José Sanchez-Marín

• PhD in Chemistry
• University of Valencia

From CCSD(T) calculations on the water dimer and B97D/CC on the water-circumcoronene complex at a large number of randomly generated conformations, interaction potentials for the physisorption of water on graphene are built, accomplishing almost sub-chemical accuracy. The force fields were constructed by decomposing the interaction in electrostatic...

The adsorption—for separation, storage and transportation—of methane, hydrogen and their mixture is important for a sustainable energy consumption in present-day society. Graphene derivatives have proven to be very promising for such an application, yet for a good design a better understanding of the optimal pore size is needed. In this work, grand...

Despite being considered completely rigid in most studies, graphene is really exible leading to out-of-plane movements. In this work, the inuence of such exibility on the adsorption of methane and nitrogen on graphene is studied using molecular dynam- ics. Indeed, we have used intramolecular force elds for graphene with in-plane and out-of-plane co...

Different force fields for the graphene–CH4 system are proposed including pseudo-atom and full atomistic models. Furthermore, different charge schemes are tested to evaluate the electrostatic interaction for the CH4 dimer. The interaction parameters are optimized by fitting to interaction energies at the DFT level, which were themselves benchmarked...

We investigate different types of potential parameters for the graphene-nitrogen interaction. Interaction energies calculated at DFT level are fitted with the semi-emperical Improved Lennard-Jones potential. Both a pseudo-atom potential and a full atomistic potential are considered. Furthermore, we consider the influence of the electrostatic part...

The interaction of CO with graphene has been studied at different theoretical levels. Quantum mechanical calculations on finite graphene models using coronene for coupled cluster calculations and circumcoronene for B97D calculations showed that there exists no preferential site for adsorption and that the most important factor is the orientation of...

Buckybowls have risen as appealing fullerene fragment derivatives. Their intrinsic curvature has been exploited in the generation of host‒guest supramolecular assemblies, not only through concave‒convex complementarity but also through less-known concave‒concave staggered arrangements. Whereas the stabilization of bowl-in-bowl dispositions has been...

In the search for efficient molecular dynamics simulation models both simplicity and acceptable accuracy matter. In the present study, a model of the graphene-H 2 physisorption system is used to explore its performance and limitations under canonical NVT and microcanonical NVE simulation conditions. The model implies several simplifications that ca...

We use large-scale MP2 calculations to investigate the physisorption of molecular hydrogen on (9,0) defective carbon nanotubes (CNT) of C72H18. These large (supra)molecular systems are typically studied using conventional DFT methods, which do not describe well the van der Waals interactions responsible for this process. Here, we use CCSD(T)-calibr...

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Code interoperability and the search for domain-specific standard data formats represent critical issues in many areas of computational science. The advent of novel computing infrastructures such as computational grids and clouds make these issues even more urgent. The design and implementation of a common data format for quantum chemistry (QC) and...

A new implementation of the approximate coupled cluster singles and doubles CC2 linear response model is reported. It employs a Cholesky decomposition of the two-electron integrals that significantly reduces the computational cost and the storage requirements of the method compared to standard implementations. Our algorithm also exploits a partitio...

A new multireference configuration interaction method using localised orbitals is proposed, in which a molecular system is divided into regions of unequal importance. The advantage of dealing with local orbitals, i.e., the possibility to neglect long range interaction is enhanced. Indeed, while in the zone of the molecule where the important phenom...

The aim of the present theoretical work is to provide data necessary for a better understanding of the electronic spectrum of the silane molecule, which is affected by the Jahn-Teller effect. By selecting an adequate distorted C(2v) geometry of SiH(4), the three lower Koopmans ionization potentials are evaluated with the equation of motion coupled...

In this work, the linear response formalism with a triples-corrected CCSD reference wave function, LR-CCSDR(3), is applied to the calculation of vertical excitation energies of singlet states of the F2CO molecule. A basis set of atomic natural orbitals augmented with a series of Rydberg functions has been used in the calculations. A large number of...

Ab initio Coupled-Cluster calculations with single and double excitations and perturbative correction to the triple, CCSD(T), have been carried out for the high-spin electronic state, (5A2), of the copper cluster Cu4 in its tetrahedral arrangement. Like alkali metals clusters, tetrahedral Cu4 presents a bound quintet state, i.e., a situation where...

