Showing papers by "José Elguero published in 2020"

Not Only Hydrogen Bonds: Other Noncovalent Interactions

Abstract: In this review, we provide a consistent description of noncovalent interactions, covering most groups of the Periodic Table. Different types of bonds are discussed using their trivial names. Moreover, the new name “Spodium bonds” is proposed for group 12 since noncovalent interactions involving this group of elements as electron acceptors have not yet been named. Excluding hydrogen bonds, the following noncovalent interactions will be discussed: alkali, alkaline earth, regium, spodium, triel, tetrel, pnictogen, chalcogen, halogen, and aerogen, which almost covers the Periodic Table entirely. Other interactions, such as orthogonal interactions and π-π stacking, will also be considered. Research and applications of σ-hole and π-hole interactions involving the p-block element is growing exponentially. The important applications include supramolecular chemistry, crystal engineering, catalysis, enzymatic chemistry molecular machines, membrane ion transport, etc. Despite the fact that this review is not intended to be comprehensive, a number of representative works for each type of interaction is provided. The possibility of modeling the dissociation energies of the complexes using different models (HSAB, ECW, Alkorta-Legon) was analyzed. Finally, the extension of Cahn-Ingold-Prelog priority rules to noncovalent is proposed.

Spodium Bonds: Noncovalent Interactions Involving Group 12 Elements.

Abstract: The term spodium (Sp) bond is proposed to refer to a net attractive interaction between any element of Group 12 and electron-rich atoms (Lewis bases or anions). These noncovalent interactions are markedly different from coordination bonds (antibonding Sp-ligand orbital involved). Evidence is provided for the existence of this interaction by calculations at the RI-MP2/aug-cc-pVTZ level of theory, atoms-in-molecules, and natural bond orbital analyses and by examining solid-state structures in the Cambridge Structure Database.

A Conceptual DFT Study of Phosphonate Dimers: Dianions Supported by H-Bonds.

Abstract: A conceptual DFT study of the dissociation of anionic and neutral phosphonate dimers has been carried out. In addition, the dianion complexes have been studied in the presence of two solvents, wate...

Metastable Dianions and Dications

Abstract: A theoretical study of metastable dianions and dications has been carried out at the CCSD(T)//MP2 level. MX3 2- and LX4 2- (M=Li and Na, L=Be and Mg, X=F and Cl) have been considered as dianions, M3 X2+ (M=Li and Na, X=F and Cl), YH3 2+ and ZH4 2+ (Y=F and Cl and Z=O, S) as dications. Minima structures are found in all cases, but they are less stable than the corresponding dissociated pair of mono-ions. The dissociation profile of the molecules in two mono-ions has been explored showing in all cases a maximum that prevent their spontaneous dissociation. The strength and nature of the chemical bond in the dianions and dications have been analyzed with the QTAIM, NBO and LMOEDA method and compared to the corresponding monoanions and monocations.

Stabilisation of dianion dimers trapped inside cyanostar macrocycles

Abstract: Interanionic H-bonds (IAHBs) are unfavourable interactions in the gas phase becoming favoured when anions are in solution. Dianion dimers are also susceptible to being trapped inside the cavities of cyanostar (CS) macrocycles, and thus, the formation of 2 : 2 anion : cyanostar aggregates is mainly supported by three kinds of interactions: IAHBs between the dianions, π–π stacking between the confronted cyanostars, and the presence of an intricate network of multiple C(sp2)H⋯O H-bonds between cyanostar ligands and the anionic moieties. An analysis of the interaction energies supported by NBO reveals a slight cooperative effect of the CSs on the IAHB stabilisation.

Regium Bonds between Silver(I) Pyrazolates Dinuclear Complexes and Lewis Bases (N2, OH2, NCH, SH2, NH3, PH3, CO and CNH)

Abstract: A theoretical study and Cambridge Structural Database (CSD) search of dinuclear Ag(I) pyrazolates interactions with Lewis bases were carried out and the effect of the substituents and ligands on the structure and on the aromaticity were analyzed. A relationship between the intramolecular Ag–Ag distance and stability was found in the unsubstituted system, which indicates a destabilization at longer distances compensated by ligands upon complexation. It was also observed that the asymmetrical interaction with phosphines as ligands increases the Ag–Ag distance. This increase is dramatically higher when two simultaneous PH3 ligands are taken into account. The calculated 109Ag chemical shielding shows variation up to 1200 ppm due to the complexation. Calculations showed that six-membered rings possessed non-aromatic character while pyrazole rings do not change their aromatic character significantly upon complexation.

Diborane Concatenation Leads to New Planar Boron Chemistry.

