In order to assess the ability of theory to describe properly the dispersive interactions that are ubiquitous in peptide and protein systems, an isolated short peptide chain has been studied using both gas-phase laser spectroscopy and quantum chemistry. The experimentally observed coexistence of an extended form and a folded form in the supersonic expansion was found to result from comparable Gibbs free energies for the two species under the high-temperature conditions (< or = 320 K) resulting from the laser desorption technique used to vaporize the molecules. These data have been compared to results obtained using a series of quantum chemistry methods, including DFT, DFT-D, and post-Hartree-Fock methods, which give rise to a wide range of relative stabilities predicted for these two forms. The experimental observation was best reproduced by an empirically dispersion-corrected functional (B97-D) and a hybrid functional with a significant Hartree-Fock exchange term (M06-2X). In contrast, the popular post-Hartree-Fock method MP2, which is often used for benchmarking these systems, had to be discarded because of a very large basis-set superposition error. The applicability of the atomic counterpoise correction (ACP) is also discussed. This work also introduces the mandatory theoretical examination of experimental abundances. DeltaH(0 K) predictions are clearly not sufficient for discussion of folding, as the conformation inversion temperature is crucial to the conformation determination and requires taking into account thermodynamical corrections (DeltaG) in order to computationally isolate the most stable conformation.

The paper collects the answers of the authors to the following questions: Is the lack of precision in the definition of many chemical concepts one of the reasons for the coexistence of many partition schemes? Does the adoption of a given partition scheme imply a set of more precise definitions of the underlying chemical concepts? How can one use the results of a partition scheme to improve the clarity of definitions of concepts? Are partition schemes subject to scientific Darwinism? If so, what is the influence of a community's sociological pressure in the “natural selection” process? To what extent does/can/should investigated systems influence the choice of a particular partition scheme? Do we need more focused chemical validation of Energy Decomposition Analysis (EDA) methodology and descriptors/terms in general? Is there any interest in developing common benchmarks and test sets for cross‐validation of methods? Is it possible to contemplate a unified partition scheme (let us call it the “standard model” of partitioning), that is proper for all applications in chemistry, in the foreseeable future or even in principle? In the end, science is about experiments and the real world. Can one, therefore, use any experiment or experimental data be used to favor one partition scheme over another? © 2019 Wiley Periodicals, Inc.

The nature of the bonding in the binary transition-metal carbonyl complex has been analyzed by topological approaches (atoms in molecules (AIM) and electron localization function (ELF)) from a series of calculations carried out at the hybrid Hartree−Fock/DFT level (B3LYP). It is shown that the interaction between a transition metal and CO should be characterized as a dative bond, in which the monosynaptic basin of the carbon plays the role of the disynaptic basin connecting the metal core to the carbon atom. For all atoms except Cr, Mn, and Cu, the multiplicity of the ground state is given by applying Hund's rule to the maximal core occupancy (i.e., [Ar]c n +2):  high-spin complexes for n < 4, low-spin for n > 5, spin-conserved for n = 4, 5, 9. The charge transfers and the spin density on the ligand are rationalized by resonance structures of the same multiplicity. In all complexes except CrCO and CuCO, the ELF function in the core has a local cylindrical symmetry that in turn favors a linear structure; moreover, 2 electrons are available for the charge transfer toward the CO moiety and for the metal nonbonding valence basin. In CrCO and CuCO whose cores have a spherical symmetry, only one electron can be shared by the net transfer and the nonbonding valence basin. The maximization of the charge transfer implies a bent geometry. Finally, we propose two new donation−back-donation schemes based on the AIM and ELF partitions. In the ELF framework, the net charge transfer is almost equal to the π back-donation, the σ-donation being negligible.

Computational chemistry currently lacks ad hoc tools for probing the nature of chemical bonds in heavy and superheavy-atom systems where the consideration of spin-orbit coupling (SOC) effects is mandatory. We report an implementation of the Quantum Theory of Atoms-In-Molecules in the framework of two-component relativistic calculations. Used in conjunction with the topological analysis of the Electron Localization Function, we show for astatine (At) species that SOC significantly lowers At electronegativity and boosts its propensity to make charge-shift bonds. Relativistic spin-dependent effects are furthermore able to change some bonds from mainly covalent to charge-shift type. The implication of the disclosed features regarding the rationalization of the labeling protocols used in nuclear medicine for (211)At radioisotope nicely illustrates the potential of the introduced methodology for investigating the chemistry of (super)heavy elements.

