New prebiotic molecules in the interstellar medium from the reaction between vinyl alcohol and CN radicals: unsupervised reaction mechanism discovery, accurate electronic structure calculations and kinetic simulations.

Vinyl alcohol (VyA) and cyanide (CN) radicals are relatively abundant in the interstellar medium (ISM). VyA is the enolic tautomer of acetaldehyde and has two low-lying conformers, characterized by the or placement of hydroxyl hydrogen with respect to the double bond. In this paper, we present a gas-phase model of the barrierless reactions of both VyA's conformers with CN employing accurate quantum chemical computations in the framework of a master equation approach based on the transition state theory.

The roto-conformational diffusion tensor as a tool to interpret molecular flexibility.

Stochastic modeling approaches can be used to rationalize complex molecular dynamical behaviours in solution, helping to interpret the coupling mechanisms among internal and external degrees of freedom, providing insight into reaction mechanisms and extracting structural and dynamical data from spectroscopic observables. However, the definition of comprehensive models is usually limited by (i) the difficulty in defining - without resorting to phenomenological assumptions - a representative reduced ensemble of molecular coordinates able to capture essential dynamical properties and (ii) the complexity of numerical or approximate treatments of the resulting equations. In this paper, we address the first of these two issues.

Charge-Flow Profiles along Curvilinear Paths: A Flexible Scheme for the Analysis of Charge Displacement upon Intermolecular Interactions.

The Charge-Displacement (CD) analysis has proven to be a powerful tool for a quantitative characterization of the electron-density flow occurring upon chemical bonding along a suitably chosen interaction axis. In several classes of interesting intermolecular interactions, however, an interaction axis cannot be straightforwardly defined, and the CD analysis loses consistency and usefulness. In this article, we propose a general, flexible reformulation of the CD analysis capable of providing a quantitative view of the charge displacement along custom curvilinear paths.

Stochastic Modelling of C NMR Spin Relaxation Experiments in Oligosaccharides.

A framework for the stochastic description of relaxation processes in flexible macromolecules including dissipative effects has been recently introduced, starting from an atomistic view, describing the joint relaxation of internal coordinates and global degrees of freedom, and depending on parameters recoverable from classic force fields (energetics) and medium modelling at the continuum level (friction tensors). The new approach provides a rational context for the interpretation of magnetic resonance relaxation experiments. In its simplest formulation, the semi-flexible Brownian (SFB) model has been until now shown to reproduce correctly correlation functions and spectral densities related to orientational properties obtained by direct molecular dynamics simulations of peptides.

Chemical bonding in cuprous complexes with simple nitriles: octet rule and resonance concepts quantitative charge-redistribution analysis.

Chemical bonding in a set of six cuprous complexes with simple nitriles (CN-, HNC, HCN, CH3NC, and CH3CN) is investigated by means of a recently devised analysis scheme framed in density-functional theory and quantitatively singling out concurrent charge flows such as σ donation and π backdonation. The results of our analysis are comparatively assessed against qualitative models for charge redistribution based on the popular concepts of octet rule and resonance structures, and the relative importance of different charge-flow channels relating to σ donation, π back-donation, polarization, and hyperconjugation is discussed on a quantitative basis.

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.

The Chemical Bond and s-d Hybridization in Coinage Metal(I) Cyanides.

We present a four-component relativistic density functional theory study of the chemical bond and s-d hybridization in the group 11 cyanides M-CN (M = Cu, Ag, and Au). The analysis is carried out within the charge-displacement/natural orbital for chemical valence (CD-NOCV) scheme, which allows us to single out meaningful contributions to the total charge rearrangement that arises upon bond formation and to quantify the components of the Dewar-Chatt-Duncanson bonding model (the ligand-to-metal donation and metal-to-ligand back-donation). The M-CN bond is characterized by a large donation from the cyanide ion to the metal cation and by two small back-donation components from the metal toward the cyanide anion.

Potential-Energy Surfaces for Ring-Puckering Motions of Flexible Cyclic Molecules through Cremer-Pople Coordinates: Computation, Analysis, and Fitting.

