Using comparative extinction risk analysis to prioritize the IUCN Red List reassessments of amphibians.

Assessing the extinction risk of species based on the International Union for Conservation of Nature (IUCN) Red List (RL) is key to guiding conservation policies and reducing biodiversity loss. This process is resource demanding, however, and requires continuous updating, which becomes increasingly difficult as new species are added to the RL. Automatic methods, such as comparative analyses used to predict species RL category, can be an efficient alternative to keep assessments up to date.

Modelling the probability of meeting IUCN Red List criteria to support reassessments.

Comparative extinction risk analysis-which predicts species extinction risk from correlation with traits or geographical characteristics-has gained research attention as a promising tool to support extinction risk assessment in the IUCN Red List of Threatened Species. However, its uptake has been very limited so far, possibly because existing models only predict a species' Red List category, without indicating which Red List criteria may be triggered. This prevents such approaches to be integrated into Red List assessments.

A standard approach for including climate change responses in IUCN Red List assessments.

The International Union for Conservation of Nature (IUCN) Red List is a central tool for extinction risk monitoring and influences global biodiversity policy and action. But, to be effective, it is crucial that it consistently accounts for each driver of extinction. Climate change is rapidly becoming a key extinction driver, but consideration of climate change information remains challenging for the IUCN.

Benchmark Structures and Conformational Landscapes of Amino Acids in the Gas Phase: A Joint Venture of Machine Learning, Quantum Chemistry, and Rotational Spectroscopy.

The accurate characterization of prototypical bricks of life can strongly benefit from the integration of high resolution spectroscopy and quantum mechanical computations. We have selected a number of representative amino acids (glycine, alanine, serine, cysteine, threonine, aspartic acid and asparagine) to validate a new computational setup rooted in quantum-chemical computations of increasing accuracy guided by machine learning tools. Together with low-lying energy minima, the barriers ruling their interconversion are evaluated in order to unravel possible fast relaxation paths.

Integration of Quantum Chemistry, Statistical Mechanics, and Artificial Intelligence for Computational Spectroscopy: The UV-Vis Spectrum of TEMPO Radical in Different Solvents.

The ongoing integration of quantum chemistry, statistical mechanics, and artificial intelligence is paving the route toward more effective and accurate strategies for the investigation of the spectroscopic properties of medium-to-large size chromophores in condensed phases. In this context we are developing a novel workflow aimed at improving the generality, reliability, and ease of use of the available computational tools. In this paper we report our latest developments with specific reference to unsupervised atomistic simulations employing non periodic boundary conditions (NPBC) followed by clustering of the trajectories employing optimized feature spaces.

L-DOPA and Droxidopa: From Force Field Development to Molecular Docking into Human β-Adrenergic Receptor.

The increasing interest in the molecular mechanism of the binding of different agonists and antagonists to β-adrenergic receptor (βAR) inactive and active states has led us to investigate protein-ligand interactions using molecular docking calculations. To perform this study, the 3.2 Å X-ray crystal structure of the active conformation of human βAR in the complex with the endogenous agonist adrenaline has been used as a template for investigating the binding of two exogenous catecholamines to this adrenergic receptor.

Unbiased disentanglement of conformational baths with the help of microwave spectroscopy, quantum chemistry, and artificial intelligence: The puzzling case of homocysteine.

An integrated experimental-computational strategy for the accurate characterization of the conformational landscape of flexible biomolecule building blocks is proposed. This is based on the combination of rotational spectroscopy with quantum-chemical computations guided by artificial intelligence tools. The first step of the strategy is the conformer search and relative stability evaluation performed by means of an evolutionary algorithm.

Development, Validation, and Pilot Application of a Generalized Fluctuating Charge Model for Computational Spectroscopy in Solution.

A general approach enforcing nonperiodic boundary conditions for the computation of spectroscopic properties in solution has been improved including an effective description of charge-transfer contributions and coordination number adjustment for explicit solvent molecules. Both contributions are obtained from a continuous description of intermolecular hydrogen bonds, which has been employed also for an effective clustering of molecular dynamics trajectories. Fine tuning of the model has been performed for several water clusters, and then its efficiency and reliability have been demonstrated by computing the absorption spectra of different creatinine tautomers in aqueous solution.

