# Emilio Martinez-NuñezUniversity of Santiago de Compostela | USC · Department of Physical Chemistry

Emilio Martinez-Nuñez

Dr

## About

133

Publications

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2,305

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Introduction

Automated discovery of reaction mechanisms

Additional affiliations

July 2007 - September 2007

September 2005 - October 2005

June 2005 - July 2005

## Publications

Publications (133)

A novel computational method to discover reaction mechanisms and solve the kinetics of transition metal-catalyzed reactions is proposed in the present work. The method does not rely on neither chemical intuition nor on assumed a priori mechanisms, working in a fully automated fashion. Its core is a procedure recently developed by one of the authors...

The potential energy surface of protonated uracil has been explored with an automated transition state search procedure, resulting in the finding of 1398 stationary points and 751 reactive channels, which can be categorized into isomerizations between pairs of isomers, unimolecular fragmentations and bimolecular reactions. The use of statistical Ri...

A procedure to automatically find the transition states (TSs) of a molecular system (MS) is proposed. It has two components: high-energy chemical dynamics simulations (CDS), and an algorithm that analyzes the geometries along the trajectories to find reactive pathways. Two levels of electronic structure calculations are involved: a low level (LL) i...

Very recently, we proposed an automated method for finding transition states of chemical reactions using dynamics simulations; the method has been termed Transition State Search using Chemical Dynamics Simulations (TSSCDS) (E. Martínez-Núñez, J. Comput. Chem., 2015, 36, 222-234). In the present work, an improved automated search procedure is develo...

Large-scale trajectory simulations of different projectiles colliding with an organic surface, as well as a gas−surface model for energy transfer, are employed to investigate the effects of the mass, size, shape, and vibrational frequency(ies) of the projectile and of the projectile−surface interaction potential on the energy-transfer dynamics. The...

Different machine learning (ML) models are proposed in the present work to predict density functional theory-quality barrier heights (BHs) from semiempirical quantum mechanical (SQM) calculations. The ML models include a multitask deep neural network, gradient-boosted trees by means of the XGBoost interface, and Gaussian process regression. The obt...

Several dimerization products of fullerene C60 are presented and thoroughly characterized with a quantum chemical DFT model augmented by dispersion. We reanalyze and expand significantly the number of known dimers from 12 to 41. Many of the novel bonding schemes were found by analyzing more than 2 nanoseconds of high energy molecular dynamics semie...

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...

Different machine learning (ML) models are proposed in the present work to predict DFT-quality barrier heights (BHs) from semiempirical quantum-mechanical (SQM) calculations. The ML models include multi-task deep neural network, gradient boosted trees by means of the XGBoost interface, and Gaussian process regression. The obtained mean absolute err...

The level of detail attained in the computational description of reaction mechanisms can be vastly improved through tools for automated chemical space exploration, particularly for systems of small to medium size. Under this approach, the unimolecular decomposition landscape for indole was explored through the automated reaction mechanism discovery...

The photoisomerization behavior of styryl 9M, a common dye used in material sciences, is investigated using tandem ion mobility spectrometry (IMS) coupled with laser spectroscopy. Styryl 9M has two alkene linkages, potentially allowing for four geometric isomers. IMS measurements demonstrate that at least three geometric isomers are generated using...

AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922). This release features a number of new capabilities: rare‐event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complexes, u...

AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922-1930). This release features a number of new capabilities: rare-event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complex...

A new approach is presented to improve the performance of semiempirical quantum mechanical (SQM) methods in the description of noncovalent interactions. To show the strategy, the PM6 Hamiltonian was selected, although, in general, the procedure can be applied to other semiempirical Hamiltonians and to different methodologies. In this way, analytica...

In many scientific fields, there is an interest in understanding the way in which complex chemical networks evolve. The chemical networks which researchers focus upon, have become increasingly complex and this has motivated the development of automated methods for exploring chemical reactivity or conformational change in a black box manner, harness...

Clocking of electronically and vibrationally state-resolved channels of the fast photodissociation of CH3I in the A-band is reexamined in a combined experimental and theoretical study. Experimentally, a femtosecond pump-probe scheme is employed in the modality of resonant probing by REMPI of the methyl fragment in different vibra- tional states and...

