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opencc-by-4.0Nov 2024View details →

Data Set "Benchmarking of Vibrational Exciton Models Against Quantum-Chemical Localized-Mode Calculations"

This data set accompanies the publication "Benchmarking of Vibrational Exciton Models Against Quantum-Chemical Localized-Mode Calculations"  by Anna M. van Bodegraven, Kevin Focke, Mario Wolter, and Christoph R. Jacob  (TU Braunschweig, Germany)  It contains the following files: Directory '01_AIM':     - input (structure.pdb, topol.top and *_input.txt) and results (*.log and       Hamiltonian/AtomPos/Dipole/Parameters.txt) from frequency calculations       with the Amide-I-maps (AIM) program for six polypeptide test cases       (1gpB_310, ala_310, ala_hairpin, ala_helix, ala_strand, and trpzip),           each in vacuo or water with three different maps (Jansen, Skinner,        Tokmakoff) for 11 snapshots based on a MD run.     To rerun the calculations, you will have to change the paths in      the *_input.txt files (topfile, trjfile, sourcedir) accordingly      Directory '02_SNF':     - results (*.dat, *.out, coord and control) from frequency calculations        using Turbomole, SNF, and LocVib for six polypeptide test cases       (1gpB_310, ala_310, ala_hairpin, ala_helix, ala_strand, and trpzip)        each in vacuo or water for snapshots based on an MD run.        Directory '03_NMA':     - coordinates and results from pyADF for NMA molecules each alligned        with a peptide bond from the six polypeptide test cases       (1gpB_310, ala_310, ala_hairpin, ala_helix, ala_strand, and trpzip)        each in water for 11 snapshots based on a MD run and input        (*_input.txt) and results (*.log and Hamiltonian/AtomPos/Dipole/Parameters.txt)        from calculations with the Amide-I-maps (AIM) program        Directory '04_Handling_Data':     - contains all used notebooks to extract the data, plot the figures        and calculate the errors     - RMSD_Error_vacuo/water.ipynb is used to calculate the overall shifts        and generates a map-dependent mean value to shift the frequencies of AIM     - Frequencies.ipynb and Couplings.ipynb are used to plot the figures      - RMSD_values_vacuo/water.ipynb show the calculations for the statistical        analysis     To use the notebooks, start with the Dictionary_setup_for_data_for_paper.ipynb      to set up the main dictionary from the calculated data

opencc-by-4.0Nov 2024View details →

Data for: Alchemical free-energy calculations at quantum-chemical precision

In the last decade, machine-learned potentials (MLP) have demonstrated the capability to predict various QM properties learned from a set of reference QM calculations. Accordingly, hybrid QM/MM simulations can be accelerated by replacement of expensive QM calculations with efficient MLP energy predictions. At the same time, alchemical free energy perturbations (FEP) remain unachievable at the QM level of theory. In this work, we extend the capabilities of the Buffer Region Neural Network (BuRNN) QM/MM scheme towards FEP. BuRNN introduces a buffer region that experiences full electronic polarization by the QM region to minimize artifacts at the QM/MM interface. A MLP is used to predict the energies for the QM region and its interactions with the buffer region. Furthermore, BuRNN allows us to implement FEP directly into the MLP Hamiltonian. Here, we describe the alchemical change from methanol to methane in water at the MLP/MM level as a proof of concept.

opencc-by-4.0Sep 2022View details →

Data Set "Accurate quantum-chemical fragmentation calculations for ion–water clusters with the density-based many-body expansion"

This data set accompanies the publication "Accurate quantum-chemical fragmentation calculations for ion–water clusters with the density-based many-body expansion" It contains: - xyz files of all considered molecular structures. - PyADF input scripts for running the eb-MBE and db-MBE calculations. - raw results data from the eb-MBE and db-MBE calculations - Jupyter notebooks for generating the plots and tables

opencc-by-4.0Dec 2018View details →

Structural Dynamics of an Excited Donor-Acceptor Complex from Ultrafast Polarized Infrared Spectroscopy, Molecular Dynamics Simulations, and Quantum Chemical Calculations

The files contains all the data that are shown in the figures  of the article: Rumble, C.; Vauthey, E. Structural Dynamics of an Excited Donor-Acceptor Complex from Ultrafast Polarized Infrared Spectroscopy, Molecular Dynamics Simulations, and Quantum Chemical Calculations. Phys. Chem. Chem. Phys. 21 (2019).  10.1039/C9CP00795D

opencc-by-4.0Nov 2022View details →

Data Set "Quantum-chemical calculation of two-dimensional infrared spectra using localized-mode VSCF/VCI"

This data set accompanies the publication "Quantum-chemical calculation of two-dimensional infrared spectra using localized-mode VSCF/VCI" It contains: -  xyz files of all considered molecular structures. - Results data from the harmonic and anharmonic vibrational calculations. - Data and code for calculating 2D-IR spectra.

opencc-by-4.0Oct 2020View details →

Insights from quantum chemical calculations into inner and outer-sphere complexation of plutonium(IV) by monoamide and carbamide extractants - Dataset

Supplementary information for "Insights from quantum chemical calculations into inner and outer-sphere complexation of plutonium(IV) by monoamide and carbamide extractants" The attached 'Pu-inner-outer.zip' unpacks two directories that contains the optimized molecular structures in xyz format. - Inner-sphere/ for the inner-sphere complexes - Outer-sphere/ for the outer-sphere complexes in their geometries I and II

opencc-by-4.0Jun 2024View details →

Equilibrium chemical composition of impact-produced hot cloud during isentropic expansion. The initial temperature T0 is 4000 K, the initial pressure P0 is 5, 20, and 80 bar. Calculations are performed using the EQL program. Abundances of considered species are presented in molar fractions.The elemental composition of impact-produced cloud is taken as a mixture of CI chondrite, mare basalts, and ferroan anorthosite with a ratio of 1:25:25 by mass as in Berezhnoy (2013).

