J. Phys. Chem. A, 116, 9205, 2012

DOI: 10.1021/jp307083g

J. E. Del Bene, I. Alkorta, G. Sanchez-Sanz, J. Elguero

Interplay of F-H...F Hydrogen Bonds and P...N Pnicogen Bonds

Ab initio MP2/aug′-cc-pVTZ calculations have been carried out to investigate the influence of F–H···F hydrogen bonds on the P···N pnicogen bond in complexes nFH:(H2FP:NFH2) for n = 1–2, and a selected complex with n = 3. The NBO analysis indicates that the N(lp) → P–Fσ* charge-transfer transition has a much greater stabilizing effect than the P(lp) → N–Fσ* transition. When hydrogen bonding occurs at P–F, charge transfer associated with the pnicogen bond and the hydrogen bond are in the same direction but are in opposite directions when hydrogen bonding occurs at N–F. As a result, the formation of F–H···F hydrogen bonds at P–F leads to shorter P···N distances, increased strength of P···N bonds, and synergistic energetic effects; hydrogen bonding at N–F has opposite effects. 31P and 15N chemical shieldings do not correlate with charges on P and N, respectively, but 31P shieldings correlate quadratically with the P–N distance. 1pJ(P–N) coupling constants do not correlate with the intermolecular P–N distance. However, when hydrogen bonding occurs only at P–F, 1pJ(P–N) decreases in absolute value as the P–N distance decreases, thereby approaching 1J(P–N) for H2P–NH2. However, the P···N bond in 3FH:(H2FP:NFH2) has little covalent character, unlike the P···P bond in the corresponding complex 3FH:(PH2F)2.

J. Chem. Theor. Comput. 8, 2320, 2012

DOI: 10.1021/ct300399y

I. Alkorta, G. Sanchez-Sanz, J. Elguero, J. E. Del Bene

Influence of Hydrogen Bonds on the P...P Pnicogen Bond

Ab initio MP2/aug′-cc-pVTZ calculations have been carried out to investigate the influence of F–H···F hydrogen bonds on the P···P pnicogen bond in complexes nFH:(PH2F)2 for n = 1–3. The formation of F–H···F hydrogen bonds leads to a shortening of the P–P distance, a lengthening of the P–F distance involved in the hydrogen bond, a strengthening of the P···P interaction, and changes in atomic populations, NMR 31P chemical shieldings, and 1pJ(P–P) coupling constants. The magnitude of these changes depends on the number of FH molecules and their positions in the complex and are relatively modest except for complexes 2FH:(PH2F)2and 3FH:(PH2F)2 that have all FH molecules hydrogen bonded to the same F-atom. For these two complexes, 1pJ(P–P) decreases as the P–P distance decreases and approaches the value of 1J(P–P) for P2H4. The dramatic changes in these two complexes reflect the changing nature of the hydrogen bonds and the pnicogen bond. Thus, the complex 3FH:(PH2F)2 acquires ion-pair character represented as [3(FH)F:(H2P–PH2F)+], and the P···P pnicogen bond acquires significant covalent character. These changes are observed to a lesser extent in 2FH:(PH2F)2.

Comput. Theor. Chem. 994, 64, 2012

DOI: 10.1016/j.comptc.2012.06.004

B.Kelly,  G. Sanchez-Sanz, F. Blanco, I. Rozas

Cation–π vs. π–π interactions: Complexes of 2-pyridinylguanidinium derivatives and aromatic systems

We have theoretically studied, using PCM–water solvation, the cation–π and π–π complexes established by the biologically relevant 5-substituted 2-pyridinylguanidinium derivatives and electron-rich and electron-depleted aromatic systems (benzene and (hexafluoro)benzene). In condensed phase using PCM–water and M06-2X/6-311++G(d,p) different cation–π and π–π complexes were found. The interactions established within these complexes have been analyzed by means of the Atoms in Molecules and Natural Bond Orbital approaches and electron density difference maps have been calculated. Finally, the effect of the cation–π and π–π complexation on the aromaticity of pyridine, benzene and hexafluorobenzene was evaluated by calculating the corresponding aromaticity indexes, NICS0, 1 and 2 as well as the NICS on the 0.001 a.u. isodensity surface.