Abstract: Diborane has long been realized to be analogous to ethylene in terms of its bonding MOs, both as to symmetries and splitting patterns. This naturally suggests an investigation to see whether other similar conjugated hydrocarbons manifest a similar boron-substituted and H 2 supplemented borane. That is, for a conjugated hydrocarbon structure with a neighbor-paired resonance pattern, we propose to look at boranes where each carbon atom is replaced by a boron atom, and an H-atom pair is added to each double bond of the resonance structure, with one H above the molecular plane and one below. This construction of con-catenated diboranes is uniformly different than that for the previously known stable boranes of 4 or more B atoms. We find from quantum-chemical computations that our so constructed polyboranes are stable. All this suggests a possible novel new chapter in borane chemistry - a chapter with some promise of understandings related to that for (alternant) conjugated hydrocarbons.

Mutual Influence of Pnicogen Bonds and Beryllium Bonds: Energies and Structures in the Spotlight

Abstract: Pnicogen bonds, which are weak noncovalent interactions (NCIs), can be significantly modified by the presence of beryllium bonds, one of the strongest NCIs known. We demonstrate the importance of this influence by studying ternary complexes in which both NCIs are present, that is, the ternary complexes formed by a nitrogen base (NH3, NHCH2, and NCH), a phosphine (fluorophosphane, PH2F) and a beryllium derivative (BeH2, BeF2, BeCl2, BeCO3, and BeSO4). Energies, structures, and nature of the chemical bonding in these complexes are studied by means of ab initio computational methods. The pnicogen bond between the nitrogen base and the phosphine and the beryllium bond between the fluorine atom of fluorophosphane and the beryllium derivative show large cooperativity effects both on energies and geometries, with dissociation energies up to 296 kJ mol-1 and cooperativity up to 104 kJ mol-1 in the most strongly bound complex, CH2HN:PH2F:BeSO4. In the complexes between the strongest nitrogen bases and the strongest beryllium donors, phosphorus-shared and phosphorus-transfer bonds are found.

Rivalry between Regium and Hydrogen Bonds Established within Diatomic Coinage Molecules and Lewis Acids/Bases

Abstract: A theoretical study of the complexes formed by Ag 2 and Cu 2 with different molecules, XH (FH, ClH, OH 2 , SH 2 , HCN, HNC, HCCH, NH 3 and PH 3 ) that can act as hydrogen bond donors (Lewis acids) or regium bond acceptors (Lewis bases) were carried out at the CCSD(T)/CBS computational level. In addition, the heteronuclear diatomic coinage molecules (AuAg, AuCu, and AgCu) have also been considered. With the exception of some of the hydrogen bonded complexes with FH, the regium bonded binary complexes are more stable. The AuAg and AuCu molecules show large dipole moments that weaken the RB bonds with Au and favours those through the Ag and Cu atoms respectively.

Hydrogen vs. Halogen Bonds in 1-Halo-Closo-Carboranes.

Abstract: A theoretical study of the hydrogen bond (HB) and halogen bond (XB) complexes between 1-halo-closo-carboranes and hydrogen cyanide (NCH) as HB and XB probe has been carried out at the MP2 computational level. The energy results show that the HB complexes are more stable than the XBs for the same system, with the exception of the isoenergetic iodine derivatives. The analysis of the electron density with the quantum theory of atoms in molecules (QTAIM) shows the presence of a unique intermolecular bond critical point with the typical features of weak noncovalent interactions (small values of the electron density and positive Laplacian and total energy density). The natural energy decomposition analysis (NEDA) of the complexes shows that the HB and XB complexes are dominated by the charge-transfer and polarization terms, respectively. The work has been complemented with a search in the CSD database of analogous complexes and the comparison of the results, with those of the 1-halobenzene:NCH complexes showing smaller binding energies and larger intermolecular distances as compared to the 1-halo-closo-carboranes:NCH complexes.

An experimental and computational NMR study of organometallic nine-membered rings: Trinuclear silver(I) complexes of pyrazolate ligands

Abstract: This work reports the calculation of the nuclear magnetic resonance (NMR) chemical shifts of eight trinuclear Ag(I) complexes of pyrazolate ligands using the relativistic program ZORA. The data from the literature concern exclusively 1 H, 13 C, and 19 F nuclei. For this reason, one of the complexes that is derived from 3,5-bis-trifluoromethyl-1H-pyrazole has been studied anew, and the 15 N and 109 Ag chemical shifts determined for the first time in solution. Solid-state NMR data of this compound have been obtained for some nuclei (1 H, 13 C, and 19 F) but not for others (14 N, 15 N, and 109 Ag).

Hybrid Boron-Carbon Chemistry.

