosine dianions and their corresponding anion radicals solvated with n=1 to 4 water molecules.

2.1. one-water-dianions.zip contains output files for guanosine dianions solvated with 1 water molecule. Ten structures prepared manually are named da-manual-x.log (x=1 to 10); models based on 200K MD simulations are named da-one-200-mx.log (x=1 to 6); models based on 300K MD simulations are named da-one-300-mx.log (x=1 to 29)

2.2. one-water-anionradicals.zip contains guanosine anion radicals solvated with 1 water molecule, based on corresponding dianions. Structures prepared manually are named ar-manual-x.log (x=1 to 10); models based on 200K MD simulations are named ar-one-200-mx.log (x=1 to 6); models based on 300K MD simulations are named ar-one-300-mx.log (x=1 to 29)

2.3. two-waters-dianions.zip contains guanosine dianions solvated with 2 water molecules. Models based on 200K MD simulations are named da-two-200-mx.log (x=1 to 7); models based on 300K MD simulations are named da-two-300-mx.log (x=1 to 29)

2.4. one-waters-anionradicals.zip contains anion radicals solvated with 2 water molecules, based on corresponding dianions. Models based on 200K MD simulations are named ar-two-200-mx.log (x=1 to 7); models based on 300K MD simulations are named ar-two-300-mx.log (x=1 to 29)

2.5. three-waters-dianions.zip contains guanosine dianions solvated with 3 water molecules. Models based on 200K MD simulations are named da-three-200-mx.log (x=1 to 6); models based on 300K MD simulations are named da-three-300-mx.log (x=1 to 25)

2.6. three-waters-anionradicals.zip contains anion radicals solvated with 3 water molecules, based on corresponding dianions. Models based on 200K MD simulations are named ar-three-200-mx.log (x=1 to 6); models based on 300K MD simulations are named ar-three-300-mx.log (x=1 to 25)

2.7. four-waters-dianions.zip contains guanosine dianions solvated with 4 water molecules. Models based on 200K MD simulations are named da-four-200-mx.log (x=1 to 10); models based on 300K MD simulations are named da-four-300-mx.log (x=1 to 33)

2.8. four-waters-anionradicals.zip contains anion radicals solvated with 4 water molecules, based on corresponding dianions. Models based on 200K MD simulations are named ar-four-200-mx.log (x=1 to 10); models based on 300K MD simulations are named ar-four-300-mx.log (x=1 to 33)