1. ABOUT THE DATASET -------------------- Title: Diffraction measurements and modelling underlying the text Trimethylamine-N-oxide depletes urea in a peptide solvation shell Creator(s): Mazin Nasralla Organisation: University of Leeds Rights-holder: Copyright 2024 University of Leeds Publication Year: 2024 Description: A data supplement to the article, 'Trimethylamine-N-oxide depletes urea in a peptide solvation shell', published in PNAS in 2024. It includes differential neutron scattering cross sections measurements, taken over the period 4-7 March 2022 at the ISIS Neutron and Muon Source, using the NIMROD diffractometer, with isotopically substituted samples of GPG tripeptide in aqueous solutions of urea, TMAO, and urea-TMAO. The EPSR working directories and centre of geometry radial distributon functions derived from DLPUTILS have been included. The data presented includes the reduced neutron diffraction measurements (the mint files), a journal that will serve as a key to mint files, i.e., to which sample they relate, and the three EPSR working directories GPG Tripeptide in: aqueous urea, aqueous TMAO, aqueous urea-TMAO. The EPSR Software is available at https://www.isis.stfc.ac.uk/Pages/Empirical-Potential-Structure-Refinement.aspx. At each iteration of EPSR, text files are output which summarise aspects of the simulation, and these are summarised in the EPSR user manual. The molecular radial distribution functions were derived from writexyz functionality in EPSR that were read by the com RDF DLPUTILS accessible at https://www.isis.stfc.ac.uk/Pages/Disordered-Materials-Software.aspx. The writexyz functionality needs to converted to a format that is readable by DLPUTILS, and that is documented with the DLPUTILS routines. Cite as: Nasralla (2024): Diffraction measurements and modelling underlying the text Trimethylamine-N-oxide depletes urea in a peptide solvation shell. University of Leeds. DOI: https://doi.org/10.5518/1368 Related publication:Trimethylamine-N-oxide depletes urea in a peptide solvation shell. Nasralla et al., 2024, PNAS. Provisionally accepted. Contact: Mr Mazin Nasralla, pymna@leeds.ac.uk 2. TERMS OF USE --------------- This dataset is licensed under a Creative Commons Attribution 4.0 International Licence: https://creativecommons.org/licenses/by/4.0/.] 3. PROJECT AND FUNDING INFORMATION ---------------------------------- Title: Exploiting Engineered Polyproteins in the Modular Design of Robust, Tuneable and Biofunctional Hydrogels Dates: 01/03/2018 - 31/01/2024 Funding organisation: EPSRC Grant no.: EP/P02288X/1 The experimental costs were supported by the funding provided by the EPSRC. 4. CONTENTS ----------- File listing Atomic_densities The measured atomic density of the GPG_urea_water, GPG_TMAO_water, and GPG_urea_TMAO_water solutions measured at ISIS. Measurements derived from a simple density measurement cltest.ato EPSR parameters used to describe the Cl ion. Sequence might be to define in jmol, import into EPSR as mol file and then input LJ parameters converting to an ato. Before mixing all atos to create a solution through mixato cltest.jmol JMOL parameters used to describe the Cl ion cltest.mol MOL parameters used to describe the Cl ion likely imported into EPSR from JMOL Diffraction measurement journal A log of the experiment run on NIMROD that assigns run numbers to each can, isotopic sample etc dirlist.txt List of ato files some if which were subsequently deleted and not used EPSR User Guide A guide to EPSR and its outputs f0_WaasKirf.dat The independent atom form factors in EPSR are obtained from a file called ‘f0_WaasKirf.dat’ which MUST exist in the home directory for the program to run correctly. fort.35 Appears to relate to the sizefactor routine which is used at the outset of the simulation to enable separation of the molecules when they are randomised in the box gnuatoms.txt A file related to gnuplot which we did not use. gnubonds.txt A file related to gnuplot which we did not use. GNUplot.plt A file related to gnuplot which we did not use. gpgcis5.ato EPSR parameters used to describe the GPG cis molecule gpgcis5.jmol JMOL parameters used to describe the GPG cis isomer gpgcis5.mol MOL parameters used to describe the gpg cis isomer gpgtrans.ato EPSR parameters used to describe the GPG trans molecule gpgtrans.jmol JMOL parameters used to describe the GPG trans isomer gpgtrans.mol MOL parameters used to describe the gpg trans isomer gpgureabox.ato The name we allocated to the simulation box through the mixato function in the initial set up of EPSR gpgureabox.nblock A file created by EPSR in relation to the writexyz function gpgureabox.pcof Inputs created by