Due to bonding orbital interaction in the 𝛔-system, atomic charges are also charged.Įlectron-donor atoms of hydrogen bonds, such as N6-H6-O4 lose 24 mili-a.u whereas N1-H3-N3 loses 46 mili-a.u. This results in a positive charge on the central hydrogen atoms and a negative charge on the edged atom from the hydrogen bond. This results in the depletion of the charge density from the central point of overlap and is directed toward the edge of the hydrogen bonds (N6-H6 makes a hydrogen bond with O4 and N1 hydrogen bonded with H3-N3). These results in charge redistribution in the 𝛔 and 𝝅-electron system.ĭue to Pauli’s repulsive and bonding orbitals interactions, these components can be further breakdown into charge rearrangement.įormation of base pair (AT) from the bases adenine (A) and guanine (T) takes place due to the effect of Pauli’s repulsion. Charge redistributionĪccording to the VDD charge decomposition analysis, it is possible to calculate the changes in atomic charge ΔQ A by the formation of base pairs from other bases and to break down them. In the case of the base pair of guanine-cytosine (GC), the above process is repeated in the same way. Similarly, the lone pair on the O4 atom of the thymine (T) make donor-acceptor interactions with 𝛔* orbitals of N6-H6 of adenine (A). For example, the lone pair on the first nitrogen atom (N1) in the adenine (A) make contact with the 𝛔* orbital on H3-N3 atoms in the thymine (T). The result of the above combination is the formation of a weak hydrogen bond.

Unoccupied 𝛔* orbital of an N-H group the other base.

Lone pair on the oxygen or nitrogen atoms in the base.

Especially 𝛔-electron system, in which orbital interactions like donor-acceptor or charge transfer occur.Īccording to Molecular Orbital (MO) analysis, the key features that are required for achieving the donor-acceptor orbital interactions are: Orbital interaction due to hydrogen bonding can be studied by considering the orbital electronic structure of DNA bases. All the protons acceptor atoms have a negative charge while corresponding protons have a positive charge. This shows DNA bases have the charge distribution for achieving the electrostatic interaction in the base pairs.

In addition, by examing the charge distribution at the atoms that are responsible for hydrogen bonding between the base pairs. Bonding orbital interactions ΔE oi (charge transfer).Pauli repulsive orbital interactions ΔE pauli between orbitals.Electrostatic attraction ΔV elstat between the unperturbed charge distribution of base pairs.Quantitatively, interaction energy ΔE int is the sum of these: On the other hand, interaction energies ΔE int are very essential and analyzed in the Kohn-Sham MO model. Geometrical changes in the DNA base pairs are minor, so the preparation energies ΔE prep are very small 4 kcal/mol or less.

The preparation energy ΔE prep is associated with the breakdown of the equilibrium structure of base pairs into their geometry or individual structures whereas actual interaction energy ΔE int is the energy that is present between these individual structures of base pairs. The bond energy is ΔE is separated into preparation energy ΔE prep and the actual interaction energy ΔE int. It is good to understand the hydrogen bonding that holds the base pair together and the importance of electrostatic interaction in the DNA. The nature of hydrogen bonds in DNA is composed of these components: According to the gas phase experiment, the strength of the hydrogen bond is -12.1kcal/mol for adenine-thymine (AT) while -21.0 kcal/mol for guanine-cytosine (GC). Adenine (A) always makes two hydrogen bonds with thymine (T), whereas guanine (G) bonds with cytosine (C) by three hydrogen bonds. These above base pairs are present in the strands of DNA where they specifically bond with each other by hydrogen bonding and connect the two strands.

These are the four nitrogenous bases in DNA: The genetic information is encoded in the DNA by the specific combination of nitrogenous bases. In DNA, hydrogen bonds play an important role in giving intrinsic stability to the molecule. They are twisted around each other and form a ladder-like structure known as a double helix. Strands of DNA are made up of nucleotides that have phosphate groups, ribose sugar, and nitrogenous bases. Deoxyribonucleic acid (DNA) has two helical strands that are connected to each other by hydrogen bonding.

Hydrogen bonds in dna