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. Building on a previously defined systematic approach to construct rigorous stochastic models of flexible molecules in solutions from basic principles, we define a manageable diffusive framework leading to a Smoluchowski equation determined by one main tensorial parameter, namely the scaled roto-conformational diffusion tensor, which accounts for the influence of both conservative and dissipative forces and describes the molecular mobility via a precise definition of internal-external and internal-internal couplings. We then show the usefulness of the roto-conformational scaled diffusion tensor as an efficient gauge of molecular flexibility through the analysis of a set of molecular systems of increasing complexity ranging from dimethylformamide to a protein domain.

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 syn or anti 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. Our results indicate that both VyA conformers feature a similar reactivity with CN, starting with a barrierless addition to the double bond and followed by different isomerization, dissociation, and/or hydrogen elimination steps. The rate constants computed for temperatures up to 600 K show that several reaction channels are open even under the harsh conditions of the ISM, with the favoured one providing the first feasible formation route of a prebiotic molecule not yet detected in the ISM, namely cyanoacetaldehyde. This finding suggests looking for cyanoacetaldehyde in regions where both VyA and CN have already been detected, like, e.g., Sagittarius B2N or G+0.693-0.027.

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. The new scheme naturally reduces to ordinary CD analysis if the path is chosen to be a straight line. An implementation based on a discrete sampling of the electron densities and a Voronoi space partitioning is described and shown in action on two test cases of a metal-carbonyl and a pyridine-ammonia complex.

Stochastic Modelling of 13C 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. Here, for the first time, we applied directly the SFB approach to the practical evaluation of high-quality 13C nuclear magnetic resonance relaxation parameters, T1 and T2, and the heteronuclear NOE of several oligosaccharides, which were previously interpreted on the basis of refined ad hoc modelling. The calculated NMR relaxation parameters were in agreement with the experimental data, showing that this general approach can be applied to diverse classes of molecular systems, with the minimal usage of adjustable parameters.

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.

Chemical bonding in cuprous complexes with simple nitriles: octet rule and resonance concepts versus 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.

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. The case of gold cyanide elucidates the peculiar role of the relativistic effects in determining the characteristics of the Au-C bond with respect to the copper and silver homologues. In AuCN, the donation and back-donation components are significantly enhanced, and the spin-orbit coupling, removing the degeneracy of the 5d atomic orbitals, induces a substantial split in the back-donation components. A simple spatial analysis of the NOCV-pair density, related to the ligand-to-metal donation component, allows us to quantify, with unprecedented accuracy, the charge rearrangement due to the s-d hybridization occurring at the metal site. The s-d hybridization plays a key role in determining the shape and size of the metal; it removes electron density from the bond axis and induces a significant flattening at the metal site in the position trans to the ligand. The s-d hybridization is present in all noble metal complexes, influencing the bond distances, and its effect is enhanced for Au, which is consistent with the preference of gold to form linear complexes. A comparative investigation of simple complexes [AuL]+/0 of Au+ with different ligands (L = F-, N-heterocyclic carbene, CO, and PH3) shows that the s-d hybridization mechanism is also influenced by the nature of the ligand.

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. Interesting conformational properties are either confirmed or established by the technique, like the eclipsed conformation of the two cyclopentadienyl rings and an intra-molecular interaction involving the OH for 3. For 4, NMR, VCD and IR spectra are compatible with dimer formation and in this case a distorted conformation is predicted. Of utmost importance for the absolute configuration assignment in mono-substituted ferrocenes, we were able to identify a diagnostic VCD band at 950 cm-1 and a (low intensity) ECD band that clearly indicate the absolute configuration of the whole series.

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. By means of two case studies on organometallic complexes, we show how familiar concepts in coordination chemistry, such as donation and back-donation charge flows, can be effectively identified and quantified to predict experimental observables. © 2018 Wiley Periodicals, Inc.

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. Based on the assignment of the rotational spectra for 7 isotopologues, an accurate semi-experimental equilibrium structure for the heavy-atom backbone of the molecular complex has been determined, which is characterized by a S⋅⋅⋅S distance (2.947(3) Å) well below the sum of van der Waals radii.

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. The conformational landscape exploration and stationary points characterization have been performed using state-of-the-art quantum-chemical computations providing significant insights on structure determination.

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)2(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. We then use theory to unravel the detailed mechanisms of chelation-bond formation in terms of partial charge flows between the molecular orbitals of the fragments. By extending the promising, recently published natural orbitals for chemical valence/charge displacement (NOCV/CD) analysis scheme we provide a thorough, quantitative description of the several charge fluxes following the metal-ligand bond formation and demonstrate that the carbonyl stretching frequencies in the considered complexes selectively respond to the σ-donation charge flow from the phosphorus lone pairs of the ligands, with the frequency shift being in quantitative correlation with the extent of the ligand-to-metal charge transfer.