the user when setting up the EPSR input file. Initially chose ereq=0.00, then once equlibrated we used ereq = 7 gpgureabox49.EPSR.d01 EPSR - difference Partial Structure Factor minus simulated Partial Structure Factor gpgureabox49.EPSR.d02 EPSR - difference Partial Structure Factor minus simulated Partial Structure Factor gpgureabox49.EPSR.d03 EPSR - difference Partial Structure Factor minus simulated Partial Structure Factor gpgureabox49.EPSR.erg "EPSR – list energy, pressure, R-factor, and absolute energy at each iteration of the simulation, plus a number of other variables" gpgureabox49.EPSR.f01 EPSR – simulated PSF gpgureabox49.EPSR.f02 EPSR – simulated PSF gpgureabox49.EPSR.f03 EPSR – simulated PSF gpgureabox49.EPSR.g01 EPSR and PARTIALS – simulated site-site g(r)s gpgureabox49.EPSR.g02 EPSR and PARTIALS – simulated site-site g(r)s gpgureabox49.EPSR.g03 EPSR and PARTIALS – simulated site-site g(r)s gpgureabox49.EPSR.inp EPSR input files. The .inpa file is used only to store some accumulators and the current EP difference coefficients and does not need to be modified by the user. gpgureabox49.EPSR.inpa EPSR input files. The .inpa file is used only to store some accumulators and the current EP difference coefficients and does not need to be modified by the user. gpgureabox49.EPSR.l01 Unknown output from EPSR. Not in the user guide gpgureabox49.EPSR.l02 Unknown output from EPSR. Not in the user guide gpgureabox49.EPSR.l03 Unknown output from EPSR. Not in the user guide gpgureabox49.EPSR.o01 EPSR – site-site reference potentials, including Morse and Gaussian terms gpgureabox49.EPSR.o02 EPSR – site-site reference potentials, including Morse and Gaussian terms gpgureabox49.EPSR.o03 EPSR – site-site reference potentials, including Morse and Gaussian terms gpgureabox49.EPSR.out EPSR – list of diagnostic values from the simulation. gpgureabox49.EPSR.p01 EPSR – site-site empirical potentials, including exponential repulsive terms gpgureabox49.EPSR.p02 EPSR – site-site empirical potentials, including exponential repulsive terms gpgureabox49.EPSR.p03 EPSR – site-site empirical potentials, including exponential repulsive terms gpgureabox49.EPSR.q01 EPSR – estimated partial structure factors “data” gpgureabox49.EPSR.q02 EPSR – estimated partial structure factors “data” gpgureabox49.EPSR.q03 EPSR – estimated partial structure factors “data” gpgureabox49.EPSR.qdr Unknown output from EPSR. Not in the user guide gpgureabox49.EPSR.r01 EPSR – Fourier transform of PSF “data” gpgureabox49.EPSR.r02 EPSR – Fourier transform of PSF “data” gpgureabox49.EPSR.r03 EPSR – Fourier transform of PSF “data” gpgureabox49.EPSR.s01 EPSR – simulated intra-molecular PSF gpgureabox49.EPSR.s02 EPSR – simulated intra-molecular PSF gpgureabox49.EPSR.s03 EPSR – simulated intra-molecular PSF gpgureabox49.EPSR.t01 EPSR – supplied diffraction data D(Q) gpgureabox49.EPSR.terg "EPSR – shows the mean energies associated with each atom type pair, separated into contributions from the reference potential, empirical potential, and total potential." gpgureabox49.EPSR.u01 EPSR – simulated diffraction data F(Q) gpgureabox49.EPSR.uni EPSR – uniform atom distribution. gpgureabox49.EPSR.v01 EPSR – difference D(Q) - F(Q) gpgureabox49.EPSR.w01 EPSR – f(r) (FT of D(Q)) gpgureabox49.EPSR.x01 EPSR – simulated f(r) (FT of F(Q)) gpgureabox49.EPSR.y01 EPSR – simulated intra-molecular site-site g(r)s gpgureabox49.EPSR.y02 EPSR – simulated intra-molecular site-site g(r)s gpgureabox49.EPSR.y03 EPSR – simulated intra-molecular site-site g(r)s gpgureabox49.EPSR.z01 EPSR – running coordination number for each site-site RDF. This is calculated assuming the first atom of the pair is at the origin. gpgureabox49.EPSR.z02 EPSR – running coordination number for each site-site RDF. This is calculated assuming the first atom of the pair is at the origin. gpgureabox49.EPSR.z03 EPSR – running coordination number for each site-site RDF. This is calculated assuming the first atom of the pair is at the origin. Neutron diffraction measurements aq urea Key to translate NIMROD measurement to sample (e.g., mint files) NIMROD00073678.mint01 Gives the merge differential scattering cross section AFTER post processing NIMROD00073678.NWTS.dat sets up the .wts file which gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns. NIMROD00073678.NWTStot.wts Gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns NIMROD00073679.mint01 Gives the merge differential scattering cross section AFTER post processing NIMROD00073679.NWTS.dat sets up the .wts file which gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns. NIMROD00073679.NWTStot.wts Gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns