cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.11588/portal.gsi.6821b00b1d19c
title: August Scherl (Bremen)
DOI: 10.11588/portal.gsi.6821b00c05ac3
title: Galerie Alice Seidel-Frank (Baden-Baden)
DOI: 10.21233/qg8e-np07
title: Antler Pond pollen dataset

description: Raw data for the Antler Pond pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/hbeg-ry40
title: Aubrey [41DN479] vertebrate fauna dataset

description: Raw data for the Aubrey [41DN479] vertebrate fauna dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.camgk6
title: Occurrence Download

description: A dataset containing 2806879 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Türkiye",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 2806879 records from 108 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025898-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g6wah3
title: Occurrence Download

description: A dataset containing 138 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leptodactylus notoaktites Heyer, 1978",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 138 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025924-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/thyp-w845
title: Akulivikchuk [DIL-00002] vertebrate fauna dataset

description: Raw data for the Akulivikchuk [DIL-00002] vertebrate fauna dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/2tz3-wt04
title: LDDsite589 water chemistry dataset

description: Raw data for the LDDsite589 water chemistry dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.11588/portal.gsi.6821b0451c682
title: Dr. Gottschewski - Dr. Schäffer (Amsterdam)
DOI: 10.11588/portal.gsi.6821b046c1c40
title: Schaeffer Galleries (New York)
DOI: 10.11588/portal.gsi.6821b0478f4fb
title: Schaeffer Galleries (London)
DOI: 10.11588/portal.gsi.6821b0486056b
title: Schaeffer Galleries (San Francisco)
DOI: 10.11588/portal.gsi.6821b04939810
title: Galerie Käthe Perls (Paris)
DOI: 10.11588/portal.gsi.6821b04a5d471
title: Perls Galleries
DOI: 10.11588/portal.gsi.6821b04b3dde7
title: Der Malik-Verlag
DOI: 10.11588/portal.gsi.6821b04c026d3
title: Der dänische Silberschmied
DOI: 10.11588/portal.gsi.6821b04cd3b9d
title: Hohenzollern-Kaufhaus für Kunst und Kunstgewerbe Zwilling. J.A. Henckels
DOI: 10.21233/2dr9-ts53
title: Harpeth Gravel Bar vertebrate fauna dataset

description: Raw data for the Harpeth Gravel Bar vertebrate fauna dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.11588/portal.gsi.6821b04db1437
title: Friedmann & Weber GmbH
DOI: 10.11588/portal.gsi.6821b04e7482b
title: Magazin für Berliner Kunstgewerbe H. Hirschwald (Filiale)
DOI: 10.11588/portal.gsi.6821b04f4bb9e
title: Magazin für Berliner Kunstgewerbe H. Hirschwald
DOI: 10.11588/portal.gsi.6821b0501dd2e
title: Friedmann & Weber Innendekorationen
DOI: 10.15468/dl.qumgyw
title: Occurrence Download

description: A dataset containing 94332 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Invazivke - Invasive Alien Species in Slovenia"
 ]
}

 The dataset includes 94332 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025919-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/znbh-jp26
title: LDDsite6172 water chemistry dataset

description: Raw data for the LDDsite6172 water chemistry dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/8c6p-d195
title: Karelia testate amoebae surface sample dataset

description: Raw data for the Karelia testate amoebae surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/y6dg-xa25
title: Loon Lake water chemistry dataset

description: Raw data for the Loon Lake water chemistry dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.b6exms
title: Occurrence Download

description: A dataset containing 494 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Amaranthus crispus (Lesp. & Thévenau) N.Terracc.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 494 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025927-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/xkmp-s187
title: Floating Island Lake pollen dataset

description: Raw data for the Floating Island Lake pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.fjrpqu
title: Occurrence Download

description: A dataset containing 7597 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Limnodynastes convexiusculus (Macleay, 1878)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 7597 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025929-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/yqms-a202
title: Mims Lake diatom surface sample dataset

description: Raw data for the Mims Lake diatom surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.mnbx6a
title: Occurrence Download

description: A dataset containing 5276 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lagerstroemia speciosa (L.) Pers.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5276 records from 147 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025928-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/0fdn-1912
title: LDDsite3009 water chemistry dataset

description: Raw data for the LDDsite3009 water chemistry dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.11588/portal.gsi.6821b0a94310c
title: Kunst und Handwerk GmbH (Kunsthag)
DOI: 10.11588/portal.gsi.6821b0aa5abd8
title: Münchener Kunsthandlung GmbH
DOI: 10.11588/portal.gsi.6821b0ab396f0
title: Ausstellung für Graphische Kunst
DOI: 10.11588/portal.gsi.6821b0ac14232
title: Die Kornscheuer (Den Haag)
DOI: 10.11588/portal.gsi.6821b0acddd9a
title: Die Kornscheuer (Warschau)
DOI: 10.11588/portal.gsi.6821b0adbf3b2
title: Die Kornscheuer (Moskau)
DOI: 10.11588/portal.gsi.6821b0ae901b9
title: Die Kornscheuer (Rom)
DOI: 10.21233/eca8-gp33
title: Short Stop vertebrate fauna dataset

