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  1. Article ; Online: Toward Reliable and Insightful Entropy Calculations on Flexible Molecules.

    Díaz, Natalia / Suárez, Dimas

    Journal of chemical theory and computation

    2022  

    Abstract: The absolute entropy of a flexible molecule can be approximated by the sum of a rigid-rotor-harmonic-oscillator (RRHO) entropy and a Gibbs-Shannon entropy associated to the Boltzmann distribution for the occupation of the conformational energy levels. ... ...

    Abstract The absolute entropy of a flexible molecule can be approximated by the sum of a rigid-rotor-harmonic-oscillator (RRHO) entropy and a Gibbs-Shannon entropy associated to the Boltzmann distribution for the occupation of the conformational energy levels. Herein, we show that such partitioning, which has received renewed interest, leads to accurate entropies of single molecules of increasing size provided that the conformational part is estimated by means of a set of discretization and expansion techniques that are able to capture the significant correlation effects among the torsional motions. To ensure a reliable entropy estimation, we rely on extensive sampling as that produced by classical molecular dynamics simulations on the microsecond time scale, which is currently affordable for small- and medium-sized molecules. According to test calculations, the gas-phase entropy of simple organic molecules is predicted with a mean unsigned error of 0.9 cal/(mol K) when the RRHO entropies are computed at the B3LYP-D3/cc-pVTZ level. Remarkably, the same protocol gives small errors [<1 cal/(mol K)] for the extremely flexible linear alkane molecules (C
    Language English
    Publishing date 2022-11-25
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.2c00858
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Colorectal adenocarcinoma with enteroblastic differentiation. Report of one case with lacunar growth pattern, microcalcifications, osseous metaplasia, and metachronous involvement of sigma and appendix.

    Suárez-Vilela, Dimas / Izquierdo, Francisco Miguel

    Pathology international

    2022  Volume 72, Issue 12, Page(s) 640–642

    MeSH term(s) Humans ; Appendix/pathology ; Adenocarcinoma/pathology ; Metaplasia ; Colorectal Neoplasms/pathology ; Calcinosis
    Language English
    Publishing date 2022-11-02
    Publishing country Australia
    Document type Case Reports ; Letter
    ZDB-ID 1194850-4
    ISSN 1440-1827 ; 1320-5463
    ISSN (online) 1440-1827
    ISSN 1320-5463
    DOI 10.1111/pin.13281
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  3. Article ; Online: Splenic Lesions and Other Findings in Kaposiform Lymphangiomatosis.

    Suárez-Vilela, Dimas / Izquierdo, Francisco M / Honrado, Emiliano / Díez-Tascón, Cristina

    The American journal of surgical pathology

    2023  Volume 47, Issue 5, Page(s) 631–633

    MeSH term(s) Humans ; Hemangioendothelioma/pathology
    Language English
    Publishing date 2023-02-16
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 752964-8
    ISSN 1532-0979 ; 0147-5185
    ISSN (online) 1532-0979
    ISSN 0147-5185
    DOI 10.1097/PAS.0000000000002026
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    Zs.A 1356: Show issues Location:
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  4. Article ; Online: Influence of charge configuration on substrate binding to SARS-CoV-2 main protease.

    Díaz, Natalia / Suárez, Dimas

    Chemical communications (Cambridge, England)

    2021  Volume 57, Issue 43, Page(s) 5314–5317

    Abstract: While the state-of-the-art computational simulations support the neutral state for the catalytic dyad of the SARS-CoV-2 main protease, the recently-reported neutron structure exhibits a zwitterionic form. To better compare the structural and dynamical ... ...

    Abstract While the state-of-the-art computational simulations support the neutral state for the catalytic dyad of the SARS-CoV-2 main protease, the recently-reported neutron structure exhibits a zwitterionic form. To better compare the structural and dynamical features of the two charge configurations, we perform a Molecular Dynamics study of the dimeric enzyme in complex with a peptide substrate. The simulations show that the enzyme charge configuration from the neutron structure is not compatible with a catalytically-competent binding mode for peptide substrates.
    MeSH term(s) Amino Acid Sequence ; Catalytic Domain ; Crystallography, X-Ray ; Molecular Dynamics Simulation ; Peptide Hydrolases/chemistry ; Peptides ; Protein Conformation ; SARS-CoV-2/enzymology
    Chemical Substances Peptides ; Peptide Hydrolases (EC 3.4.-)
    Language English
    Publishing date 2021-05-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/d1cc01449h
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: A Quantum Chemical Topology Picture of Intermolecular Electrostatic Interactions and Charge Penetration Energy.

    Jiménez-Grávalos, Fernando / Suárez, Dimas

    Journal of chemical theory and computation

    2021  Volume 17, Issue 8, Page(s) 4981–4995

    Abstract: Based on the Interacting Quantum Atoms approach, we present herein a conceptual and theoretical framework of short-range electrostatic interactions, whose accurate description is still a challenging problem in molecular modeling. For all the noncovalent ... ...

    Abstract Based on the Interacting Quantum Atoms approach, we present herein a conceptual and theoretical framework of short-range electrostatic interactions, whose accurate description is still a challenging problem in molecular modeling. For all the noncovalent complexes in the S66 database, the fragment-based and atomic decomposition of the electrostatic binding energies is performed using both the charge density of the dimers and the unrelaxed densities of the monomers. This energy decomposition together with dispersion corrections gives rise to a pairwise approximation to the total binding energy. It also provides energetic descriptors at varying distance that directly address the atomic and molecular electrostatic interactions as described by point-charge or multipole-based potentials. Additionally, we propose a consistent definition of the charge penetration energy within quantum chemical topology, which is mainly characterized in terms of the intramolecular electrostatic energy. Finally, we discuss some practical implications of our results for the design and validation of electrostatic potentials.
    Language English
    Publishing date 2021-07-19
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.1c00263
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Book ; Online: SARS-CoV-2 Main Protease

    Dimas Suárez / Natalia Díaz

    A Molecular Dynamic Study

    2020  

    Abstract: We provide results from a molecular dynamics simulation of the SARS-CoV-2 main protease in the monomer and dimer states of the native enzyme and also bound to a peptide substrate. ...