AutoMeKin is an automated reaction discovery tool.
This web server (https://rxnkin.usc.es/amk/) allows you to unravel the reaction mechanisms (with intermediates and transition states) of your system, just providing an equilibrium structure (reactant). As a bonus, you will also obtain kinetics results at the desired temperature or energy. The full...

The rare event acceleration method BXDE is interfaced in the present work with the automated reaction discovery method AutoMeKin. To test the efficiency of the combined AutoMeKin-BXDE procedure, the ozonolysis of a-pinene is studied in comparison with standard AutoMeKin. AutoMeKin-BXDE locates intermediates and transition states that are more dense...

The rare event acceleration method “Boxed Molecular Dynamics in Energy space” (BXDE) is interfaced in the present work with the automated reaction discovery method AutoMeKin. To test the efficiency of the combined AutoMeKin‐BXDE procedure, the ozonolysis of α‐pinene is studied in comparison with standard AutoMeKin. AutoMeKin‐BXDE locates intermedia...

We present Specific Reaction Parameter Multigrid POTFIT (SRP-MGPF), an automated methodology for the generation of global potential energy surfaces (PES), molecular properties surfaces, e.g. dipole, polarizabilities, etc. using a single random geometry as input. The SRP-MGPF workflow integrates: (i) a fully automated procedure for the global topogr...

We present a generalization of the transition state search using chemical dynamics simulations (TSSCDS) methodology (discussed in a previous study) which allows the topographical characterization of intermolecular potential energy surfaces (IPES) for non‐covalently bound complexes (vdW‐TSSCDS). Starting from a single random input geometry, we show...

We aim at simulating full quantum mechanically (nuclei and electrons) the processes of adsorption and photoreactivity of NO2 adsorbed on soot (modeled as large Polycyclic Aromatic Hydrocarbons, PAHs) in atmospheric conditions. A detailed description of these processes is necessary to understand the differential day-nighttime behavior of the product...

Low-energy collision induced dissociation (CID) of deprotonated L-cysteine S-sulfate, [cysS-SO3]⁻, delivered in the gas phase by electrospray ionization, has been found to provide a means to form deprotonated L-cysteine sulfenic acid, a fleeting intermediate in biological media. The reaction mechanism underlying this process is the focus of the pre...

The tsscds method, recently developed in our group, discovers chemical reaction mechanisms with minimal human intervention. It employs accelerated molecular dynamics, spectral graph theory, statistical rate theory and stochastic simulations to uncover chemical reaction paths and to solve the kinetics at the experimental conditions. In the present r...

The tsscds method, recently developed in our group, discovers chemical reaction mechanisms with minimal human intervention. It employs accelerated molecular dynamics, spectral graph theory, statistical rate theory and stochastic simulations to uncover chemical reaction paths and to solve the kinetics at the experimental conditions. In the present r...

The method tsscds, recently developed in our group, discovers chemical reaction mechanisms with minimal human intervention. It employs accelerated molecular dynamics, spectral graph theory, statistical rate theory and stochastic simulations to uncover chemical reaction paths and to solve the kinetics at the experimental conditions. In the present r...

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 code for the automated discovery of reaction mechanisms

To understand and simulate the dynamics behaviour of the title reaction, QCT calculations were performed on a recently developed global analytical potential energy surface, PES-2017. These calculations combine the classical description of the dynamics with pseudo-quantization in the reactants and products to perform a theoretical/experimental compa...

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...

Motivated by the possibility that cyano containing hydrocarbons may act as photolytic sources for HCN and HNC in astrophysical environments, we conducted a combined experimental and theoretical investigation of the 193 nm photolysis of the cyano-ester, methyl cyanoformate (MCF). Experimentally, nanosecond time-resolved infrared emission spectroscop...

In this Introduction, we show the basic problems of non-statistical and non-equilibrium phenomena related to the papers collected in this themed issue. Over the past few years, significant advances in both computing power and development of theories have allowed the study of larger systems, increasing the time length of simulations and improving th...

GAFit is a computational package for non-linear fitting purposes, which is equipped with several graphical tools that help the user to prepare the input files and visualize the output results. Examples of applications:
1) Potential energy surfaces and force-field parameterizations.
2) Specific reaction parameters of a semiempirical Hamiltonian.
3)...

