ORIGINAL ARTICLE Correlation Between Molecular Modelling and Spectroscopic Techniques in Investigation With DNA Binding Interaction of Ruthenium(II) Complexes B. Thulasiram 1 & C. Shobha devi 2 & Yata Praveen Kumar 3 & Rajeshwar Rao Aerva 4 & S. Satyanarayana 3 & Penumaka Nagababu 1 Received: 11 September 2016 /Accepted: 9 November 2016 # Springer Science+Business Media New York 2016 Abstract The DNA binding studies of rutheniumu(II) polypyridyl complexes {[Ru(phen) 2 Mipc] 2+ , [Ru(bpy) 2 Mipc] 2+ , [Ru(dmb) 2 Mipc] 2+ , [Ru(phen) 2 BrIPC] 2+ , [Ru(bpy) 2 BrIPC] 2+ , [Ru(dmb) 2 BrIPC] 2+ , [Ru(phen) 2 PIP- Cl] 2+ , [Ru(bpy) 2 PIP-Cl] 2+ , [Ru(dmb) 2 PIP-Cl] 2+ , [Ru(phen) 2 IPPBA] 2+ , [Ru(bpy) 2 IPPBA] 2+ , [Ru(dmb) 2 IPPBA] 2+ } with DNA investigated by electronic absorption titration, emission and molecular modelling studies to identify the binding interactions. All these complexes are showing good binding constant values ~10 4 to 10 5 . The intercalative ligands makes the binding of the ruthenium(II) complex with DNA as intercalation mode. The ancillary li- gands 1,10-phenanthroline (phen), 4,4′ -Dimethyl-2,2′ - dipyridyl (dmb) and 2,2′-dipyridine (bpy) having been discov- ered found to be involved in bond formation with the phos- phate backbone of nucleotide base pairs in ruthenium(II) com- plex–DNA docked complex. The molecular docking results are good agreement with experimental results. The molecular modelling technic should help to extend knowledge about the nature (or) mode of binding of these ruthenium(II) complexes with (calf thymus) CT-DNA. Keywords Molecular modelling . DNA-binding . Electronic absorption . Emission studies Introduction Molecular modelling techniques can be utilized to speed up drug discovery process for obtaining new drug molecules. Today, al- most every industry, involved in drug discovery has adopted molecular modelling techniques at different stages of the design process. The crucial challenges in drug design is to predict can- didate molecules for clinical treatment. It includes all theoretical methods and computational techniques. The common feature of molecular mechanics (MM) techniques is the atomistic level de- scription of the molecular systems, in other words the lowest level of information is individual atoms. The docking is a method in MM studies, which says the preferred coordination of one molecule to a second one when bound to each other to form a stable complex [1]. Knowledge of the preferred orientation in turn may be used to predict the strength of binding affinity be- tween chemical and biological molecules. Molecular docking, most commonly using methods in the drug design and mecha- nistic study by placing a molecule into the binding site of the target macromolecule in a non-covalent mode of interaction [2]. Recently, there has been a rising interest in electro and spectrochemical investigation of interaction between drug and DNA [3]. The binding of drug- DNA is importance for consid- ering the molecular mechanism of drug interaction and for the design of specific DNA targeted drugs. Also, modelling methods can be applied to better knowledge about the interaction of drug and DNA for saving lot of money and time, particularly since the reactivity of newly designed drugs with their targeted DNA mol- ecules can be predicted prior to chemical synthesis [ 4]. Covalent binding can take place to the phosphodiester backbone or sugar residues as well as bases. Covalent binding in DNA is * Penumaka Nagababu babupenumaka@gmail.com 1 Inorganic & Physical Chemistry Division, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, Telangana State, India 2 Department of Chemistry, RGUKT, Basar, Telangana State, India 3 Department of Chemistry, Osmania University, Tarnaka, Hyderabad, Telangana State, India 4 Department of Chemical Engineering, Eritrea Institute of Technology, Asmara, Eritrea J Fluoresc DOI 10.1007/s10895-016-1986-x