Abstract: The recently proved one-to-one structural equivalence between a conjugated hydrocarbon CnHm and the corresponding borane BnHm+n is applied here to hybrid systems, where each C=C double bond in the hydrocarbon is consecutively substituted by planar B(H2)B moieties from diborane(6). Quantum chemical computations with the B3LYP/cc-pVTZ method show that the structural equivalences are maintained along the substitutions, even for non-planar systems. We use as benchmark aromatic and antiaromatic (poly)cyclic conjugated hydrocarbons: cyclobutadiene, benzene, cyclooctatetraene, pentalene, benzocyclobutadiene, naphthalene and azulene. The transformation of these conjugated hydrocarbons to the corresponding boranes is analyzed from the viewpoint of geometry and electronic structure.

The Lewis acidities of gold(I) and gold(III) derivatives: a theoretical study of complexes of AuCl and AuCl3

Abstract: Chloride complexes of gold(I) (seventeen) and gold(III) (seventeen) with different ligands (including H, C, N, O, P, S as interacting atoms) have been studied at the CCSD(T)/CBS level. The computed geometries were compared with those found in the Cambridge Structural Database and the dissociation energies related with those previously reported in the literature by Yamamoto et al. Some special processes catalysed by these gold complexes such as bond-breaking (dihydrogen, cyclopropane) and arenes reactivity were studied in detail.

A Computational Study of Metallacycles Formed by Pyrazolate Ligands and the Coinage Metals M = Cu(I), Ag(I) and Au(I): (pzM) n for n = 2, 3, 4, 5 and 6. Comparison with Structures Reported in the Cambridge Crystallographic Data Center (CCDC)

Abstract: The structures reported in the Cambridge Structural Database (CSD) for neutral metallacycles formed by coinage metals in their valence (I) (cations) and pyrazolate anions were examined. Depending on the metal, dimers and trimers are the most common but some larger rings have also been reported, although some of the larger structures are not devoid of ambiguity. M06-2x calculations were carried out on simplified structures (without C-substituents on the pyrazolate rings) in order to facilitate a comparison with the reported X-ray structures (geometries and energies). The problems of stability of the different ring sizes were also analyzed.

Complexes H2CO:PXH2 and HCO2H:PXH2 for X = NC, F, Cl, CN, OH, CCH, CH3, and H: Pnicogen Bonds and Hydrogen Bonds

Abstract: Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to investigate H2 CO : PXH2 pnicogen-bonded complexes and HCO2 H : PXH2 complexes that are stabilized by pnicogen bonds and hydrogen bonds, with X=NC, F, Cl, CN, OH, CCH, CH3 , and H. The binding energies of these complexes exhibit a second-order dependence on the O-P distance. DFT-SAPT binding energies correlate linearly with MP2 binding energies. The HCO2 H : PXH2 complexes are stabilized by both a pnicogen bond and a hydrogen bond, resulting in greater binding energies for the HCO2 H : PXH2 complexes compared to H2 CO : PXH2 . Neither the O-P distance across the pnicogen bond nor the O-P distance across the hydrogen bond correlates with the binding energies of these complexes. The nonlinearity of the hydrogen bonds suggests that they are relatively weak bonds, except for complexes in which the substituent X is either CH3 or H. The pnicogen bond is the more important stabilizing interaction in the HCO2 H : PXH2 complexes except when the substituent X is a more electropositive group. EOM-CCSD spin-spin coupling constants 1p J(O-P) across pnicogen bonds in H2 CO:PXH2 and HCO2 H : PXH2 complexes increase as the O-P distance decreases, and exhibit a second order dependence on that distance. There is no correlation between 2h J(O-P) and the O-P distance across the hydrogen bond in the HCO2 H : PXH2 complexes. 2h J(O-P) coupling constants for complexes with X=CH3 and H have much greater absolute values than anticipated from their O-P distances.

Interaction between Trinuclear Regium Complexes of Pyrazolate and Anions, a Computational Study.

Abstract: The geometry, energy and electron density properties of the 1:1, 1:2 and 1:3 complexes between cyclic (Py-M)3 (M = Au, Ag and Cu) and halide ions (F-, Cl- and Br-) were studied using Moller Plesset (MP2) computational methods. Three different configurations were explored. In two of them, the anions interact with the metal atoms in planar and apical dispositions, while in the last configuration, the anions interact with the CH(4) group of the pyrazole. The energetic results for the 1:2 and 1:3 complexes are a combination of the specific strength of the interaction plus a repulsive component due to the charge:charge coulombic term. However, stable minima structures with dissociation barriers for the anions indicate that those complexes are stable and (Py-M)3 can hold up to three anions simultaneously. A search in the CSD confirmed the presence of (Pyrazole-Cu)3 systems with two anions interacting in apical disposition.