Ring-puckering motion in 12 flexible cyclic molecules is investigated by calculation and analysis of two-dimensional potential-energy surfaces (PESs) using the so-called ring-puckering coordinates proposed by Cremer and Pople. The PESs are calculated by means of density-functional theory using a B2PLYP-D3BJ exchange-correlation functional with a maug-cc-pVTZ basis set, and results are compared to the available experimental and theoretical data. Special care is devoted to the aspect of symmetry in such two-dimensional PESs, which are here reported for the first time also for molecules whose planar form has symmetry lower than D or C.

Ferrocenes with simple chiral substituents: an in-depth theoretical and experimental VCD and ECD study.

Circular dichroism spectra in the IR range (VCD = vibrational circular dichroism) and in the UV range (ECD = electronic circular dichroism) have been recorded for both enantiomers of simple mono-substituted ferrocenes containing chiral pendants: 1-acetoxyethylferrocene, 1, 1-methoxyethylferrocene, 2, and 1-hydroxyethylferrocene, 3; the related disubstituted 1,1'-bis(1-hydroxyethyl)ferrocene, 4, was also considered. These two types of spectra, with the support of DFT calculations, concur to unequivocally confirm the absolute configuration for 1-4. In particular, our computational results point out the clear advantage of using an anharmonic oscillator model for the interpretation of VCD spectra of chiral ferrocenes.

Unveiling the Sulfur-Sulfur Bridge: Accurate Structural and Energetic Characterization of a Homochalcogen Intermolecular Bond.

By combining rotational spectroscopy in supersonic expansion with the capability of state-of-the-art quantum-chemical computations in accurately determining structural and energetic properties, the genuine nature of a sulfur-sulfur chalcogen bond between dimethyl sulfide and sulfur dioxide has been unveiled in a gas-jet environment free from collision, solvent and matrix perturbations. A SAPT analysis pointed out that electrostatic S⋅⋅⋅S interactions play the dominant role in determining the stability of the complex, largely overcoming dispersion and C-H⋅⋅⋅O hydrogen-bond contributions. Indeed, in agreement with the analysis of the quadrupole-coupling constants and of the methyl internal rotation barrier, the NBO and NOCV/CD approaches show a marked charge transfer between the sulfur atoms.

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.

Theory Meets Experiment for Noncovalent Complexes: The Puzzling Case of Pnicogen Interactions.

A gas-phase nitrogen-nitrogen noncovalent interaction has been unveiled in the nitroethane-trimethylamine complex in an environment free from solvent and matrix effects using rotational spectroscopy in supersonic expansion. Different quantum chemical models (NOCV/CD and NBO) agree in indicating that this interaction largely prevails over the C-H⋅⋅⋅O and C-H⋅⋅⋅N hydrogen bonds. Furthermore, a SAPT analysis shows that electrostatic and dispersion interactions play a comparable role in stabilizing the complex.

Exploiting coordination geometry to selectively predict the σ-donor and π-acceptor abilities of ligands: a back-and-forth journey between electronic properties and spectroscopy.

Through an analysis of eighty tetrahedral and square-planar metal carbonyls of general formula [M(CO)(L')(L)] including newly synthesized chlorocarbonyl rhodium complexes with chelating atropoisomeric diphosphanes, we show how coordination geometry can switch the carbonyl stretching frequency into a selective probe of the σ-donor and π-acceptor abilities of the ligands. We thus provide a framework whereby the σ-donation and π-backdonation constituents of the Dewar-Chatt-Duncanson model can be quantitatively predicted through spectroscopic data on coordinated CO moieties and vice versa.

Charge-Displacement Analysis via Natural Orbitals for Chemical Valence in the Four-Component Relativistic Framework.

We have recently introduced a simple yet powerful tool for analyzing quantitatively the coordination bond in terms of the donation and back-donation constituents of the Dewar-Chatt-Duncanson model. Our approach is based on the decomposition, via natural orbitals for chemical valence (NOCV), of the so-called charge-displacement (CD) function into additive chemically meaningful components (Bistoni et al. J.

On the relation between carbonyl stretching frequencies and the donor power of chelating diphosphines in nickel dicarbonyl complexes.

The relation between spectroscopic observables and the detailed metal-ligand bonding features in chelation complexes is addressed using both experimental and state-of-the-art theoretical and computational methods. We synthesized and characterized a set of six nickel dicarbonyl complexes of general formula [Ni(CO)(PP)], where PP is an atropoisomeric chelating diphosphine ligand. The analysis of the obtained experimental data and the basicity and oxidative potentials of the free ligands suggests a close relation between the donor ability of the chelating ligand and the carbonyl stretching frequencies observed in the complexes.