Considered species include ions, neutral gas-phase species, and condensates. Ions are written as ...(+) (for example, Al(+)). Condensates (solids and liquids) are written as ...(c) or ...(c;...). Examples of condensates are Al2O3(c) and Al2O3(c; gamma). For species marked in theirs names as (cr, l) in Gurvich et al. (1989) (for example, Al2O3(cr, l)) it is possible to determine a state of matter (liquid or solid). The content of studied species is 0 if the relative molar fraction is less than 1e-21.  The elemental composition of impact-produced cloud is taken as a mixture of CI chondrite, mare basalts, and ferroan anorthosite with a ratio of 1:25:25 by mass as in Berezhnoy (2013).   Calculations of the equilibrium chemical composition of impact-produced clouds were performed starting from an initial temperature of 4000 K at different initial pressures of 5, 20, and 80 bar, corresponding to entropies equal to 7.2, 5.56, and 4.25 kJ / (kg×K), respectively.  Berezhnoy, A.A., 2013. Chemistry of impact events on the Moon. Icarus 226, 205-211. Gurvich L.V., Veitz I.V. et al. Thermodynamic properties of individual substances. Fourth edition in 5 volumes. Hemisphere Pub Co. New York-London, 1989.

opennotspecifiedJul 2021View details →

Fig. 5. Linear correlation between the experimental and calculated 13C NMR chemical shifts for 1A and 1B in (±)-hyperzewalsins A D, four pairs of nor-monocyclic polyprenylated acylphloroglucinols with immunosuppressive activity from hypericum przewalskii maxim

Fig. 5. Linear correlation between the experimental and calculated 13C NMR chemical shifts for 1A and 1B.

Fig. 4 in Dihydro-furanones from Hyptis species: Chemical correlations and DFT-NMR/ECD calculations for stereochemical assignments

Fig. 4. The four most relevant global-minimum energy conformations of 1 modeled in CHCl3 solution accounting for the 78% of the total population.

Fig. 3. Chemical correlations between 5,6 in Dihydro-furanones from Hyptis species: Chemical correlations and DFT-NMR/ECD calculations for stereochemical assignments

Fig. 3. Chemical correlations between 5,6-dihydro-2H-pyran-2-ones and 2(5H)-furanones. A possible biogenetic correlation is indicated by a dotter arrow.

Fig. 1. 1H in Dihydro-furanones from Hyptis species: Chemical correlations and DFT-NMR/ECD calculations for stereochemical assignments

Fig. 1. 1H NMR spectral sections of peracetylated montecofuranolide (2). (A) Simulated spectrum using DFT 3J of peracetyl-5′-epi-synrotolide (5) in gas H,H phase with chemical shifts of the experimental spectrum of compound 2 and coupling constants of monticolide A (6) for J ′ ′ 3 -4 proS = 8.7 Hz, J ′ ′ 3 -4 proR = 4 Hz to simulate the multiplicity for H-4′. (B) Fully simulated spectrum obtained by iteration of chemical shifts, 3J, and linewidths of compound 2. (C) ExperiH,H mental spectrum in CDCl3 (400 MHz).

opencc-zeroDec 2017View details →

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Data from: Accurate geometries for "mountain pass" regions of the Ramachandran plot using quantum chemical calculations

Unusual local arrangements of protein in Ramachandran space is not well represented by standard geometry tools used in either protein structure refinement using simple harmonic geometry restraints or in protein simulations using molecular mechanics force fields. By contrast, quantum chemical computations using small poly-peptide molecular models can predict accurate geometries for any well-defined backbone Ramachandran orientation. For conformations along transition regions – ϕ from -60 to 60° – a very good agreement with representative high-resolution experimental X-ray (≤1.5 Å) protein structures is obtained for both backbone C^{-1}-N-C_{alpha} angle and the nonbonded O^{-1}…C distance, while "standard geometry" leads to the "clashing" of O…C atoms and Amber FF99SB predicts distances too large by about 0.15 Å. These results confirm that quantum chemistry computations add valuable support for detailed analysis of local structural arrangements in proteins, providing improved or missing data for less understood high-energy or unusual regions.

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Fig. 4. Experimental and calculated ECD spectra for 1 and 10 in Chemical constituents of Entandrophragma angolense and their anti-inflammatory activity

Fig. 4. Experimental and calculated ECD spectra for 1 and 10.

opennotspecifiedSep 2022View details →

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Fig. 2 in Dihydro-furanones from Hyptis species: Chemical correlations and DFT-NMR/ECD calculations for stereochemical assignments

Fig. 2. ECD spectra of monticofuranolide (1 in red) and pectinolide O (11 in blue).