Showing papers by "José Elguero published in 2013"

On the Reliability of Pure and Hybrid DFT Methods for the Evaluation of Halogen, Chalcogen, and Pnicogen Bonds Involving Anionic and Neutral Electron Donors.

Abstract: In this article, we report a comprehensive theoretical study of halogen, chalcogen, and pnicogen bonding interactions using a large set of pure and hybrid functionals and some ab initio methods. We have observed that the pure and some hybrid functionals largely overestimate the interaction energies when the donor atom is anionic (Cl– or Br–), especially in the halogen bonding complexes. To evaluate the reliability of the different DFT (BP86, BP86-D3, BLYP, BLYP-D3, B3LYP, B97-D, B97-D3, PBE0, HSE06, APFD, and M06-2X) and ab initio (MP2, RI-MP2, and HF) methods, we have compared the binding energies and equilibrium distances to those obtained using the CCSD(T)/aug-cc-pVTZ level of theory, as reference. The addition of the latest available correction for dispersion (D3) to pure functionals is not recommended for the calculation of halogen, chalcogen, and pnicogen complexes with anions, since it further contributes to the overestimation of the binding energies. In addition, in chalcogen bonding interactions,...

Pnicogen Bonded Complexes of PO2X (X = F, Cl) with Nitrogen Bases

Abstract: An ab initio MP2/aug′-cc-pVTZ study has been carried out on complexes formed between PO2X (X = F and Cl) as the Lewis acids and a series of nitrogen bases ZN, including NH3, H2C═NH, NH2F, NP, NCH, NCF, NF3, and N2. Binding energies of these complexes vary from −10 to −150 kJ/mol, and P—N distances from 1.88 to 2.72 A. Complexes ZN:PO2F have stronger P...N bonds and shorter P—N distances than the corresponding complexes ZN:PO2Cl. Charge transfer from the N lone pair through the π-hole to the P—X and P—O σ* orbitals leads to stabilization of these complexes, although charge-transfer energies can be evaluated only for complexes with binding energies less than −71 kJ/mol. Complexation of PO2X with the strongest bases leads to P···N bonds with a significant degree of covalency, and P—N distances that approach the P—N distances in the molecules PO2NC and PO2NH2. In these complexes, the PO2X molecules distort from planarity. Changes in 31P absolute chemical shieldings upon complexation do not correlate with chan...

Pnicogen-bonded cyclic trimers (PH2X)3 with X = F, Cl, OH, NC, CN, CH3, H, and BH2

Abstract: Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to determine the structures and binding energies of cyclic trimers (PH2X)3 with X = F, Cl, OH, NC, CN, CH3, H, and BH2. Except for [PH2(CH3)]3, these complexes have C3h symmetry and binding energies between -17 and -63 kJ mol(-1). Many-body interaction energy analyses indicate that the two-body terms are dominant, accounting for 97-103% of the total binding energy. Except for the trimer [PH2(OH)]3, the three-body terms are stabilizing. Charge transfer from the lone pair on one P atom to an antibonding σ* orbital of the P atom adjacent to the lone pair plays a very significant role in stabilization. The charge-transfer energies correlate linearly with the trimer binding energies. NBO, AIM, and ELF analyses have been used to characterize bonds, lone pairs, and the degree of covalency of the P···P pnicogen bonds. The NMR properties of chemical shielding and (31)P-(31)P coupling constants have also been evaluated. Although the (31)P chemical shieldings in the five most strongly bound trimers increase relative to the corresponding isolated monomers, there is no correlation between the chemical shieldings and the charges on the P atoms. EOM-CCSD (31)P-(31)P spin-spin coupling constants computed for four (PH2X)3 trimers fit nicely onto a plot of (1p)J(P-P) versus the P-P distance for (PH2X)2 dimers. A coupling constant versus distance plot for the four trimers has a second-order trendline which has been used to predict the values of (1p)J(P-P) for the remaining trimers.