Comput. Theor. Chem. 994, 81, 2012

DOI: 10.1016/j.comptc.2012.06.019

C. Trujillo, G. Sanchez-Sanz, I. Alkorta, J. Elguero

Thermodynamic and hydrogen-bond basicity of phosphine oxides: Effect of the ring strain

A theoretical study of acidity and hydrogen bond acceptor properties of tetrahedric phosphine oxide derivatives have been carried out by means of MP2 computational methods. The results obtained for the mentioned complexes have been compared with the analogous ones of trimethylphosphine oxide. The strain decreases the complexation energy with metallic atoms as well as the thermodynamic and hydrogen bond acceptor (HBA) ability of the tetrahedric derivatives.

ARKIVOC ii, 85, 2012

http://www.arkat-usa.org/get-file/45154/

I. Alkorta, G. Sanchez-Sanz, C. Trujillo, J. Elguero, R. M. Claramunt

A theoretical study of the parent NH-benzazoles (benzimidazoles,indazoles and benzotriazoles): geometries, energies, acidity and basicity, NMR properties and molecular electrostatic potentials

The three parent N H-benzazoles, benzimidazole, indazole and benzotriazole, have been studied theoretically at the B3LYP/6-311++G(d,p) level. Optimized geometries have been compared with those obtained by X-ray crystallography, energ ies with studies about tautomerism, acidbase properties with pKas, and chemical shifts with those reported in the literature. As aromaticity probe, Schleyer's Nuclear Independent Chemical Shifts (NICS) were used and represented in two 3D isosurfaces of the electron density.

Phys. Chem. Chem. Phys. 14, 11468, 2012

 DOI: 10.1039/C2CP41230F

 G. Sánchez-Sanz , I. Alkorta , J. Elguero , M. Yañez, O. Mó

Strong interactions between copper halides and unsaturated systems: new metallocycles? Or the importance of deformation

The complexes formed by CuF with CC double and triple bonds have been studied at the MP2 and CCSD(T) computational levels. The interaction of CuF with acetylene, ethylene and their fluoro derivatives is very strong, with interaction energies close to those of conventional covalent bonds. Hence, these complexes could be actually viewed as a new kind of metallocycles, with significantly strong Cu–C linkages. All electronic indexes analyzed by means of the AIM, ELF and NBO formalisms, indicate that the strength of the interaction should increase with the number of fluorine substituents in both series of compounds. Surprisingly, however, although both series of compounds exhibit the same bonding arrangements, they follow opposite stability trends and the expected increase of the interaction energies with the number of fluorine substituents is only observed in the acetylene series. The reason for this unexpected behavior is once more associated with the effects triggered by the distortion of the interacting subunits. Deformation not only has a direct energetic cost but dramatically affects the intrinsic properties of the interacting systems.

Tetrahedron, 68, 6548, 2012

DOI: 10.1016/j.tet.2012.05.056

G. Sanchez-Sanz, I. Alkorta, C. Trujillo, J. Elguero

A theoretical NMR study of the structure of benzynes and some of their carbocyclic and heterocyclic analogs

This work reports the theoretical study of the aromaticity of a series of carbocycles (benzene, cyclohexane, bent and planar cyclooctatetraene) and heterocycles (pyridine, furan, thiophene,  pyrrole) and their didehydro forms (arynes and hetarynes). As aromaticity probe Schleyer's NICS  were used and represented in two 3D isosurfaces of the electron density. The spatial 3D  representation of the NICS is shown to be a powerful tool to visualize the aromaticity (or its  absence) of different molecules.