Gauge origin independent calculations of nuclear magnetic shielding tensors are carried out inside the formalism of the continuous transformation of the origin of the current density leading to formal annihilation of its diamagnetic contribution (CTOCD-DZ). We employ the unrelaxed linear response approach with a hierarchy of different coupled clust...

Size-consistent self-consistent multireference singles and doubles configuration interaction (SC)2–MR–SDCI, and linear response coupled cluster of singles and doubles including triples LR–CCSDR(3) methods, with a basis set of ANO’s augmented with a single series of molecular Rydberg functions, have been applied to the calculation of vertical excita...

Although for planar conjugated hydrocarbons the out-of-plane component of proton magnetic shielding is an unquestionable quantitative aromaticity indicator, the same is not true for tetraazanaphthalenes. As in these compounds the (core + sigma)-currents associated to the nitrogen nuclei diminish the perpendicular component of shielding, abnormal va...

Theoretical absorption oscillator strengths for transitions involving Rydberg states in molecular formaldehyde as well as cross sections for photoionization Rydberg channels associated with the production of the lowest parent ion electronic state are reported. The calculations have been performed with the molecular quantum defect orbital (MQDO) met...

This study has been focused on the ϵ(0,0) band of the nitric oxide molecule, associated with the absorption electronic transition D2Σ+←X 2Π, in the energetic vacuum ultraviolet region. A temperature of 295 K has been considered. The Molecular Quantum Defect Orbital (MQDO) methodology, with which reliable spectroscopic data have been reached in the...

The high-spin electronic states for lithium, sodium, and potassium four-atom clusters were studied. In particular, we performed coupled cluster geometry optimization of the quintet state in tetrahedral geometry. The quintet state of these systems is characterized by having all the valence electron unpaired, giving rise to the so-called no-pair bond...

An all-electron full configuration interaction (FCI) calculation of the adiabatic potential energy curves of some of the lower states of BeH molecule is presented. A moderately large ANO basis set of atomic natural orbitals (ANO) augmented with Rydberg functions has been used in order to describe the valence and Rydberg states and their interaction...

The transition intensities supplied in this Letter are directly connected with a description of the discrete and continuum spectrum of BeH. An attempt to meet our goal requires the calculation of the absorption oscillator strengths of several transitions to Rydberg states of BeH, together with differential oscillator strengths which give rise to di...

A series of electric and magnetic properties of hexafluorobenzene have been calculated, including the electric dipole polarizability, magnetizability, electric quadrupole moment, and nonlinear mixed electric dipole-magnetic dipole-electric quadrupole hyperpolarizabilities needed to obtain estimates of the Kerr, Cotton-Mouton, Buckingham, Jones, and...

Vertical excitation energies belonging to some different Rydberg series of hydrogen chloride have been determined with a coupled-cluster theoretical approach. These excitation energies have allowed us to calculate electric dipole transition intensities in HCl and allow additional assessment of the calculation approach presently used to provide an a...

Coupled-cluster calculations are used to compute the energy of conversion between the neutral and the zwitterionic forms of beta-carboline. The stability of the different species is discussed in terms of charge separation and aromatic character, which is related to magnetic criteria. By means of a linear response formalism the vertical excitation e...

Coupled-cluster calculations are used to compute the energy of conversion between the neutral and the zwitterionic forms of β-carboline. The stability of the different species is discussed in terms of charge separation and aromatic character, which is related to magnetic criteria. By means of a linear response formalism the vertical excitation ener...

The Li4 cluster low lying electronic states were studied. In particular we investigated the tetrahedral geometry at full CI and coupled cluster level, with basis sets of increasing quality. The 5A2 electronic state, characterized by having all the valence electrons unpaired, forming a quite stable no-pair bonding state, was studied in greater detai...

The all-electron full configuration interaction (FCI) vertical excitation energies for some low lying valence and Rydberg excited states of BeH are presented in this article. A basis set of valence atomic natural orbitals has been augmented with a series of Rydberg orbitals that have been generated as centered onto the Be atom. The resulting basis...