Molecular Dynamics Simulations Enforcing Nonperiodic Boundary Conditions: New Developments and Application to the Solvent Shifts of Nitroxide Magnetic Parameters.

Multiscale methods combining quantum mechanics and molecular mechanics (QM/MM) have become the most suitable and effective strategies for the investigation of the spectroscopic properties of medium-to-large size chromophores in condensed phases. In this context, we are developing a novel workflow aimed at improving the generality, reliability, and ease of use of the available computational tools. In this paper, we report our latest developments with specific reference to a general protocol based on atomistic simulations, carried out under nonperiodic boundary conditions (NPBC).

Analysis of L-DOPA and droxidopa binding to human β-adrenergic receptor.

Over the last two decades, an increasing number of studies has been devoted to a deeper understanding of the molecular process involved in the binding of various agonists and antagonists to active and inactive conformations of β-adrenergic receptor (βAR). The 3.2 Å x-ray crystal structure of human βAR active state in combination with the endogenous low affinity agonist adrenaline offers an ideal starting structure for studying the binding of various catecholamines to adrenergic receptors.

Integration of theory, simulation, artificial intelligence and virtual reality: a four-pillar approach for reconciling accuracy and interpretability in computational spectroscopy.

The established pillars of computational spectroscopy are theory and computer based simulations. Recently, artificial intelligence and virtual reality are becoming the third and fourth pillars of an integrated strategy for the investigation of complex phenomena. The main goal of the present contribution is the description of some new perspectives for computational spectroscopy, in the framework of a strategy in which computational methodologies at the state of the art, high-performance computing, artificial intelligence and virtual reality tools are integrated with the aim of improving research throughput and achieving goals otherwise not possible.

4-Fluoro-Threonine: From Diastereoselective Synthesis to pH-Dependent Conformational Equilibrium in Aqueous Solution.

4-Fluoro-threonine, the only fluoro amino acid of natural origin discovered so far, is an interesting target for both synthetic and theoretical investigations. In this work, we lay the foundation for spectroscopic characterization of 4-fluoro-threonine. First, we report a diastereoselective synthetic route, which is suitable to produce synthetic material for experimental characterization.

Elusive Coordination of the Ag Ion in Aqueous Solution: Evidence for a Linear Structure.

X-ray absorption spectroscopy (XAS) has been employed to study the coordination of the Ag ion in aqueous solution. The conjunction of extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) data analysis provided results suggesting the preference for a first shell linear coordination with a mean Ag-O bond distance of 2.34(2) Å, different from the first generally accepted tetrahedral model with a longer mean Ag-O bond distance.

Unsupervised search of low-lying conformers with spectroscopic accuracy: A two-step algorithm rooted into the island model evolutionary algorithm.

The fruitful interplay of high-resolution spectroscopy and quantum chemistry has a long history, especially in the field of small, semi-rigid molecules. However, in recent years, the targets of spectroscopic studies are shifting toward flexible molecules, characterized by a large number of closely spaced energy minima, all contributing to the overall spectrum. Here, artificial intelligence comes into play since it is at the basis of powerful unsupervised techniques for the exploration of soft degrees of freedom.

Computational Spectroscopy in Solution by Integration of Variational and Perturbative Approaches on Top of Clusterized Molecular Dynamics.

Multiscale QM/MM approaches have become the most suitable and effective methods for the investigation of spectroscopic properties of medium- or large-size chromophores in condensed phases. On these grounds, we are developing a novel workflow aimed at improving the generality, reliability, and ease of use of the available tools. In the present paper, we report the latest developments of such an approach with specific reference to a general workplan starting with the addition of acetonitrile to the panel of solvents already available in the General Liquid Optimized Boundary (GLOB) model enforcing nonperiodic boundary conditions (NPBC).

Molecular Perception for Visualization and Computation: The Proxima Library.

Proxima is a molecular perception library designed with a double purpose: to be used with immersive molecular viewers (thus providing any required feature not supported by third party libraries) and to be integrated in workflow managers thus providing the functionalities needed for the first steps of molecular modeling studies. It thus stands at the boundary between visualization and computation. The purpose of the present article is to provide a general introduction to the first release of Proxima, describe its most significant features, and highlight its performance by means of some case studies.

Chemical promenades: Exploring potential-energy surfaces with immersive virtual reality.