Characterizing complexes with pnicogen bonds involving sp2 hybridized phosphorus atoms: (H2C═PX)2 with X = F, Cl, OH, CN, NC, CCH, H, CH3, and BH2.

Abstract: Ab initio MP2/aug'-cc-pVTZ searches of the potential surfaces of (H2C═PX)2 complexes, with X = F, Cl, OH, CN, NC, CCH, H, CH3, and BH2, have been carried out to identify and characterize the properties of complexes with P···P pnicogen bonds. All (H2C═PX)2 form equilibrium conformation A dimers with C(2h) symmetry in which A-P···P-A approaches a linear alignment, with A the atom of X directly bonded to P. Conformation A dimers containing the more electronegative substituents are stabilized by a P···P pnicogen bond, have shorter P-P distances, and have binding energies which correlate with the P-P distance. Dimers stabilized by a P···P pnicogen bond and two P···H(b) interactions consist of those with the more electropositive substituents, have shorter P-H(b) distances, and have binding energies which are too high for their P-P distances. Conformation A complexes with P···H(b) interactions in addition to the P···P bond are more stable than the corresponding (PH2X)2 complexes, while with only one exception, complexes stabilized by only a P···P bond are less stable than the corresponding (PH2X)2 complexes. In the region of the potential surfaces with C-P···P-C approaching linearity (conformation B), the only planar equilibrium complex is (H2C═POH)2, which is stabilized primarily by two O-H···P hydrogen bonds. The remaining (H2C═PX)2 complexes are not stabilized by pnicogen bonds, but by π interactions between the two H2C═PX monomers which are in parallel planes. When A-P···P-C approaches linearity, two types of equilibrium structures with P···P bonds exist. Of the conformation C dimers, (H2C═POH)2 is planar and the most stable, with a P···P pnicogen bond and an O-H···P hydrogen bond. (H2C═PH)2 and (H2C═PCH3)2 are also planar, and stabilized by a P···P pnicogen bond and a P···H(b) interaction. The absence of a P···H(b) interaction results in nonplanar C' conformations with structures in which the monomers essentially retain their symmetry plane, but the plane of one molecule is rotated about the P···P bond relative to the other. C and C' dimers are less stable than the corresponding A dimers, except for (H2C═PCH3)2. (31)P chemical shielding patterns are consistent with the changing nature of the interactions which stabilize (H2C═PX)2 complexes. EOM-CCSD (31)P-(31)P spin-spin coupling constants increase quadratically as the P-P distance decreases.

Properties of complexes H2C═(X)P:PXH2, for X = F, Cl, OH, CN, NC, CCH, H, CH3, and BH2: P···P pnicogen bonding at σ-holes and π-holes.

Abstract: Ab initio MP2/aug′-cc-pVTZ calculations have been carried out on complexes H2C═(X)P:PXH2, for X = F, Cl, OH, CN, NC, CCH, H, CH3, and BH2. Three sets of complexes have been found on the potential surfaces. Conformation A complexes have A–P···P–A approaching linearity, with A the atom of X directly bonded to P. Conformation B complexes have A–P···P linear, but the P···P═C orientation of H2C═PX may differ significantly from linearity. Conformation C complexes are unique, since the pnicogen bond involves π-electron donation and acceptance by H2C═PX. The order of binding energies of the three conformations of H2C═(X)P:PXH2 is C > A > B, with two exceptions. Although the binding energies of conformation C complexes tend to be greater than the corresponding conformation A complexes, intermolecular distances in conformation C tend to be longer than those in conformation A. Charge transfer stabilizes H2C═(X)P:PXH2 complexes. The preferred direction of charge transfer is from H2C═PX to PXH2. In conformations A and...

Can Conventional Bases and Unsaturated Hydrocarbons Be Converted into Gas‐Phase Superacids That Are Stronger than Most of the Known Oxyacids? The Role of Beryllium Bonds

Abstract: This work has been partially supported by the DGI projects nos. CTQ2012-35513-C02 and CTQ2010-17006, by the project MADRISOLAR2 (Ref.: S2009PPQ/1533) of the Comunidad de Madrid, and by the Consolider on Molecular Nanoscience (CSC2007-00010). A generous allocation of computing time at the CTI (CSIC) and at the CCC of the UAM is also acknowledged.