Using correlated ab initio methods, the polarizability of large [4n+2]-annulenes is determined, showing that there exists an almost linear relation between the exaltation of magnetic susceptibility (a measure of aromaticity) and an equivalent enlargement of polarizability.

Coupled cluster linear response formalism has been used to compute the vertical excitation energies and oscillator strengths of the lowest valence singlet states of dimethyl sulfide (DMS) and dimethyl sulphoxide (DMSO). Unless for one exception, the results are in very good agreement with experiment, but a new assignment of one DMSO transition is p...

Vertical excitation energies of the CF(3)Cl molecule have been obtained from a response function approach with a CC reference function to determine absolute photoabsorption oscillator strengths in the molecular-adapted quantum defect orbital formalism (MQDO). The present work covers more highly excited Rydberg states than have been experimentally r...

Ab initio quantum-chemistry programs produce and use large amounts of data, which are usually stored on disk in the form of binary files. A FORTRAN library, named Q5Cost, has been designed and implemented in order to allow the storage of these data sets in a special data format built with the HDF5 technology. This data format allows the data to be...

Without Abstract

The size-consistent self-consistent configuration interaction method, (SC)2-CI, is a procedure based on the matrix dressing formulation of the intermediate hamiltonian theory, which aims to correct the size-extensivity problem in truncated or selected configuration interaction (CI) calculations. Corrected energies and CI-like functions are obtained...

Vertical excitation energies as well as related absolute photoabsorption oscillator strength data are very scarce in the literature for methane. In this study, we have characterized the three existing series of low-lying Rydberg states of CH4 by computing coupled cluster linear response (CCLR) vertical excitation energies together with oscillator s...

Investigations into the charge-separated states and electron-transfer transitions in tetracyanoethylene (TCNE) complexes have recently generated much interest. In this work we present theoretical calculations showing that the most stable structure of the dianion TCNE2- has D2d symmetry in vacuum as well as in the solvents dichloromethane and aceton...

We present the results of an extended computational study of the electric and magnetic properties connected to Cotton-Mouton birefringences, on the trifluoro- and trichloroborides in the gas phase. The electric dipole polarizabilities, magnetizabilities, quadrupole moments, and higher-order hypersusceptibilities--expressed as quadratic and cubic fr...

A recently developed algorithm to generate localized molecular orbitals (LMO) is applied to the study of excited states along a photodissociation process. The LMOs allow for the selection of a consistent complete active space (CAS) for the simultaneous description of all the electronic states involved in a multistate process on the basis of simple...

We present the results of an extended computational study of the electric and magnetic properties connected to Cotton-Mouton birefringences, on the trifluoro-and trichloroborides in the gas phase. The electric dipole polarizabilities, magnetizabilities, quadrupole moments, and higher-order hypersusceptibilities—expressed as quadratic and cubic freq...

The full configuration interaction (FCI) study of the singlets vertical spectrum of the neutral beryllium trimer has been performed using atomic natural orbitals [3s2p1d] basis set. The FCI triangular equilibrium structure of the ground state has been used to calculate the FCI vertical excitation energies up to 4.8 eV. The FCI vertical ionization p...

The full configuration interaction (FCI) study of the ground state of the neutral beryllium trimer has been performed using an atomic natural orbitals [3s2p1d] basis set. Both triangular and linear structures have been considered for the Be(3) cluster. The optimal geometry for the equilateral triangle has been calculated. The potential energy cut s...

The molecular electric quadrupole moment (Θ) of Cl2 has been calculated using SDCI, and (SC)2-SDCI wave functions as well as CCSD, CCSD(T), and CC3 methods. All these correlation methods are single reference. All of them, but SDCI, are free of the size-extensivity error. The variation of Θ from the separated atoms to the equilibrium region is repor...

The open shell (SC)(2)-CAS-SDCI method along with a basis set of atomic natural orbitals (ANO) has been applied for calculating the main ionization potentials of acetylene, as well as the manifold of excited states of the different symmetries up to 32 eV. In this method, the single and double excitations of a CAS space are generated and the corresp...

