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Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.

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., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

The complete mol-ecule of the binuclear title complex, bis-[μ-1 H -1,2,4-triazole-5(4 H )-thione-κ 2 S : S ]bis-{(thio-cyanato-κ S )[1 H -1,2,4-triazole-5(4 H )-thione-κ S ]silver(I)}, [Ag 2 (SCN) 2 (C 2 H 3 N 3 S) 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 (μ 2 ) bridging mode to provide a link between two Ag I centres. Each Ag I atom is also coordinated by a terminal S-bound thio-cyanate ligand, resulting in a distorted AgS 4 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., (© Kreaunakpan et al. 2020.)

Combined quantum mechanical molecular mechanics (QM/MM) calculations have become a popular methodology for efficient and accurate description of large molecular systems. In this work we introduce our development of a QM/MM framework based on two well-known codes-NWChem and AMBER. As an initial application area we are focused on excited state properties of small molecules in an aqueous phase using an analogue of the green fluorescent protein (GFP) chromophore as a particular test case. Our approach incorporates high level coupled cluster theory for the analysis of excited states providing a reliable theoretical analysis of effects of an aqueous solvation environment on the photochemical properties of the GFP chromophore. Using a systematic approach, which involves comparison of gas phase and aqueous phase results for different protonation states and conformations, we resolve existing uncertainties regarding the theoretical interpretation of experimental data. We observe that the impact of aqueous environment on charged states generally results in blue shifts of the absorption spectra, but the magnitude of the effect is sensitive to both protonation state and conformation and can be rationalized based on charge movement into the area of higher/lower external electrostatic potentials. At neutral pH levels the experimentally observed absorption signal is most likely coming from the phenol protonated form. Our results also show that the high level electron correlated method is essential for a proper description of excited states of GFP. © 2017 Wiley Periodicals, Inc., (© 2017 Wiley Periodicals, Inc.)