Antonio Fernández-Ramos

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

The formation of complex organic molecules in the interstellar medium (ISM) is central to astrochemistry and prebiotic chemistry, as these species may act as precursors to biomolecules essential for life. Although glyceraldehyde (HOCH2CH(OH)C(O)H, GCA) has not yet been detected in the ISM, the presence of structurally related compounds in various a...

A widely used procedure for obtaining the complete-basis set (CBS) limit of an electronic structure method is extrapolating results from a sequence of correlation-consistent basis sets. A recent study by Xi et al. trained two-point extrapolation schemes against a new extensive dataset using aug-cc-pVXZ (X = D, T, Q, 5, and 6) basis set pairs. Their...

We present the systematic exploration of various potential energy surfaces for systems with C 6 H 6– x ( x = 0, 1, 2, or 3) empirical formula using an automatic search approach. The primary objective of this study is to identify reaction pathways that lead to the creation of benzene, o -benzyne, and other rings. These pathways initiate with a barri...

Acetonitrile (CH 3 CN) is present in the interstellar medium (ISM) in a variety of environments. However, at the ultracold temperatures of the ISM, radical-molecule reactions are not widely investigated because of...

Zr-based metal–organic frameworks (MOFs) are excellent heterogeneous porous catalysts due to their thermal stability. Their tunability via node and linker modifications makes them amenable for theoretical studies on catalyst design. However, detailed benchmarks on MOF-based reaction mechanisms combined with kinetics analysis are still scarce. Thus,...

Polyrate is a suite of computer programs for the calculation of chemical reaction rates of polyatomic species (including atoms and diatoms as special cases) by variational transition state theory (VTST); conventional transition state theory is also supported. Polyrate can calculate the rate constants for both bimolecular reactions and unimolecular...

The advent of recent technological developments in software engineering has enabled the exploration of reaction mechanisms inside intricate reaction networks, thereby propelling the beginning of a new era in ab initio kinetics. While it is feasible to consider a substantial number of reactions, determining their rate constants with precision remain...

Our automated reaction discovery program, AutoMeKin, has been utilized to investigate the formation of glycolonitrile (HOCH2CN) in the gas phase under the low temperatures of the interstellar medium (ISM). The feasibility of a proposed pathway depends on the absence of barriers above the energy of reactants and the availability of the suggested pre...

The equilibrium structure of selenophenol has been investigated using rotational spectroscopy and high-level quantum mechanical calculations, offering electronic and structural insight into the scarcely studied selenium compounds. The jet-cooled broadband microwave spectrum was measured in the 2–8 GHz cm-wave region using broadband (chirped-pulse)...

Our automated reaction discovery program, AutoMeKin, has been utilized to investigate the formation of glycolonitrile (HOCH$_{2}$CN) in the gas phase under the low temperatures of the interstellar medium (ISM). The feasibility of a proposed pathway depends on the absence of barriers above the energy of reactants and the availability of the suggeste...

The structure and interactions of oxygenated aromatic molecules are of atmospheric interest due to their toxicity and as precursors of aerosols. Here, we present the analysis of 4-methyl-2-nitrophenol (4MNP) using chirped pulse and Fabry–Pérot Fourier transform microwave spectroscopy in combination with quantum chemical calculations. The rotational...

Nitrogen-bearing molecules, like methylamine (CH3NH2), can be the building blocks of amino acids in the interstellar medium (ISM). At the ultralow temperatures of the ISM, it is important to know its gas-phase reactivity towards interstellar radicals and the products formed. In this work, the kinetics of the OH + CH3NH2 reaction was experimentally...

Correction for 'An integrated protocol to study hydrogen abstraction reactions by atomic hydrogen in flexible molecules: application to butanol isomers' by David Ferro-Costas et al., Phys. Chem. Chem. Phys., 2022, DOI: 10.1039/d1cp03928h.

In this work, we introduce , a user-friendly software written in Python 3 and designed to find all the torsional conformers of flexible acyclic molecules in an automatic fashion. For the mapping of the torsional potential energy surface, the algorithm implemented in combines two searching strategies: preconditioned and stochastic. The former is a t...

