A Fundamental Relation of Molecular Informatics on the Information-Carrying Properties of Density Functions

2007 ◽  
Vol 72 (2) ◽  
pp. 153-163 ◽  
Author(s):  
Paul G. Mezey
Keyword(s):  
Electron Density ◽  
Complete Information ◽  
Molecular Shape ◽  
Density Theorem ◽  
Fundamental Relation ◽  
Electron Densities ◽  
Large Molecules ◽  
Topological Features ◽  
Fundamental Information ◽  
Molecular Electron

The molecular electron density carries the complete information about the molecule. This information is stored in the shape and more general topological features of molecular electron densities. A fundamental relation of molecular informatics, building on the Hohenberg-Kohn theorem, is the holographic electron density theorem: any nonzero volume part of a molecular electron density in a non-degenerate electronic ground state contains the complete information about all properties of the entire molecule. This fundamental feature of all molecules applies to all exhibited and also to all latent molecular properties, where latent properties are those not normally exhibited, only in response to some external stimulus. Recently it has become feasible to compute ab initio quality electron densities and approximate forces acting on individual nuclei in large molecules, even those beyond the thousand atom range, such as proteins. The newly expanded size range where reliable modelling methods can be also applied extends the role of detailed molecular shape analysis to macromolecules. In this context, it has become possible to study how the fundamental information-carrying properties of electron density take a newly recognized role influencing the predominance of specific nuclear conformations within the family of astronomically many potentially stable conformations of some macromolecules. Some special problems and results are discussed.

scholarly journals Positron annihilation and electron densities in organic liquids

1974 ◽  
Vol 27 (5) ◽  
pp. 1125 ◽  
Author(s):  
BJ Brown
Keyword(s):  
Positron Annihilation ◽  
Electron Density ◽  
Chain Length ◽  
Atomic Number ◽  
Aliphatic Hydrocarbons ◽  
Organic Liquids ◽  
Electron Densities ◽  
Effective Electron ◽  
Molecular Electron ◽  
Aromatic Systems

The effective electron density for positron annihilation in substituted aliphatic and aromatic liquid compounds has been determined. For the aliphatic hydrocarbons the molecular electron density Ne increases linearly with an increase in chain length and is equal to the sum of the partial electron densities of the substituent methyl (Ne(CH3) = 1.18) and methylene (Ne(CH2) = 1.28) groups.The values are approximately 10% lower for aromatic systems. The partial electron densities of substituted halogen atoms increase with atomic number and are: fluorine (9.3), chlorine (10.0), bromine (14.4) and iodine (23.0). For the aliphatic alcohols the partial Ne(OH) value decreases from 1.35 in methanol to 0.86 in octanol.

scholarly journals Localizing electron density errors in density functional theory

2019 ◽  
Vol 21 (37) ◽  
pp. 20927-20938 ◽  
Author(s):  
Rubén Laplaza ◽  
Victor Polo ◽  
Julia Contreras-García
Keyword(s):  
Density Functional Theory ◽  
Electron Density ◽  
Quantum Chemical ◽  
Density Functional ◽  
Electron Densities ◽  
Functional Theory ◽  
Chemical Topology ◽  
Molecular Electron ◽  
Quantum Chemical Topology

The accuracy of different density functional approximations is assessed through the use of quantum chemical topology on molecular electron densities.

MOLECULAR FACE — A NOVEL MOLECULAR MODEL SHOWING BOTH MOLECULAR SPATIAL CONTOUR AND FRONTIER ELECTRON DENSITY

2008 ◽  
Vol 07 (03) ◽  
pp. 303-315 ◽  
Author(s):  
DONG-XIA ZHAO ◽  
ZHONG-ZHI YANG
Keyword(s):  
Electron Density ◽  
Molecular Model ◽  
Molecular Shape ◽  
Spatial Knowledge ◽  
Significant Feature ◽  
Molecular Fingerprint ◽  
Molecular Electron ◽  
Frontier Electron Density ◽  
Van Der Waals Surface ◽  
Accessible Surface

The spatial knowledge is the first one of all information about an object. Molecular shape and size, molecular van der Waals surface and/or solvent-accessible surface etc. have been widely studied and applied. This paper is to show that a molecular face (MF) for a molecule may be defined uniquely and intrinsically via the molecular intrinsic characteristic contours (MICC) with coding the molecular electron density (ED) as the fourth dimension. The significant feature of an MF provides both molecular spatial appearance and its frontier electron density, being an intuitive picture as a molecular fingerprint or face. With simple examples, the physical significance of an MF is then demonstrated.

PubChem and ChEMBL Beyond Lipinski

2019 ◽  
Author(s):  
Jean-Louis Reymond ◽  
Mahendra Awale ◽  
Daniel Probst ◽  
Alice Capecchi
Keyword(s):  
Nearest Neighbor ◽  
Molecular Shape ◽  
Biological Properties ◽  
Web Based ◽  
Large Molecules ◽  
Interactive Tools ◽  
Small Molecule Drugs ◽  
Pubchem Database ◽  
Nearest Neighbor Searches ◽  
Insight Into