We have developed a software package based on a genetic algorithm that fits an analytic function to a given set of data points. The code, called GAFit, was also interfaced with the CHARMM and MOPAC programs in order to facilitate force field parameterizations and fittings of specific reaction parameters (SRP) for semiempirical Hamiltonians. The pre...

The effect of the metal ion and ligand design on the enantioselectivity and linkage isomerization of neutral cobalt and zinc bisthiosemicarbazone metallohelicates has been investigated in this work. The electrochemical synthesis has afforded the enantioselective formation of chiral pure cobalt helicates, and the isomer of a single enantiomer ha...

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...

We present a combined experimental and theoretical investigation of the 193 nm photolysis of the cyano-ester, methyl cyanoformate (MCF). Specifically, nanosecond time-resolved infrared emission spectroscopy was used to monitor the ro-vibrationally excited photoproducts generated in the photolysis reaction. The signal-to-noise of all time-resolved s...

The ground electronic state potential energy surface of acryloyl chloride, CH2CHC(O)Cl, has been mapped using an automated transition state search procedure. A total of 174 minima, 527 TSs, and 20 different dissociation channels have been found. Among others, three novel HCl elimination pathways, namely, a five-center mechanism and two three-body d...

The ground electronic state potential energy surface of acryloyl chloride, CH 2 CHC(O)Cl, has been mapped using an automated transition state search procedure. A total of 174 minima, 527 TSs, and 20 different dissociation channels have been found. Among others, three novel HCl elimination pathways, namely, a five-center mechanism and two three-body...

Mechanistic pathways for the cyclization of 1,5-alkynylacetal with N2CHTMS in the presence of Cp- and Cp RuCl(cod) to afford (Z)- and (E)-(trimethylsilyl)vinyl spiroacetals have been calculated. Calculations show the presence of three conformers in equilibrium for the initially formed ruthenium carbenes. Differences in the stabilities and reactivit...

The different HCN elimination pathways from vinyl cyanide (VCN) are studied in this paper using RRKM, Kinetic Monte Carlo (KMC), and quasi-classical trajectory (QCT) calculations. A new HCN elimination pathway proves to be very competitive with the traditional 3-center and 4-center mechanisms, particularly at low excitation energies. However, low e...

In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to p...

In this article we briefly review the Boxed Molecular Dynamics (BXD) method, which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this article, we review previous applications of BXD...

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...

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...

The collision-induced dissociation (CID) of the [Li(uracil)](+) complex with Xe is studied by means of quasi-classical trajectory calculations. The potential energy surface is obtained "on the fly" from AM1 semiempirical calculations, supplemented with two-body analytical potentials to model the intermolecular interactions. The simulations show tha...

A modification of the energy transfer model recently proposed by two of us (ref 4) is tested in this work by an extensive comparison with the simulation results for O3 scattering from a perfluorinated self-assembled monolayer (F-SAM) as well as with previous NO + FSAM and Ar + F-SAM scattering results. The model fits very well the trajectory data o...

Analytical potential energy functions were developed for interactions of SiNCS+ and (CH3)2SiNCS+ ions with perfluorinated self-assembled monolayer (F-SAM) surfaces. Two model compounds were used to represent an F-SAM: CF4 and nine chains of perfluorobutane forming a miniSAM structure. Density functional theory plus dispersion (DFT-D) calculations w...

In this paper, the dynamics of NO scattering off a perfluorinated self-assembled monolayer was studied by means of chemical dynamics simulations. An analytical function was developed for the interaction between the projectile and the surface, based on focal point-CCSD(T)/CBS ab initio results. The trajectories that perform a minimum number of moder...

We present a semiempirical Hamiltonian that provides an accurate description of the first singlet and triplet potential energy surfaces of azobenzene for use in direct simulations of the excited-state dynamics. The parameterization made use of spectroscopic and thermochemical data and the best ab initio results available to date. Two-dimensional po...

Ab initio CCSD and CCSD(T) calculations with the 6-311+G(2d,2p) and the 6-311++G(3df,3pd) basis sets were carried out to characterize the vinyl cyanide (C(3)H(3)N) dissociation channels leading to hydrogen cyanide (HCN) and its isomer hydrogen isocyanide (HNC). Our computations predict three elimination channels giving rise to HCN and another four...