We present a quantitative evaluation of the influence of the electron transfer on the magnetic properties of mixed-valence polyoxometalates reduced by two electrons. For that purpose, we extract from valence-spectroscopy ab initio calculations on embedded fragments the value of the transfer integrals between W nearest-neighbor atoms in a mixed-vale...

The vertical electronic spectrum of formaldehyde has been studied by means of (SC)2-MR-SDCI and CCLR methods. Two basis sets of atomic natural orbitals (ANOs) complemented with a one-centre series of Rydberg orbitals were used. The first was taken from the CASPT2 study by Merchán, M., and Roos, B. O., 1995, Theoret. Chim. Acta, 92, 221, and may be...

Coupled Cluster and related size-consistent methods can be employed for an accurate ab initio estimate of the Molecular Electric Quadrupole Moment (MEQM). The difficulties and accuracy that can be achieved are illustrated by the calculation of the MEQM of the Chlorine diatomic [1]. For Chlorine gas three experimental values are available. The ab-in...

A new method is presented, which allows an important reduction of the size of some Configuration Interaction (CI) matrices. Starting from a Complete Active Space (CAS), the numerous configurations that have a small weight in the CAS wave function are eliminated. When excited configurations (e.g., singly and doubly excited) are added to the referenc...

The size-consistent self-consistent singles and doubles configuration interaction method using both multireference (MR) and complete active space (CAS) as SDCI generator spaces has been used to calculate both vertical excitation energies and vertical ionization potentials for the H2S molecule. A basis set of ANO functions, [4s3p2d1f] for S and [2s1...

The UV fluorescence excitation and dispersed fluorescence spectra of jet-cooled p-methylaniline have been obtained for the S1←S0 transition. The main spectral bands have been assigned by comparison with those of other relevant substituted benzenes and with the help of computed vibrational frequencies. The structure of p-methylaniline in both the S0...

A method for the computation of a dimension index D is implemented in program TOPO and applied to calculate the solvent-accessible surfaces of molecules. Our algorithm distinguishes external from internal atoms, and uses such a feature to give two fractal-like dimension indices, D and D′. The D′- D difference is a sensitive method to elucidate the...

The size-consistent self-consistent singles and doubles configuration interaction method (SDCI) has been used to get size-extensive excitation energies into the framework of the SDCI space. The method is applied through a matrix dressing operator that usually accounts for the dressing effects carried by the doubles. This operator has been modified...

A general mechanism for the reactions of the NO3 radical with 2-butene, isobutene, 2-methyl-2-butene, and 2,3-dimethyl-2-butene is proposed on the basis of density functional theory (DFT) calculations. This mechanism is compared with previously reported model experimental kinetic studies at low pressures and temperatures in anaerobic conditions. In...

A mechanism for the reaction of the NO3 radical with vinyl chloride is proposed on the basis of B3LYP and CASSCF quantum chemistry calculations. Two initial transition states lead to the Markownikoff and contra-Markownikoff addition of NO3 to chloroethene. From the two initial adducts different interconnected pathways start. We have found epoxichlo...

A general mechanism for the reactions of the NO3 radical with 1,2-dichloroethene, 1,1-dichloroethene, trichloroethene, and tetrachloroethene is proposed from ab initio DFT calculations. The calculated mechanism shows three main parallel reaction pathways. For the systems where the two carbon atoms are differently substituted, the study includes bot...

A general mechanism for the reactions of the NO3 radical with 2-butene, isobutene, 2-methyl-2-butene, and 2,3-dimethyl-2-butene is proposed on the basis of density functional theory (DFT) calculations. This mechanism is compared with previously reported model experimental kinetic studies at low pressures and temperatures in anaerobic conditions. In...

The UV fluorescence excitation and dispersed fluorescence spectra of a jet-cooled m-methylaniline have been obtained for the S1<--S0 transition, in which some of the bands have been observed for the first time. The main spectral bands have been assigned by comparison with those of other relevant substituted benzenes. It was found that the spectra e...

The size-consistent self-consistent matrix dressing method has been applied on an open-shell single-configuration reference state. Once the reference state is converged, several low-lying roots can be obtained for the dressed configuration interaction (CI) matrices of appropriate symmetry. The CI matrices were built with a complete-active-space sin...

