A Step toward the Quantification of Noncovalent Interactions in Large Biological Systems: The Independent Gradient Model-Extremely Localized Molecular Orbital Approach

Wieduwilt, Erna K.; Boisson, Jean-Charles; Terraneo, Giancarlo; Hénon, Éric; Genoni, Alessandro

doi:10.1021/acs.jcim.0c01188

Cited by 15 publications

(12 citation statements)

References 66 publications

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“…The blue region shows hydrogen bond, which is mainly located near carbonyl oxygen, methyl oxygen, and phenolic hydroxyl oxygen. In the scatter plot, ρ stands for the total electron density, λ 2 stands for the sign of the second eigenvalue of the electron density hessian [ 27 ], δ g is the local descriptor which reflects the interaction region between two (or more) fragments [ 28 ]. The green, blue and red represented van der Waals force, hydrogen bond and repulsion effect, respectively.…”

Section: Resultsmentioning

confidence: 99%

Interaction between Curcumin and β-Casein: Multi-Spectroscopic and Molecular Dynamics Simulation Methods

2021

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Effect of temperature and pH on the interaction of curcumin with β-casein was explored by fluorescence spectroscopy, ultraviolet-visible spectroscopy and molecular dynamics simulation. The spectroscopic results showed that curcumin could bind to β-casein to form a complex which was driven mainly by electrostatic interaction. The intrinsic fluorescence of β-casein was quenched by curcumin through static quenching mechanism. The binding constants of curcumin to β-casein were 6.48 × 104 L/mol (298 K), 6.17 × 104 L/mol (305 K) and 5.73 × 104 L/mol (312 K) at pH 2.0, which was greater than that (3.98 × 104 L/mol at 298 K, 3.90 × 104 L/mol at 305 K and 3.41 × 104 L/mol at 312 K) at pH 7.4. Molecular docking study showed that binding energy of β-casein-curcumin complex at pH 2.0 (−7.53 kcal/mol) was lower than that at pH 7.4 (−7.01 kcal/mol). The molecular dynamics simulation study showed that the binding energy (−131.07 kJ/mol) of β-casein-curcumin complex was relatively low at pH 2.0 and 298 K. α-Helix content in β-casein was decreased and random coil content was increased in the presence of curcumin. These results can promote a deep understanding of interaction between curcumin and β-casein and provide a reference for improving the bioavailability of curcumin.

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Section: Resultsmentioning

confidence: 99%

Interaction between Curcumin and β-Casein: Multi-Spectroscopic and Molecular Dynamics Simulation Methods

2021

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“…Several analytical tools derived from QTAIM can qualitatively and quantitatively address the relevance of NCIs within RCs. NCIPLOT, IQA, the independent gradient model (IGM), and the intrinsic bond strength index (IBSI) provide qualitative and quantitative levers to address local NCIs at the key “reactant complex” stage (Figure a). These new tools represent a promising arsenal to address the question of reactivity analysis and prediction.…”

Section: Reactivitymentioning

confidence: 99%

“…(a) IGM and IBSI analyses , , of weak interactions and NCIs in an RC as an expedient to rationalize chemoselectivity toward products ( P1 and P2 ). A and B are any user-defined fragments of the considered RC.…”

Section: Reactivitymentioning

confidence: 99%

Noncovalent Interactions in Organometallic Chemistry: From Cohesion to Reactivity, a New Chapter

Cornaton

Djukic

2021

Acc. Chem. Res.