description: Raw data for the Short Stop vertebrate fauna dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.11588/portal.gsi.6821b0af787b7
title: Die Kornscheuer (New York)
DOI: 10.11588/portal.gsi.6821b0b04d9e3
title: Galerie Rheinland GmbH
DOI: 10.11588/portal.gsi.6821b0b11fbc1
title: H. Lipke. Fabrik und Verkauf von Wohnungseinrichtungen und Möbeln
DOI: 10.11588/portal.gsi.6821b0b1ef502
title: Camilla Speth Buch- und Kunsthandlung
DOI: 10.11588/portal.gsi.6821b0b2cdf44
title: H. Pfuhl Kunsthandlung und Wohnungs-Einrichtungen
DOI: 10.11588/portal.gsi.6821b0b38e4bf
title: Bruno Cassirer (Publishers) Ltd.
DOI: 10.5281/zenodo.15268109
title: Supplementary data for: "Conformational Free Energy Landscape of β-glucose in the Gas-Phase and Aqueous Solution: Energetic, Structural and Electronic Changes"

description: This data set contains files related to the article "Conformational Free Energy Landscape of β-glucose in the Gas-Phase and Aqueous Solution: Energetic, Structural and Electronic Changes" by Qinghua Liao, Mariana A.B. Morais, Carme Rovira and Alba Nin-Hill

 

ABSTRACT

The conformational flexibility of β-glucose is critical for the enzymatic breakdown of carbohydrates such as cellulose and starch. Detailed knowledge of its ring conformations supports the rational design of therapeutic agents and functional molecules, including glucosidase activity-based probes. Although quantum mechanical methods have been employed to study β-glucose conformations, a comprehensive analysis of the Cremer−Pople conformational space, particularly accounting for solventeffects, remains incomplete. Using density functional theory (DFT), we systematically characterize β-glucose conformations in both gas and aqueous phases. We apply three metadynamics approaches-standard, well-tempered, and parallel bias-using Cremer−Pople polar coordinates and ring dihedral angles as collective variables. Consistent conformational stability trends are observed across methods and environments. In both gas and aqueous phases, the free energy landscape (FEL) identifies the 4C1 chair as the global minimum, followed by equatorial conformers and the inverted 1C4 chair, which is less stable in solution than in the gas phase. In the gas phase, the most stable distorted conformers (in the 2SO−B3,O−1S3 region) exhibit structural and electronic features characteristic of an oxocarbenium ion, including a high C1−O1/C1−O5 bond length ratio, a pronounced anomeric effect, and negative charge accumulation at O1 and O5. These features are significantly diminished in aqueous solution, suggesting that the gas-phase FEL better reflects the conformational preferences of the saccharide at the -1 subsite in enzyme−substrate complexes of glucosidases. These findings provide a valuable framework for investigating saccharide conformations, establishing β-glucose as a model system for computational and methodological benchmarking.

 

DESCRIPTION OF THE DATASET

The data is compressed in two different .zip files in where we could find the trajectory files generated from the ab initio and QM/MM molecular dynamics simulations.



bGlc_pbmetad-mw.zip: Data related to the gas phase and aqueous simulations of the β-glucose molecule using parallel bias metadynamics with multiple walkers and the dihedral torsions as CVs. 

bGlc_metad_cremerpople.zip: Data related to the gas phase and aqueous simulations of the β-glucose molecule using standard and well-tempered metadynamics and the cartesian Cremer and Pople coordinates as CVs.
DOI: 10.5281/zenodo.15268110
title: Supplementary data for: "Conformational Free Energy Landscape of β-glucose in the Gas-Phase and Aqueous Solution: Energetic, Structural and Electronic Changes"

description: This data set contains files related to the article "Conformational Free Energy Landscape of β-glucose in the Gas-Phase and Aqueous Solution: Energetic, Structural and Electronic Changes" by Qinghua Liao, Mariana A.B. Morais, Carme Rovira and Alba Nin-Hill

 

