How many types of atoms are there
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Types of Atoms: A Comprehensive Overview
Introduction to Atom Types
Atoms, the fundamental building blocks of matter, can be classified into various types based on their properties and interactions. This article synthesizes research findings to provide a clear understanding of the different types of atoms identified in scientific studies.
Classification Based on Atomic Properties
Quantum Chemical Topology (QCT) Atom Types
Quantum Chemical Topology (QCT) offers a method to classify atoms by computing their properties directly from molecular electron densities. In a study involving 20 amino acids and smaller derived molecules, researchers identified 760 topological atoms, which were further categorized into specific types based on seven atomic properties. These properties include kinetic energy, volume, population, and various multipole moments. The study distinguished 21 types of carbon atoms, 7 types of hydrogen, 2 types of nitrogen, 6 types of oxygen, and 6 types of sulfur atoms3.
Force-Field Design and Atom Types
The QCT method was compared with the assisted model building with energy refinement (AMBER) force field, revealing that QCT provides a more unbiased and accurate classification of atom types. This comparison highlighted the potential of QCT in designing new force fields or improving existing ones3.
Crystalline Networks and Atom Types
Enumeration of Crystalline Networks
In the context of crystalline structures, atoms can be part of various networks. A significant study enumerated all possible networks of atoms in inorganic structures, focusing on 4-connected networks where each atom is connected to exactly four neighbors. This research identified 9 uninodal, 117 binodal, and 926 trinodal topological types of networks derived from simple tilings based on tetrahedra. Additionally, 145 more distinct uninodal networks were identified based on more complex tiling units2.
Atomic Physicochemical Parameters
Hydrophobicity and Atom Types
Another approach to classifying atom types involves their physicochemical parameters, particularly hydrophobicity. A study classified carbon, hydrogen, oxygen, nitrogen, sulfur, and halogens into 110 atom types based on their hydrophobic contributions. These contributions were evaluated using the log P (water-octanol partition coefficient) values of 494 molecules. This classification method provided a robust model for predicting the hydrophobicity of various compounds5.
Conclusion
The classification of atoms into different types is a complex but essential task in understanding their behavior and interactions. Methods such as Quantum Chemical Topology and systematic enumeration of crystalline networks provide detailed and accurate classifications. These classifications are crucial for applications in force-field design, material science, and understanding molecular interactions. The ongoing research continues to refine and expand our understanding of the diverse types of atoms in various contexts.
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Number of Single, Double, and Triple Clusters in a System Containing Two Types of Atoms
The probability of a type A atom being in a cluster of one, two, or three A atoms in a lattice varies with concentration, and is influenced by the number of atoms in the lattice.
Highly CitedSystematic enumeration of crystalline networks
This study identifies 9,117 and 926 distinct topological types of 4-connected uninodal, binodal, and trinodal networks, providing a partial solution to the systematic enumeration of crystalline networks in inorganic structures.
Highly CitedAtomic properties of amino acids: computed atom types as a guide for future force-field design.
Quantum chemical topology (QCT) is a useful guide for designing new force fields or improving existing ones, as it provides unbiased atom type determination compared to chemical intuition and assumptions.
Highly CitedAtomic properties of selected biomolecules: quantum topological atom types of carbon occurring in natural amino acids and derived molecules.
This study identifies 213 unique quantum topological carbons in natural amino acids and derived molecules, revealing their atomic properties and their role in determining the structure of these molecules.
Atomic Physicochemical Parameters for Three‐Dimensional Structure‐Directed Quantitative Structure‐Activity Relationships I. Partition Coefficients as a Measure of Hydrophobicity
Atomic physicochemical parameters can effectively predict hydrophobicity in compounds, aiding in three-dimensional receptor mapping and structure-activity relationships.
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A minimal set of 18 atom types efficiently represents the spectrum of packing in proteins, revealing inconsistencies in traditional chemical typing schemes.
Virtual Exploration of the Chemical Universe up to 11 Atoms of C, N, O, F: Assembly of 26.4 Million Structures (110.9 Million Stereoisomers) and Analysis for New Ring Systems, Stereochemistry, Physicochemical Properties, Compound Classes, and Drug Discovery
The GDB database contains 26.4 million molecules (110.9 million stereoisomers) and offers potential for drug discovery by virtual screening for kinase inhibitors, G-protein coupled receptor ligands, and ion-channel modulators.
Highly CitedThe number of atoms in a primefree atomic domain
An atomic domain with precisely n atoms and m maximal ideals can exist without prime elements, using commutative algebra, algebraic number theory, and additive number theory.
Atom, atom-type, and total linear indices of the "molecular pseudograph's atom adjacency matrix": application to QSPR/QSAR studies of organic compounds.
The molecular pseudograph's atom adjacency matrix effectively predicts boiling point, partition coefficient, specific rate constant, and antibacterial activity of organic compounds, offering potential for computer-aided drug design.
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