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Metrics & More Article Recommendations * sı Supporting Information CONSPECTUS: Noncovalent interactions (NCIs) have long interested a vast community of chemists who investigated their "canonical categories" derived from descriptive crystallography, e.g., H-bonds, π−π interactions, halogen/chalcogen/tetrel bonds, cation−π and C−H−π interactions, metallophilic interactions in the broad sense, etc. Recent developments in theoretical chemistry have enabled the treatment of noncovalent interactions under new auspices: dispersion-force-inclusive density functionals have emerged, which are reliable for modeling small to large molecular systems. It is possible to perform the full analysis of the contributions of London, Debye, and Keesom forces, i.e., the main components of van der Waals forces, by the DFT-D and ab initio methods at a reasonable computational cost. Our research has been focusing for now 15 years on the role of NCIs in the cohesion of organometallic complexes. NCIs are not only effective in Werner's secondary coordination sphere but also in the metal's primary one. The stabilization of electron-unsaturated transition metal complexes by hemichelation, metal−metal donor−acceptor complexes, and self-aggregation of cationic Rh(I) chromophores have indeed outlined the significance of the London dispersion force as an attractive force operating throughout the whole molecule or molecular assembly. The recent outburst of interest in C−H bond functionalization led us to address the broader question of reaction and catalyst engineering: although one can now satisfactorily analyze bonding and molecular cohesion in transition-metalbased organometallic systems, can modern theoretical methods guide reactivity exploration and the engineering of novel catalytic systems? We addressed this question by investigating the ambiphilic metal−ligand activation/concerted metalation−deprotonation mechanism involved in transition-metal-catalyzed directed C−H bond functionalization. This endeavor was initiated having in scope the construction of a rationale for the transposition of 4−5d metal chemistry to earth-abundant 3d metals. In this base-assisted mechanism of C−H bond metalation, agostic interactions are necessary but not sufficient because C−H bond breaking actually relies on the attractive NCI coding of a proton-transfer step and the minimization of metal−H repulsion. This Account introduces the recent shift of our research toward the construction of an NCI-inclusive paradigm of chemical reactivity engineering based on experimental efforts propped up by state-of-the-art theoretical tools.

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“…Along the same lines, the ELMO libraries have also been recently interfaced with the IGM, for which the ELMO-based analyses were shown to be better than the promolecular ones even from a quantitative point of view. 43 As mentioned above, the second important limitation of the standard NCI index descriptions used to be the complete absence of quantitative information. In response to this shortcoming, some of us have recently proposed an improved version of the NCI index technique, 24 where integrals of powers of the electron density over regions of noncovalent interactions are exploited to extract quantitative values that can be directly associated with interaction energies (see Subsection 2.1 for more details).…”

Section: Introductionmentioning

confidence: 99%

Extracting Quantitative Information at Quantum Mechanical Level from Noncovalent Interaction Index Analyses

Wieduwilt

Boto

Macetti

et al. 2023

J. Chem. Theory Comput.

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The noncovalent interaction (NCI) index is nowadays a well-known strategy to detect NCIs in molecular systems. Even though it initially provided only qualitative descriptions, the technique has been recently extended to also extract quantitative information. To accomplish this task, integrals of powers of the electron distribution were considered, with the requirement that the overall electron density can be clearly decomposed as sum of distinct fragment contributions to enable the definition of the (noncovalent) integration region. So far, this was done by only exploiting approximate promolecular electron densities, which are given by the sum of spherically averaged atomic electron distributions and thus represent too crude approximations. Therefore, to obtain more quantum mechanically (QM) rigorous results from NCI index analyses, in this work, we propose to use electron densities obtained through the transfer of extremely localized molecular orbitals (ELMOs) or through the recently developed QM/ELMO embedding technique. Although still approximate, the electron distributions resulting from the abovementioned methods are fully QM and, above all, are again partitionable into subunit contributions, which makes them completely suitable for the NCI integral approach. Therefore, we benchmarked the integrals resulting from NCI index analyses (both those based on the promolecular densities and those based on ELMO electron distributions) against interaction energies computed at a high quantum chemical level (in particular, at the coupled cluster level). The performed test calculations have indicated that the NCI integrals based on ELMO electron densities outperform the promolecular ones. Furthermore, it was observed that the novel quantitative NCI−(QM/)ELMO approach can be also profitably exploited both to characterize and evaluate the strength of specific interactions between ligand subunits and protein residues in protein−ligand complexes and to follow the evolution of NCIs along trajectories of molecular dynamics simulations. Although further methodological improvements are still possible, the new quantitative ELMO-based technique could be already exploited in situations in which fast and reliable assessments of NCIs are crucial, such as in computational high-throughput screenings for drug discovery.

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A Step toward the Quantification of Noncovalent Interactions in Large Biological Systems: The Independent Gradient Model-Extremely Localized Molecular Orbital Approach

Cited by 15 publications

References 66 publications

Interaction between Curcumin and β-Casein: Multi-Spectroscopic and Molecular Dynamics Simulation Methods

Interaction between Curcumin and β-Casein: Multi-Spectroscopic and Molecular Dynamics Simulation Methods

Noncovalent Interactions in Organometallic Chemistry: From Cohesion to Reactivity, a New Chapter

Extracting Quantitative Information at Quantum Mechanical Level from Noncovalent Interaction Index Analyses

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