The virtual-reality framework AVATAR (Advanced Virtual Approach to Topological Analysis of Reactivity) for the immersive exploration of potential-energy landscapes is presented. AVATAR is based on modern consumer-grade virtual-reality technology and builds on two key concepts: (a) the reduction of the dimensionality of the potential-energy surface to two process-tailored, physically meaningful generalized coordinates, and (b) the analogy between the evolution of a chemical process and a pathway through valleys (potential wells) and mountain passes (saddle points) of the associated potential energy landscape. Examples including the discovery of competitive reaction paths in simple A + BC collisional systems and the interconversion between conformers in ring-puckering motions of flexible rings highlight the innovation potential that augmented and virtual reality convey for teaching, training, and supporting research in chemistry.

Deciphering Copper Coordination in the Mammalian Prion Protein Amyloidogenic Domain.

Prions are pathological isoforms of the cellular prion protein that is responsible for transmissible spongiform encephalopathies (TSE). Cellular prion protein interacts with copper, Cu(II), through octarepeat and nonoctarepeat (non-OR) binding sites. The molecular details of Cu(II) coordination within the non-OR region are not well characterized yet.

Two-level stochastic search of low-energy conformers for molecular spectroscopy: implementation and validation of MM and QM models.

The search for stationary points in the molecular potential energy surfaces (PES) is a problem of increasing relevance in different fields of molecular sciences especially for large, flexible systems characterized by several large-amplitude internal motions leading to shallow minima with comparable energies and separated by small barriers. After structural biology and medicinal chemistry, also high-resolution molecular spectroscopy, which is the focus of our research activity, is nowadays shifting its attention to this kind of molecular systems. In such circumstances, accurate geometrical structures and relative stabilities of all these minima are a mandatory prerequisite for the vis-à-vis comparison between computed and experimental spectra.

Assessment of Multi-Scale Approaches for Computing UV-Vis Spectra in Condensed Phases: Toward an Effective yet Reliable Integration of Variational and Perturbative QM/MM Approaches.

Computational simulation of UV/vis spectra in condensed phases can be performed starting from converged molecular dynamics (MD) simulations and then performing quantum mechanical/molecular mechanical (QM/MM) computations for a statistically significant number of snapshots. However, the need of variational solutions (e.g.

Mechanistic insights into metal ions transit through threefold ferritin channel.

Background: The mechanism of how the hydrophilic threefold channel (C3) of ferritin nanocages facilitates diffusion of diverse metal ions into the internal cavity remains poorly explored.

Methods: Computational modeling and free energy estimations were carried out on R. catesbeiana H´ ferritin.

Towards the SMART workflow system for computational spectroscopy.

Is it possible to convert highly specialized research in the field of computational spectroscopy into robust and user-friendly aids to experiments and industrial applications? What kind of tools should be created to increase the interactions between researchers with different backgrounds and push towards new frontiers in computational chemistry? The outstanding advances in computational spectroscopy and the wide availability of computational and analytical tools are paving the route toward the study of problems that were previously difficult or impossible to solve and enable the imagination of even more ambitious targets for fundamental and applied research. The combination of new computer- and data-centric technologies is transforming data analysis from an uncommon and retrospective practice into a proactive process of strategic decision and action. This paper starts from these premises and proposes a perspective for a new cyberinfrastructure aimed at integrating developments in theory, algorithms and software with new tools for workflow management, data mining and visualization.

Diving into chemical bonding: An immersive analysis of the electron charge rearrangement through virtual reality.

An integrated environment for the analysis of chemical bonding based on immersive virtual reality is presented. Using a multiscreen stereoscopic projection system, researchers are cast into the world of atoms and molecules, where they can visualize at a human scale the electron charge rearrangement (computed via state-of-the-art quantum-chemical methods) occurring on bond formation throughout the molecular region. Thanks to specifically designed features, such a virtual laboratory couples the immediacy of an immersive experience with a powerful, recently developed method yielding quantitative, spatially detailed pictures of the several charge flows involved in the formation of a chemical bond.

Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties.

The UV-vis spectrum of Tyrosine and its response to different backbone protonation states have been studied by applying the Perturbed Matrix Method (PMM) in conjunction with molecular dynamics (MD) simulations. Herein, we theoretically reproduce the UV-vis absorption spectrum of aqueous solution of Tyrosine in its zwitterionic, anionic and cationic forms, as well as of aqua-p-Cresol (i.e.