Phys. Chem. Chem. Phys. 14, 9880, 2012

DOI: 10.1039/C2CP40949F

G. Sanchez-Sanz , C. Trujillo , I. Alkorta, J. Elguero
 
Weak interactions between hypohalous acids and dimethylchalcogens

The complexes formed between dimethylchalcogens X(CH3)2 (X = S, Se, and Te) and hypohalous acids YOH (Y = F, Cl, Br, and I) have been studied at the MP2/aug'-cc-pVTZ computational level, five minima structures being located. Two of them correspond to hydrogen bonds (HB), another two to halogen bonds (XB) with the chalcogen acting as an electron donor, the last one showing a C–HO contact. The most stable complexes of IOH and BrOH acids present halogenchalcogen interactions with interaction energies, Ei, up to −49 kJ mol−1. In the case of the ClOH and FOH molecules, the hydrogen bonded complexes are more stable with interaction energies between −27 and −34 kJ mol−1. Linear correlations between the molecular electrostatic potential (MEP) stationary points at the van der Waals surface and the interaction energy have been found. The contribution of the different energy terms to the total interaction energy was analyzed by means of the DFT–SAPT theory finding that the electrostatic attractive term is dominant in the complexes with HB and XB, excepting a few cases in which the dispersion and induction terms become more important than the electrostatic one.

Chem. Phys. Lett. 538, 14, 2012

DOI: 10.1016/j.cplett.2012.04.039

J. E. Del Bene, I. Alkorta, G. Sanchez-Sanz, J. Elguero

Homo- and heterochiral dimers (PHFX)2, X = Cl, CN, CH3, NC: To what extent do they differ?

Ab initio MP2/aug’-cc-pVTZ calculations have been performed to determine if intermolecular P–P distances, Z–P–P angles, binding energies, 31P chemical shieldings, or EOM–CCSD spin–spin coupling constants can differentiate between corresponding C2 (homochiral) and Ci (heterochiral) dimers (PHFX)2, X = Cl, CN, CH3, NC. With one exception, Ci isomers have shorter P–P distances than corresponding C2 isomers. Neither binding energies, Z–P–P angles, chemical shieldings, nor spin–spin coupling constants 1pJ(P–P) exhibit patterns which distinguish between corresponding C2 and Ci isomers. 1pJ(P–P) values correlate linearly with P–P distances, so that experimental values of 1pJ(P–P) could be used to extract intermolecular P–P distances.

Chem. Phys. Lett. 538, 5, 2012

DOI: 10.1016/j.cplett.2012.04.034

J. E. Del Bene, I. Alkorta, G. Sanchez-Sanz, J. Elguero

Variations in the structures and binding energies of binary complexes with HBO

Ab initio MP2/aug’-cc-pVTZ calculations have been carried out to determine the structures and binding energies of binary complexes formed by HBO with a series of small molecules A. Three different types of structures have been identified, which depend on the nature of A. In one structure A:HBO, HBO acts as a weak proton donor. In the second HBO:A, HBO is a relatively strong base. The third type of complex A||HBO has HBO and A in an approximately parallel arrangement. The dipole moment of A influences both the type of complex formed and its binding energy.

J. Phys. Chem. A 116, 5199, 2012

DOI: 10.1021/jp300540z

M. Solimannejad, V. Ramezani, C. Trujillo, I. Alkorta, G. Sanchez-Sanz, J. Elguero

Competition and Interplay between sigma-Hole and pi-Hole Interactions: A Computational Study of 1:1 and 1:2 Complexes of Nitryl Halides (O2NX) with Ammonia