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. Li, L.-S. Wang, X. C. Zeng, PNAS 2006, 103, 8326-8330]. These unique triangulations of a sphere are related to fullerene duals having exactly 12 vertices of degree five, and the icosahedral hollow gold cages previously postulated are related to the Goldberg-Coxeter transforms of C20 starting from a triangulated surface (hexagonal lattice, dual of a graphene sheet). This also relates topologically the (chiral) gold nanowires observed to the (chiral) carbon nanotubes. In fact, the Mackay icosahedra well known in gold cluster chemistry are related topologically to the dual halma transforms of the smallest possible fullerene C20 . The basic building block here is the (111) fcc sheet of bulk gold which is dual to graphene. Because of this interesting one-to-one relationship through Euler's polyhedral formula, there are as many golden fullerene isomers as there are fullerene isomers, with the number of isomers Niso increasing polynomially as O(Niso9 ). For the recently observed Au16- , Au17- , and Au18- we present simulated photoelectron spectra including all isomers. We also predict the photoelectron spectrum of Au32- . The stability of the golden fullerenes is discussed in relation with the more compact structures for the neutral and negatively charged Au12 to Au20 and Au32 clusters. As for the compact gold clusters we observe a clear trend in stability of the hollow gold cages towards the (111) fcc sheet. The high stability of the (111) fcc sheet of gold compared to the bulk 3D structure explains the unusual stability of these hollow gold cages.

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. Grid Comput. 2010, 8, 571-586). The scheme is based on a space-reduced formulation of the so-called bond-order variables allowing for a balanced representation of the attractive and repulsive regions of a diatom configuration space. Uniform grids based on space-reduced bond-order variables are proven to outperform those defined on the more conventional bond-length variables in converging the fitted/interpolated PES to the computed ab initio one with increasing number of grid points. Benchmarks are performed on the one- and three-dimensional prototype systems H2 and H3 using both a local-interpolation (modified Shepard) and a global-fitting (Aguado-Paniagua) scheme.

Thermal Rate Coefficients for the Astrochemical Process C + CH+ → C2+ + H by Ring Polymer Molecular Dynamics.

Thermal rate coefficients for the astrochemical reaction C + CH+ → C2+ + 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. In the absence of any rigorous quantum mechanical or experimental results, the computed RPMD rate coefficients represent state-of-the-art estimates to be included in astrochemical databases and kinetic networks.

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. Calculations were carried out for Au-E (E = Hg, Cn, Pb, Fl, Xe, Rn, Uuo), Au7- and Au20-E (E = Hg, Cn, Pb, Fl, Rn) complexes, where Au7 (planar) and Au20 (pyramidal) are experimentally determined clusters having structures of increasing complexity. Results are analysed both in terms of the energetics of the complexes and of the electron charge rearrangement accompanying their formation. In line with the available experimental data, Cn and more markedly Fl are found to be less reactive than their lighter homologues. On the contrary, Uuo is found to be more reactive than Rn and Xe. Cn forms the weakest bond with the gold atom, compared to Fl and Uuo. The reactivity of Fl decreases with increasing gold-fragment size more rapidly than that of Cn and, as a consequence, the order of the reactivity of these two elements is inverted upon reaching the Au20-cluster adduct. Density difference maps between adducts and fragments reveal similarities in the behaviour of Cn and Xe, and in that of Uuo and the more reactive species Hg and Pb. These findings are given a quantitative ground via charge-displacement analysis.

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., Angew. Chem., Int. Ed. 52, 11599 (2013)]. The symmetry constraints exclude of course from the analysis most systems of interest in coordination chemistry. In this paper, we show how to entirely overcome this limitation by taking advantage of the properties of the natural orbitals for chemical valence [M. Mitoraj and A. Michalak, J. Mol. Model. 13, 347 (2007)]. A general scheme for disentangling donation and back-donation in the CD function of both symmetric and non-symmetric systems is presented and illustrated through applications to M-ethyne (M = Au, Ni and W) coordination bonds, including an explicative study on substrate activation in a model reaction mechanism.

Code interoperability and standard data formats in quantum chemistry and quantum dynamics: The Q5/D5Cost data model.

Code interoperability and the search for domain-specific standard data formats represent critical issues in many areas of computational science. The advent of novel computing infrastructures such as computational grids and clouds make these issues even more urgent. The design and implementation of a common data format for quantum chemistry (QC) and quantum dynamics (QD) computer programs is discussed with reference to the research performed in the course of two Collaboration in Science and Technology Actions. The specific data models adopted, Q5Cost and D5Cost, are shown to work for a number of interoperating codes, regardless of the type and amount of information (small or large datasets) to be exchanged. The codes are either interfaced directly, or transfer data by means of wrappers; both types of data exchange are supported by the Q5/D5Cost library. Further, the exchange of data between QC and QD codes is addressed. As a proof of concept, the H + H2 reaction is discussed. The proposed scheme is shown to provide an excellent basis for cooperative code development, even across domain boundaries. Moreover, the scheme presented is found to be useful also as a production tool in the grid distributed computing environment.

An extension of the grid empowered molecular simulator to quantum reactive scattering.

Within the activities of the D37 COST Action, we have further developed the quantum dynamics framework of the grid empowered molecular simulator (GEMS) implemented on the segment of the European grid available to the COMPCHEM (computational chemistry) virtual organization. GEMS does now include in a full ab initio approach, the evaluation of the detailed quantum (both time dependent and time independent) dynamics of small systems starting from the calculation of the electronic structure properties as well as the direct calculation of thermalized properties. Illustrative, full dimensional applications of the extended simulator to the H + H(2) , N + N(2) , and O + O(2) systems are presented.