Jesus Rodriguez-Otero

• PhD
• Professor (Associate) at University of Santiago de Compostela

Analytical corrections were developed to improve the accuracy of the PM6 and GFN2-xTB semiempirical quantum mechanical (SQM) methods for the evaluation of noncovalent interaction energies in alkanes and alkenes. We followed the approach of functional group corrections (FGC), wherein the atom-atom pair corrections depend on the nature of the interac...

The nature of the interaction in benzene-containing dimers has been analysed by means of Symmetry Adapted Perturbation Theory (SAPT). The total interaction energy and the preference for the dimers to adopt slipped structures are, apparently, consequence of the balance between repulsion and dispersion. However, our results indicate that this only ho...

Recently, we reported a new approach to develop pairwise analytical corrections to improve the description of noncovalent interactions, by approximate methods of electronic structures, such as semiempirical quantum mechanical (SQM) methods. In particular, and as a proof of concept, we used the PM6 Hamiltonian and we named the method PM6-FGC, where...

Curvature and size effects in halogen interactions with extended aromatic species have been evaluated, employing computational methods, in dimers formed by dihalogens Cl2, Br2 and I2 with both planar (coronene and circumcoronene) and curved (corannulene, sumanene and C60) aromatic systems. The main controlling factor in these interactions is disper...

The substituent effect in monosubstituted benzene dimers mostly follows changes on electrostatics mainly controlled by the direct interaction of the substituent and the other phenyl ring, whereas the contribution from the interacting rings is smaller. As the substituent is located further away the two contributions become of similar magnitude, so t...

[10]cycloparaphenylene ([10]CPP) effectively encapsulates ionic endofullerenes M+C60 (M = Li+, Na+, K+) as revealed by dispersion-corrected density functional theory methods. The interaction between the [10]CPP and these fullerenes is dominated by dispersion, though it is stronger than with pristine C60 due to a reinforcement of electrostatic and i...

Using dispersion-corrected DFT methods, an exhaustive computational study of all possible complexes between the carbon nanorings, CNRs, [10]CPP and [6]CPPA with the fullerenes C50 and C76 was carried out. For C50, the two more favorable isomers (with D5h and D3 symmetry) were chosen, and for C76, the isomer with D2 symmetry (the most favorable isom...

Complexes formed by fullerenes C60/C70 and substituted cycloparaphenylenes with the capability to act as donor/acceptor pairs ([10]CPAq and [10]CPTcaq nanohoops), have been studied using density functional theory methods empirically corrected for dispersion. All nanohoops form stable complexes with fullerenes, with complexation energies amounting t...

Stacking interactions have been evaluated, employing computational methods, in dimers formed by analogous aliphatic and aromatic species of increasing size. Changes in stability as the systems become larger are mostly controlled by the balance of increasing repulsion and dispersion contributions, while electrostatics plays a secondary but relevant...

The potential energy surface involved in the thermal decomposition of 1-propanol radicals was investigated in detail using automated codes (tsscds2018 and Q2DTor). From the predicted elementary reactions, a relevant reaction network was constructed to study the decomposition at temperatures in the range 1000  2000 K. Specifically, this relevant ne...

The ability of the carbon nanoring [11]cycloparaphenylene ([11]CPP) for coordinating fullerenes has been tested using a series of hosts, including the pristine fullerenes C60, C70, C76 and C78, the clusterfullerene Sc3N@C80, monometallic endofullerenes Y@C82 and Tm@C82, and dimetallic endofullerenes Y2@C82 and Lu2@C82. A systematic theoretical stud...

The characteristics of the concave–convex π-π interactions are evaluated in 32 buckybowl dimers formed by corannulene, sumanene, and two substituted sumanenes (with S and CO groups), using symmetry-adapted perturbation theory [SAPT(DFT)] and density functional theory (DFT). According to our results, the main stabilizing contribution is dispersion,...

The complexation of the pristine fullerenes C60, C70, and the endohedral fullerenes Sc3N@C80 and Sc3N@C68 has been tested with a series of hosts of different nature, including the buckybowls corannulene and sumanene, a zinc porphyrin, a chloro boron subphthalocyanine, and a corannulene pentasubstituted with nitrile groups. A systematic theoretical...

The characteristics of the interaction in aliphatic-aliphatic (σ-σ), aliphatic-aromatic (σ-π), and aromatic-aromatic (π-π) dimers have been studied employing benzene, cyclohexane and some of their fluorinated derivatives. Though fluorination dramatically changes the electrostatic properties of the molecules, the interaction only changes notably whe...

