J. Phys. Condensed Matter, 25, 415504, 2013

DOI:10.1088/0953-8984/25/41/415504

A. J. Salkeld, M. F. Reid, J-P. R. Wells, G. Sánchez-Sanz, L. Seijo and Z. Barandiarán. 

Effective-Hamiltonian parameters for ab initio energy-level calculations of SrCl2 :Yb2+ and CsCaBr3:Yb2+.

Calculated energy levels from recent ab initio studies of the electronic structure of SrCl2:Yb2+ and CsCaBr3:Yb2+ are fitted with a semi-empirical 'crystal-field' Hamiltonian, which acts within the model space 4f14 + 4f135d + 4f136s. Parameters are obtained for the minima of the potential energy curves for each energy level and also for a range of anion–cation separations. The parameters are compared with published parameters fitted to experimental data and to atomic calculations. The states with significant 4f136s character give a good approximation to the impurity-trapped exciton states that appear in the ab initio calculations.

J. Phys. Chem. B. 117, 11608, 2013

DOI: 10.1021/jp407339v

F. Blanco, B. Kelly, G. Sánchez-Sanz, C. Trujillo, I. Alkorta , J. Elguero , I. Rozas

Non-Covalent Interactions: Complexes of Guanidinium with DNA and RNA Nucleobases

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.

Phys. Chem. Chem. Phys. 15, 14310, 2013

DOI: 10.1039/c3cp52312h

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

Orthogonal interactions between nitryl derivatives and electron donors: pnictogen bonds

Pnictogen complexes between nitryl derivatives (NO2X, X = CN, F, Cl, Br, NO2, OH, CCH, and C2H3) and molecules acting as Lewis bases (H2O, H3N, CO, HCN, HNC and HCCH) have been obtained at the MP2/aug-cc-pVTZ computational level. A total of 53 minima have been located. Their energy, geometry, DFT-SAPT energy terms, electronic properties (NBO, AIM, ELF, and NCI) and NMR shieldings have been calculated and analyzed. Finally, a search in the CSD database has been carried out, showing a large number of similar interactions in crystallographic structures.

Tetrahedron, 69, 7333, 2013

DOI:/10.1016/j.tet.2013.06.072

G. Sánchez-Sanz, C. Trujillo, I. Rozas, J. Elguero

A theoretical study on the aromaticity of benzene and related derivatives incorporating a C–Ctriple bond; length of mdashC–C fragment

Dedicated to Professor Ibon Alkorta on the occasion of his 50th anniversary

Continuing with our interest in aromaticity, we have studied the influence that replacement of formal C–C single bonds by C–Ctriple bond; length of mdashC–C fragments, in a series of mono- (cyclobutadiene, benzene, and cyclooctatetraene) and fused-carbocycles (naphthalene and azulene), has in their properties, focusing mostly on NMR and aromaticity. We have analyzed the effect of such substitution not only in the aromaticity of the different structures, but also in the influence of low and high spin states by means of NICS values over the rings and 3D NICS isosurfaces. We have found that, in most of the cases, the substitution induces a loss of aromaticity in singlet states (both restricted and unrestricted) that can be recovered when triplet states are taken into account.

Comp. Rend. Chim. 16, 937, 2013

DOI: 10.1016/j.crci.2013.05.016

D. Sanz, R. M. Claramunt, F. Mathey, I. Alkorta, G. Sánchez-Sanz, J. Elguero

Intermolecular spin–spin coupling constants between 31P atoms

This paper reports the study by NMR spectroscopy and ab initio methods of the structure of 3,4-dimethyl-1-cyanophosphole and its dimer. The dimer presents a P...P interaction of the pnictogen type due to the presence ofs-holes. NMR of the monomer was recorded in CDCl3 solution while NMR of the dimer corresponds to the solid state (CPMAS) experiments. The 2pJPP spin–spin coupling constan thas not been measured, but calculated at the B3LYP level. AIM, NBO and ELF methodologies have been used to describe the electronic structure of the dimer

J. Mol. Struct. 108, 138, 2013

DOI: 10.1016/j.molstruc.2013.04.069

C. Trujillo, G. Sánchez-Sanz, I. Alkorta, J. Elguero, O. Mó, M. Yáñez

Resonance assisted hydrogen bonds in open-chain and cyclic structures of malonaldehyde enol: A theoretical study

In 1989 Gilli, Bellucci, Ferretti and Bertolasi introduced the notion of Resonance Assisted Hydrogen Bonding (RAHB) one of the most fruitful concepts in structural chemistry. After reviewing our previous contributions to this topic, the present work analyzes theoretically this concept especially in non-cyclic structures. Geometries, electron densities and Laplacian at the bond critical points, cooperativity through many body interaction energies, deformation energies as well as NMR properties (chemical shifts and 2hJOO coupling constants) are used for the discussion.