A review of recent progress (2002-2012) on the biological activities of pyrazoles

Abstract: In this review, we report the structures of 243 pyrazoles with their corresponding biological activities. All of them are represented around the common structure of the pyrazole ring even in those cases where the heterocycle is only a minor part of the molecule. The classification we have used is based on chemical structure considerations and not in terms of the therapeutic area which is the more common approach. Some general conclusions have been drawn linking structures with activities.

Complexes between dihydrogen and amine, phosphine, and arsine derivatives. Hydrogen bond versus pnictogen interaction.

Abstract: A theoretical study of the complexes between dihydrogen, H2, and a series of amine, phosphine, and arsine derivatives (ZH3 and ZH2X, with Z = N, P, or As and X = F, Cl, CN, or CH3) has been carried out using ab initio methods (MP2/aug-cc-pVTZ). Three energetic minima configurations have been characterized for each case with the H2 molecule in the proximity of the pnictogen atom (Z). In configuration A, the σ-electrons of H2 interact with σ-hole region of the pnictogen atom generated by the of X-Z bond. These complexes can be ascribed as pnictogen bonded. In configuration C, the lone electron pair of Z acts as the Lewis base, and H2 plays the role of the Lewis acid. Finally, configuration B presents a variety of noncovalent interactions depending on the binary complex considered. The atoms-in-molecules theory (AIM), natural bond orbitals (NBO) method as well as the density functional theory-symmetry adapted perturbation theory (DFT-SAPT) approach were used in this study to deepen the nature of the interactions considered.

Linear free energy relationships in halogen bonds

Abstract: Four models of halogen bonds were used to quantify this bond using the DFT B97D/6-311+G(d) computational level: para-substituted iodobenzenes, para- and meta-substituted bromobenzenes complexed with three simple Lewis bases (NH3, NCH and CNH), 1-bromo-4-substituted-bicyclo[2.2.2]octanes with NH3 and 3- and 4-substituted pyridines complexed with BrCl and BrF. In addition, the combination of the para-substituted bromobenzenes with the 4-substituted pyridines has been studied. A total of 459 complexes have been optimized and are discussed in the present article. The energetic and geometric results have been analyzed based on the properties of the substituents and the isolated molecules involved in the interaction. The Hammett–Taft parameters provide reasonable correlations with the interaction energies. However, excellent correlations are obtained in all the cases when the electrostatic properties of the two molecules involved in the interaction are considered (R2 > 0.99).

Enhancing and modulating the intrinsic acidity of imidazole and pyrazole through beryllium bonds.

Abstract: The structure and electronic properties of the complexes formed by the interaction of imidazole and pyrazole with different BeXH(BeX2) (X = H, Me, F, Cl) derivatives have been investigated via B3LYP/6−311+G(3df,2p)//B3LYP/6−31+G(d,p) calculations. The formation of these azole:BeXH(BeX2) complexes is accompanied by a dramatic enhancement of the intrinsic acidity of the azole, as the deprotonated azole is much more stable after the aforementioned interaction. Most importantly, the increase in acidity is so large that the azole:BeXH or azole:BeX2 complexes behave as NH acids, which are stronger than typical oxyacids such as phosphoric acid and oxalic acid. Interestingly, the increase in acidity can be tuned through appropriate selection of the substituents attached to the Be atom, permitting us to modulate the electron-accepting ability of the BeXH or BeX2 molecule.

Non-covalent interactions: complexes of guanidinium with DNA and RNA nucleobases.

