We utilized molecular dynamics (MD) simulations and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) free energy calculations to investigate the specificity of two oligonucleotide probes, namely probe B and probe D, in detecting single-stranded DNA (ssDNA) within three bacteria families: Enterobacteriaceae, Pasteurellaceae, and Vibrionaceae. Due to the limited understanding of molecular mechanisms in the previous research, we have extended the discussion to focus specifically on investigating the binding process of bacteria-probe DNA duplexes, with an emphasis on analyzing the binding free energy. The role of electrostatic contributions in the specificity between the oligonucleotide probes and the bacterial ssDNAs was investigated and found to be crucial. Our calculations yielded results that were highly consistent with the experimental data. Through our study, we have successfully exhibited the benefits of utilizing in-silico approaches as a powerful virtual-screening tool, particularly in research areas that demand a thorough comprehension of molecular interactions.
The complete mol-ecule of the binuclear title complex, bis-[μ-1H-1,2,4-triazole-5(4H)-thione-κ2 S:S]bis-{(thio-cyanato-κS)[1H-1,2,4-triazole-5(4H)-thione-κS]silver(I)}, [Ag2(SCN)2(C2H3N3S)4], is generated by crystallographic inversion symmetry. The independent triazole-3-thione ligands employ the exocyclic-S atoms exclusively in coordination. One acts as a terminal S-ligand and the other in a bidentate (μ2) bridging mode to provide a link between two AgI centres. Each AgI atom is also coordinated by a terminal S-bound thio-cyanate ligand, resulting in a distorted AgS4 tetra-hedral coordination geometry. An intra-molecular N-H⋯S(thio-cyanate) hydrogen bond is noted. In the crystal, amine-N-H⋯S(thione), N-H⋯N(triazol-yl) and N-H⋯N(thio-cyanate) hydrogen bonds give rise to a three-dimensional architecture. The packing is consolidated by triazolyl-C-H⋯S(thio-cyanate), triazolyl-C-H⋯N(thiocyanate) and S⋯S [3.2463 (9) Å] inter-actions as well as face-to-face π-π stacking between the independent triazolyl rings [inter-centroid separation = 3.4444 (15) Å]. An analysis of the calculated Hirshfeld surfaces shows the three major contributors are due to N⋯H/H⋯N, S⋯H/H⋯S and C⋯H/H⋯C contacts, at 35.8, 19.4 and 12.7%, respectively; H⋯H contacts contribute only 7.6% to the overall surface.