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Electrical potential surface of paracetamol showing polar areas in red and blue. The polar surface area (PSA) or topological polar surface area (TPSA) of a molecule is defined as the surface sum over all polar atoms or molecules, primarily oxygen and nitrogen, also including their attached hydrogen atoms.
The van der Waals surface of a molecule is an abstract representation or model of that molecule, illustrating where, in very rough terms, a surface might reside for the molecule based on the hard cutoffs of van der Waals radii for individual atoms, and it represents a surface through which the molecule might be conceived as interacting with other molecules.
Accessible surface area is often used when calculating the transfer free energy required to move a biomolecule from an aqueous solvent to a non-polar solvent, such as a lipid environment. The LCPO method is also used when calculating implicit solvent effects in the molecular dynamics software package AMBER .
The van der Waals force of adhesion is also dependent on the surface topography. If there are surface asperities, or protuberances, that result in a greater total area of contact between two particles or between a particle and a wall, this increases the van der Waals force of attraction as well as the tendency for mechanical interlocking.
The position of each atom is determined by the nature of the chemical bonds by which it is connected to its neighboring atoms. The molecular geometry can be described by the positions of these atoms in space, evoking bond lengths of two joined atoms, bond angles of three connected atoms, and torsion angles (dihedral angles) of three consecutive ...
N is the number of atoms in the surface slab. E bulk is the bulk energy per atom. A is the surface area. For a slab, we have two surfaces and they are of the same type, which is reflected by the number 2 in the denominator. To guarantee this, we need to create the slab carefully to make sure that the upper and lower surfaces are of the same type.
When oxygen atoms release energy after colliding with solar particles, the sky turns red and green, while nitrogen atoms paint it purple and pink. #10 Pink Beach, Padar Island, Komodo National Park
A molecule is composed of one or more chemical bonds between molecular orbitals of different atoms. A molecule may be polar either as a result of polar bonds due to differences in electronegativity as described above, or as a result of an asymmetric arrangement of nonpolar covalent bonds and non-bonding pairs of electrons known as a full ...