Abstract: Considering that guanidine-based derivatives are good DNA minor groove binders, we have theoretically studied, using the Polarizable Continuum model mimicking water solvation, the complexes formed by the biologically relevant guanidinium cation and the DNA and RNA nucleobases (adenine, guanine, cytosine, thymine, and uracil). The interactions established within these complexes both by hydrogen bonds and by cation−π interactions have been analyzed by means of the Atoms in Molecules and Natural Bond Orbital approaches. Moreover, maps of electron density difference have been produced to understand the cation−π complexes. Finally, the NICS and three-dimensional NICS maps of the cation−π complexes have been studied to understand the effect of the guanidinium cation on the aromaticity of the nucleobases.

Structure of NH-benzazoles (1H-benzimidazoles, 1H- and 2H-indazoles, 1H- and 2H-benzotriazoles)

Abstract: The structure and properties (crystallography, NMR, theoretical calculations) of the three N-unsubstituted benzazoles (1H-benzimidazoles, 1H- and 2H-indazoles, 1H- and 2H-benzotriazoles) have been reviewed for the period 2000–2012 with some results from previous years. The study of these compounds will greatly increase in the coming years and it is expected that the present review will contribute to it.

Structure and Thermodynamical Properties of Metformin Salicylate

Abstract: The behavior under thermal conditions of the cocrystal formed by metformin and salicylic acid was studied by DSC, crystallography (single-crystal), and powder diffraction (WAXS). Metformin salicylate crystallizes in space group P21/c, with the salicylate anion showing a planar structure, stabilized by strong intramolecular hydrogen bonds. The more flexible metformin cations link through the oxygen atoms of salicylate, forming a dense hydrogen-bonding network. The compound exists initially as a salt, metformin salicylate, but after melting and cooling, it is transformed into a glass form that crystallizes and melts again, showing different behaviors depending on the heating rate.

The structure of azines derived from C-formyl-1H-imidazoles in solution and in the solid state: tautomerism, configurational and conformational studies.

Abstract: The structures of three azines derived from 2-formylimidazole, 4(5)-formylimidazole, and 4(5)-formyl-5(4)-methylimidazole have been determined in solution and in the solid state. Density Functional Theory (DFT) Polarizable Continuum Model (PCM) calculations (geometries, energies, and chemical shifts), NMR [solution and cross polarization magic-angle spinning (CPMAS)], and X-ray crystallography [azine of 4(5)-formylimidazole] have been used. The configuration around the central C = N bonds has been determined and some insights about prototropic tautomerism and conformation have been gained. Copyright © 2013 John Wiley & Sons, Ltd.

HOMA parameters for the boron–boron bond: How the introduction of a BB bond influences the aromaticity of selected hydrocarbons

Abstract: An extension of the harmonic oscillator model of aromaticity (HOMA) model for systems with boron–boron bonds is presented. For the first time, the parameters of the HOMA model are estimated using only theoretically calculated bond lengths. The HOMA parameters obtained make geometric aromaticity studies possible for a large number of compounds containing the boron–boron bond. The derived HOMA parameters have been used to investigate how the introduction of the boron–boron moiety in the structure of selected hydrocarbons modifies their aromaticity. The conclusion is that the insertion of a boron–boron bond usually strongly decreases the aromaticity of the boron-containing compounds in comparison to their parent hydrocarbons.

Conformational Preference and Chiroptical Response of Carbohydrates D‑Ribose and 2‑Deoxy‑D‑ribose in Aqueous and Solid Phases

Abstract: This work targets the structural preferences of d-ribose and 2-deoxy-d-ribose in water solution and solid phase. A theoretical DFT (B3LYP and M06-2X) and MP2 study has been undertaken considering the five possible configurations (open-chain, α-furanose, β-furanose, α-pyranose, and β-pyranose) of these two carbohydrates with a comparison of the solvent treatment using only a continuum solvation model (PCM) and the PCM plus one explicit water molecule. In addition, experimental vibrational studies using both nonchiroptical (IR-Raman) and chiroptical (VCD) techniques have been carried out. The theoretical and experimental results show that α- and β-pyranose forms are the dominant configurations for both compounds. Moreover, it has been found that 2-deoxy-d-ribose presents a non-negligible percentage of open-chain forms in aqueous solution, while in solid phase this configuration is absent.

