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WIREs Comput Mol Sci
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NCIPLOT and the analysis of noncovalent interactions using the reduced density gradient

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Abstract Noncovalent interactions are of utmost importance. However, their accurate treatment is still difficult. This is partially induced by the coexistence of many types of interactions and physical phenomena, which hampers generality in simple treatments. The NCI index has been successfully used for nearly over 10 years in order to identify, analyze, and understand noncovalent interactions in a wide variety of systems, ranging from proteins to molecular crystals. In this work, the development and implications of the method will be reviewed, and modern implementations will be presented. Afterward, some sophisticated examples will be given that showcase the current advances toward the fast, robust, and intuitive identification of noncovalent interactions in real space. This article is categorized under: Software > Molecular Modeling Quantum Computing > Theory Development Structure and Mechanism > Computational Biochemistry and Biophysics
ρ and s along the internuclear axis of a model system that is governed by two weakly interacting exponential cusps
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Evolution of sign(λ2)ρ2 along the 100 dynamics frames of NIAD‐4/Aβ40 integrated over three ranges of sign(λ2)ρ: −0.05 to −0.01 (attractive), −0.01 to 0.01 (van der Waals), 0.01 to 0.05 (repulsive). Black lines are guides to the eyes
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Evolution of sign(λ2)ρ2 along the 100 dynamics frames of Thioflavin‐T/Aβ40 integrated over three ranges of sign(λ2)ρ: −0.05 to −0.01 (attractive), −0.01 to 0.01 (van der Waals), 0.01 to 0.05 (repulsive). Black lines are guides to the eyes
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Structure of an amyloid‐β(1–40) fibril, PDB code 2LMN, and of Thioflavin‐T and NIAD‐4, fluorescent markers for amyloid detection
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Integrals over time for different sign(λ2)ρ intervals. Integration was performed with γref = 0.95 and sref(r) = 1.0
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s(r) = 0.3 isosurface in an intramolecular calculation fo a DNA fragment
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CO2 adsorption on top of different graphene‐like flakes: (a) B‐doped graphene, (b) N‐doped graphene flake, (c) nonsubstituted graphene flake
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s(r) = 0.5 isosurfaces colored by sign(λ2)ρ(r) for several tetrel bonds: (a) FCH3⋯OH2 (b) FCH3⋯NH3 (c) FCH3⋯OCH2 (d) FSiH3⋯OH2 (e) FSiH3⋯NH3 (f) FSiH3⋯OCH2. C, H, Si, F, N, and O atoms are colored gray, white, orange, green, blue, and red, respectively
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Schematic representation of a three‐step adaptive grid procedure with αl = 2. Active regions are colored purple, colorless areas are inactive
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s(r) against ρ(r) plots for (a) the acetic acid molecule and (b) the acetic acid dimer as in Figure 3
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2D NCI analysis of the acetic acid dimer using densities from different sources: (a) DFT calculation on the dimer (b) atomic densities (promolecular)
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s(r) = 0.5 isosurfaces colored by sign(λ2)ρ(r) for the acetic acid dimer with densities from different sources: (a) DFT calculation of the dimer. (b) Natural‐Bond Orbital localized DFT calculation of each monomer. (c) DFT calculation on each monomer. (d) s(r) = 0.4 isosurface using atomic densities (promolecular)
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s(r) = 0.5 isosurfaces and corresponding 2D plots colored by sign(λ2)ρ(r) for several dimers in 3D and 2D. (a) Hypoxanthine–adenine, (b) hypoxanthine–cytosine, (c) hypoxanthine–uracil
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s(r) = 0.5 isosurfaces on the acetic acid dimer. (a) with a ρ(r) = 0.05 cutoff (b) with a ρ(r) = 0.08 cutoff (c) without any cutoff
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χ, ELF, and LOL along the Z‐axis of the CO2 molecule. Nuclear positions are indicated by the respective atomic symbols
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Structure and Mechanism > Computational Biochemistry and Biophysics
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