The present work studies the interaction of two extended curved π-systems (corannulene and sumanene) with various cations (sodium, potassium, ammonium, tetramethylammonium, guanidinium and imidazolium). The polyatomic cations are models of groups found in important biomolecules in which the cation-π interaction plays a fundamental role. The results...

A comprehensive computational analysis of all possible complexes between the carbon-nanorings, CNRs, [10]CPP and [6]CPPA with the fullerenes C60 and C70, was carried out. The B97-D2 functional together with the def2-TZVP basis set was used through the work, although comparisons with other different functionals (BLYP-D2, B3LYP-D3(BJ), TPSS-D3(BJ), P...

With the aim of enhancing the comprehension of the cation-π interaction, a computational study of the interaction established between sumanene molecule and various cations was performed. Sumanene is a polycyclic aromatic hydrocarbon with a bowl-shaped structure. The curvature of the molecule causes an asymmetry in the distribution of its molecular...

Non-local effects are crucial in order to give a proper description of substituent effects in extended aromatic systems. As a consequence, the predictions based on the currently accepted through-space picture can lead to large errors in the strength of cation···π interactions, especially for the rings furthest from the substituent.

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Complexes formed by imidazolium cation and the aromatic amino acids, phenylalanine, tyrosine, tryptophan, and histidine have been studied by using computational methods. Complexation energies estimated at the MP2.X level amount to -123.3, -124.6, -131.5 and -145.5 kJ/mol for Phe, Tyr, Trp and His, respectively. The results obtained for Phe, Tyr and...

In 2007, Sygula and co-workers introduced a novel type of molecular tweezers with buckybowl pincers that have attracted a substantial interest of researchers due their ideal architecture for recognizing fullerenes by concave-convex π···π interactions (A. Sygula et al. J. Am. Chem. Soc. 2007, 129, 3842). Although in recent years some modifications h...

A series of buckybowls with different size and structure have been tested as potential receptors of fullerenes C60, C70 and C40. Among these bowls are corannulene (C20H10), sumanene (C21H12), pinakene (C28H14), hemifullerene (C30H12), circumtrindene (C36H12), pentaindenocorannulene (C50H20) and bowl-shaped hexabenzocoronene derivatives. An exhausti...

The properties of ternary indole-cation-anion (IMX) complexes are theoretically studied as simplified models of real systems in which some of the fragments used are parts of bigger and complicated structures, like proteins. The electro-neutrality of real systems and the presence of ions of both charges interacting simultaneously with aromatic resid...

A systematic study based on the non-covalent interactions (NCI) index was carried out in order to analyze the characteristics of the cation⋯π interaction in complexes formed by alkaline cations (Li+, Na+, K+, Rb+, and Cs+) and molecular bowls of increasing size, going from corannulene, C20H10, to the fully closed buckminsterfullerene, C60. For this...

The simultaneous interactions of an anion and a cation with a π system have been investigated using MP2 and M06-2X theoretical calculations. Indole was chosen as a model π system for its relevance in biological environments. Two different orientations of the anion: interacting with the N H and with the C H groups of indole, have been considered. Th...

The interaction of guanidinium cation and phenylalanine, tyrosine and tryptophan has been studied with a variety of computational methods. Benchmark values for the interaction have been estimated with the CCSD(T) method extrapolated to the complete basis set limit, indicating that the complexation energy amounts to -123.0, -124.4 and 134.2 kJ/mol f...

Stacking interactions between substituted buckybowls (corannulene and sumanene) with fullerenes (C60 and C70) were studied at the B97-D2/TZVP level. Corannulene and sumanene monomers were substituted with five and six Br, Cl, CH3, C2H or CN units, respectively. A comprehensive study was conducted, analyzing the interaction of corannulenes and suman...

b Stacking p/p interactions of ring-annelated corannulenes with fullerenes C 60 and C 70 were studied at the B97-D level. For this purpose three-, four-, and five-membered rings (saturated and unsaturated) were annelated to the five rim bonds of corannulene. Substitution effects with NH, O and S units on each one of the five saturated five-membered...

Complexes formed by substituted buckybowls derived from corannulene and sumanene with sodium cation or chloride anion have been computationally studied by using a variety of methods. Best results have been obtained with the SCS-MP2 method extrapolated to basis set limit, which reproduces the highest-level values obtained with the MP2.X method. All...

Complexes formed by CN-substituted corannulene and sumanene with monovalent anions have been computationally studied in order to evaluate the effect of anion's nature and solvent upon the interaction. The results indicate that the most stable complex arrangement corresponds in all cases to the anion located by the center of the concave face of the...

