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  • 1.
    Di Meo, Florent
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Bayach, Imene
    University of Limoges, France.
    Trouillas, Patrick
    University of Limoges, France; Palacky University, Czech Republic.
    Sancho-Garcia, Juan-Carlos
    University of Alicante, Spain.
    Unraveling the performance of dispersion-corrected functionals for the accurate description of weakly bound natural polyphenols2015In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 21, no 11, p. 291-Article in journal (Refereed)
    Abstract [en]

    Long-range non-covalent interactions play a key role in the chemistry of natural polyphenols. We have previously proposed a description of supramolecular polyphenol complexes by the B3P86 density functional coupled with some corrections for dispersion. We couple here the B3P86 functional with the D3 correction for dispersion, assessing systematically the accuracy of the new B3P86-D3 model using for that the well-known S66, HB23, NCCE31, and S12L datasets for non-covalent interactions. Furthermore, the association energies of these complexes were carefully compared to those obtained by other dispersion-corrected functionals, such as B(3) LYP-D3, BP86-D3 or B3P86-NL. Finally, this set of models were also applied to a database composed of seven non-covalent polyphenol complexes of the most interest.

  • 2.
    Fourre, Isabelle
    et al.
    University of Paris 06, France.
    Di Meo, Florent
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering. University of Limoges, France.
    Podloucka, Pavlina
    Palacky University, Czech Republic.
    Otyepka, Michal
    Palacky University, Czech Republic.
    Trouillas, Patrick
    University of Limoges, France; Palacky University, Czech Republic.
    Dimerization of quercetin, Diels-Alder vs. radical-coupling approach: a joint thermodynamics, kinetics, and topological study2016In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 22, no 8, p. 190-Article in journal (Refereed)
    Abstract [en]

    Quercetin is a prototypical antioxidant and prominent member of flavonoids, a large group of natural polyphenols. The oxidation of quercetin may lead to its dimerization, which is a paradigm of the more general polyphenol oligomerization. There exist two opposing mechanisms to describe the dimerization process, namely radical-coupling or Diels-Alder reactions. This work presents a comprehensive rationalization of this dimerization process, acquired from density functional theory (DFT) calculations. It is found that the two-step radical-coupling pathway is thermodynamically and kinetically preferred over the Diels-Alder reaction. This is in agreement with the experimental results showing the formation of only one isomer, whereas the Diels-Alder mechanism would yield two isomers. The evolution in bonding, occurring during these two processes, is investigated using the atoms in molecules (AIM) and electron localization function (ELF) topological approaches. It is shown that some electron density is accumulated between the fragments in the transition state of the radical-coupling reaction, but not in the transition state of the Diels-Alder process.

  • 3.
    Franco-Gonzalez, Juan Felipe
    et al.
    Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Madrid, Spain.
    Cruz, Victor L
    Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Madrid, Spain.
    Ramos, Javier
    Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Madrid, Spain.
    Martínez-Salazar, Javier
    Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Madrid, Spain.
    Conformational flexibility of the ErbB2 ectodomain and trastuzumab antibody complex as revealed by molecular dynamics and principal component analysis.2013In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 19, no 3, p. 1227-1236Article in journal (Refereed)
    Abstract [en]

    Human epidermal growth factor receptor 2 (ErbB2) is a transmembrane oncoprotein that is over expressed in breast cancer. A successful therapeutic treatment is a monoclonal antibody called trastuzumab which interacts with the ErbB2 extracellular domain (ErbB2-ECD). A better understanding of the detailed structure of the receptor-antibody interaction is indeed of prime interest for the design of more effective anticancer therapies. In order to discuss the flexibility of the complex ErbB2-ECD/trastuzumab, we present, in this study, a multi-nanosecond molecular dynamics simulation (MD) together with an analysis of fluctuations, through a principal component analysis (PCA) of this system. Previous to this step and in order to validate the simulations, we have performed a detailed analysis of the variable antibody domain interactions with the extracellular domain IV of ErbB2. This structure has been statically elucidated by x-ray studies. Indeed, the simulation results are in excellent agreement with the available experimental information during the full trajectory. The PCA shows eigenvector fluctuations resulting in a hinge motion in which domain II and C(H) domains approach each other. This move is likely stabilized by the formation of H-bonds and salt bridge interactions between residues of the dimerization arm in the domain II and trastuzumab residues located in the C(H) domain. Finally, we discuss the flexibility of the MD/PCA model in relation with the static x-ray structure. A movement of the antibody toward the dimerization domain of the ErbB2 receptor is reported for the first time. This finding could have important consequences on the biological action of the monoclonal antibody.