NIMROD00073680.mint01 Gives the merge differential scattering cross section AFTER post processing NIMROD00073680.NWTS.dat sets up the .wts file which gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns. NIMROD00073680.NWTStot.wts Gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns NIMROD00073681.mint01 Gives the merge differential scattering cross section AFTER post processing NIMROD00073681.NWTS.dat sets up the .wts file which gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns. NIMROD00073681.NWTStot.wts Gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns plot_defaults Summary of the plots available from EPSR runepsr EPSR text file to run simplest script. The user defines a .txt file name of their choosing which will instruct EPSR what to do at the end of each iteration. Most simply runepsr until interrupted. runepsr_plus EPSR text file to run EPSR plus a utility in this case writexyz runflag.txt EPSR file. I think this is automatically created when running scripts system_commands Documents locations of software such as Java required to run EPSR system_commands_gui Documents locations of software such as Java required to run EPSR TMAO.ato EPSR parameters used to describe the TMAO molecule TMAO.jmol JMOL parameters used to describe the TMAO molecule TMAO.mol MOL parameters used to describe the TMAO molecule in EPSR urea_131.ato EPSR parameters used to describe the Urea molecule urea_131.mol MOL parameters used to describe the Urea molecule in EPSR vanderWaalsRadii.txt An initial file created in the set-up process used to define the van der waals radii of the atom types Water.ato EPSR parameters used to describe the Water molecule Water.jmol JMOL parameters used to describe the Water molecule Water.mol MOL parameters used to describe the Water molecule in EPSR aqureainterim.rdf11 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function aqureainterim.rdf12 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function aqureainterim.rdf13 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function aqureainterim.rdf14 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function aqureainterim.rdf21 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function aqureainterim.rdf22 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function aqureainterim.rdf23 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function aqureainterim.rdf24 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function aqureainterim.rdf31 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function aqureainterim.rdf32 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function aqureainterim.rdf33 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function aqureainterim.rdf34 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function aqureainterim.rdf41 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function aqureainterim.rdf42 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function aqureainterim.rdf43 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function aqureainterim.rdf44 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function gpgureaboxappend5.xyz The molecular trajectory written from EPSR rdf_key.txt Key to the rdf outputs Atomic_densities The measured atomic density of the GPG_urea_water, GPG_TMAO_water, and GPG_urea_TMAO_water solutions measured at ISIS. Measurements derived from a simple density measurement cltest.ato EPSR parameters used to describe the Cl ion. Sequence might be to define in jmol, import into EPSR as mol file and then input LJ parameters converting to an ato. Before mixing all atos to create a solution through mixato cltest.jmol JMOL parameters used to describe the Cl ion cltest.mol MOL parameters used to describe the Cl ion likely imported into EPSR from JMOL delfit.dat Unknown file from EPSR. Not documented in the EPSR guide. I have included files that I do not understand because other users may derive their significance and some files are system requirements Diffraction measurement journal A log of the experiment run on NIMROD that assigns run numbers to each can, isotopic sample etc dirlist.txt List of ato files some if which were subsequently deleted and not used EPSR User Guide A guide to EPSR and its outputs f0_WaasKirf.dat The independent atom form factors in EPSR are obtained from a file called ‘f0_WaasKirf.dat’ which MUST exist in the home directory for the program to run correctly. fort.35 Appears to relate to the sizefactor routine which is used at the outset of the simulation to enable separation of the molecules when they are randomised in the box gnuatoms.txt A file related to gnuplot which we did not