Complexes formed by guanidinium cation and a pair of aromatic molecules among benzene, phenol, or indole have been computationally studied to determine the characteristics of the cation···π interaction in ternary systems modeling amino acid side chains. Guanidinium coordinates to the aromatic units preferentially in the following order: indole, phe...

The characteristics of the interaction of microhydrated guanidinium cation with the aromatic moieties present in the aromatic amino acids side chains have been studied by means of computational methods. The most stable minima found for non-hydrated complexes correspond in all cases to structures with guanidinium oriented toward the ring and interac...

A computational study has been carried out in complexes formed by pyrrolidinium cation and aromatic units present in amino acid side chains. The interaction is stronger with indole (-21.9 kcal mol(-1) at the CCSD(T) complete basis set level) than with phenol (-17.4 kcal mol(-1)) or benzene (-16.1 kcal mol(-1)). Most stable structures show a N-Hπ co...

A computational study has been performed in order to characterize the interactions in ternary systems formed by an ion pair of ionic liquids (ILs): C1mim+BF4-,C1mim+NO3- and [C1mim+][CF3COO−], and one water molecule. Using CCSD(T) values extrapolated to basis set limit as reference, the performance of six different functionals has been assessed giv...

Stacking interactions between substituted buckybowls (corannulene and sumanene) with fullerenes (C 60 and C 70) were studied at the B97-D2/TZVP level. Corannulene and sumanene monomers were substituted with five and six Br, Cl, CH 3, C 2H or CN units, respectively. This work was carried out for supplement our previous work of the study of substitue...

A computational study has been performed for studying the characteristics of the interaction of phenol with ammonium and methylammonium cations. The effect of the presence of water molecules has also been considered by microhydrating the clusters with up to three water molecules. Clusters of phenol with ammonium and methylammonium cations present s...

Corannulene is an unsaturated hydrocarbon composed of fused rings, with one central five-membered ring and five peripheral six-membered rings. Its structure can be considered as a portion of C(60). Corannulene is a curved π surface, but unlike C(60), it has two accessible different faces: one concave (inside) and one convex (outside). In this work,...

The performance of a variety of DFT-D functionals with empirical dispersion correction (B97-D, PBE-D, B-LYP-D, BP86-D) and specialized functionals for the treatment the non-covalent interactions (M05-2X, M06-2X) has been evaluated on four representative groups of complexes with π⋯π interactions: (1) dispersion–dominated complexes taken from the S22...

The mechanism of the decomposition of ethyl and ethyl 3-phenyl glycidate in gas phase was studied by density functional theory (DFT) and MP2 methods. A proposed mechanism for the reaction indicates that the ethyl side of the ester is eliminated as ethylene through a concerted six-membered cyclic transition state, and the unstable intermediate glyci...

The properties of complexes formed by phenol and K+, Na+, Li+ and Mg2+ in the presence of up to four water molecules have been studied by means of computational methods. The interaction becomes stronger as the size of the cation decreases, showing almost no preference between coordinating to the aromatic ring or to the hydroxyl oxygen. As water mol...

The interaction of anions with cation-π complexes formed by the guanidinium cation and benzene was thoroughly studied by means of computational methods. Potential energy surface scans were performed in order to evaluate the effect of the anion coming closer to the cation-π pair. Several structures of guanidinium-benzene complexes and anion approach...

The characteristics of the interaction of anions with naphthalendiimides, the basic structural motif of a newly synthesized anion channel based on anion···π interactions, are studied by computational methods. Stable complexes are formed with bromide, chloride, fluoride or hydroxide anions, which exhibit strong anion···π interactions in the gas phas...

Corannulene dimers made up of corannulene monomers with different curvature and substituents were studied using M06-2X, B97D and ωB97XD functionals and 6-31+G* basis set. Corannulene molecules were substituted with five alternating Br, Cl, CH(3), C(2)H or CN units. Geometric results showed that substituents gave rise to small changes in the curvatu...

The effect of microhydration on the interaction of guanidinium cation with benzene has been studied by employing ab initio calculations. Four different structural arrangements were considered for the guanidinium···benzene interaction to which up to six water molecules were added. T-shaped structures are usually the most stable, but as water molecul...

Complexes formed by anions and substituted molecular bowls were studied by means of computational methods. The bowls consisted of corannulene molecules substituted with five or ten F, Cl, or CN groups, whereas Cl(-), Br(-) and BF(4)(-) were the anions considered. Substitution with F, Cl and CN hardly affects the geometry of the bowl, but produces a...