 Quantum calculations at the MP2 cc-pVTZ, MP2 aug-cc-pVTZ, and CCSD(T) cc-pVTZ levels have been used to examine 1:1 and 1:2 complexes between O2NX (X = Cl, Br, and I) with NH3. The 1:1 complexes can easily be differentiated using the stretching frequency of the N–X bond. Thus, those complexes with σ-hole interaction show a blue shift of the N–X bond stretching whereas a red shift is observed in the complexes along the π-hole. The SAPT-DFT methodology has been used to gain insight on the source of the interaction energy. In the 1:2 complexes, the cooperative and diminutive energetic effects have been analyzed using the many-body interaction energies. The nature of the interactions has been characterized with the atoms in molecules (AIM) and natural bond orbital (NBO) methodologies. Stabilization energies of 1:1 and 1:2 complexes including the variation of the zero point vibrational energy (ΔZPVE) are in the ranges 7–26 and 14–46 kJ mol–1, respectively.

Comput. Theor. Chem. 991, 124, 2012

DOI: 10.1016/j.comptc.2012.04.007

G. Sanchez-Sanz, C. Trujillo, I. Alkorta, J. Elguero

Electron density shift description of non-bonding intramolecular interactions

A new methodology is described for the study of the electron density shift in intramolecular interactions. The methodology has been tested in an intermolecular complex and compared to the electron density shift obtained as the difference between the complex and the isolated monomers. The molecular fragmentation procedures and its application to hydrogen bonds, chalcogen–chalcogen interactions, nitrogen–boron interactions, dihydrogen interactions and silicon–nitrogen interactions are described. A careful selection of the fragmentation scheme is necessary in order to describe correctly the electron density shift in the intramolecular interactions. For this reason, different orders of fragmentation have been studied and analyzed pointing out the problems and limitations which are inherent to the methodology. It has been found that this methodology is a new tool which provides a good qualitative description of the electron density shift within the interacting region between two or more contacts, in both inter and intramolecular contacts with a reasonable low computational cost.

Struct. Chem. 23, 1245, 2012

DOI: 10.1007/s11224-012-9991-4

I. Alkorta, L. M. Azofra, G. Sanchez-Sanz, J. Elguero

A theoretical study of six-membered rings containing the -N=S-S=N- motif

The sulfur electronic structure allows for the existence of hypervalent molecules that were discussed as early as 1939 by Schomaker and Pauling. In the present paper, we report a theoretical study of three hypothetical possible six-membered rings that contain the –N=S–S=N– motif carried out at the MP2/aug-cc-pVDZ level. Three minima have been found, of which two of them are six-membered rings with all covalent bonds. Since they do not have a planar structure, we have calculated the aromaticity index NICS through the symmetry axis perpendicular to the mid-plane and at various points in space. Benzene, cyclohexane, and 1,2,5-thiadiazole have served as points of comparison.

J. Phys. Chem. A, 116, 3056, 2012

DOI: 10.1021/jp300763d

J. E. Del Bene, I. Alkorta, G. Sánchez-Sanz, J. Elguero

Structures, Binding Energies, and Spin-Spin Coupling Constants of Geometric Isomers of Pnicogen Homodimers (PHFX)2, X = F, Cl, CN, CH3, NC

Ab initio MP2/aug′-cc-pVTZ calculations have been carried out to determine the structures and binding energies of homodimers (PHFX)2 for X = F, Cl, CN, CH3, and NC. Geometric isomers of these complexes with Ci symmetry exist, which are differentiated in terms of the nature of the atoms (F–P···P–F, H–P···P–H, or A–P···P–A, with A being the atom of X directly bonded to P), which approach a nearly linear alignment. Of these, isomers having F–P···P–F linear are the most stable. Binding energies, intermolecular distances, and EOM-CCSD spin–spin coupling constants are sensitive to both the nature of X and the atoms that assume the linear alignment.