use. gnubonds.txt A file related to gnuplot which we did not use. GNUplot.plt A file related to gnuplot which we did not use. gpgcis5.ato EPSR parameters used to describe the GPG cis molecule gpgcis5.jmol JMOL parameters used to describe the GPG cis isomer gpgcis5.mol MOL parameters used to describe the gpg cis isomer gpgtmaobox.ato The name we allocated to the simulation box through the mixato function in the initial set up of EPSR gpgtmaobox.pcof Inputs created by the user when setting up the EPSR input file. Initially chose ereq=0.00, then once equlibrated we used ereq = 14.5 gpgtmaobox2.EPSR.d01 EPSR - difference Partial Structure Factor minus simulated Partial Structure Factor gpgtmaobox2.EPSR.d02 EPSR - difference Partial Structure Factor minus simulated Partial Structure Factor gpgtmaobox2.EPSR.d03 EPSR - difference Partial Structure Factor minus simulated Partial Structure Factor gpgtmaobox2.EPSR.erg "EPSR – list energy, pressure, R-factor, and absolute energy at each iteration of the simulation, plus a number of other variables" gpgtmaobox2.EPSR.f01 EPSR – simulated PSF gpgtmaobox2.EPSR.f02 EPSR – simulated PSF gpgtmaobox2.EPSR.f03 EPSR – simulated PSF gpgtmaobox2.EPSR.g01 EPSR and PARTIALS – simulated site-site g(r)s gpgtmaobox2.EPSR.g02 EPSR and PARTIALS – simulated site-site g(r)s gpgtmaobox2.EPSR.g03 EPSR and PARTIALS – simulated site-site g(r)s gpgtmaobox2.EPSR.inp EPSR input files. The .inpa file is used only to store some accumulators and the current EP difference coefficients and does not need to be modified by the user. gpgtmaobox2.EPSR.inpa EPSR input files. The .inpa file is used only to store some accumulators and the current EP difference coefficients and does not need to be modified by the user. gpgtmaobox2.EPSR.l01 Unknown output from EPSR. Not in the user guide gpgtmaobox2.EPSR.l02 Unknown output from EPSR. Not in the user guide gpgtmaobox2.EPSR.l03 Unknown output from EPSR. Not in the user guide gpgtmaobox2.EPSR.o01 EPSR – site-site reference potentials, including Morse and Gaussian terms gpgtmaobox2.EPSR.o02 EPSR – site-site reference potentials, including Morse and Gaussian terms gpgtmaobox2.EPSR.o03 EPSR – site-site reference potentials, including Morse and Gaussian terms gpgtmaobox2.EPSR.out EPSR – list of diagnostic values from the simulation. gpgtmaobox2.EPSR.p01 EPSR – site-site empirical potentials, including exponential repulsive terms gpgtmaobox2.EPSR.p02 EPSR – site-site empirical potentials, including exponential repulsive terms gpgtmaobox2.EPSR.p03 EPSR – site-site empirical potentials, including exponential repulsive terms gpgtmaobox2.EPSR.q01 EPSR – estimated partial structure factors “data” gpgtmaobox2.EPSR.q02 EPSR – estimated partial structure factors “data” gpgtmaobox2.EPSR.q03 EPSR – estimated partial structure factors “data” gpgtmaobox2.EPSR.qdr Unknown output from EPSR. Not in the user guide gpgtmaobox2.EPSR.r01 EPSR – Fourier transform of PSF “data” gpgtmaobox2.EPSR.r02 EPSR – Fourier transform of PSF “data” gpgtmaobox2.EPSR.r03 EPSR – Fourier transform of PSF “data” gpgtmaobox2.EPSR.s01 EPSR – simulated intra-molecular PSF gpgtmaobox2.EPSR.s02 EPSR – simulated intra-molecular PSF gpgtmaobox2.EPSR.s03 EPSR – simulated intra-molecular PSF gpgtmaobox2.EPSR.t01 EPSR – supplied diffraction data D(Q) gpgtmaobox2.EPSR.terg "EPSR – shows the mean energies associated with each atom type pair, separated into contributions from the reference potential, empirical potential, and total potential." gpgtmaobox2.EPSR.u01 EPSR – simulated diffraction data F(Q) gpgtmaobox2.EPSR.uni EPSR – uniform atom distribution. gpgtmaobox2.EPSR.v01 EPSR – difference D(Q) - F(Q) gpgtmaobox2.EPSR.w01 EPSR – f(r) (FT of D(Q)) gpgtmaobox2.EPSR.x01 EPSR – simulated f(r) (FT of F(Q)) gpgtmaobox2.EPSR.y01 EPSR – simulated intra-molecular site-site g(r)s gpgtmaobox2.EPSR.y02 EPSR – simulated intra-molecular site-site g(r)s gpgtmaobox2.EPSR.y03 EPSR – simulated intra-molecular site-site g(r)s gpgtmaobox2.EPSR.z01 EPSR – running coordination number for each site-site RDF. This is calculated assuming the first atom of the pair is at the origin. gpgtmaobox2.EPSR.z02 EPSR – running coordination number for each site-site RDF. This is calculated assuming the first atom of the pair is at the origin. gpgtmaobox2.EPSR.z03 EPSR – running coordination number for each site-site RDF. This is calculated assuming the first atom of the pair is at the origin. gpgtrans.ato EPSR parameters used to describe the GPG trans molecule gpgtrans.jmol JMOL parameters used to describe the GPG trans isomer gpgtrans.mol MOL parameters used to describe the gpg trans isomer Neutron diffraction measurements aq urea Key to