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A molecule is a group of atoms held together in a specific arrangement by chemical bonds. For example, one water molecule H2O, is consisted of two hydrogens atom and one oxygen atom held together by covalent bond.
One water molecule is considered as a discrete molecule. Water itself is made up of a lot of discrete water molecules held together by bonds.
The regular arrangement of molecules can be explained by the electronic arrangement of the molecule itself. Electrons are shared between hydrogen and oxygen atom. However, the share is not equal. Oxygen atom is occupying the shared electrons most of the time. As a result, the oxygen atom is slightly charged negatively, while the hydrogen atoms are charged slightle positively.
The negative part of the water molecule (oxygen part) attracts the positive part of another water molecule (hydrogen part of another water molecule). This is the bonding between water molecules and the negative always attracts positive, so the arrangment is regular.