In this work, we introduce TorsiFlex, a user-friendly software written in Python 3 and designed to find all the torsional conformers of flexible acyclic molecules in an automatic fashion. For the mapping of the torsional potential energy surface, the algorithm implemented in TorsiFlex combines two searching strategies: preconditioned and stochastic...

This work presents a protocol designed to study hydrogen abstraction reactions by atomic hydrogen in molecules with multiple conformations. The protocol starts with the search and location of the conformers of the equilibrium structures using the TorsiFlex program. By a simple modification of the starting geometry of reactants, a Python script gene...

Recent developments of low-temperature techniques are providing valuable knowledge about chemical processes that manifest in the quantum regimen. The tunneling effect from the vibrational ground-state is the main mechanism of these reactions, which usually involves the motion or transfer of hydrogen atoms. Theoretical methods can enrich the informa...

The chapter brings a brief description of semiclassical methods and their application to the calculation of ground-state and state-selected tunnelling splittings, with a special emphasis on the instanton theory. The methodologies are presented following a historical timeline, and in this journey malonaldehyde is the touchstone. For years, malonalde...

Pilgrim is a program written in Python and designed to use direct dynamics in the calculation of thermal rate constants of chemical reactions by the variational transition state theory (VTST), based on electronic structure calculations for the potential energy surface. Pilgrim can also simulate reaction mechanisms using kinetic Monte Carlo (KMC). F...

We propose an algorithm that is a combination of systematic variation of the torsions and Monte Carlo (or stochastic) search. It starts with a trial geometry in internal coordinates and with a set of preconditioned torsional angles, i.e., torsional angles at which minima are expected according to the chemical knowledge. Firstly, the optimization of...

ion from ethanol by atomic hydrogen in aqueous solution is studied using two theoretical approaches; multi-path variational transition state theory (MP-VTST) and a path integral formalism in combination with free-energy perturbation and umbrella sampling (PI-FEP/UM). The performance of the models is compared to experimental values of H kinetic isot...

The Q 2DTor program (Quantum 2-Dimensional Torsions) is designed to calculate accurate rotational–vibrational partition functions (also called rovibrational partition functions) and thermodynamic functions for molecular systems having two [1] or more torsions. Systems with more than two torsions can also be studied by treating the torsions by pairs...

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...

A theoretical study is reported of a system of two identical symmetric hydrogen bonds, weakly coupled such that the two mobile protons can move either separately (stepwise) or together (concerted). It is modeled by two equivalent quartic potentials interacting through dipolar and quadrupolar coupling terms. The tunneling Hamiltonian has two imagina...

In this Reply we answer the two main arguments raised in the Comment. The first argument is related to the binding energy of the methanol dimer and its influence on the dimerization rate constant. We show that the dimerization rate constants calculated in the Comment are unphysically low. We report values that are about two orders of magnitude high...

The OH radical is the most important radical in combustion and in the atmosphere, and methanol is a fuel and antifreeze additive, model biofuel, and trace atmospheric constituent. These reagents are also present in interstellar space. Here we calculate the rate constants, branching ratios, and kinetic isotope effects (KIEs) of the hydrogen abstract...

In this work we present the extended two-dimensional torsion (E2DT) method and use it to analyze the performance of several methods that incorporate torsional anharmonicity more approximately for calculating rotational-vibrational partition functions. Twenty molecules having two hindered rotors were studied for temperatures between 100 and 2500~K....

The kinetics of the reaction of methanol with hydroxyl radicals is revisited in light of the reported new kinetic data, measured in cold expansion beams. The rate constants exhibit an approximately 10(2)-fold increase when the temperature decreases from 200 to 50 K, a result that cannot be fully explained by tunneling, as we confirm by new calculat...

In this work we present a novel application of the two-dimensional non-separable (2D-NS) method to the calculation of torsional tunneling splittings in systems with two hindered internal rotors. This method could be considered an extension of one-dimensional methods for the case of compounds with two tops. The 2D-NS method includes coupling between...

In this work we apply multipath canonical variational transition state theory with small-tunneling corrections (MP-CVT/SCT) to the hydrogen abstraction reaction from ethanol by atomic hydrogen in aqueous solution at room temperature. This reaction presents two transition states which can interconvert by internal rotations about single bonds and ano...

