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Introducing Hydrogen atoms to a molecule







To introduce hydrogen atoms to molecules so as to balance all the atoms in the molecule according to their valency. 





Hydrogen is the first element in periodic table with the symbol H. It is formed by a nucleus with one unit of positively charged proton and one unit of negatively charged electron. In normal conditions it is colorless, non-toxic, tasteless, odorless and highly explosive gas formed by diatomic molecules, H2. It is the most abundant chemical element and main compound of almost all organic matter. The atomic number of hydrogen is 1 and the atomic weight 1,00797 g/mol. Since hydrogen has the lowest atomic weight of any substance, it has very low density in its liquid and gaseous states.


There are three naturally occupying hydrogen isotopes are there. They are protium, deuterium and tritium. Protium contains a nucleus with a single proton and no neutron, Deuterium contains a single proton and single neutron. Tritium contains one proton and two neutrons. Proton has a positive electrical charge whereas an electron has a negative electrical charge. A neutron has no charge. The bonding between hydrogen atoms is strong. Since it is highly reactive, hydrogen can make bond with other elements also.


Figure 1: Hydrogen

image src: http://en.wikipedia.org/wiki/File:Electron_shell_001_Hydrogen_-_no_label.svg


Hydrogen can make bonds with hydrogen, nitrogen, fluorine, oxygen etc. Hydrogen bonding is very specific. It can form ionic bonds, covalent bonds and hydrogen bonds. Ionic bonds form between two atoms that have large electronegativity difference. Electronegativity is the tendency of an atom to attract electrons toward it. Covalent bond is the sharing of electron pairs between atoms. A hydrogen bond is forming between a polar hydrogen atom and any electronegative atom such as oxygen, nitrogen, fluorine etc. Hydrogen bond is weaker than ionic or covalent bond. A hydrogen atom always has an attraction towards electronegative atoms. There are two types of hydrogen bonds; intermolecular hydrogen bond and intramolecular hydrogen bond. The bond between two different molecules in same substance or different substance is called intermolecular hydrogen bond. The hydrogen bond in water molecules is an example for this type of bond. The bond between the hydrogen atom and a highly electro negative atom that present in same molecule is called an intramolecular hydrogen bond.


Why adding hydrogen to molecules?


Most of the structure databases obtain the 3D structure of biological macromolecules from techniques like X-ray crystallography, NMR Spectroscopy, Small angle X-ray scattering, Electron microscopy etc. These files are saved in either pdb or mmCIF format and stored in the databases like PDB, Structure(NCBI) etc. In PDB, about 90% of the 3D structures are obtained through the method X-ray crystallography. In X-ray crystallography, the position of hydrogen atoms cannot be determined due to its small size, large thermal motion and lesser number of electrons. It has only 1 electron which does not get projected like the other atoms which has a bigger electronic cloud. So hydrogen is not included in the PDB files. Therefore only a part of the molecule may be included in almost all PBD entries. In the case of structure of symmetrical molecules in PDB entry, it includes only a single subunit of the complex. So the coordinates for quaternary structure of a protein should calculate from the coordinate of the subunit. Biologically, all the protein molecules have hydrogen atom and all the bonds are satisfied to obtain a stable conformation. When one does any analysis like docking with the protein molecule, the structures have to be added with hydrogen and satisfy the bonds. So this is an important step before any structure analysis. 





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