J. Phys. Chem. A, 117, 3133, 2013

DOI: 10.1021/jp401480y

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

Phosphorus As a Simultaneous Electron-Pair Acceptor in Intermolecular P···N Pnicogen Bonds and Electron-Pair Donor to Lewis Acids

Ab initio MP2/aug’-cc-pVTZ calculations have been performed to investigate the structures and energies of binary complexes LA:PH2F and LA:PH3 and of ternary complexes LA:H2FP:NFH2 and LA:H3P:NH3 in which the pnicogen-bonded P atom also acts as an electron-pair donor to a Lewis acid (LA), for LA = BH3, NCH, ClH, FH, FCl, and HLi. Hydrogen bonds, halogen bonds, and dative covalent bonds are found at P in some cases, depending on the nature of the Lewis acid. HLi forms a lithium bond with P only in the binary complex HLi:PH3. The binding energies of ternary complexes exhibit a classical synergistic effect, although the computed cooperativity may be overestimated due to neglect of the interaction of the Lewis acid with NH2F or NH3 in some cases. The hydrogen-bonding Lewis acids appear to have little effect on the strength of the P···N bond, while the remaining Lewis acids strengthen the pnicogen bond. 31P absolute chemical shieldings increase in LA:H2FP:NFH2complexes relative to the corresponding LA:PH2F complexes as the positive charge on P decreases, while chemical shieldings decrease in LA:H3P:NH3 relative to the corresponding LA:PH3 complexes as the positive charge increases. Absolute values of 1pJ(P–N) spin–spin coupling constants in complexes LA:H2FP:NFH2 decrease as the P–N distance decreases. It appears that this behavior is associated with the presence of a second intermolecular interaction, whether electron-donation by P or hydrogen bond formation at P–F.

ChemPhysChem, 14, 1656, 2013

DOI: 10.1002/cphc.201300145

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

Intramolecular Pnicogen Interactions in PHF(CH2)nPHF (n=2–6) Systems

A computational study of the intramolecular pnicogen bond in PHF[BOND](CH2)n[BOND]PHF (n=2–6) systems was carried out. For each compound, two different conformations, (R,R) and (R,S), were considered on the basis of the chirality of the phosphine groups. The characteristics of the closed conformers, in which the pnicogen interaction occurs, were compared with those of the extended conformer. In several cases, the closed conformations are more stable than the extended conformations. The calculated interaction energies of the pnicogen contact, by means of isodesmic reactions, provide values between −3.4 and −26.0 kJ mol−1. Atoms in molecules and electron localization function analysis of the electron density showed that the systems in the closed conformations with short P⋅⋅⋅P distances have a partial covalent character in this interaction. The calculated absolute chemical shieldings of the P atoms showed an exponential relationship with the P⋅⋅⋅P distance. In addition, a search in the Cambridge crystallographic database was carried out to detect those compounds with a potential intramolecular pnicogen bond in the solid phase.

Z. Phys. Chem. 227, 821, 2013

DOI: 10.1524/zpch.2013.0367

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

Ab Initio Study of Cooperative Effects in Complexes X:HBO:Z, with X, Z=LiH, HNC, HF, HCN, HCl, ClF, and HBO: Structures, Binding Energies, and Spin-Spin Coupling Constants across Intermolecular Bonds

A systematic ab initio investigation has been carried out to determine the structures, binding energies, and spin-spin coupling constants of ternary complexes X:HBO:Z for X, Z=LiH, HNC, HF, HCN, HCl, ClF, and HBO. All complexes X:HBO:Z are linear with C∞v symmetry, except for HCl:HBO:Z and ClF:HBO:Z which have Cs symmetry, thereby reflecting the structures of the corresponding X:HBO and HBO:Z complexes. Cooperative effects on energies are synergistic in all ternary complexes. The enhanced binding energies of complexes X:HBO:Z correlate with the binding energies of the X:HBO and HBO:Z complexes. Coupling constants 1J(B-H) and 2hJ(B-A) across B-H···A hydrogen bonds correlate with the B-A distance, and exhibit synergistic effects due to the presence of Z. 1hJ(H-A) indicates that these bonds have little proton-shared character. Coupling constants across D-H···O hydrogen bonds, H-Li···O lithium bonds, and F-Cl···O halogen bonds are also sensitive to the synergistic effects arising from the presence of X. D-H···O hydrogen bonds in ternary complexes are traditional (normal) hydrogen bonds.