A laser flash photolysis technique and quasi-classical trajectory (QCT) calculations have been used to determine the rate coefficients for the title process. The experimental high-pressure-limiting rate coefficient is 7.0 x 10(-11) cm(3) s(-1) at T = 300 K, which compares with the computed QCT value for the Mg(+) + H(2)O capture rate of 2.75 +/- 0....

In this paper, we present classical and coupled coherent states quantum dynamics simulations to investigate intramolecular vibrational energy redistribution (IVR) from an excited (v = 1-10) OH stretch within the HOSO(2) complex to the other molecular bath modes. Using an analytical PES derived from electronic structure theory calculations, the resu...

The dynamics of collisions of CO2 with a perfluorinated alkanethiol self-assembled monolayer (F-SAM) on gold were investigated by classical trajectory calculations using explicit atom (EA) and united atom (UA) models to represent the F-SAM surface. The CO2 molecule was directed perpendicularly to the surface at initial collision energies of 1.6, 4....

Following photodissociation of 2-chloropropene (H(2)CCClCH(3)) at 193 nm, vibration-rotationally resolved emission spectra of HCl (upsilon < or = 6) in the spectral region of 1900-2900 cm(-1) were recorded with a step-scan time-resolved Fourier-transform spectrometer. All vibrational levels show a small low-J component corresponding to approximatel...

Quasiclassical trajectory (QCT) calculations were carried out to evaluate relative translational energy distributions, P(Et), of the HF elimination that takes place in the photodissociation of fluorobenzene. Three excitation energies were selected, which correspond to photon wavelengths of 248, 193, and 157 nm. The trajectories were initiated at th...

Dynamics of Ar atom collisions with a perfluorinated alkanethiol self-assembled monolayer (F-SAM) surface on gold were investigated by classical trajectory simulations and atomic beam scattering techniques. Both explicit-atom (EA) and united-atom (UA) models were used to represent the F-SAM surface; in the UA model, the CF3 and CF2 units are repres...

Linear molecules with degenerate bending modes have states, which may be represented by the quantum numbers N and L. The former gives the total energy for these modes and the latter identifies their vibrational angular momentum jz. In this work, the classical mechanical analog of the N,L-quantum states is reviewed, and an algorithm is presented for...

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...

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,...

Electronic structure calculations (MP2, B3LYP, and MC3BB) were performed to characterize the stationary points involved in the elimination of HX (X = F, Cl) from chlorofluoroethylene. The calculations predict 10 different HX elimination channels, being the HF elimination energetically favoured over the HCl elimination. The relative product abundanc...

Chemical dynamics simulations at collision energies of 3.0, 10.6, and 20.0 kcal/mol were performed to study energy transfer in perpendicular (θi = 0°) collisions of carbon dioxide with a perfluorinated octanethiol self-assembled monolayer (F-SAM) surface. An accurate carbon dioxide + F-SAM intermolecular potential was developed from ab initio calcu...

The three-center (3C) and four-center (4C) HBr eliminations in the photodissociation of vinyl bromide at 193 nm were investigated by direct quasiclassical trajectory (QCT) calculations using a semiempirical AM1 Hamiltonian with specific reaction parameters. The trajectories were initiated at the corresponding transition states under microcanonical...

We investigate the role of vibrational energy excitation of methane and two deuterated species (CD(4) and CH(2)D(2)) in the collision-induced dissociation (CID) process with argon at hyperthermal energies. The quasi-classical trajectory method has been applied, and the reactive Ar + CH(4) system has been modeled by using a modified version of the C...

In this article phase space constrained classical mechanics (PSCCM), a version of accelerated dynamics, is suggested to speed up classical trajectory simulations of slow chemical processes. The approach is based on introducing constraints which lock trajectories in the region of the phase space close to the dividing surface, which separates reactan...

Classical trajectory calculations have been performed to investigate the collision-induced dissociation (CID) of the CH(3)SH(+) cation with Ar atoms. A new intramolecular potential energy surface for the CH(3)SH(+) cation is evaluated by interpolation of 3000 ab initio data points calculated at the MP2/6-311G(d,p) level of theory. The new potential...

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...

Non-adiabatic direct dynamics calculations were carried out to investigate the radical and molecular decomposition channels of formic acid. The calculations show, in agreement with experiment, that the HCO + OH dissociation channel accounts for similar to 70% of the product yields. In addition, the molecular eliminations of CO and CO2 are minor cha...

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...