Thermal Rate Coefficients for the Astrochemical Process C + CH → C + H by Ring Polymer Molecular Dynamics.

Thermal rate coefficients for the astrochemical reaction C + CH → C + H were computed in the temperature range 20-300 K by using novel rate theory based on ring polymer molecular dynamics (RPMD) on a recently published bond-order based potential energy surface and compared with previous Langevin capture model (LCM) and quasi-classical trajectory (QCT) calculations. Results show that there is a significant discrepancy between the RPMD rate coefficients and the previous theoretical results that can lead to overestimation of the rate coefficients for the title reaction by several orders of magnitude at very low temperatures. We argue that this can be attributed to a very challenging energy profile along the reaction coordinate for the title reaction, not taken into account in extenso by either the LCM or QCT approximation.

Hollow Gold Cages and Their Topological Relationship to Dual Fullerenes.

Golden fullerenes have recently been identified by photoelectron spectra by Bulusu et al. [S. Bulusu, X.

How π back-donation quantitatively controls the CO stretching response in classical and non-classical metal carbonyl complexes.

The CO stretching response upon coordination to a metal M to form [(L) M(CO)] complexes (L is an auxiliary ligand) is investigated in relation to the σ donation and π back-donation components of the M-CO bond and to the electrostatic effect exerted by the ligand-metal fragment. Our analysis encompasses over 30 carbonyls, in which the relative importance of donation, back-donation and electrostatics are varied either through the ligand in a series of [(L)Au(CO)] gold(i) complexes, or through the metal in a series of anionic, neutral and cationic homoleptic carbonyls. Charge-displacement analysis is used to obtain well-defined, consistent measures of σ donation and π back-donation charges, as well as to quantify the σ and π components of CO polarization.

Configuration-Space Sampling in Potential Energy Surface Fitting: A Space-Reduced Bond-Order Grid Approach.

Potential energy surfaces (PESs) for use in dynamics calculations of few-atom reactive systems are commonly modeled as functional forms fitting or interpolating a set of ab initio energies computed at many nuclear configurations. An automated procedure is here proposed for optimal configuration-space sampling in generating this set of energies as part of the grid-empowered molecular simulator GEMS (Laganà et al., J.

Gold-superheavy-element interaction in diatomics and cluster adducts: A combined four-component Dirac-Kohn-Sham/charge-displacement study.

The chemistry of superheavy elements (Z ≥ 104) is actively investigated in atom-at-a-time experiments of volatility through adsorption on gold surfaces. In this context, common guidelines for interpretation based on group trends in the periodic table should be used cautiously, because relativistic effects play a central role and may cause predictions to fall short. In this paper, we present an all-electron four-component Dirac-Kohn-Sham comparative study of the interaction of gold with Cn (Z = 112), Fl (Z = 114), and Uuo (Z = 118) versus their lighter homologues of the 6th period, Hg, Pb, and Rn plus the noble gas Xe.

Charge-displacement analysis via natural orbitals for chemical valence: charge transfer effects in coordination chemistry.

We recently devised a simple scheme for analyzing on quantitative grounds the Dewar-Chatt-Duncanson donation and back-donation in symmetric coordination complexes. Our approach is based on a symmetry decomposition of the so called Charge-Displacement (CD) function quantifying the charge flow, upon formation of a metal (M)-substrate (S) bond, along the M-S interaction axis and provides clear-cut measures of donation and back-donation charges in correlation with experimental observables [G. Bistoni et al.

Full Parallel Implementation of an All-Electron Four-Component Dirac-Kohn-Sham Program.

A full distributed-memory implementation of the Dirac-Kohn-Sham (DKS) module of the program BERTHA (Belpassi et al., Phys. Chem.

An ab Initio Benchmark and DFT Validation Study on Gold(I)-Catalyzed Hydroamination of Alkynes.

High level ab initio calculations have been carried out on an archetypal gold(I)-catalyzed reaction: hydroamination of ethyne. We studied up to 12 structures of possible gold(I)-coordinated species modeling different intermediates potentially present in a catalytic cycle for the addition of a protic nucleophile to an alkyne. The benchmark is used to evaluate the performances of some popular density functionals for describing geometries and relative energies of stationary points along the reaction profile.