translate NIMROD measurement to sample (e.g., mint files) NIMROD00073610.NWTS.dat sets up the .wts file which gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns. NIMROD00073610.NWTStot.wts Gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns NIMROD00073610_5.mint01 Gives the merge differential scattering cross section AFTER post processing NIMROD00073611.NWTS.dat sets up the .wts file which gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns. NIMROD00073611.NWTStot.wts Gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns NIMROD00073611_5.mint01 Gives the merge differential scattering cross section AFTER post processing NIMROD00073612.NWTS.dat sets up the .wts file which gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns. NIMROD00073612.NWTStot.wts Gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns NIMROD00073612_5.mint01 Gives the merge differential scattering cross section AFTER post processing NIMROD00073613.NWTS.dat sets up the .wts file which gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns. NIMROD00073613.NWTStot.wts Gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns NIMROD00073613_5.mint01 Gives the merge differential scattering cross section AFTER post processing NIMROD00073614.NWTS.dat sets up the .wts file which gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns. NIMROD00073614.NWTStot.wts Gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns NIMROD00073614_5.mint01 Gives the merge differential scattering cross section AFTER post processing NIMROD00073616.NWTS.dat sets up the .wts file which gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns. NIMROD00073616.NWTStot.wts Gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns NIMROD00073616_5.mint01 Gives the merge differential scattering cross section AFTER post processing NIMROD00073617.NWTS.dat sets up the .wts file which gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns. NIMROD00073617.NWTStot.wts Gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns NIMROD00073617_5.mint01 Gives the merge differential scattering cross section AFTER post processing plot_defaults Summary of the plots available from EPSR runepsr EPSR text file to run simplest script. The user defines a .txt file name of their choosing which will instruct EPSR what to do at the end of each iteration. Most simply runepsr until interrupted. runepsr_plus EPSR text file to run EPSR plus a utility in this case writexyz runflag.txt EPSR file. I think this is automatically created when running scripts system_commands Documents locations of software such as Java required to run EPSR system_commands_gui Documents locations of software such as Java required to run EPSR TMAO.ato EPSR parameters used to describe the TMAO molecule TMAO.jmol JMOL parameters used to describe the TMAO molecule TMAO.mol MOL parameters used to describe the TMAO molecule in EPSR vanderWaalsRadii.txt An initial file created in the set-up process used to define the van der waals radii of the atom types Water.ato EPSR parameters used to describe the Water molecule Water.jmol JMOL parameters used to describe the Water molecule Water.mol MOL parameters used to describe the Water molecule in EPSR gpgtmao2results.rdf11 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function gpgtmao2results.rdf12 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function gpgtmao2results.rdf13 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function gpgtmao2results.rdf14 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function gpgtmao2results.rdf21 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function gpgtmao2results.rdf22 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function gpgtmao2results.rdf23 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function gpgtmao2results.rdf24 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function gpgtmao2results.rdf31 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function gpgtmao2results.rdf32 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function gpgtmao2results.rdf33 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function gpgtmao2results.rdf34 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function gpgtmao2results.rdf41 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function gpgtmao2results.rdf42 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function gpgtmao2results.rdf43 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function gpgtmao2results.rdf44 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function gpgtmaoboxappend.xyz The molecular trajectory written from EPSR rdf_key.txt Key to the rdf outputs Atomic_densities The measured atomic