J. Phys. Org. Chem. 26, 378, 2013

DOI: 10.1002/poc.3099

I. Rozas, G. Sanchez-Sanz, I. Alkorta, J. Elguero
 
Solvent effects on guanidinium-anion interactions and the problem of guanidinium Y-aromaticity
 

We have calculated the complexes formed by guanidine/guanidinium and HCl/Cl, HNO3/NO3 and H2SO4/HSO4 both in the gas and aqueous Polarizable Continuum Model (PCM) phase to understand the effect that solvation has on their interaction energies. In the gas phase, the cation–anion complexes are much more stable than the rest; however, when PCM-water is considered, this energetic difference is not as large due to the extra stabilization that the ions suffer when in aqueous solution. All the complexes were analyzed in terms of their AIM and NBO properties. In all cases, water solvation seems to “dampen” those properties observed in the gas phase. The values of Nucleus Independent Chemical Shift (NICS)(1) and NICS(2) indicate a huge influence of the proximity of the carbon atom for short distances; thus, the 3D NICS values on the van der Waal isosurfaces have been used to evaluate the possible Y-aromaticity of the guanidinium system. The isosurface in this system is more similar to cyclohexane than to benzene as indication of poor aromaticity.

CrystEngComm, 15, 3178, 2013

DOI: 10.1039/C2CE26786A

I. Alkorta, G. Sánchez-Sanz, J. Elguero

Linear free energy relationships in halogen bonds

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).

Struct. Chem. 24, 1145, 2013

DOI:10.1007/s11224-012-0134-8

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

A theoretical investigation of the mechanism of formation of a simplified analog of the green fluorescent protein (GFP) from a peptide model

Theoretical calculations at the B3LYP/6-311++G(d,p) level have been carried out on the reaction path connecting a dipeptide to an imidazolinone as a model for the formation of GFP. In addition, we have studied the hydration effects on the processes, adding a water molecule to assist the cyclization. The solvent effects have been taken into account by introducing the monohydrated molecules into a solvent cavity with a polarized continuum model. Significant reductions of the energy barriers for the reaction path can be observed within the water-assisted processes. The solvent effects account for a barrier lowering of 4–5 kJ mol−1.

J. Phys. Chem. A, 117, 183, 2013

DOI: 10.1021/jp3100816

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

Exploring (NH2F)2, H2FP:NFH2, and (PH2F)2 Potential Surfaces:Hydrogen Bonds or Pnicogen Bonds?

An ab initio MP2/aug’-cc-pVTZ study has been carried out to identify local minima on the (NH2F)2, H2FP:NFH2, and (PH2F)2 potential surfaces, to characterize the types of interactions which stabilize the complexes found at these minima, and to evaluate their binding energies. With one exception, (NH2F)2 complexes are stabilized by N–H···N or N–H···F hydrogen bonds. Only one complex, that with the smallest binding energy, has a pnicogen N···N bond. In contrast, (PH2F)2 complexes are stabilized by P···P or P···F pnicogen bonds or by an antiparallel alignment of the dipole moment vectors of the two monomers, but not by hydrogen bonds. The most stable complex has an F–P···P–F alignment which approaches linearity. Both hydrogen-bonded and pnicogen-bonded complexes exist on the H2FP:NFH2surface, with the most stable being the pnicogen-bonded complex with F–P···N–F approaching a linear arrangement. Charge transfer transitions from a lone pair on a P, N, or F atom in one molecule to an antibonding σ* orbital of the other stabilize these complexes. These transitions are most important for complexes with pnicogen bonds. Although net charge transfer occurs in complexes in which the two monomers are inequivalent, charges on N and P do not correlate with N and P absolute chemical shieldings. Rather, these shieldings also reflect charge distributions and overall bonding patterns. EOM-CCSD two-bond spin–spin coupling constants 2hJ(X–Y) across X–H···Y hydrogen bonds tend to be small, due in part to the nonlinearity of many of the hydrogen bonds. 1pJ values across a particular kind of pnicogen bond are relatively large and vary significantly but do not correlate with corresponding distances.

Onlain free bet offers here.