cclib 2.0: An updated architecture for interoperable computational chemistry.

Interoperability in computational chemistry is elusive, impeded by the independent development of software packages and idiosyncratic nature of their output files. The cclib library was introduced in 2006 as an attempt to improve this situation by providing a consistent interface to the results of various quantum chemistry programs. The shared API across programs enabled by cclib has allowed users to focus on results as opposed to output and to combine data from multiple programs or develop generic downstream tools. Initial development, however, did not anticipate the rapid progress of computational capabilities, novel methods, and new programs; nor did it foresee the growing need for customizability. Here, we recount this history and present cclib 2, focused on extensibility and modularity. We also introduce recent design pivots-the formalization of cclib's intermediate data representation as a tree-based structure, a new combinator-based parser organization, and parsed chemical properties as extensible objects.

Overreact, an in silico lab: Automative quantum chemical microkinetic simulations for complex chemical reactions.

Today's demand for precisely predicting chemical reactions from first principles requires research to go beyond Gibbs' free energy diagrams and consider other effects such as concentrations and quantum tunneling. The present work introduces overreact, a novel Python package for propagating chemical reactions over time using data from computational chemistry only. The overreact code infers all differential equations and parameters from a simple input that consists of a set of chemical equations and quantum chemistry package outputs for each chemical species. We evaluate some applications from the literature: gas-phase eclipsed-staggered isomerization of ethane, gas-phase umbrella inversion of ammonia, gas-phase degradation of methane by chlorine radical, and three solvation-phase reactions. Furthermore, we comment on a simple solvation-phase acid-base equilibrium. We show how it is possible to achieve reaction profiles and information matching experiments.

Platinum-Triggered Bond-Cleavage of Pentynoyl Amide and N-Propargyl Handles for Drug-Activation.

The ability to create ways to control drug activation at specific tissues while sparing healthy tissues remains a major challenge. The administration of exogenous target-specific triggers offers the potential for traceless release of active drugs on tumor sites from antibody-drug conjugates (ADCs) and caged prodrugs. We have developed a metal-mediated bond-cleavage reaction that uses platinum complexes [K2PtCl4 or Cisplatin (CisPt)] for drug activation. Key to the success of the reaction is a water-promoted activation process that triggers the reactivity of the platinum complexes. Under these conditions, the decaging of pentynoyl tertiary amides and N-propargyls occurs rapidly in aqueous systems. In cells, the protected analogues of cytotoxic drugs 5-fluorouracil (5-FU) and monomethyl auristatin E (MMAE) are partially activated by nontoxic amounts of platinum salts. Additionally, a noninternalizing ADC built with a pentynoyl traceless linker that features a tertiary amide protected MMAE was also decaged in the presence of platinum salts for extracellular drug release in cancer cells. Finally, CisPt-mediated prodrug activation of a propargyl derivative of 5-FU was shown in a colorectal zebrafish xenograft model that led to significant reductions in tumor size. Overall, our results reveal a new metal-based cleavable reaction that expands the application of platinum complexes beyond those in catalysis and cancer therapy.

Quest for Insight into Ultrashort C-H···π Proximities in Molecular "Iron Maidens".

Molecular iron maidens are a strained type of cyclophane in which a methine hydrogen, by the action of the bridges, is placed closer to the center of an aromatic ring. Such constrained molecular frameworks are in fact a noteworthy synthetic challenge. The present study provides a comprehensible theoretical analysis that elucidates unique structural and energetic aspects of this class of molecules, evaluating, in the light of quantum chemistry, both the influence of the aromatic moiety, from π-basic to π-acid, and the nature of the heteroatoms located at the bridges. Our results not only propose the shortest intramolecular centered C-H···π distance to date, which is supported by calculated 1H chemical shifts, but also shed light on the main factors that rationalize and justify such proximity. QTAIM, NBO, and NCI analyses allow us prematurely to conclude that the ultrashort C-H···π distance is sustained by an interplay between a large stabilizing electrostatic component with a non-negligible covalent character. However, the energetics involving such strained molecular scaffolds, addressed by means of isodesmic reactions, revealed that the C-H···π proximity is modulated mainly by the capacity of the bridges to support the strain imposed by the whole structure, hence compressing the C-H bond against the π-system.

Evaluation of Electron Donation as a Mechanism for the Stabilisation of Chalcogenate-Protected Gold Nanoclusters.

Models based on Au(111) face have been extensively used to describe self-assembled monolayers, as well nanoparticles and nanoclusters. However, for very small clusters (<2 nm), the chemisorption of ligands leads to surface reconstruction, making necessary the use of a more reliable model that is able to simulate the main electronic and geometrical features of these small systems. In this work, a simple model to describe the geometries and the metal-ligand bonding in chalcogenate-protected gold nanoclusters is proposed. Three different models with Aun+ and [XCH3 ]- (n=10, 15, 19, 22 and X=S, Se, Te) are used in this work. The obtained structures are in close agreement not only with the available crystallographic data, but also with much more expensive computational procedures, confirming that the proposed models are robust enough to describe the metal-ligand bonding. The results reveal that the Au-X distances are dependent on both the nature of the chalcogen and the coordination mode. The shortest Au-X distances are observed in the face-centred cubic mode, indicating that the central gold atom seems to play a role in determining the adsorption strength. The proposed models show unambiguously chalcogen→cluster σ-donation, as supported by energy decomposition analysis coupled with the natural orbitals for chemical valence and natural bond orbital analyses. In all cases, the metal-ligand interactions are characterised as being more covalent than electrostatic.