density of the GPG_urea_water, GPG_TMAO_water, and GPG_urea_TMAO_water solutions measured at ISIS. Measurements derived from a simple density measurement cltest.ato EPSR parameters used to describe the Cl ion. Sequence might be to define in jmol, import into EPSR as mol file and then input LJ parameters converting to an ato. Before mixing all atos to create a solution through mixato cltest.jmol JMOL parameters used to describe the Cl ion cltest.mol MOL parameters used to describe the Cl ion likely imported into EPSR from JMOL delfit.dat Unknown file from EPSR. Not documented in the EPSR guide. I have included files that I do not understand because other users may derive their significance and some files are system requirements Diffraction measurement journal A log of the experiment run on NIMROD that assigns run numbers to each can, isotopic sample etc dirlist.txt List of ato files some if which were subsequently deleted and not used EPSR User Guide A guide to EPSR and its outputs f0_WaasKirf.dat The independent atom form factors in EPSR are obtained from a file called ‘f0_WaasKirf.dat’ which MUST exist in the home directory for the program to run correctly. fort.35 Appears to relate to the sizefactor routine which is used at the outset of the simulation to enable separation of the molecules when they are randomised in the box gnuatoms.txt A file related to gnuplot which we did not use. gnubonds.txt A file related to gnuplot which we did not use. GNUplot.plt A file related to gnuplot which we did not use. gpgcis5.ato EPSR parameters used to describe the GPG cis molecule gpgcis5.jmol JMOL parameters used to describe the GPG cis isomer gpgcis5.mol MOL parameters used to describe the gpg cis isomer gpgtrans.ato EPSR parameters used to describe the GPG trans molecule gpgtrans.jmol JMOL parameters used to describe the GPG trans isomer gpgtrans.mol MOL parameters used to describe the gpg trans isomer gpgureatmaobox.ato The name we allocated to the simulation box through the mixato function in the initial set up of EPSR gpgureatmaobox.nblock A file created by EPSR in relation to the writexyz function gpgureatmaobox.pcof Inputs created by the user when setting up the EPSR input file. Initially chose ereq=0.00, then once equlibrated we used ereq = 14.5 gpgureatmaobox2.EPSR.d01 EPSR - difference Partial Structure Factor minus simulated Partial Structure Factor gpgureatmaobox2.EPSR.d02 EPSR - difference Partial Structure Factor minus simulated Partial Structure Factor gpgureatmaobox2.EPSR.d03 EPSR - difference Partial Structure Factor minus simulated Partial Structure Factor gpgureatmaobox2.EPSR.d04 EPSR - difference Partial Structure Factor minus simulated Partial Structure Factor gpgureatmaobox2.EPSR.erg "EPSR – list energy, pressure, R-factor, and absolute energy at each iteration of the simulation, plus a number of other variables" gpgureatmaobox2.EPSR.f01 EPSR – simulated PSF gpgureatmaobox2.EPSR.f02 EPSR – simulated PSF gpgureatmaobox2.EPSR.f03 EPSR – simulated PSF gpgureatmaobox2.EPSR.f04 EPSR – simulated PSF gpgureatmaobox2.EPSR.g01 EPSR and PARTIALS – simulated site-site g(r)s gpgureatmaobox2.EPSR.g02 EPSR and PARTIALS – simulated site-site g(r)s gpgureatmaobox2.EPSR.g03 EPSR and PARTIALS – simulated site-site g(r)s gpgureatmaobox2.EPSR.g04 EPSR and PARTIALS – simulated site-site g(r)s gpgureatmaobox2.EPSR.inp EPSR input files. The .inpa file is used only to store some accumulators and the current EP difference coefficients and does not need to be modified by the user. gpgureatmaobox2.EPSR.inpa EPSR input files. The .inpa file is used only to store some accumulators and the current EP difference coefficients and does not need to be modified by the user. gpgureatmaobox2.EPSR.l01 Unknown output from EPSR. Not in the user guide gpgureatmaobox2.EPSR.l02 Unknown output from EPSR. Not in the user guide gpgureatmaobox2.EPSR.l03 Unknown output from EPSR. Not in the user guide gpgureatmaobox2.EPSR.l04 Unknown output from EPSR. Not in the user guide gpgureatmaobox2.EPSR.o01 EPSR – site-site reference potentials, including Morse and Gaussian terms gpgureatmaobox2.EPSR.o02 EPSR – site-site reference potentials, including Morse and Gaussian terms gpgureatmaobox2.EPSR.o03 EPSR – site-site reference potentials, including Morse and Gaussian terms gpgureatmaobox2.EPSR.o04 EPSR – site-site reference potentials, including Morse and Gaussian terms gpgureatmaobox2.EPSR.out EPSR – list of diagnostic values from the simulation. gpgureatmaobox2.EPSR.p01 EPSR – site-site empirical potentials, including exponential repulsive terms gpgureatmaobox2.EPSR.p02 EPSR – site-site empirical potentials, including exponential repulsive