ABSTRACT

The conformational flexibility of β-glucose is critical for the enzymatic breakdown of carbohydrates such as cellulose and starch. Detailed knowledge of its ring conformations supports the rational design of therapeutic agents and functional molecules, including glucosidase activity-based probes. Although quantum mechanical methods have been employed to study β-glucose conformations, a comprehensive analysis of the Cremer−Pople conformational space, particularly accounting for solventeffects, remains incomplete. Using density functional theory (DFT), we systematically characterize β-glucose conformations in both gas and aqueous phases. We apply three metadynamics approaches-standard, well-tempered, and parallel bias-using Cremer−Pople polar coordinates and ring dihedral angles as collective variables. Consistent conformational stability trends are observed across methods and environments. In both gas and aqueous phases, the free energy landscape (FEL) identifies the 4C1 chair as the global minimum, followed by equatorial conformers and the inverted 1C4 chair, which is less stable in solution than in the gas phase. In the gas phase, the most stable distorted conformers (in the 2SO−B3,O−1S3 region) exhibit structural and electronic features characteristic of an oxocarbenium ion, including a high C1−O1/C1−O5 bond length ratio, a pronounced anomeric effect, and negative charge accumulation at O1 and O5. These features are significantly diminished in aqueous solution, suggesting that the gas-phase FEL better reflects the conformational preferences of the saccharide at the -1 subsite in enzyme−substrate complexes of glucosidases. These findings provide a valuable framework for investigating saccharide conformations, establishing β-glucose as a model system for computational and methodological benchmarking.

 

DESCRIPTION OF THE DATASET

The data is compressed in two different .zip files in where we could find the trajectory files generated from the ab initio and QM/MM molecular dynamics simulations.



bGlc_pbmetad-mw.zip: Data related to the gas phase and aqueous simulations of the β-glucose molecule using parallel bias metadynamics with multiple walkers and the dihedral torsions as CVs. 

bGlc_metad_cremerpople.zip: Data related to the gas phase and aqueous simulations of the β-glucose molecule using standard and well-tempered metadynamics and the cartesian Cremer and Pople coordinates as CVs.
DOI: 10.21233/8b3z-4912
title: Margaret Lake pollen surface sample dataset

description: Raw data for the Margaret Lake pollen surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/f2s4-wr34
title: LDDsite5 water chemistry dataset

description: Raw data for the LDDsite5 water chemistry dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/nzq2-j505
title: East Lily Peatland testate amoebae surface sample dataset

description: Raw data for the East Lily Peatland testate amoebae surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/bkgx-9h20
title: Mott 1974 Site 2 pollen surface sample dataset

description: Raw data for the Mott 1974 Site 2 pollen surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.4121/bb39045d-6660-4a47-ac73-a5d41bccdf1b.v1
title: Data underlying the publication: A tale of scale: Different factors influence the range boundaries and habitat use of a generalist mammalian carnivore

description: The data available in this dataset was used for the species distribution modelling of brown hyenas in southern Africa, including occurrence points, environmental predictors and R code to run the analysis. Occurrence points are at ~10km resolution, collected by 100+ data contributors, through camera traps, direct observations, telemetry, scats and spoor, and collated by the IUCN SSC Hyaena Specialist Group. The environmental predictors were collected from open access sources, cropped tot he modelling region (southern Africa - Angola, Zambia, Malawi, Mozambique, Zimbabwe, Botswana, Namibia, South Africa, Lesotho, Eswatini), transformed into a normal distribution when possible, and standardized to a mean of 0 and standard deviation of 1. The R file includes code used to run the ensembled species distribution analysis.
DOI: 10.21233/jkma-e793
title: Grad Cave vertebrate fauna dataset

description: Raw data for the Grad Cave vertebrate fauna dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.wybk36
title: Occurrence Download

description: A dataset containing 113 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((15.34 47.08,15.39 47.08,15.39 47.13,15.34 47.13,15.34 47.08))",
 "HasCoordinate is true",
 "IucnRedListCategory is one of (EX, EW, CR, EN, VU, NT)",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 113 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025930-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pq8wcz
title: Occurrence Download

description: A dataset containing 6494 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Arundina graminifolia (D.Don) Hochr."
 ]
}

 The dataset includes 6494 records from 180 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025931-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/ygk-jh6-dt4
title: Heliacus variegatus (Gmelin, 1791)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/r21-56e-drg
title: Americardia guppyi (Thiele, 1910)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5lh-ysr-xt3
title: Neritopsis radula (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6h3-hl8-crg
title: Segmentina nitida (O. F. Müller, 1774)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kf1-2kf-k5v
title: Nassarius subspinosus (Lamarck, 1822)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/d10-2rp-0sm
title: Haliotis gigantea Gmelin, 1791

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/aeg-p3j-w2t
title: Similipecten nanus (A. E. Verrill & K. J. Bush, 1897)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/f64-x5p-lla
title: Dosinia lupinus (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1bw-1hx-5pz
title: Crassinella martinicensis (A. d'Orbigny, 1853)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/bv3-h02-0np
title: Vasticardium pectiniforme (Born, 1780)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7ah-z3v-9kx
title: Conus striatus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hrm-x3h-y4b
title: Agathistoma lividomaculatum (C. B. Adams, 1845)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gkr-rfy-7e2
title: Oliva pacifica Marrat, 1870

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mfb-rmb-a67
title: Ena montana (Draparnaud, 1801)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6fg-7tg-rq2
title: Turbo chrysostomus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2gq-g41-tj0
title: Vokesimurex chrysostoma (G. B. Sowerby II, 1834)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7lt-6cx-y2d
title: Viviparus Montfort, 1810

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.