Computational modelling of intermolecular interactions in bio, organic and nano molecules

  • Anitha Ramraj

Student thesis: Phd


We have investigated the noncovalent interactions in carbohydrate-aromatic interactionswhich are pivotal to the recognition of carbohydrates in proteins. We have employedquantum mechanical methods to study carbohydrate-aromatic complexes. Due to theimportance of dispersion contribution to the interaction energy, we mainly use densityfunctional theory augmented with an empirical correction for the dispersion interactions(DFT-D). We have validated this method with a limited number of high level ab initiocalculations. We have also analysed the vibrational and NMR chemical shiftcharacteristics using the DFT-D method. We have mainly studied the complexesinvolving β-glucose with 3-methylindole and p-hydroxytoluene, which are analogues oftryptophan and tyrosine, respectively. We find that the contribution for interactionenergy mainly comes from CH/pie and OH/pie interactions. We find that the interactionenergy of complexes involving CH/pie and OH/pie interactions is reflected in the associatedblue and red shifts of vibrational spectrum. We also find that the interactions involving3-methylindole are somewhat greater than those for p-hydroxytoluene. The C-H blueshifts are also in parallel with the predicted NMR proton shift. We have also testeddifferent density functionals including both standard density functionals and newlydeveloped M0x functionals and MP2 method for studying carbohydrate-aromaticcomplexes. The DFT-D method and M06 functionals of the M0x family are found toperform better, while B3LYP and BLYP functionals perform poorly. We find that theinclusion of a dispersion term to BLYP is found to perform better. The dispersionenergy dominates over the interaction energy of carbohydrate-aromatic complexes.From the DFT-D calculations, we found that the complexes would be unstable withoutthe contribution from dispersive energy. We have also studied the importance ofnoncovalent interactions in functionalization of nanotubes by nucleic acid bases andaromatic aminoacids by using semi-empirical methods with dispersion term such asPM3-D and PM3-D*. We find that the both semi-empirical schemes give reasonableinteraction energies with respect to DFT-D interaction energies. We have also usedPM3-D method to study the adsorption of organic pollutants on graphene sheet and onnanotubes. We found that the semi-empirical schemes, which are faster and cheaper, aresuitable to study these larger molecules involving noncovalent interactions and can beused as an alternative to DFT-D method. We have also studied the importance ofdispersion interaction and the effect of steric hindrance in aggregation of functionalizedanthracenes and pentacenes. We have also employed molecular dynamics simulationmethods to study the aggregation of anthracene molecules in toluene solution.
Date of Award1 Aug 2011
Original languageEnglish
Awarding Institution
  • The University of Manchester
SupervisorIan Hillier (Supervisor) & Neil Burton (Supervisor)


  • Intermolecular interactions,aromatic-aromatic interactions,London dispersion forces,Computational modelling, carbophydrates, nanotubes, thin-film transistors, aromatic molcules, nucleic acid bases, organic molecules, arenes
  • Quantum mechanics, molecular dynamics, DFT-D, PM3-D, PM3-D*, MUSE, M0x functionals

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