The characteristics of the interaction between water and hydrogen sulfide with indole and a series of analogs obtained by substituting the NH group of indole by different heteroatoms have been studied by means of ab initio calculations. In all cases, minima were found corresponding to structures where water and hydrogen sulfide interact by means of...

A comprehensive MP2/6-311 + G(d,p) and B3LYP/6-311 + G(d,p) study of the aromatic character of phospholes, Pn (CH)4-n PH with n = 0-4 was conducted. For this purpose, the structures for these compounds were optimized at both theoretical levels and different magnetic properties (magnetic susceptibility anisotropy, χanis, and the nucleus-independent...

This work is focused in three topical subjects: intermolecular interactions, metal ions, and aromaticity. A comprehensive MP2/6-31 + G and B3LYP/6-31 + G study of the influence of cation-π interactions on the aromatic character of phosphole was conducted. For this purpose, the structures of complexes were optimized at both theoretical level and dif...

A systematic study of the interaction of alkaline cations with curved π systems (molecular bowls) derived from fullerene (C(60)) shows the ability of these structures to form stable cation-π complexes with both of their sides: concave and convex. In all cases, complexes with the cation in the convex side are more stable than its corresponding partn...

A computational study of dimers formed by aniline and one or two CH3X molecules, X being CN, Cl or F, was carried out to elucidate the main characteristics of the interacting systems. Two different structures were found for each of the dimers, depending on the relative location of the CH3X molecule with respect to the NH2 hydrogen atoms. The most s...

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

The mechanism for the decarbonylation of (E)-2-butenal and (E)-2-methyl-3-pheny-2-propenal was studied with different levels of ab initio and DFT methods. Reactants, products and transition structures were optimized for two kinds of reaction channel: a one-step reaction which involves a three-membered cyclic transition state, and a two-step reactio...

Density functional theory has been used to study an alternative mechanism for the ruthenium(II)-catalyzed [2 + 2 + 2] cycloaddition between 1,6-diynes and tricarbonyl compounds, proposing a multistep-pathway different from that which we previously reported. The dimerization mechanism to obtain the minority product of the reaction has also been stud...

A computational study has been carried out for determining the characteristics of the interaction between one water and hydrogen sulfide molecule with a series of polycyclic aromatic hydrocarbons of increasing size, namely, benzene, anthracene, triphenylene, coronene, circumcoronene, and dicircumcoronene. Potential energy curves were calculated for...

Irigoras et al. found two isomers of the ferrocene–lithium cation complex by DFT calculations [Irigoras, A.; Mercero, J. M.; Silanes, I.; Ugalde, J. J. Am. Chem. Soc.2001, 123, 5040–5043]. The most stable isomer (I) of this complex has Li+ on top of one of the cyclopentadienyls, while in the least stable isomer (II) Li+ binds to the central iron me...

Density functional theory has been employed to study the mechanism of the [2+2+2] ruthenium(II)-catalyzed cycloaddition between 1,6-diynes and tricarbonyl compounds, proposing a viable multistep-pathway according with that was previously suggested, but clarifying some aspects. This process is compared with the one-step reaction in absence of cataly...

The acid-catalyzed 1,4- and 1,3-cycloadditions between methyl glyoxylate oxime (1) and cyclopentadiene were investigated using various Lewis and/or Bronsted acids at different temperatures in dichloromethane as solvent. Besides the expected new adducts, (+/-)-methyl [(3-exo)-2-hydroxy-2-azabicyclo[2.2.1]hept-5-ene]-3-carboxylate (2) and (+/-)-methy...

The intermolecular [5+2]-cycloaddition mechanism of cyclopropyl imines and alkynes catalyzed by [Rh(CO)2Cl]2 has been studied using density functional theory, comparing this multistep process with the two-step reaction in the absence of catalyst. Calculations show that a similar mechanism to that found for dihydroazepines could also lead to the for...

A computational study was carried out for studying the characteristics of the interaction between azulene and water or hydrogen sulfide. In azulene...water complex the water molecule is located with both hydrogen atoms pointing toward the aromatic cloud but displaced to the five-membered ring. Hydrogen sulfide adopts a similar arrangement but locat...

The characteristics of the interaction between the pi cloud of naphthalene and up to two H2O or H2S molecules were studied. Calculations show that clusters formed by naphthalene and one H2O or H2S molecule have similar geometric features, and also present similar interaction energies. Our best estimates for the interaction energy amount to -2.95 an...

The role of lithium cation in the isomerization from diademane to triquinacene and in the Claisen reaction from phenyl allyl ether to 6-allyl-2,4-cyclohexadienone was analyzed. The nature of the interaction of the lithium ion with the reacting molecules in the transition state was studied using supermolecule and perturbational methods. The aromatic...