A mechanism for the reaction of the NO3 radical with propene is proposed on the basis of B3LYP and CASSCF calculations. The mechanism involves initially both Markownikoff and contra-Markownikoff oriented addition on the double bond. From the initial radical adducts several interconnected pathways have been found, giving 1,2-epoxypropane, propanal,...

In previous works, the size-consistent self-consistent matrix dressing method has been applied to single reference as well as to complete active space singles and doubles configuration interaction. The wave function of the dressed state was assumed to be dominated by a closed shell determinant. Here, the method has been extended to systems where th...

We outline a method for the calculation of molecular dipole and quadrupole moments and dipole–dipole polarizabilities which we have successfully applied to a series of reference molecules, amino acids and model peptides. The results for are in line with CPHF reference calculations. In particular, the calculated positive value of CO is in agreement...

We use a method for the calculation of the molecular dipole ( μ ¯ ) and quadrupole ( θ = ) moments and dipole-dipole ( α = ), dipole-quadrupole ( A ≡ ) and quadrupole-quadrupole ( C ≣ ) polarizabilities which we have successfully applied to the benzothiazole (A)-benzobisthiazole (B) linear oligomer A-B13-A. Two model rotational isomers have been ch...

AMYR is a computer program for the calculation of molecular associations using Fraga's pairwise atom-atom potential. The interaction energy is evaluated through a expansion. The electrostatic energy is calculated through either the one-centre-per atom or the three-centres-per atom model by Hunter and Sanders. A pairwise dispersion energy term is in...

The self-consistent size consistent on a complete active space singly and doubly configuration interaction (SC)2CAS-SDCI method is applied to excited states. The (SC)2 correction is performed on a closed shell state, and the excited states are obtained by diagonalization of the dressed matrix. A theoretical justification of the transferability of t...

A mechanism for the reaction of the NO(3) radical with the simplest alkene, ethene, is proposed. The mechanism involves three paths leading to three main different products: oxirane, ethanal, and nitric acid. The three paths start from the same initial intermediate, an NO(3)-ethene adduct. The calculated energy barriers show that the oxirane is the...

The size-consistent self-consistent configuration interaction operator (SC)2CI has been applied to a hierarchy of SDCI approaches. It has been obtained for the ground state of N2 at the equilibrium distance. It has been applied to calculate excited roots of dressed SDCI built on single-reference, multi-reference (MR) and complete active space (CAS)...

The concept of fractal has been applied to a number of properties of proteins. The structure and shape of the polypeptide chain of proteins are determined by the hybridized states of atomic orbitals in the molecular chain. The fractal dimension in the range of short distances (1-10 Å) of the tertiary structures of some proteins covering various str...

We have outlined a method for the calculation of atomic net charges and molecular dipole-dipole, α, dipole-quadrupole, A, and quadrupole-quadrupole, C, polarizabilities which we have successfully applied to benzothiazole (A)-benzobisthiazole (B) oligomers in the series AB1A to AB13A, and the results have been extrapolated to give predictions...

Limited previous experience with the mean value total dressing (MVTD) method had shown that MVTD energies for closed shell systems are generally better than CCSD(T) ones compared to FCI. The method, previously published as total dressing 2′(td-2′), is based on the single reference intermediate Hamiltonian theory. It is not a CC method but deals in...

Using the intermediate hamiltonian theory as a unique conceptual frame and the technique of CI matrix dressing, a wide series of single-reference methods for the treatment of the ground state correlation are reviewed, compared, and sometimes improved. These methods range from independent excitation approximation (the very next step beyond MP2) to c...

We outline a method for the calculation of multipole moments and molecular dipole-dipole (), dipole-quadrupole (), and quadrupole-quadrupole () polarizabilities, which we have successfully applied to benzothiazole (A)-benzobisthiazole (B) oligomer A-B13-A. Three model rotational isomers have been characterized: (1) the fully planar (000) rotational...

The size-consistent self-consistent configuration interaction (SC)2CI method is applied to the calculation of excitation energies. This method diagonalizes a dressed SDCI matrix built for the ground state but it is shown that the extra eigenvalues are not phony solutions but represent the excited roots of the system. Numerical tests are encouraging...