J. Mol. Struct., 1015,138, 2012

DOI:10.1016/j.molstruc.2012.02.013

P. López-Tarifa, G. Sánchez-Sanz, I. Alkorta, J. Elguero, D. Sanz, A. Perona, R. M. Claramunt

The tautomeric structures of 3(5),3′(5′)-azopyrazole [(E)-1,2-di(1H-pyrazol-3(5)-yl)diazene)]: The combined use of NMR and electronic spectroscopies with DFT calculations

An azo derivative of 1H-pyrazole has been chosen to study the information obtained from different techniques for determining the structure of a non-crystalline compound in the solid-state and in solution. Syn–antiisomerism of the azo group, prototropic tautomerism of the 1H-pyrazole and rotation about the pyrazole–azo group resulted in 20 structures that were analyzed. Energy calculations, 13C and 15N chemical shifts, 1H–1H coupling constants and electronic spectra reduced the 20 possible structures to only one, the 3,3′-Z,Z-anti-azopyrazole.

J. Phys. Chem. A, 116, 2300, 2012

DOI: 10.1021/jp211451y

I. Alkorta, G. Sánchez-Sanz, J. Elguero, J.E. Del Bene

FCl:PCX Complexes: Old and New Types of Halogen Bonds

MP2/aug′-cc-pVTZ calculations have been performed to investigate the halogen-bonded complexes FCl:PCX, for X = NC, CN, F, H, CCH, CCF, CH3, Li, and Na. Although stable complexes with a F–Cl···P halogen bond exist that form through the lone pair at P (configuration I), except for FCl:PCCN, the more stable complexes are those in which FCl interacts with the C≡P triple bond through a perturbed π system (configuration II). In complexes I, the nature of the halogen bond changes from traditional to chlorine-shared and the interaction energies increase, as the electron-donating ability of X increases. The anionic complex FCl:PC has a chlorine-transferred halogen bond. SAPT analyses indicate that configuration I complexes with traditional halogen bonds are stabilized primarily by the dispersion interaction. The electrostatic interaction is the most important for configuration I complexes with chlorine-shared halogen bonds and for configuration II complexes except for FCl:PCNa for which the induction term is most important. The F–Cl stretching frequency is red-shifted upon complexation. EOM-CCSD/(qzp,qz2p) spin–spin coupling constants have been obtained for all FCl:PCX complexes with configuration I. 1J(F–Cl) decreases upon complexation. 2XJ(F–P) values are quadratically dependent upon the F–P distance and are very sensitive to halogen-bond type. 1XJ(Cl–P) tends to increase as the Cl–P distance decreases but then decreases dramatically in the chlorine-transferred complex FCl:PC as the Cl–P interaction approaches that of a covalent Cl–P bond. Values of 1J(F–Cl) for configuration II are reduced relative to configuration I, reflecting the longer F–Cl distances in II compared to those of the neutral complexes of I. Although the F–P and Cl–P distances in configuration II complexes are shorter than these distances in the corresponding configuration I complexes,2XJ(F–P) and 1XJ(Cl–P) values are significantly reduced, indicating that coupling through the perturbed C–P π bond is less efficient. The nature of F–P coupling for configuration II is also significantly different, as evidenced by the relative importance of PSO, FC, and SD components.

Struct.Chem. 23, 873, 2012

DOI: 10.1007/s11224-012-9947-8

I. Alkorta, G. Sanchez-Sanz, C. Trujillo, L. M. Azofra, J. Elguero

A theoretical reappraisal of the cyclol hypothesis

Theoretical calculations at the B3LYP/6-31G(d) level have been carried out on the isomerization of cyclic-tri-glycine into the corresponding tri-cyclol. The results confirmed that the cyclol hypothesis was untenable both from a thermodynamic as well as from a kinetic point of view.

