Transferability, adjustability, and additivity of fuzzy electron density fragments

Mezey, Paul G.

doi:10.1007/0-306-46943-x_4

Cited by 5 publications

(4 citation statements)

References 111 publications

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“…An important special application of these fuzzy fragments is in linear scaling macromolecular quantum chemistry methods. − For a macromolecule M, the nuclear families, eq , are chosen, and for each nuclear family f k a smaller, artificial “parent molecule” M k is constructed. In each M k , the family f k has the same local arrangement and surroundings within some d distance as in the macromolecule M; often, several additional nuclear families f k ′ , surrounding f k are included.…”

Section: Fuzzy Electron Density Fragments In Efficient Linear Scaling...mentioning

confidence: 99%

“…The two main macromolecular AFDF methods are the numerical electron density assembler MEDLA − (molecular electron density “loge” assembler, or molecular electron density “lego” assembler) based on numerically stored electron densities and the more efficient density matrix approach ADMA − (adjustable density matrix assembler), both with a large number of ab initio quality applications to proteins, including bovine insulin, HIV-1 protease, hemoglobin, and other large systems, well over 1000 atoms.…”

Section: Fuzzy Electron Density Fragments In Efficient Linear Scaling...mentioning

confidence: 99%

“…Whereas there are limitations on fragment transferability, adjustability, and additivity, as set by the Hohenberg–Kohn theorem , and by its extension, the holographic electron density theorem, − still, it is possible to obtain better than 1 kcal/mol accuracy by the linear scaling fuzzy fragment approach for proteins relative to traditional and expensive nonfragment quantum chemistry methods …”

Section: Fuzzy Electron Density Fragments In Efficient Linear Scaling...mentioning

confidence: 99%

“…30 Another application, the use of precomputed fuzzy fragments in a "combinatorial quantum chemistry" approach for the quick generation of a large number of approximate macromolecular densities has also been advocated. 31−34 Whereas there are limitations on fragment transferability, adjustability, and additivity, 35 as set by the Hohenberg−Kohn theorem 36,37 and by its extension, the holographic electron density theorem, 38−40 still, it is possible to obtain better than 1 kcal/mol accuracy by the linear scaling fuzzy fragment approach for proteins relative to traditional and expensive nonfragment quantum chemistry methods. 25 ■ QUANTUM CHEMICAL FUNCTIONAL GROUPS DEFINED BY FUZZY ELECTRON DENSITY FRAGMENTS The approach uses some analogies with a pair of interacting molecules, relying on molecular isodensity contour surfaces, MIDCOs, defined for threshold value a as…”

Section: ■ Fuzzy Electron Density Fragments Inmentioning

confidence: 99%

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Fuzzy Electron Density Fragments in Macromolecular Quantum Chemistry, Combinatorial Quantum Chemistry, Functional Group Analysis, and Shape–Activity Relations

Mezey

2014

Acc. Chem. Res.

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Conspectus Just as complete molecules have no boundaries and have "fuzzy" electron density clouds approaching zero density exponentially at large distances from the nearest nucleus, a physically justified choice for electron density fragments exhibits similar behavior. Whereas fuzzy electron densities, just as any fuzzy object, such as a thicker cloud on a foggy day, do not lend themselves to easy visualization, one may partially overcome this by using isocontours. Whereas a faithful representation of the complete fuzzy density would need infinitely many such isocontours, nevertheless, by choosing a selected few, one can still obtain a limited pictorial representation. Clearly, such images are of limited value, and one better relies on more complete mathematical representations, using, for example, density matrices of fuzzy fragment densities. A fuzzy density fragmentation can be obtained in an exactly additive way, using the output from any of the common quantum chemical computational techniques, such as Hartree-Fock, MP2, and various density functional approaches. Such "fuzzy" electron density fragments properly represented have proven to be useful in a rather wide range of applications, for example, (a) using them as additive building blocks leading to efficient linear scaling macromolecular quantum chemistry computational techniques, (b) the study of quantum chemical functional groups, (c) using approximate fuzzy fragment information as allowed by the holographic electron density theorem, (d) the study of correlations between local shape and activity, including through-bond and through-space components of interactions between parts of molecules and relations between local molecular shape and substituent effects, (e) using them as tools of density matrix extrapolation in conformational changes, (f) physically valid averaging and statistical distribution of several local electron densities of common stoichiometry, useful in electron density databank mining, for example, in medicinal drug design, and (g) tools for combinatorial quantum chemistry approaches using fuzzy fragment databanks and rapid construction of a large number of approximate electron densities for large sets of related molecules, relevant in theoretical molecular and nanostructure design.

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Section: Fuzzy Electron Density Fragments In Efficient Linear Scaling...mentioning

confidence: 99%

Section: Fuzzy Electron Density Fragments In Efficient Linear Scaling...mentioning

confidence: 99%

Section: Fuzzy Electron Density Fragments In Efficient Linear Scaling...mentioning

confidence: 99%

Section: ■ Fuzzy Electron Density Fragments Inmentioning

confidence: 99%

See 2 more Smart Citations

Fuzzy Electron Density Fragments in Macromolecular Quantum Chemistry, Combinatorial Quantum Chemistry, Functional Group Analysis, and Shape–Activity Relations

Mezey

2014

Acc. Chem. Res.

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show abstract

Accurate and efficient flux-corrected finite volume approximation for the fragmentation problem

2023

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Fundamental Constraints on Linear Scaling Methods: Relations between the Parts and the Whole in Molecules

Mezey¹,

Maroulis²,

Simos³

2009

AIP Conference Proceedings

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Transferability, adjustability, and additivity of fuzzy electron density fragments

Cited by 5 publications

References 111 publications

Fuzzy Electron Density Fragments in Macromolecular Quantum Chemistry, Combinatorial Quantum Chemistry, Functional Group Analysis, and Shape–Activity Relations

Fuzzy Electron Density Fragments in Macromolecular Quantum Chemistry, Combinatorial Quantum Chemistry, Functional Group Analysis, and Shape–Activity Relations

Accurate and efficient flux-corrected finite volume approximation for the fragmentation problem

Fundamental Constraints on Linear Scaling Methods: Relations between the Parts and the Whole in Molecules

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