terms gpgureatmaobox2.EPSR.p03 EPSR – site-site empirical potentials, including exponential repulsive terms gpgureatmaobox2.EPSR.p04 EPSR – site-site empirical potentials, including exponential repulsive terms gpgureatmaobox2.EPSR.q01 EPSR – estimated partial structure factors “data” gpgureatmaobox2.EPSR.q02 EPSR – estimated partial structure factors “data” gpgureatmaobox2.EPSR.q03 EPSR – estimated partial structure factors “data” gpgureatmaobox2.EPSR.q04 EPSR – estimated partial structure factors “data” gpgureatmaobox2.EPSR.qdr Unknown output from EPSR. Not in the user guide gpgureatmaobox2.EPSR.r01 EPSR – Fourier transform of PSF “data” gpgureatmaobox2.EPSR.r02 EPSR – Fourier transform of PSF “data” gpgureatmaobox2.EPSR.r03 EPSR – Fourier transform of PSF “data” gpgureatmaobox2.EPSR.r04 EPSR – Fourier transform of PSF “data” gpgureatmaobox2.EPSR.s01 EPSR – simulated intra-molecular PSF gpgureatmaobox2.EPSR.s02 EPSR – simulated intra-molecular PSF gpgureatmaobox2.EPSR.s03 EPSR – simulated intra-molecular PSF gpgureatmaobox2.EPSR.s04 EPSR – simulated intra-molecular PSF gpgureatmaobox2.EPSR.t01 EPSR – supplied diffraction data D(Q) gpgureatmaobox2.EPSR.terg "EPSR – shows the mean energies associated with each atom type pair, separated into contributions from the reference potential, empirical potential, and total potential." gpgureatmaobox2.EPSR.u01 EPSR – simulated diffraction data F(Q) gpgureatmaobox2.EPSR.uni EPSR – uniform atom distribution. gpgureatmaobox2.EPSR.v01 EPSR – difference D(Q) - F(Q) gpgureatmaobox2.EPSR.w01 EPSR – f(r) (FT of D(Q)) gpgureatmaobox2.EPSR.x01 EPSR – simulated f(r) (FT of F(Q)) gpgureatmaobox2.EPSR.y01 EPSR – simulated intra-molecular site-site g(r)s gpgureatmaobox2.EPSR.y02 EPSR – simulated intra-molecular site-site g(r)s gpgureatmaobox2.EPSR.y03 EPSR – simulated intra-molecular site-site g(r)s gpgureatmaobox2.EPSR.y04 EPSR – simulated intra-molecular site-site g(r)s gpgureatmaobox2.EPSR.z01 EPSR – running coordination number for each site-site RDF. This is calculated assuming the first atom of the pair is at the origin. gpgureatmaobox2.EPSR.z02 EPSR – running coordination number for each site-site RDF. This is calculated assuming the first atom of the pair is at the origin. gpgureatmaobox2.EPSR.z03 EPSR – running coordination number for each site-site RDF. This is calculated assuming the first atom of the pair is at the origin. gpgureatmaobox2.EPSR.z04 EPSR – running coordination number for each site-site RDF. This is calculated assuming the first atom of the pair is at the origin. Neutron diffraction measurements aq urea-tmao.txt Key to translate NIMROD measurement to sample (e.g., mint files) NIMROD00073643.mint01 Gives the merge differential scattering cross section AFTER post processing NIMROD00073643.NWTS.dat sets up the .wts file which gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns. NIMROD00073643.NWTStot.wts Gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns NIMROD00073644.mint01 Gives the merge differential scattering cross section AFTER post processing NIMROD00073644.NWTS.dat sets up the .wts file which gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns. NIMROD00073644.NWTStot.wts Gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns NIMROD00073645.mint01 Gives the merge differential scattering cross section AFTER post processing NIMROD00073645.NWTS.dat sets up the .wts file which gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns. NIMROD00073645.NWTStot.wts Gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns NIMROD00073646.mint01 Gives the merge differential scattering cross section AFTER post processing NIMROD00073646.NWTS.dat sets up the .wts file which gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns. NIMROD00073646.NWTStot.wts Gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns NIMROD00073647.mint01 Gives the merge differential scattering cross section AFTER post processing NIMROD00073647.NWTS.dat sets up the .wts file which gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns. NIMROD00073647.NWTStot.wts Gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns NIMROD00073648.mint01 Gives the merge differential scattering cross section AFTER post processing NIMROD00073648.NWTS.dat sets up the .wts file which gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns. NIMROD00073648.NWTStot.wts Gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns NIMROD00073649.mint01 Gives the merge differential scattering cross section AFTER post processing NIMROD00073649.NWTS.dat sets up the .wts file which gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns. NIMROD00073649.NWTStot.wts Gives the relative