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- Brinck, Tore, Professor, 1965-, et al.
(författare)
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The Importance of Electrostatics and Polarization for Noncovalent Interactions : Ionic Hydrogen Bonds vs Ionic Halogen Bonds
- 2022
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Ingår i: Journal of Molecular Modeling. - : Springer Nature. - 1610-2940 .- 0948-5023. ; 28:9
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Tidskriftsartikel (refereegranskat)abstract
- A series of 26 hydrogen-bonded complexes between Br- and halogen, oxygen and sulfur hydrogen-bond (HB) donors is investigated at the M06-2X/6-311 +G(2df,2p) level of theory. Analysis using a model in which Br- is replaced by a point charge shows that the interaction energy (Delta E-Int) of the complexes is accurately reproduced by the scaled interaction energy with the point charge (Delta E-Int(PC)). This is demonstrated by Delta E-Int = 0.86 Delta E-Int(PC) with a correlation coefficient, R-2=0.999. The only outlier is (Br-H-Br)(-), which generally is classified as a strong charge-transfer complex with covalent character rather than a HB complex. Delta E-Int(PC) can be divided rigorously into an electrostatic contribution (Delta E-ES(PC)) and a polarization contribution (Delta E-pol(PC)).Within the set of HB complexes investigated, the former varies between -7.2 and -32.7 kcal mol(-1), whereas the latter varies between -1.6 and -11.5 kcal mol(-1). Compared to our previous study of halogen-bonded (XB) complexes between Br and C-Br XB donors, the electrostatic contribution is generally stronger and the polarization contribution is generally weaker in the HB complexes. However, for both types of bonding, the variation in interaction strength can be reproduced accurately without invoking a charge-transfer term. For the Br-center dot center dot center dot HF complex, the importance of charge penetration on the variation of the interaction energy with intermolecular distance is investigated. It is shown that the repulsive character of Delta E-Int at short distances in this complex to a large extent can be attributed to charge penetration.
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| 3. |
- Houshmand, F., et al.
(författare)
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Exciton effect in new generation of carbon nanotubes : graphdiyne nanotubes
- 2020
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Ingår i: Journal of Molecular Modeling. - : Springer. - 1610-2940 .- 0948-5023. ; 26:7, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- Graphdiyne-based nanotubes (GDNTs) are a novel type of carbon nanotubes. While conventional carbon nanotubes (CNTs) aregenerated by rolling graphene sheets, GDNTs are generated by rolling sheets that are similar to graphene but where the edges areelongated by the introduction of additional acetylene bonds between vertices (C6 aromatic rings). Such nanotubes are predicted tohave many useful practical applications, but a thorough understanding of the relationship between their structure and theirphysical properties is still missing. We present a theoretical study of the electronic and optical properties of GDNTs. Thestructural, electronic, and optical properties of GDNTs with different diameters (i.e., 2–10 additional acetylene bonds) havebeen studied systematically by using density function theory (DFT) and self-consistent charge density functional tight-binding(SCC-DFTB) and by solving the Bethe–Salpeter equation (BSE), with and without considering the electron-hole interactions.The results indicate that the GDNTs are semiconductors with the direct band gap in close range, which is beneficial forphotoelectronic devices and applications. Moreover, the absorption spectra of the GDNTs with different edge structures, (armchair,and zigzag) revealed little differences between the optical spectra of armchair and zigzag GDNTs, which could mean thatfine separation between those structures (a process that is likely difficult and expensive in practice) will not be necessary.Importantly, the nanotubes were highly stable based on their cohesive energies, and their exciton binding energies were as largeas about ~ 1 eV. From a methodological point of view, SCC-DFTB was found to be in agreement with more elaborate DFTcalculations for most systems.
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| 4. |
- Rovaletti, Anna, et al.
(författare)
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QM/MM study of the binding of H2 to MoCu CO dehydrogenase : development and applications of improved H2 van der Waals parameters
- 2021
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Ingår i: Journal of Molecular Modeling. - : Springer Science and Business Media LLC. - 1610-2940 .- 0948-5023. ; 27:3
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Tidskriftsartikel (refereegranskat)abstract
- The MoCu CO dehydrogenase enzyme not only transforms CO into CO2 but it can also oxidise H2. Even if its hydrogenase activity has been known for decades, a debate is ongoing on the most plausible mode for the binding of H2 to the enzyme active site and the hydrogen oxidation mechanism. In the present work, we provide a new perspective on the MoCu-CODH hydrogenase activity by improving the in silico description of the enzyme. Energy refinement—by means of the BigQM approach—was performed on the intermediates involved in the dihydrogen oxidation catalysis reported in our previously published work (Rovaletti, et al. “Theoretical Insights into the Aerobic Hydrogenase Activity of Molybdenum–Copper CO Dehydrogenase.” Inorganics 7 (2019) 135). A suboptimal description of the H2–HN(backbone) interaction was observed when the van der Waals parameters described in previous literature for H2 were employed. Therefore, a new set of van der Waals parameters is developed here in order to better describe the hydrogen–backbone interaction. They give rise to improved binding modes of H2 in the active site of MoCu CO dehydrogenase. Implications of the resulting outcomes for a better understanding of hydrogen oxidation catalysis mechanisms are proposed and discussed.
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| 5. |
- Zhu, Lijuan, et al.
(författare)
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Binding modes of cabazitaxel with the different human beta-tubulin isotypes : DFT and MD studies
- 2020
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Ingår i: Journal of Molecular Modeling. - : Springer Science and Business Media LLC. - 1610-2940 .- 0948-5023. ; 26:6
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Tidskriftsartikel (refereegranskat)abstract
- Taxanes (paclitaxel, docetaxel, cabazitaxel) are anticancer drugs as microtubule inhibitors. Following our previous studies on paclitaxel and docetaxel, in this work, we examine cabazitaxel and compare these three taxenes. The binding interaction of three taxanes with various beta-tubulin isotypes is studied by homology modeling, molecular docking, and molecular dynamics simulations. The results show that the effects of docetaxel on beta I-tubulin (- 29.5 kcal/mol) and of paclitaxel on beta IIa-tubulin (- 25.5 kcal/mol) are much stronger than their effects on beta III-tubulin (- 17.8 kcal/mol and - 8.6 kcal/mol, respectively). However, the effect of cabazitaxel on beta III-tubulin (- 23.0 kcal/mol) is comparable with that on beta I-tubulin (- 24.0 kcal/mol) and beta IIa-tubulin (- 25.9 kcal/mol), consistent with the fact that overexpression of beta III-tubulin increases the drug resistance to paclitaxel and docetaxel, but has little influence for cabazitaxel. This theoretical research supports the use of cabazitaxel for patients who are resistant to the action of paclitaxel and docetaxel.
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