Zero-point and excited level splittings due to double-proton tunneling are calculated for porphycene and the results are compared with experiment. The calculation makes use of a multidimensional imaginary-mode Hamiltonian, diagonalized directly by an effective reduction of its dimensionality. Porphycene has a complex potential energy surface with n...

A multidimensional Hamiltonian for tunneling is formulated, based on the mode with imaginary frequency of the transition state as a reaction coordinate. To prepare it for diagonalization, it is transformed into a lower-dimension Hamiltonian by incorporating modes that move faster than the tunneling into a coordinate-dependent kinetic energy operato...

Dynamics simulations were performed to study soft landing of SiNCS+ and (CH3)2SiNCS+ ions on a self-assembled monolayer of perfluorinated alkanethiols on gold (F-SAM). Using classical trajectories, the short-time collision dynamics (picosecond scale) were investigated to analyze trapping probabilities for these silyl ions. Thermal desorption of tra...

This work reports a detailed theoretical study of the hydrogen abstraction reactions from ethanol by atomic hydrogen. The calculated thermal rate constants take into account torsional anharmonicity and conformational flexibility, in addition to the variational and tunneling effects. Specifically, the kinetics calculations were performed by using mu...

We present the application of an accurate quantum treatment, called two-dimensional non-separable (2D-NS), to the calculation of internal rotation partition functions of molecules with two rotors. This methodology involves full coupling in the kinetic and potential energies; the later is written as a Fourier series type potential. The resulting Ham...

The hydrogen abstraction reaction of fluorine with ammonia represents a true chemical challenge because it is very fast, is followed by secondary abstraction reactions which are also extremely fast, and it presents an experimental/theoretical controversy about rate constants. Using a previously developed full-dimensional analytical potential energy...

Zero-point tunneling splittings are calculated and compared with experiment for four compounds in which the splittings are due to multiple-proton transfer along hydrogen bonds. These compounds are three binary complexes, namely the formic acid and benzoic acid dimer and the 2-pyridone-2-hydroxypyridine complex, in which the protons move in pairs, a...

The enol-keto transition rate constants in 2 '-methylacetophenone observed by Grellmann et al. [3] are calculated from first principles. The results reinterpret the proposed mechanism and show that proton tunneling is preceded by dissociation of a substrate-solvent complex rather than by rotamer interconversion.

The correct interpretation is provided of how tunneling proceeds at low temperatures in the proton transfer Reactions (1) and (3) involving thiotropolone and tropolone (see the Arrhenius plots). It is also shown that the variational transition-state theory calculations carried out by Jose and Datta (Angew. Chem. 2012, 124, 9523; Angew. Chem. Int. E...

Five symmetry-based selection rules are formulated that relate the tunneling splitting of a vibrationally excited level to that of the ground level in molecules with a symmetric double-minimum potential. The rules, which explain why excited levels frequently have smaller splittings than zero-point levels, are used to interpret the observed and calc...

The tunneling splitting associated with double proton transfer recently observed in the dimeric complex 2-pyridone · 2-hydroxypyridine is studied theoretically. Direct dynamics calculations based on the approximate instanton method applied to a multidimensional potential-energy surface evaluated at the DFT-B3LYP/6-311++G(d,p) level satisfactorily r...

This work presents an accurate way for calculating partition functions of strongly coupled hindered rotors in two dimensions. The two-dimensional torsional potential is generated from electronic structure calculations and fitted to Fourier series. The kinetic energy includes off-diagonal terms which are allowed to vary with the torsional angles, an...

A new instanton approach is reported to tunneling at zero-temperature in multidimensional (MD) systems in which a "light particle" is transferred between two equivalent "heavy" sites. The method is based on two concepts. The first is that an adequate MD potential energy surface can be generated from input of the stationary configurations only, by c...

The thermal isomerization reaction converting previtamin D to vitamin D is an intramolecular [1,7]-sigmatropic hydrogen shift with antarafacial stereochemistry. We have studied the dynamics of this reaction by means of the variational transition-state theory with multidimensional corrections for tunneling in both gas-phase and n-hexane environments...

We report a detailed theoretical study of the hydrogen abstraction reaction from methanol by atomic hydrogen. The study includes the analysis of thermal rate constants, branching ratios, and kinetic isotope effects. Specifically, we have performed high-level computations at the MC3BB level together with direct dynamics calculations by canonical var...

