Energy Decomposition Analysis (EDA)

We're going to build a A:T (adenine-thymine) DNA base pair, to study hydrogen-bonding between the bases.

1. Construct the A:T base pair by clicking on the benzene ring within AMSinput, then select [DNA]:[AT] and click
2. Choose the following setup:
   • XC functional: S12g-D3 (GGA-D)
   • Relativity: Scalar
   • Basis set: TZ2P
   • Frozen core: Small
   • Numerical quality: Good
3. Go to [Model]:[Regions]
4. Select one molecule, and click on the [+] sign
5. Select the other molecule, and click again on [+]
6. Go to [Multilevel]:[Fragments], and select [Use fragments]:[Yes]
7. Save
8. Run

Analysis

1. Once the job has run, go to [SCM]:[Levels], to see how the molecular orbitals of the two fragments are combined into the MOs of the base pair
2. Go to [SCM]:[Output] to see the output, and then go to [Properties]:[Bonding Energy Decomposition] to inspect the bonding energy (-19.2 kcal·mol^-1), and its components
3. Go to [SCM]:[Output] to see the output, then to [Properties]:[Voronoi Charge Analysis] to inspect the Voronoi Deformation Density (VDD) charges

Further reading

• M. Swart, C. Fonseca Guerra and F.M. Bickelhaupt
  "Hydrogen Bonds of RNA Are Stronger than Those of DNA, But NMR Monitors Only Presence of Methyl Substituent in Uracil/Thymine"
  J. Am. Chem. Soc. 2004, 126, 16718-16719 Abstract
  10.1021/ja045276b
• C. Fonseca Guerra, F.M. Bickelhaupt, J.G. Snijders, and E.J. Baerends
  "The Nature of the Hydrogen Bond in DNA Base Pairs: The Role of Charge Transfer and Resonance Assistance"
  Chem. Eur. J. 1999, 5, 3581-3594 [abstract]
  DOI: 10.1002/(SICI)1521-3765(19991203)5:12<3581::AID-CHEM3581>3.0.CO;2-Y
• C. Fonseca Guerra, F.M. Bickelhaupt, J.G. Snijders, and E.J. Baerends
  "Hydrogen Bonding in DNA Base Pairs:  Reconciliation of Theory and Experiment"
  J. Am. Chem. Soc. 2000, 122, 4117-4128 [abstract]
  DOI: 10.1021/ja993262d