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Panadés-Barrueta RL, Duflot D, Soto J, Martínez-Núñez E, Peláez D. Automatic Determination of the Non-Covalent Stable Conformations of the NO 2-Pyrene Cluster in Full Dimensionality (81D) Using the vdW-TSSCDS Approach. Chemphyschem 2024; 25:e202301001. [PMID: 38662437 DOI: 10.1002/cphc.202301001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/27/2024] [Indexed: 05/24/2024]
Abstract
We present the detailed topographical characterisation (stationary points and minimum energy paths connecting them) of the full dimensional (81D) intermolecular potential energy surface associated with the non-covalent interactions between the NO2 radical and the pyrene (C16H10) molecule. The whole procedure is (quasi) fully automated. We have used our recent algorithm vdW-TSSCDS as implemented on the freely-available AutoMekin software package. To this end, a series of inexpensive classical trajectories using forces from a low-level (semi-empirical) theory are used to sample the configuration space of the system in the search for candidates to first order saddle points. These guess structures are determined by means of a graph-theory based algorithm using the concept of adjacency matrix. Low-level optimizations are followed by re-optimizations at a final high-level of theory (DFT and CCSD(T)-F12 in our case.). The resulting set of stationary points and paths connecting them constitutes the so-called reaction network. In the case of NO2-pyrene, this network exhibits four major basins which can be characterized by their point-group symmetry. A central one, of global C2 symmetry, comprises the global minimum (as well as all other permutationally related conformers) together with the corresponding C2v saddle points connecting them. This central basin is connected to three others of lower C1 symmetry. The latter can be distinguished by the projection of the position of the NO2 nitrogen atom on the pyrene plane in combination with the relative orientation of the oxygen pair pointing either inwards, outwards, upwards or downwards.
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González D, Canosa A, Martínez-Núñez E, Fernández-Ramos A, Ballesteros B, Agúndez M, Cernicharo J, Jiménez E. Effect of temperature on the gas-phase reaction of CH 3CN with OH radicals: experimental ( T = 11.7-177.5 K) and computational ( T = 10-400 K) kinetic study. Phys Chem Chem Phys 2024; 26:3632-3646. [PMID: 38224163 DOI: 10.1039/d3cp04944b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Acetonitrile (CH3CN) 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 the experimental handicap of getting organic molecules in the gas phase by conventional techniques. The CRESU (French acronym for Reaction Kinetics in a Uniform Supersonic Flow) technique solves this problem. For this reason, we present in this work the kinetic study of the gas-phase reaction of CH3CN with one of the most ubiquitous radicals, the hydroxyl (OH) radical, as a function of temperature (11.7-177.5 K). The kinetic technique employed to investigate the CH3CN + OH reaction was the pulsed laser photolysis-laser induced fluorescence. The rate coefficient for this reaction k(T) has been observed to drastically increase from 177.5 K to 107.0 K (about 2 orders of magnitude), while the increase in k(T) from 107.0 K to 11.7 K was milder (around 4 times). The temperature dependent expressions for k(T) are provided in the two distinct T-ranges, excluding the upper limit obtained for k(177.5 K): In addition, the rate coefficients estimated by the canonical competitive unified statistical (CCUS) theory show a similar behaviour to the experimental results, when evaluated within the high-pressure limit. This is consistent with the experimentally observed independence of k(T) with total gas density at selected temperatures. Astrochemical networks, such as the KIDA database or UMIST, do not include the CH3CN + OH reaction as a potential depletion process for acetonitrile in the ISM because the current studies predict very low rate coefficients at IS temperatures. According to the model (T = 10 K), the impact of the titled reaction on the abundances of CH3CN appears to be negligible in dark molecular clouds of the ISM (∼1% of the total depletion reactions included in UMIST network). With respect to the potential formation of the CH2CN radical in those environments, even in the most favourable scenario, where this radical could be formed in a 100% yield from the CH3CN + OH reaction, this route would only contribute around 2% to the current assumed formation routes by the UMIST network.
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Ballotta B, Martínez-Núñez E, Rampino S, Barone V. New prebiotic molecules in the interstellar medium from the reaction between vinyl alcohol and CN radicals: unsupervised reaction mechanism discovery, accurate electronic structure calculations and kinetic simulations. Phys Chem Chem Phys 2023; 25:22840-22850. [PMID: 37584420 DOI: 10.1039/d3cp02571c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Vinyl alcohol (VyA) and cyanide (CN) radicals are relatively abundant in the interstellar medium (ISM). VyA is the enolic tautomer of acetaldehyde and has two low-lying conformers, characterized by the syn or anti placement of hydroxyl hydrogen with respect to the double bond. In this paper, we present a gas-phase model of the barrierless reactions of both VyA's conformers with CN employing accurate quantum chemical computations in the framework of a master equation approach based on the transition state theory. Our results indicate that both VyA conformers feature a similar reactivity with CN, starting with a barrierless addition to the double bond and followed by different isomerization, dissociation, and/or hydrogen elimination steps. The rate constants computed for temperatures up to 600 K show that several reaction channels are open even under the harsh conditions of the ISM, with the favoured one providing the first feasible formation route of a prebiotic molecule not yet detected in the ISM, namely cyanoacetaldehyde. This finding suggests looking for cyanoacetaldehyde in regions where both VyA and CN have already been detected, like, e.g., Sagittarius B2N or G+0.693-0.027.