Theoretical calculations of the chemical shifts of cyclo[n]phosphazenes for n = 2, 3, 4 and 5 (X2PN)n with X = CH3, F, Cl and Br: the effect of relativistic corrections

Abstract: Di, tri, tetra and pentacyclophosphazenes substituted on the phosphorus atoms by CH3, F, Cl and Br atoms corresponding to (X2PN)n structures have been studied theoretically at the B3LYP/6-3...

Hydrogen bonds and halogen bonds in complexes of carbones L→C←L as electron donors to HF and ClF, for L = CO, N2, HNC, PH3, and SH2.

Abstract: Ab initio MP2/aug’-cc-pVTZ calculations have been carried out to determine the structures and binding energies of the carbone complexes in which the carbone L→C←L acts as an electron pair donor to one and two HF or ClF molecules, for L = CO, N2, HNC, PH3, and SH2. The binding energies increase with respect to the ligand in the order CO < NN < CNH ≪ PH3 < SH2, and increase with respect to the acid in the order HF < 2 HF < ClF < 2 ClF. The complexes with the ligands CO, N2 and PH3 have C2v symmetry while those with CNH and SH2 have Cs symmetry, except for H2S→C←SH2:2HF which has C2 symmetry and a unique structure among all of the carbone complexes. F–H and Cl–F stretching frequencies in the complexes decrease as the F–H and Cl–F distances, respectively, increase. EOM-CCSD spin–spin coupling constants 2hJ(F–C) increase with decreasing F–C distance. Although the F–H⋯C hydrogen bonds gain some proton-shared character in the most tightly bound complexes, the hydrogen bonds remain traditional hydrogen bonds. 1xJ(Cl–C) values indicate that the Cl⋯C halogen bonds have chlorine shared character even at the longest distances. 1xJ(Cl–C) then increases as the Cl–C distance decreases, and reaches a maximum for chlorine-shared halogen bonds. As the Cl–C distance further decreases, the halogen bond becomes a chlorine-transferred halogen bond.

Regiospecific synthesis and structural studies of 3,5-dihydro-4h-pyrido[2,3-b][1,4]diazepin-4-ones and comparison with 1,3-dihydro-2h-benzo[b][1,4]diazepin-2-ones

Abstract: Nine 3,5-dihydro-4H-pyrido[2,3-b][1,4]diazepin-4-ones (17-25), some of which contain fluoro-substituents, have been regiospecifically prepared by reaction of 2,3-diaminopyridines with ethyl aroylacetates. In two cases, open intermediates have been isolated and these are related to the reaction pathway. The X-ray crystal structure of 1-methyl-4-phenyl-3,5-dihydro-4H-pyrido[2,3-b][1,4]diazepin-4-one (23) has been solved (formula, C15H13N3O; crystal system, monoclinic; space group, C2/c). This is an asymmetric unit constituted by a single nonplanar molecule and its conformational enantiomer due to the presence of the seven-membered diazepin-2-one moiety, which introduces a certain degree of torsion in the adjacent pyridine ring. The 1H, 13C, 15N, and 19F NMR spectra were obtained and the chemical shifts, together with those of the previously published 1,3-dihydro-2H-benzo[b][1,4]diazepin-2-ones (1-16), i.e., a total of 544 values, were successfully compared with the chemical shifts calculated at the gauge invariant atomic orbital (GIAO)/Becke, three-parameter, Lee-Yang-Parr (B3LYP)/6-311++G(d,p) level. The seven-membered ring inversion barrier in 5-benzyl-2-phenyl-3,5-dihydro-4H-pyrido[2,3-b][1,4]diazepin-4-one (25) was determined and, in conjunction with the data from the literature, compared with the B3LYP/6-311++G(d,p) computed values. This allowed the determination of several structural effects. The rotation about the exocyclic N1-CR bond was also calculated and its dynamic properties were discussed.

Theoretical studies of perimidine and its derivatives: structures, energies, and spectra

Abstract: Theoretical calculations at the B3LYP/6-311++G(d,p) level plus GIAO calculations for NMR absolute shieldings have been carried out for the parent perimidine and several of its derivatives. These include its anion and cation and the acid-base equilibria and other examples of annular tautomerism, such as the 2-hydroxy (and their radical cations), 2-thiol, 2-amino, and 2-alkyl perimidines, and the functional tautomers, such as the benzologues of perimidone. The protonation of 2-aminoperimidines (cyclic guanidines) and the properties of perimidine carbene (dimerization and addition to carbon dioxide), biperimidine, dihydroperimidine, and spiro bidihydroperimidine were also studied.