The intramolecular [6+2] cycloaddition mechanism of 2-vinylcyclobutanones and alkenes catalyzed by the [Rh(CO)2Cl]2 rhodium dimer has been studied using density functional theory, comparing this multi-step process with the one-step reaction in the absence of catalyst. According to our results the calculated mechanism agrees with what was previously...

The characteristics of the interaction between phenol and acetonitrile, methyl fluoride and methyl chloride were studied. The most stable structures for clusters containing one or two CH3X molecules and one phenol moiety were located by means of ab initio and density functional theory calculations. Phenol-acetonitrile dimer presents two almost equa...

The [2+2+2+1] cycloaddition mechanism of enediynes and carbon monoxide catalyzed by the [Rh(CO)2Cl]2 rhodium dimer has been studied using density functional theory, comparing this multistep process with the two-step reaction in the absence of a catalyst. According to our results, the multistep mechanism agrees with that previously suggested. The gr...

The performance of DFT to reproduce noncovalent interactions like H-bonds was assessed. Three DFT hybrid functionals (B3LYP, BHandHLYP from Jaguar5E5, and BHandHLYP from G03) were used to calculate the interaction energies and H-bond distances of several host-guest complexes theoretically designed. Two reference systems (whose experimental data wer...

NICS methodology has been applied to study the change in aromaticity in several aromatic rings on complexation with several ions. From the calculated values of NICS(1) and NICSZZ(1) the only relevant conclusion is that a very small change in aromaticity takes place. Moreover, a large discrepancy between the results from the two aromatic descriptors...

NICS methodology has been applied to study the change in aromaticity in several aromatic rings (benzene, pyrrol, triazine, hexafluorobenzene) on complexation with several ions (Li + , Na + , K + . F -, Cl -). For this purpose all the isolated and complexed rings have been optimized at the MP2/6-31++G(d,p) level of theory. Using GIAO method to calcu...

A comprehensive B3LYP/6-31+G∗ study of the influence of BF3 on the [4+2] cycloaddition of vinylketene with formaldimine was conducted. For this purpose, the complete pathway was determined and changes in different magnetic properties (magnetic susceptibility, χ, magnetic susceptibility anisotropy, χanis, and the nucleus-independent chemical shifts,...

A computational study of clusters containing azulene and up to two molecules of water or hydrogen sulfide was carried out to elucidate the main characteristics of these X-H···π interacting systems. For clusters with one H 2 X molecule only one structure was found interacting with the aromatic cloud of azulene, with an interaction energy of -3.1 kca...

Methylidencyclopropabenzene (MCPB) 1 and Fulvalenes 2–4 are molecules of special interest due to the relation between structure and aromaticity. The aim of this work was to analyze this relation and to quantify the aromaticity in 1–4 using different methods. Magnetic properties are directly related with aromaticity; here we studied the magnetic sus...

A comprehensive B3LYP/6-31+G∗ study of the nature of the [4+2] cycloadditions of conjugated ketenes, vinylketene, imidoylketene and formylketene, with formaldimine was conducted. For each reaction, the complete pathway was determined and changes in different magnetic properties (magnetic susceptibility, χ, magnetic susceptibility anisotropy, χanis,...

Electrocyclization reactions of o-divinylbenzene and several derivatives were studied by performing density functional theory (DFT) calculations together with the 6-31+G∗ basis set. Reactants, products and transition states for each reaction were localized and the path connecting reactants and products was also obtained. Along the reaction path, ma...

The geometries of the different stationary points of reactants, products, and transition states of the nucleophilic addition of water to cyanoketene and methylcarboxyketene have been identified by optimizing every degree of freedom by density functional theory at the B3LYP/6-31++G** level of theory. The computational results for methylcarboxyketene...

A comprehensive B3LYP/6-31+G* study of the nature of 6pi electrocyclizations of four different dienylketenes (2-furanyl, 2-pyrrolyl, cyclopenta-1,3-dienyl, and 2-thiophenyl-substituted ketenes) to corresponding cyclohexadienones was carried out. An analogous system ((3Z)-4-(3H-pyrrol-2-yl)buta-1,3-dien-1-one) was also analyzed. For this purpose, th...

A theoretical study of the ‘walk’ rearrangement in bicyclo[2.1.0]pentene and perfluorotetramethyl (Dewar thiophene) exo-S-oxide has been carried out. Despite the differences between them, the results for both reactions show an enhancement of aromaticity in the transition state, which is consistent with a pericyclic behavior. NBO calculations show t...