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Several sets of OPLS parameters have been published. There is OPLS-ua (united atom), which includes hydrogen atoms next to carbon implicitly in the carbon parameters, and can be used to save simulation time. OPLS-aa (all atom) includes every atom explicitly.
The total Coulomb energy is a sum over all pairwise combinations of atoms and usually excludes 1, 2 bonded atoms, 1, 3 bonded atoms, as well as 1, 4 bonded atoms [clarify]. [ 10 ] [ 11 ] [ 12 ] Atomic charges can make dominant contributions to the potential energy, especially for polar molecules and ionic compounds, and are critical to simulate ...
A major obstacle was the poor definition of atomic charges in molecular models, especially for inorganic compounds, due to reliance on quantum chemistry calculations and partitioning methods that may be suitable for field-based but not for point-based charge distributions necessary in force fields.
Like the periodic table, the list below organizes the elements by the number of protons in their atoms; it can also be organized by other properties, such as atomic weight, density, and electronegativity. For more detailed information about the origins of element names, see List of chemical element name etymologies.
An ion is an atom (or group of atoms) that has lost one or more electrons, giving it a net positive charge (cation), or that has gained one or more electrons, giving it a net negative charge (anion). Monatomic ions are formed from single atoms, while polyatomic ions are formed from two or more atoms that have been bonded together, in each case ...
In atomic physics, the effective nuclear charge of an electron in a multi-electron atom or ion is the number of elementary charges an electron experiences by the nucleus. It is denoted by Z eff . The term "effective" is used because the shielding effect of negatively charged electrons prevent higher energy electrons from experiencing the full ...
In chemistry, the oxidation state, or oxidation number, is the hypothetical charge of an atom if all of its bonds to other atoms are fully ionic. It describes the degree of oxidation (loss of electrons) of an atom in a chemical compound. Conceptually, the oxidation state may be positive, negative or zero.
This page shows the electron configurations of the neutral gaseous atoms in their ground states. For each atom the subshells are given first in concise form, then with all subshells written out, followed by the number of electrons per shell. For phosphorus (element 15) as an example, the concise form is [Ne] 3s 2 3p 3.