Following a previous study by de Courcy et al. ((2009) Interdiscip. Sci. Comput. Life Sci. 1, 55-60), we demonstrate in this contribution, using quantum chemistry, that metal cations exhibit a specific topological signature in the electron localization of their density interacting with ligands according to its “soft” or “hard” character. Introducing the concept of metal cation subvalence, we show that a metal cation can split its outer-shell density (the so-called subvalent domains or basins) according to it capability to form a partly covalent bond involving charge transfer. Such behaviour is investigated by means of several quantum chemical interpretative methods encompasing the topological analysis of the Electron Localization Function (ELF) and Bader's Quantum Theory of Atoms in Molecules (QTAIM) and two energy decomposition analyses (EDA), namely the Restricted Variational Space (RVS) and Constrained Space Orbital Variations (CSOV) approaches. Further rationalization is performed by computing ELF and QTAIM local properties such as electrostatic distributed moments and local chemical descriptors such as condensed Fukui Functions and dual descriptors. These reactivity indexes are computed within the ELF topological analysis in addition to QTAIM offering access to non atomic reactivity local index, for example on lone pairs. We apply this “subvalence” concept to study the cation selectivity in enzymes involved in blood coagulation (GLA domains of three coagulation factors). We show that the calcium ions are clearly able to form partially covalent charge transfer networks between the subdomain of the metal ion and the carboxylate oxygen lone pairs whereas magnesium does not have such ability. Our analysis also explains the different role of two groups (high affinity and low affinity cation binding sites) present in GLA domains. If the presence of Ca(II) is mandatory in the central “high affinity” region to conserve a proper folding and a charge transfer network, external sites are better stabilised by Mg(II), rather than Ca(II), in agreement with experiment. The central role of discrete water molecules is also discussed in order to understand the stabilities of the observed X-rays structures of the Gla domain. Indeed, the presence of explicit water molecules generating indirect cation-protein interactions through water networks is shown to be able to reverse the observed electronic selectivity occuring when cations directly interact with the Gla domain without the need of water.

Context. Over 20 of the ∼150 different species detected in the interstellar and circumstellar media have also been identified in icy environments. For most of the species observed so far in the interstellar medium (ISM), the most abundant isomer of a given generic chemical formula is the most stable one (minimum energy principle -MEP) with few exceptions such as, for example, CH 3 COOH/HCOOCH 3 and CH 3 CH 2 OH/CH 3 OCH 3 , whose formation is thought to occur on the icy mantles of interstellar grains. Aims. We investigate whether differences found in the compositions of molecular ices and the surrounding gas phase could originate from differences between the adsorption of one isomer from that of another at the ice surface. Methods. We performed a coherent and concerted theoretical/experimental study of the adsorption energies of the four molecules mentioned above, i.e. acetic acid (AA)/methyl formate (MF) and ethanol (EtOH)/dimethyl ether (DME) on the surface of water ice at low temperature. The question was first addressed theoretically at LCT using solid state periodic density functional theory (DFT) to represent the organized solid support. The experimental determination of the ice/molecule interaction energies was then carried out independently by two teams at LPMAA and LERMA/LAMAp using temperature programmed desorption (TPD) under an ultra-high vacuum (UHV) between 70 and 160 K. Results. For each pair of isomers, theory and experiments both agree that the most stable isomer (AA or EtOH) interacts more efficiently with the water ice than the higher energy isomer (MF or DME). This differential adsorption can be clearly seen in the different desorption temperatures of the isomers. It is not related to their intrinsic stability but instead to both AA and EtOH producing more and stronger hydrogen bonds with the ice surface. Conclusions. We show that hydrogen bonding may play an important role in the release of organic species from grains and propose that, depending on the environment, differential adsorption should not be rejected as a possible way of interpreting MEP exceptions.

We present an original formulation of the electron localization function (ELF) in the field of relativistic two-component DFT calculations. Using I2 and At2 species as a test set, we show that the ELF analysis is suitable to evaluate the spin-orbit effects on the electronic structure. Beyond these examples, this approach opens up new opportunities for the bonding analysis of large molecular systems involving heavy and superheavy elements.

We propose here an evaluation of chemically intuitive distributed electrostatic moments using the topological analysis of the electron localization function (ELF). As this partition of the total charge density provides an accurate representation of the molecular dipole, the distributed electrostatic moments based on the ELF partition (DEMEP) allows computing of local moments located at non atomic centers such as lone pairs, sigma bonds and pi systems. As the local dipole contribution can be decomposed in polarization and charge transfer components, our results indicate that local dipolar polarization of the lone pairs and chemical reactivity are closely related whereas the charge transfer contribution is the key factor driving the local bond dipole. Results on relevant molecules show that local dipole contributions can be used to rationalize inductive polarization effects in alcohols derivatives and typical hydrogen bond interactions. Moreover, bond quadrupole polarization moments being related to a pi character enable to discuss bond multiplicities, and to sort families of molecules according to their bond order. That way, the nature of the C-O bond has been revisited for several typical systems by means of the DEMEP analysis which appears also helpful to discuss aromaticity. Special attention has been given to the carbon monoxide molecule, to the CuCO complex and to a weak intramolecular N|-CO interaction involved in several biological systems. In this latter case, it is confirmed that the bond formation is mainly linked to the CO bond polarization. Transferability tests show that the approach is suitable for the design of advanced force fields.