    Abstract We provide results from a molecular dynamics simulation of the SARS-CoV-2 main protease in the monomer and dimer states of the native enzyme and also bound to a peptide substrate.
    Keywords Computational Chemistry and Modeling ; COVID-19 ; Molecular Dynamics Simulation Study ; Main Protease Mpro ; covid19
    Publishing date 2020-05-27T05:47:07Z
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: SARS-CoV-2 Main Protease: A Molecular Dynamics Study.

    Suárez, Dimas / Díaz, Natalia

    Journal of chemical information and modeling

    2020  Volume 60, Issue 12, Page(s) 5815–5831

    Abstract: Herein, we investigate the structure and flexibility of the hydrated SARS-CoV-2 main protease by means of 2.0 μs molecular dynamics (MD) simulations in explicit solvent. After having performed electrostatic ... ...

    Abstract Herein, we investigate the structure and flexibility of the hydrated SARS-CoV-2 main protease by means of 2.0 μs molecular dynamics (MD) simulations in explicit solvent. After having performed electrostatic p
    MeSH term(s) Amino Acid Sequence ; COVID-19/metabolism ; Catalytic Domain ; Coronavirus 3C Proteases/metabolism ; Dimerization ; Humans ; Molecular Dynamics Simulation ; Peptides/chemistry ; Peptides/metabolism ; Protein Conformation ; SARS-CoV-2/metabolism ; Static Electricity ; Structure-Activity Relationship ; Substrate Specificity ; Thermodynamics
    Chemical Substances Peptides ; Coronavirus 3C Proteases (EC 3.4.22.28)
    Keywords covid19
    Language English
    Publishing date 2020-08-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.0c00575
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    Zs.A 1230: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (1.OG)
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  8. Article ; Online: Understanding the Conformational Properties of Fluorinated Polypeptides: Molecular Modelling of Unguisin A.

    Díaz, Natalia / Suárez, Dimas

    Journal of chemical information and modeling

    2020  Volume 61, Issue 1, Page(s) 223–237

    Abstract: In this work, we investigate the conformational properties of unguisin A, a natural macrocyclic heptapeptide that incorporates a γ-aminobutyric acid (Gaba), and four of its difluorinated stereoisomers at the Gaba residue. According to nuclear magnetic ... ...

    Abstract In this work, we investigate the conformational properties of unguisin A, a natural macrocyclic heptapeptide that incorporates a γ-aminobutyric acid (Gaba), and four of its difluorinated stereoisomers at the Gaba residue. According to nuclear magnetic resonance (NMR) experiments, their secondary structure depends dramatically on the stereochemistry of the fluorinated carbon atoms. However, many molecular details of the structure and flexibility of these systems remain unknown, so that a rationale of the conformational changes induced by the fluorine atoms in the macrocycle is still missing. To fill this gap, we apply enhanced molecular dynamics (MD) techniques to explore the peptide conformational space in dimethyl sulfoxide solution followed by 4-8 μs of conventional MD simulations that provide extensive equilibrium sampling. The simulations, which compare reasonably well with the NMR-based observations, show that the secondary structure of the macrocycle is altered substantially upon fluorination, except for the (
    MeSH term(s) Molecular Dynamics Simulation ; Peptides ; Peptides, Cyclic ; Protein Conformation ; Protein Structure, Secondary
    Chemical Substances Peptides ; Peptides, Cyclic ; unguisin A
    Language English
    Publishing date 2020-12-16
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.0c00746
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1230: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    ab Jg. 2022: Lesesaal (EG)

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  9. Article: Influence of charge configuration on substrate binding to SARS-CoV-2 main protease

    Díaz, Natalia / Suárez, Dimas

    Chemical communications. 2021 May 27, v. 57, no. 43

    2021  

    Abstract: While the state-of-the-art computational simulations support the neutral state for the catalytic dyad of the SARS-CoV-2 main protease, the recently-reported neutron structure exhibits a zwitterionic form. To better compare the structural and dynamical ... ...

    Abstract While the state-of-the-art computational simulations support the neutral state for the catalytic dyad of the SARS-CoV-2 main protease, the recently-reported neutron structure exhibits a zwitterionic form. To better compare the structural and dynamical features of the two charge configurations, we perform a Molecular Dynamics study of the dimeric enzyme in complex with a peptide substrate. The simulations show that the enzyme charge configuration from the neutron structure is not compatible with a catalytically-competent binding mode for peptide substrates.
    Keywords Severe acute respiratory syndrome coronavirus 2 ; molecular dynamics ; neutrons ; peptides ; proteinases ; zwitterions
    Language English
    Dates of publication 2021-0527
    Size p. 5314-5317.
    Publishing place The Royal Society of Chemistry
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/d1cc01449h
    Database NAL-Catalogue (AGRICOLA)

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  10. Book ; Online: SARS-CoV-2 Main Protease

    Suárez, Dimas / Díaz, Natalia

    A Molecular Dynamic StudySARS-CoV-2 Main Protease: A Molecular Dynamics Study of Native Enzyme and Its Complex with a Peptide Substrate

    2020  

    Keywords covid19
    Publisher American Chemical Society (ACS)
    Publishing country us
    Document type Book ; Online
    DOI 10.26434/chemrxiv.12366584
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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