Complexes Between Adamantane Analogues B4X6 -X = {CH2, NH, O ; SiH2, PH, S} - and Dihydrogen, B4X6:nH2 (n = 1–4)

Abstract: In this work, we study the interactions between adamantane-like structures B4X6 with X = {CH2, NH, O ; SiH2, PH, S} and dihydrogen molecules above the Boron atom, with ab initio methods based on perturbation theory (MP2/aug-cc-pVDZ). Molecular electrostatic potentials (MESP) for optimized B4X6 systems, optimized geometries, and binding energies are reported for all B4X6:nH2 (n = 1–4) complexes. All B4X6:nH2 (n = 1–4) complexes show attractive patterns, with B4O6:nH2 systems showing remarkable behavior with larger binding energies and smaller B···H2 distances as compared to the other structures with different X.

Are Anions of Cyclobutane Beryllium Derivatives Stabilized through Four-Center One-Electron Bonds?

Abstract: High-level G4 ab initio calculations allowed us to show that C4H4(BeX)4 (X = H, Cl) derivatives behave as rather efficient electron capturers due to their ability to trap the extra electron through the formation of a four-membered beryllium ring. This finding is in agreement with previous work showing the ability of highly electron-deficient atoms, such as beryllium, to lead to multicenter one-electron bonds. In our particular case, the formation of the four-center bond is characterized, in very good harmony, by different topological methods such as quantum theory of atoms in molecules (QTAIM), the electron localization function (ELF), and the noncovalent interactions (NCI) approach and is accompanied by large electron affinity values, around 300 kJ·mol-1, in the gas phase. Preliminary results may anticipate that the ability of groups of beryllium atoms to trap electrons decays on going to bigger systems.

Theoretical and Spectroscopic Characterization of API-Related Azoles in Solution and in Solid State.

Abstract: Azoles are a family of five-membered azacyclic compounds with relevant biological and pharmacological activity. Different subclasses of azoles are defined depending on the atomic arrangement and the number of nitrogen atoms present in the ring: pyrazoles, indazoles, imidazoles, benzimidazoles, triazoles, benzotriazoles, tetrazoles and pentazoles. The complete characterization of their structure and the knowledge about their crystal packing and physical and chemical properties are of vital importance for the advancement in the design of new azole-containing drugs. In this review, we report the latest recent contributions to azole chemistry, in particular, those in which theoretical studies have been performed.

From Very Strong to Inexistent Be-Be Bonds in the Interactions of Be2 with π-Systems.

Abstract: Isolated Be2 is a typical example of a weakly bound system, but interaction with other systems may give rise to surprising bonding features. The interactions between Be2 and a set of selected neutral Cn Hn (n=2-8) π-systems have been analyzed through the use of G4 and G4MP2 ab initio methods, along with multireference CASPT2//CASPT2 calculations. Our results systematically show that the Cn Hn -Be2 -Cn Hn clusters formed are always very stable. However, the nature of this interaction is completely different when the π-system involved is a closed shell species (n=2, 4, 6, 8), or a radical (n=3, 5, 7). In the first case, the interaction does not occur with the π-system as a whole, but with specific C centers yielding rather polar but strong C-Be bonds. Nonetheless, although the Be-Be distances in these complexes are similar to the ones in compounds with ultra-strong Be-Be bonds, a close examination of their electron density distribution reveals that no Be-Be bonds exist. The situation is totally different when the interaction involves two π-radicals, Cn Hn -Be2 -Cn Hn (n=3, 5, 7). In these cases, a strong Be-Be bond is formed. Indeed, even though Be is electron deficient, the Be2 moiety behaves as an efficient electron donor towards the two π-radicals, so that the different Cn Hn -Be2 -Cn Hn (n=3, 5, 7) clusters are the result of the interaction between Be2 2+ and two L- anions. The characteristics of these two scenarios do not change when dealing with bicyclic π-compounds, such as naphthalene and pentalene, because the interaction with the Be2 moiety is localized on one of the unsaturated cycles, the other being almost a spectator.

A C(π-hole)⋯Cl–Zn tetrel interaction driving a metal–organic supramolecular assembly

Abstract: A brominated pyrimidinyl triazolopyridine ligand (bptpy) forms a C(π-hole)⋯Cl–Zn tetrel interaction that plays a determining role in the formation of supramolecular layers through chain assembly in 18 membered metallacycle [(ZnCl2)2(μ-bptpy)2] crystals. Supramolecular chains are formed through C–H⋯X interactions. The observed interactions are supported by DFT calculations using model dimers.