or absolute neutron weight factors of individual PSFs in the input neutron diffraction patterns plot_defaults.txt Summary of the plots available from EPSR runepsr.txt EPSR text file to run simplest script. The user defines a .txt file name of their choosing which will instruct EPSR what to do at the end of each iteration. Most simply runepsr until interrupted. runepsr_plus.txt EPSR text file to run EPSR plus a utility in this case writexyz runflag.txt EPSR file. I think this is automatically created when running scripts system_commands.txt Documents locations of software such as Java required to run EPSR system_commands_gui.txt Documents locations of software such as Java required to run EPSR urea_131.ato EPSR parameters used to describe the TMAO molecule urea_131.mol JMOL parameters used to describe the TMAO molecule TMAO.ato MOL parameters used to describe the TMAO molecule in EPSR TMAO.jmol EPSR parameters used to describe the Urea molecule TMAO.mol MOL parameters used to describe the Urea molecule in EPSR vanderWaalsRadii.txt An initial file created in the set-up process used to define the van der waals radii of the atom types Water.ato EPSR parameters used to describe the Water molecule Water.jmol JMOL parameters used to describe the Water molecule Water.mol MOL parameters used to describe the Water molecule in EPSR gpgureatmaoboxappend.xyz The molecular trajectory written from EPSR rdf_key.txt Key to the rdf outputs tmao_urea.rdf11 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf12 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf13 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf14 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf15 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf21 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf22 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf23 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf24 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf25 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf31 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf32 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf33 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf34 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf35 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf41 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf42 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf43 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf44 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf45 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf51 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf52 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf53 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf54 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function tmao_urea.rdf55 centre of geometry rdf derived from the RDF function of DLPUTILS that utilised the gpgureaboxappend5.xyz file written from EPSR by the writexyz function 5. METHODS ---------- Please see the the 'Material and Methods' section of the main text 'Trimethylamine-N-oxide depletes urea in a peptide solvation shell' that document the methodology. The vast majority of the data documented here was generated by Empirical Potential Structure Refinement (EPSR), software that can be run on a windows machine and is available at the ISIS web-site. A user manual documents the procedures, and the user has the choice of using EPSR through a shell, or GUI interface. The simulation boxes were equilibrated using an initial size factor of 20 0.9 0.0 in EPSR, otherwise it was found to be difficult to unravel entangled GPG peptide molecules, and a ref intra setting of 0.0 1.0 was used to minimise the close approach of GPG atoms. At each iteration, EPSR generates a host of text based files that summarise aspects of the simulation including the radial distribution functions (RDF). In addition to the atomic RDF, our text described molecular RDF that were derived from the software DLPUTILS accessible at https://www.isis.stfc.ac.uk/Pages/Disordered-Materials-Software.aspx. In order to use this functionality the user needs to run the writexyz function in EPSR to generate a cumulative xyz molecular trajectory file that once converted to the appropriate format can be interrogated by a whole suite of additonal programs in DLPUTILS. The DLPUTILS utility for the molecular rdf is the program 'RDF'. At the time of writing this does not produce a centre of mass (COM) RDF because the writexyz routine does not generate an atomic mass, however the user may find that more recent versions of EPSR have been updated to allow for a genuine COM RDF.