In this review we discuss a recently introduced method of calculating hydrogen tunnelling rates and tunnelling splittings in medium and large molecules. It is a non-empirical, direct-dynamics method that uses ab initio quantum-chemical output as input data for the calculation of dynamic properties by means of the instanton approach. This approach i...

We present two new direct dynamics algorithms for calculating transmission coefficients of polyatomic chemical reactions by the multidimensional least-action tunneling approximation. The new algorithms are called the interpolated least-action tunneling method based on one-dimensional interpolation (ILAT1D) and the double interpolated least-action t...

The accurate evaluation of quantum effects is of great importance in many reaction processes. Variational transition state theory with multidimensional tunneling is the natural choice for the study of these reactions, because it incorporates quantum effects through a multiplicative transmission coefficient and it can deal with large systems. Curren...

We present a new least-action variational approximation for tunneling in polyatomic reactions based on the procedure developed by Garrett and Truhlar for atom−diatom reactions.(63) The method calculates the semiclassical ground-state tunneling probability at every tunneling energy by minimizing the value of imaginary action integral along a family...

An analytical two-dimensional (2D) potential-energy surface based on two equal hydrogen bonds coupled by a correlation term. recently introduced [J. Chem. Phys. 127 (2007) 174513] to describe the dynamics of double proton transfer, is reviewed and generalized. It is then applied to the evaluation of proton transfer dynamics in a number of realistic...

The reversed order of the levels in which a CO-stretch fundamental in the formic acid dimer is split, as recently observed and ascribed to perturbation by a nearby state, is interpreted as due to accidental degeneracy between the CO-stretch level and a combination level. This interpretation allows a proper assessment of the hindering effect of anti...

The dynamics of double-proton transfer reactions is studied on a model of transfer along two identical hydrogen bonds represented by quartic double-minimum potentials. Correlation between the proton motions is introduced by a coupling term that is bilinear in the two proton coordinates; it is shown that this form properly accounts for the polarity...

This article shows how to evaluate rotational symmetry numbers for different molecular configurations and how to apply them to transition state theory. In general, the symmetry number is given by the ratio of the reactant and transition state rotational symmetry numbers. However, special care is advised in the evaluation of symmetry numbers in the...

Multiconfigurational CASSCF and CASPT2 calculations were performed to investigate the enol --> keto tautomerization in the lowest singlet excited state of the 7-hydroxyquinoline.(NH3)3 cluster. Two different reaction mechanisms were explored. The first one corresponds to that proposed previously by Tanner et al. (Science 2003, 302, 1736) on the bas...

To determine whether the tautomerization of porphycene is a concerted or a stepwise process, we characterize its stationary points on the potential energy surface employing density functional theory as well as M?ller-Plesset perturbation theory, and calculate proton-transfer rates and the zero-level tunneling splitting using the approximate instant...

Direct-dynamics canonical variational transition-state theory calculations with microcanonically optimized multidimensional transmission coefficient (CVT/muOMT) for tunneling were carried out at the MPWB1K/6-31+G(d,p) level to study the [1,7] sigmatropic hydrogen rearrangement in 7-methylocta-1,3(Z),5(Z)-triene. This compound has seven conformers,...

This review describes the application of variational transition state theory (VTST) to the calculation of chemical reaction rates. In 1985 two of us, together with Alan D. Isaacson, wrote a book chapter on this subject entitled âGeneralized Transition State Theory❠for the multi-volume series entitled Theory of Chemical Reaction Dynamics.1 Since t...

A review of the theoretical and computational modeling of bimolecular reactions is given. The review is divided into several sections which are as follows: gas-phase thermal reactions; gas-phase state-selected reactions and product state distributions; and condensed-phase bimolecular reactions. The section on gas-phase thermal reactions covers the...

Protons, like electrons, are light enough to tunnel through potential-energy barriers, an ability that provides them with a high mobility. However, while electrons can jump over distances of 10 Å or more, proton jumps are typically limited to 1 to 1.5 Å. Nevertheless, protons manage to travel over much larger distances, e.g., across cell membranes....