  • 4.
    Franco-Gonzalez, Juan Felipe
    et al.
    BIOPHYM, Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Serrano 113 bis, 28006, Madrid, Spain .
    Ramos, Javier
    BIOPHYM, Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Serrano 113 bis, 28006, Madrid, Spain .
    Cruz, Victor L
    BIOPHYM, Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Serrano 113 bis, 28006, Madrid, Spain .
    Martínez-Salazar, Javier
    BIOPHYM, Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Serrano 113 bis, 28006, Madrid, Spain .
    Simulation of homology models for the extracellular domains (ECD) of ErbB3, ErbB4 and the ErbB2-ErbB3 complex in their active conformations.2013In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 19, no 2, p. 931-941Article in journal (Refereed)
    Abstract [en]

    Epidermal growth factor receptors (EGFR) are associated with a number of biological processes and are becoming increasingly recognized as important therapeutic targets against cancer. In this work, we provide models based on homology for the extracellular domains (ECD) of ErbB3 and ErbB4 in their active conformations, including a Heregulin ligand, followed by further refinement of the models by molecular dynamics simulations at atomistic scale. We compare the results with a model built for ErbB2 based on crystallographic information and analyze the common features observed among members of the family, namely, the periscope movement of the dimerization arm and the hinge displacement of domain IV. Finally, we refine a model for the interaction of the ECDs corresponding to a ErbB2-ErbB3 heterodimer, which is widely recognized to have a high impact in cancer development.

  • 5.
    Liu, Yuan
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
    Ojamäe, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
    Fingerprints in IR OH vibrational spectra of H2O clusters from different H-bond conformations by means of quantum-chemical computations2014In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 20, no 6, p. 2281-Article in journal (Refereed)
    Abstract [en]

    The thermodynamic stabilities and IR spectra of the three water clusters (H2O)(20), (H2O)(54,), and (H2O)(100) are studied by quantum-chemical computations. After full optimization of the (H2O)(20,54,100) structures using the hybrid density functional B3LYP together with the 6-31+G(d,p) basis set, the electronic energies, zero-point energies, internal energies, enthalpies, entropies, and Gibbs free energies of the water clusters at 298 K are investigated. The OH stretching vibrational IR spectra of (H2O)(20,54,100) are simulated and split into sub-spectra for different H-bond groups depending on the conformations of the hydrogen bonds. From the computed spectra the different spectroscopic fingerprint features of water molecules in different H-bond conformations in the water clusters are inferred.

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  • 6.
    Oruganti, Baswanth
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    On the possibility to accelerate the thermal isomerizations of overcrowded alkene-based rotary molecular motors with electron-donating or electron-withdrawing substituents2016In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 22, no 9, p. 219-Article in journal (Refereed)
    Abstract [en]

    We employ computational methods to investigate the possibility of using electron-donating or electron-withdrawing substituents to reduce the free-energy barriers of the thermal isomerizations that limit the rotational frequencies achievable by synthetic overcrowded alkene-based molecular motors. Choosing as reference systems one of the fastest motors known to date and two variants thereof, we consider six new motors obtained by introducing electron-donating methoxy and dimethylamino or electron-withdrawing nitro and cyano substituents in conjugation with the central olefinic bond connecting the two (stator and rotator) motor halves. Performing density functional theory calculations, we then show that electron-donating (but not electron-withdrawing) groups at the stator are able to reduce the already small barriers of the reference motors by up to 18 kJ mol(-1). This result outlines a possible strategy for improving the rotational frequencies of motors of this kind. Furthermore, exploring the origin of the catalytic effect, it is found that electron-donating groups exert a favorable steric influence on the thermal isomerizations, which is not manifested by electron-withdrawing groups. This finding suggests a new mechanism for controlling the critical steric interactions of these motors.

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