Struct. Chem. 23, 847, 2012

DOI: 10.1007/s11224-011-9931-8

M. Solimannejad, M. Gharabaghi, I. Alkorta, G. Sanchez-Sanz
 
A theoretical study of 1:1 and 1:2 complexes of acetylene with nitrosyl hydride
 
Ab initio calculations at MP2 computational level using aug-cc-pVTZ basis set were used to analyze the interactions between 1:1 and 1:2 complexes of acetylene and nitrosyl hydride. The structures obtained have been analyzed with the atoms in molecules and the density functional theory–symmetry adapted perturbation theory methodologies. Four minima were located on the potential energy surface of the 1:1 complex. Twenty-four different structures have been obtained for the 1:2 complexes. Five types of interactions are observed, CH···O, CH···N, NH···π hydrogen bonds and orthogonal interactions between the π clouds of triple bond, or the lone pair of oxygen with the electron-deficient region of the nitrogen atom. Stabilization energies of the 1:1 and 1:2 clusters including basis set superposition error and ZPE are in the range 3–8 and 6–17 kJ mol−1 at MP2/aug-cc-pVTZ computational level, respectively. Blue shift of NH bond upon complex formation in the ranges between 18–30 and 20–96 cm−1 is predicted for 1:1 and 1:2 clusters, respectively. The total nonadditive energy in the 1:2 cluster, calculated as the sum of the supermolecular nonadditive MP2 energy and the three-body dispersion energy, presents values between −1.48 and 1.20 kJ mol−1.

ChemPhysChem, 13, 496, 2012

DOI: 10.1002/cphc.201100830

G. Sánchez-Sanz, C. Trujillo, I. Alkorta, J. Elguero
 
Intermolecular Weak Interactions in HTeXH Dimers (X=O, S, Se, Te): Hydrogen Bonds, Chalcogen-Chalcogen Contacts and Chiral Discrimination
 
A theoretical study of the HTeXH (X=O, S, Se and Te) monomers and homodimers was carried out by means of second-order Møller-Plesset perturbation theory (MP2) computational methods. In the case of monomers, the isomerization energy from HTeXH to H2Te=X and H2X=Te (X=O, S, Se, and Te) and the rotational transition-state barriers were obtained. Due to the chiral nature of these compounds, homo and heterochiral dimers were found. The electron density of the complexes was characterized with the atoms-in-molecules (AIM) methodology, finding a large variety of interactions. The charge transfer within the dimers was analyzed by means of natural bond orbitals (NBO). The density functional theory-symmetry adapted perturbation theory (DFT-SAPT) method was used to compute the components of the interaction energies. Hydrogen bonds and chalcogen–chalcogen interactions were characterized and their influence analyzed concerning the stability and chiral discrimination of the dimers.

Mag. Reson. Chem. 50, 246, 2012

DOI: 10.1002/mrc.2868

D. Sanz, R, M. Claramunt, I. Alkorta, G. Sanchez-Sanz, J. Elguero

The structure of glibenclamide in the solid state

The structure of glibenclamide, 5-chloro-N-(2-{4-[(cyclohexylamino)carbonyl] aminosulfonyl}phenyl) ethyl)-2-methoxybenzamide, an important antidiabetic drug, has been studied both in solution and in the solid state by a combination of NMR spectroscopy and theoretical calculations. The possibility that glibenclamide suffers a tautomerization under melting to afford a desmotrope was rejected.

J. Heteroc. Chem. 49, 1257, 2012

 DOI: 10.1002/jhet.1076

N. Fresno, R. Pérez-Fernández, M. L. Jimeno, I. Alkorta, G. Sánchez-Sanz, J. Elguero, J. E. Del Bene.

Multinuclear NMR Characterization of Cyanuric Fluoride (2,4,6-Trifluoro-1,3,5-triazine)

Although 2,4,6-trifluoro-1,3,5-triazine, C3F3N3, is a highly symmetrical molecule, its NMR parameters can be obtained by reducing its symmetry through the introduction of 14N/15N and 12C/13C isotopomers. Experimental and computed chemical shifts of cyanuric fluoride have been obtained for 13C, 15N, and 19F. Spin-spin coupling constants have been measured and compared with previous experimental data and with the complete set of computed EOM-CCSD coupling constants.

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