Deuterium-labeling of substrates is an effective way to gather information on enzymatic reactions involving hydrogen transfer. If deuterium substitution reduces the rate of the reaction substantially, it implies that hydrogen transfer is a rate-determining step and that this step proceeds by quantummechanical tunneling. Large kinetic effects of deu...

An ab initio interpolated potential energy surface (PES) for the F + CH4 reactive system has been constructed using the interpolation method of Collins and co-workers. The ab initio calculations have been performed using second-order Möller-Plesset (MP2) perturbation theory to build the initial PES. Scaling all correlation (SAC) methodology has bee...

Quasiclassical trajectory calculations are employed to investigate the dynamics of collision-induced dissociation (CID) of Cr(CO)6 + with Xe atoms at collision energies ranging from 1.3 to 5.0 eV. The trajectory simulations show that direct elimination of CO ligands, during the collision, becomes increasingly important as the collision energy incre...

We present a new algorithm for carrying out large-curvature tunneling calculations that account for extreme corner-cutting tunneling in hydrogen atom, proton, and hydride transfer reactions. The algorithm is based on two-dimensional interpolation in a physically motived set of variables that span the space of tunneling paths and tunneling energies....

Large-scale classical trajectory calculations have been performed to study the reaction Ar + CH4--> CH3 +H + Ar in the temperature range 2500 < or = T/K < or = 4500. The potential energy surface used for ArCH4 is the sum of the nonbonding pairwise potentials of Hase and collaborators (J. Chem. Phys. 2001, 114, 535) that models the intermolecular in...

Direct dynamics calculations based on instanton techniques are reported of tunneling splittings due to double proton transfer in formic and benzoic acid dimers. The results are used to assign the observed splittings to levels for which the authors of the high-resolution spectra could not provide a definitive assignment. In both cases the splitting...

A direct dynamics calculation based on instanton techniques is reported of tunneling splittings in the formic acid dimer and its deuterated isotopomers for the zero-point level and the lowest vibrationally excited level of a nontotally symmetric CO-stretch vibration. A new method is introduced to calculate the effect of anharmonic couplings for ske...

Tunneling splittings have been observed in the eigenstate-resolved electronic spectrum of the 2-hydroxypyridine/2-pyridone dimer in the gas phase. Deuterium substitution experiments show that these splittings are caused by a concerted double proton transfer reaction along the O-H...O and N...H-N hydrogen bonds that hold the dimer together, substitu...

Product energy distributions (PEDs) for the photodissociation of acetone at 266, 248, and 193 nm were evaluated by direct classical trajectory calculations on the lowest triplet potential energy surface. CASSCF(8,7) and MRCI+Q calculations were first performed to obtain a set of high-level ab initio data with which the semiempirical parameters were...

The near threshold photodissociation of propanal via the HCO+C 2H5 channel on the triplet surface is studied by direct PM3-SRP classical trajectory calculations. The initial conditions for the trajectories are selected by either the quasi-classical or the Wigner distribution function. The HCO translational energy and rotational distributions obtain...

Direct AM1 with specific reaction parameters (AM1-SRP) trajectory calculations were performed to investigate the photodissociation of vinyl chloride at 193 nm. Marked differences were found between the trajectories run from the transition states to the products for the four-center (4C) and three-center (3C) dissociation channels. The average intern...

Photodissociation of acetaldehyde at 308 nm via the radical CH3 + HCO channel has been studied on the triplet state surface by DFT classical trajectory calculations using the B3LYP/6-31G* electronic structure method. A rotational analysis of product HCO predicts a non-Boltzmann distribution and that the energy is partitioned preferentially along th...

Direct quasi-classical trajectories were carried out to calculate translational energy distributions, P(E T ), for the elimination of molecular hydrogen from 1,1- and 1,2-difluoroethylene (DFE) at 193 nm. A reasonably good agreement is found between the calculated and the experimental distributions. The calculations corroborate that the elimination...

Thermal rate constants and H/D kinetic isotope effects for the Cl+C2H6→HCl+C2H5 reaction were computed by microcanonical variational transition state theory on a high-level ab initio potential energy surface (PES). The calculations show that the reaction proceeds through a “loose” transition state, and so the consideration of variational effects is...