<p>Seven million of the currently 94 million entries in the PubChem database break at least one of the four Lipinski constraints for oral bioavailability, 183,185 of which are also found in the ChEMBL database. These non-Lipinski PubChem (NLP) and ChEMBL (NLC) subsets are interesting because they contain new modalities that can display biological properties not accessible to small molecule drugs. Unfortunately, the current search tools in PubChem and ChEMBL are designed for small molecules and are not well suited to explore these subsets, which therefore remain poorly appreciated. Herein we report MXFP (macromolecule extended atom-pair fingerprint), a 217-D fingerprint tailored to analyze large molecules in terms of molecular shape and pharmacophores. We implement MXFP in two web-based applications, the first one to visualize NLP and NLC interactively using Faerun (http://faerun.gdb.tools/), the second one to perform MXFP nearest neighbor searches in NLP (http://similaritysearch.gdb.tools/). We show that these tools provide a meaningful insight into the diversity of large molecules in NLP and NLC. The interactive tools presented here are publicly available at http://gdb.unibe.ch and can be used freely to explore and better understand the diversity of non-Lipinski molecules in PubChem and ChEMBL.</p>

Understanding the molecular mechanism of the stereoselective conversion of N-trialkylsilyloxy nitronates into bicyclic isoxazoline derivatives

2021 ◽  
Author(s):  
Agnieszka Kącka-Zych ◽  
Radomir Jasinski
Keyword(s):  
Density Functional Theory ◽  
Molecular Mechanism ◽  
Electron Density ◽  
Density Functional ◽  
Dft Method ◽  
Functional Theory ◽  
Molecular Electron ◽  
Molecular Electron Density Theory

Conversion of N-trialkylsilyloxy nitronates into bicyclic isoxazoline derivatives has been explored using Density Functional Theory (DFT) method within the context of the Molecular Electron Density Theory (MEDT) at the B97XD(PCM)/6-311G(d,p)...

scholarly journals A molecular electron density theory study of the [3 + 2] cycloaddition reaction of nitrones with ketenes

2017 ◽  
Vol 15 (7) ◽  
pp. 1618-1627 ◽  
Author(s):  
Mar Ríos-Gutiérrez ◽  
Andrea Darù ◽  
Tomás Tejero ◽  
Luis R. Domingo ◽  
Pedro Merino
Keyword(s):  
Electron Density ◽  
Cycloaddition Reaction ◽  
Molecular Electron ◽  
One Step ◽  
Molecular Electron Density Theory ◽  
Electrophilic Character

The zw-type 32CA reactions of nitrones with ketenes are controlled by the nucleophilic character of the nitrone and the electrophilic character of the ketene. They are chemo- and regio-selective and the use of electrophilic ketenes changes the mechanism from one-step to two-step.

scholarly journals ELECTRON DENSITY STUDIES ON THE REGIOSELECTIVITY OF DEPROTONATION REACTIONS

2014 ◽  
Vol 70 (a1) ◽  
pp. C287-C287
Author(s):  
Juan Van der Maelen ◽  
Javier Cabeza
Keyword(s):  
Electron Density ◽  
Theoretical Calculations ◽  
Density Ratio ◽  
Atomic Charge ◽  
Heterocyclic Ring ◽  
Bond Critical Point ◽  
Electron Densities ◽  
Total Energy Density ◽  
Topological Parameters ◽  
Alkyl Groups

The C-alkyl groups of cationic triruthenium cluster complexes of the type [Ru3(µ-H)(µ-κ2N1,C2-EtnMemPyHk)(CO)10]+ (EtnMemPyHk represents a generic C-alkyl-N-methyl-pyrazium species) have been deprotonated to give kinetic products that contain unprecedented C-alkylidene derivatives and maintain the original edge-bridged decacarbonyl structure. When the starting complexes contain various C-alkyl groups, the selectivity of these deprotonation reactions is related to the atomic charges of the alkyl H atoms, as suggested by DFT/natural-bond orbital (NBO) calculations. Three additional electronic properties of the C-alkyl C-H bonds have also been found to correlate with the experimental regioselectivity since, in all cases, the deprotonated C-H bond has the smallest electron density at the bond critical point (bcp), the greatest Laplacian of the electron density at the bcp, and the greatest total energy density ratio at the bcp (computed by using the quantum theory of atoms in molecules, QTAIM). The kinetic decacarbonyl products evolve, under appropriate reaction conditions that depend upon the position of the C-alkylidene group in the heterocyclic ring, towards face-capped nonacarbonyl derivatives (thermodynamic products). Theoretical calculations support the proposal that the selectivity of these deprotonation reactions is primarily determined by the atomic charge of the alkyl H atoms: the higher the charge the easier the deprotonation when the starting complexes contain various C-alkyl groups. On the other hand, although QTAIM results have been obtained here only from theoretical electron densities for the above clusters, comparisons with local and integral topological parameters derived from both experimental and theoretical electron densities for the related triruthenium complex [Ru3(μ-H)2(μ3-MeImCH)(CO)9] (Me2Im = 1,3-dimethylimidazol-2-ylidene) may easily be made.

Unveiling the Regioselectivity in Electrophilic Aromatic Substitution Reactions of Deactivated Benzenes through Molecular Electron Density Theory

2021 ◽  
Author(s):  
Luis R. Domingo ◽  
Mar Ríos-Gutiérrez ◽  
María José Aurell
Keyword(s):  
Electron Density ◽  
Electrophilic Aromatic Substitution ◽  
Benzene Derivatives ◽  
Aromatic Substitution ◽  
Substitution Reactions ◽  
Molecular Electron ◽  
Molecular Electron Density Theory

The origin of the meta regioselectivity in electrophilic aromatic substitution (EAS) reactions of deactivated benzene derivatives is herein analysed through Molecular Electron Density Theory (MEDT). To this end, the EAS...

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