A previously proposed procedure including the linked and unlinked contributions due to Triple and Quadruple excitations into a size-consistent SDCI-like model has been applied to HF and F2 single-bond systems. The procedure is a non-iterative approximation to the more general total dressing model, which is based on the intermediate Hamiltonians the...

We report a detailed ab initio study of the molecular structure and conformational behavior of 2,2'-bithiophene. Fully optimized torsional potentials keeping planar the thiophene rings; are calculated at the HF/3-21G*, HF/6-31G*, and MP2/6-31G* computational levels. The optimized geometries are analyzed in terms of conjugative effects and nonbondin...

The fluoranthene-fluoranthene association has been studied using an atom-atom pair potential proposed by S. Fraga. Two models have been selected to compute the electrostatic interaction: the standard one punctual charge per atom, and a model proposed by Hunter and Sanders for π-systems. Four stacked-displaced structures are predicted to be actual m...

Using the intermediate Hamiltonian formalism, it is shown that coupled-cluster doubles (CCD) or singles and doubles (CCSD) may be formulated as an eigenvalue problem by dressing properly the doubles or singles and doubles configuration interaction matrix. The dressing may be either diagonal or non-diagonal. The so-formulated CC method converges eve...

Intermediate Hamiltonians are effective Hamiltonians which are defined on an N‐dimensional model space but which only provide n<N exact eigenvalues and the projections of the corresponding eigenvectors onto the model space. For a single root research, the intermediate Hamiltonian may be obtained from the restriction of the Hamiltonian to the model...

The importance of characterizing the stationary points of the intermolecular potential by means of Hessian eigenvalues is illustrated for the calculation of the benzene–benzene interaction using an atom-to-atom pair potential proposed by Fraga (FAAP). Two models, the standard one-center-per atom and another using three-centers-per atom due to Hunte...

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A convenient procedure has been proposed recently to insure the size-consistence of Singles and Doubles CI; the method goes through a self-consistent dressing of the energies of the excited determinants which incorporates the unlinked effects of the Triples and Quadruples. Two strategies are proposed here to add thelinked contributions of the Tripl...

We present extensive ab initio calculations on the low‐lying electronic states of trans‐1,3‐butadiene within the multireference configuration interaction (MRCI) framework by selecting the configurations with a perturbative criterion. The X 1Ag ground state and 1 3Bu, 1 3Ag, 2 1Ag, and 1 1Bu valence excited states have been calculated at a fixed geo...

Calculations of molecular aggregation using Fraga's intennolecular potential plus dispersion energy term were performed for dimers, trimers and tetramers of coronene. The program (AMYR) was adapted in order to include geometry optimization of more than one pair of systems. The results indicate that the most stable dimer corresponds to a stacked-dis...

Program AMYR, originally written by S. Fraga (University of Alberta, Canada), allows for the calculation of molecular associations using a pair-wise atom-atom potential. The interaction energy is evaluated through a 1/R expansion. Our improved version includes a dispersion energy term in the potential corrected by damping functions, the possibility...

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The program AMYRVF is a vectorized and largely modified version of a previous program called AMYR for calculating molecular associations by means of Fraga's pair-wise atom-atom potential. Three new minimization procedures have been implemented as well as other improvements such as the inclusion of new pair-wise dispersion energy terms with damping...

Aggregation is a well-known phenomenon in phthalocyanine chemistry. Interactions can occur between adjacent phthalocyanine rings, both in organic and aqueous phases, resulting in coupling between the electronic states of two, or more, phthalocyanine units [1].

The assignment of some parameters in an atom-atom pair potential proposed by Fraga is checked through calculations of some azine stacked dimers. So, the use of Mulliken net charges and interpolated polarizabilities instead of the standard Fraga's procedure reveals to be a reliable method to maintain the generality and simplicity of Fraga's potentia...

Using non-empirical pseudopotentials, we have performed a theoretical study on the last step of the propylene partial oxidation mechanism, the acrolein desorption from the catalyst surface. To represent the catalyst we have used a simplified model of a catalyst active site. We have study the C3H4CuO complex, analysing the dissociation process of th...