The photodissociation of ethylene at 193 nm was studied by a B3LYP/6-31G(d) direct trajectory method, in which the trajectories were initialized from the two exit barriers associated to molecular hydrogen formation. The calculated translational energies and the H 2 rotational and vibrational states distributions are in good agreement with the exper...

A global ground-state potential energy surface for the dissociation reactions of difluoroethylenes (DFEs) was computed by B3LYP and QCISD calculations, using the standard 6-311G(2d,2p) basis set. RRKM calculations were performed to compute relative abundances of hydrogen fluoride (HF) and molecular hydrogen produced from 1,1-DFE and from 1,2-DFE (c...

Direct dynamics calculations on the HF elimination channels from cis- and trans-1,2-difluorotethylene (1,2-DFE) were carried out considering five different elimination mechanisms involving four-center and three-center eliminations and also H atom migrations from the cis and trans isomers. The results were compared with experimental HF vibrational s...

The rate constant of the reaction catalyzed by the enzyme carbonic anhydrase II, which removes carbon dioxide from body fluids, is calculated for a model of the active site. The rate-determining step is proton transfer from a zinc-bound water molecule to a histidine residue via a bridge of two or more water molecules. The structure of the active si...

Abstract: Rate constants and kinetic isotope effects for the 1,2-H shift of methoxyl and benzyloxyl radicals were studied in the presence of water molecules. The electronic structure calculations were carried out at the UB3LYP/6-31G* level, and the dynamics calculations were performed using the variational transition state theory with semiclassical...

The linearized initial value representation (LIVR) method introduces barrier recrossing and tunneling effects into dynamics calculations based on classical trajectories. Provided the barrier can be approximated by an inverted parabola, the corrections, implemented by using the Wigner distribution of initial coordinates and momenta as a weighting fu...

Rate constants for Cl + CH4 → ClH + CH3 (forward and reverse reactions) were computed by the linearized semiclassical-initial value representation (LSC-IVR) method. Also, the H/D kinetic isotope effects for the forward reaction were calculated. Two statistical theories, specifically, conventional transition state theory (TST) and canonical unified...

We present a new algorithm for carrying out large-curvature tunneling (LCT) calculations. The new algorithm, called interpolated LCT (or ILCT) is based on interpolation by splines under tension. It is tested on five hydrogen-atom transfer reactions. We find that the cost of LCT calculations can be reduced by more than an order of magnitude.

Ab initio density functional theory and approximate instanton methods are used to study proton transfer processes in the first excited electronic state of 3,6-bis(benzoxazolyl)pyrocatechol (BBPC). Geometries of di-enol, keto-enol, and di-ketone tautomers as well as transition states for single and double proton transfer processes and the correspond...

We present a new algorithm for carrying out large-curvature tunneling (LCT) calculations. The new algorithm, called interpolated LCT (or ILCT) is based on interpolation by splines under tension. It is tested on five hydrogen-atom transfer reactions. We find that the cost of LCT calculations can be reduced by more than an order of magnitude.

The variational transition state theory (VTST) is used to calculate thermal rate constants for the reactions H + O3 → OH + O2 (R1) and O + HO2 → OH + O2 (R2). Both reactions are studied using a double many-body expansion (DMBE) potential energy surface for ground state HO3. The VTST results are compared with quasiclassical trajectory calculations (...

Reaction paths are calculated for a simple model for RNA cleavage catalyzed by large ribozymes. Stationary structures and energies are compared for uncatalyzed solvolysis induced by methanol and methoxide anion in the gas phase with special emphasis on the proposed catalytic effect of internal hydrogen bonding in the ribose moiety at the cleavage s...

The structure, energetics and vibrational force field of calix[4]arene (CA) are calculated for the chiral equilibrium configuration and the symmetric transition state for coherent quadruple proton transfer. The corresponding proton and deuteron tunneling splittings are evaluated with the instanton approach. The calculated zero-point proton tunnelin...

Rate constants and kinetic isotope effects are calculated for the CH3+H2→CH4+H reaction by two theoretical methods: variational transition state theory with semiclassical corrections for tunneling and an approximate (linearized) semiclassical initial-value representation method, recently proposed by H. Wang, X. Sun, W.H. Miller [J. Chem. Phys. 108...