Structure of 1,5-benzodiazepinones in the solid state and in solution: Effect of the fluorination in the six-membered ring

Abstract: Two novel tetrafluorinated 1,5-benzodiazepinones were synthesized and their X-ray structures determined. 6,7,8,9-Tetrafluoro-4-methyl-1,3-dihydro-2H-1,5-benzodiazepin-2-one crystallizes in the monoclinic P21/c space group and 6,7,8,9-tetrafluoro-1,4-dimethyl-1,3-dihydro-2H-1,5-benzodiazepin-2-one in the triclinic P−1 space group. Density functional theory studies at the B3LYP/6-311++G(d,p) level were carried out on these compounds and on four non-fluorinated derivatives, allowing to calculate geometries, tautomeric energies and ring-inversion barriers, that were compared with the experimental results obtained by static and dynamic NMR in solution and in solid state.

Theoretical studies of parent 1-, 2-, 3-pyrazolines and their methylated derivatives

Abstract: A theoretical study of the minima of 1-, 2-, and 3-pyrazolines as well as some methyl derivatives was performed using B3LYP/6-311++G(d,p) and CCSD(T) calculations. Conformation, tautomerism, basicity, protonation as well as NMR properties have been computationally studied. In general, the agreement with the available experimental results is excellent, highlighting the predictive potential of this type of study in the consideration of new compounds.

Atropisomerization in N-aryl-2(1H)-pyrimidin-(thi)ones: a ring-opening/rotation/ring-closure process in place of a classical rotation around the pivot bond.

Abstract: Uncatalyzed racemization processes in atropisomeric diphenyl-like frameworks are classically described as the result of the rotation around the pivotal single bond linking two planar frameworks. Se...

A Facile Method to Determine the Absolute Structure of Achiral Molecules: Supramolecular‐Tilt Structures

Abstract: Achiral compounds 4-me- thoxy-4-(p-methoxyphenyl)cyclohexa- noneethylene ketal (2), 4-hydroxy-4-(p- methoxy phenyl)cyclohexanoneethyl- A ketal (3), and 3,5-dimethyl-4-nitro- pyrazole (4) crystallized in chiral struc- tures and the samples showed an enan- tiomeric excess. We have determined the absolute structures of these com- pounds by using X-ray diffraction with copper radiation at low temperatures. Moreover, we have also established the prevalent absolute structures in these samples, by comparing their calculated and solid-state vibrational circular di- chroism (VCD) spectra. The consisten- cy of this method was confirmed by using (R,R)-2,8-diiodo-4,10-dimethyl- 6 H,12H-5,11-methano-dibenzoA A Trcger's base, (R,R)-1, as a chiral compound of known abso- lute configuration.

Theoretical and Experimental NMR Study of a Series of Five Nitrobenzene-1,2-Diamines

Abstract: 1H-, 13C-, and 15N-NMR studies of five nitrobenzene-1,2-diamines in solution and solid state have been achieved and the experimental chemical shifts and coupling constants agree with the theoretical values obtained at the B3LYP/6-311 + +G(dp) computational level using the geometries fully optimized with the hybrid HF/DFT B3LYP method and the 6-31G(d) basis set. The GIAO approximation has been used to calculate the absolute shieldings. The contribution of the substituents to the 15N chemical shifts of the amino groups could be quantified using a presence/absence matrix and a multiple regression.

A tris(pyrazol-1-yl)methane bearing carboxylic acid groups at position 4: {1-[bis(4-carboxy-3,5-dimethyl-1H-pyrazol-1-yl)methyl]-3,5-dimethyl-1H-pyrazole- 4-carboxylato}sodium dihydrate

Abstract: A low-resolution X-ray molecular structure of the title hydrated salt, [Na(C19H21N6O6)]·2H2O, displays scorpionate character and resolves apparent ambiguities between solution and solid-state NMR spectroscopies. The (13)C NMR CPMAS spectrum is consistent with this structure showing some splittings, which have been rationalized using GIAO/B3LYP/6-311++G(d,p) theoretical calculations.