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Guerrero-Méndez L, Lema-Saavedra A, Jiménez E, Fernández-Ramos A, Martínez-Núñez E. Gas-phase formation of glycolonitrile in the interstellar medium. Phys Chem Chem Phys 2023; 25:20988-20996. [PMID: 37503548 DOI: 10.1039/d3cp02379f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
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 precursors in the ISM. Based on these criteria, several radical-radical reactions and a radical-molecule reaction have been identified as viable formation routes in the ISM. Among the radical-radical reactions, OH + CH2CN appears to be the most relevant, considering the energy of the radicals and its ability to produce glycolonitrile in a single step. However, our analysis reveals that this reaction produces hydrogen isocyanide (HNC) and formaldehyde (CH2O), with rate coefficients ranging from (7.3-11.5) × 10-10 cm3 molecule-1 s-1 across the temperature range of 10-150 K. Furthermore, the identification of this remarkably efficient pathway for HNC elimination from glycolonitrile significantly broadens the possibilities for any radical-radical mechanism proposed in our research to be considered as a feasible pathway for the formation of HNC in the ISM. This finding is particularly interesing given the persistently unexplained overabundance of hydrogen isocyanide in the ISM. Among the radical-molecule reactions investigated, the most promising one is OH + CH2CHNH, which forms glycolonitrile and atomic hydrogen with rate coefficients in the range (0.3-6.6) × 10-10 cm3 molecule-1 s-1 within the 10-150 K temperature range. Our calculations indicate that the formation of both hydrogen isocyanide and glycolonitrile is efficient under the harsh conditions of the ISM.
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González D, Lema-Saavedra A, Espinosa S, Martínez-Núñez E, Fernández-Ramos A, Canosa A, Ballesteros B, Jiménez E. Reaction of OH radicals with CH 3NH 2 in the gas phase: experimental (11.7-177.5 K) and computed rate coefficients (10-1000 K). Phys Chem Chem Phys 2022; 24:23593-23601. [PMID: 36134502 DOI: 10.1039/d2cp03414j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
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 and theoretically investigated at low- and high-pressure limits (LPL and HPL) between 10 and 1000 K. Moreover, the CH2NH2 and CH3NH yields were computed in the same temperature range for both pressure regimes. A pulsed CRESU (French acronym for Reaction Kinetics in a Uniform Supersonic Flow) apparatus was employed to determine the rate coefficient, k(T), in the 11.7-177.5 K range. A drastic increase of k(T) when the temperature is lowered was observed in agreement with theoretical calculations, evaluated by the competitive canonical unified statistical (CCUS) theory, below 300 K in the LPL regime. The same trend was observed in the HPL regime below 350 K, but the theoretical k(T) values were higher than the experimental ones. Above 200 K, the calculated rate coefficients are improved with respect to previous computational studies and are in excellent agreement with the experimental literature data. In the LPL, the formation of CH3NH becomes largely dominant below ca. 100 K. Conversely, in the HPL regime, CH2NH2 is the only product below 100 K, whereas CH3NH becomes dominant at 298 K with a branching ratio similar to the one found in the LPL regime (≈70%). At T > 300 K, both reaction channels are competitive independently of the pressure regime.
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Garay-Ruiz D, Álvarez-Moreno M, Bo C, Martínez-Núñez E. New Tools for Taming Complex Reaction Networks: The Unimolecular Decomposition of Indole Revisited. ACS PHYSICAL CHEMISTRY AU 2022; 2:225-236. [PMID: 36855573 PMCID: PMC9718323 DOI: 10.1021/acsphyschemau.1c00051] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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 program AutoMeKin. Nevertheless, the sheer complexity of the obtained mechanisms might be a hindrance regarding their chemical interpretation. In this spirit, the new Python library amk-tools has been designed to read and manipulate complex reaction networks, greatly simplifying their overall analysis. The package provides interactive dashboards featuring visualizations of the network, the three-dimensional (3D) molecular structures and vibrational normal modes of all chemical species, and the corresponding energy profiles for selected pathways. The combination of the joined mechanism generation and postprocessing workflow with the rich chemistry of indole decomposition enabled us to find new details of the reaction (obtained at the CCSD(T)/aug-cc-pVTZ//M06-2X/MG3S level of theory) that were not reported before: (i) 16 pathways leading to the formation of HCN and NH3 (via amino radical); (ii) a barrierless reaction between methylene radical and phenyl isocyanide, which might be an operative mechanism under the conditions of the interstellar medium; and (iii) reaction channels leading to both hydrogen cyanide and hydrogen isocyanide, of potential astrochemical interest as the computed HNC/HCN ratios greatly exceed the calculated equilibrium value at very low temperatures. The reported reaction networks can be very valuable to supplement databases of kinetic data, which is of remarkable interest for pyrolysis and astrochemical studies.
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Carrascosa E, Bull JN, Martínez-Núñez E, Scholz MS, Buntine JT, Bieske EJ. Photoisomerization of Linear and Stacked Isomers of a Charged Styryl Dye: A Tandem Ion Mobility Study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2842-2851. [PMID: 34787413 PMCID: PMC8640989 DOI: 10.1021/jasms.1c00264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/21/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
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 electrospray ionization with the most abundant forms assigned to a combination of EE (major) and ZE (minor) geometric isomers, which are difficult to distinguish using IMS as they have similar collision cross sections. Two additional but minor isomers are generated by collisional excitation of the electrosprayed styryl 9M ions and are assigned to the EZ and ZZ geometric isomers, with the latter predicted to have a π-stacked configuration. The isomer assignments are supported through calculations of equilibrium structures, collision cross sections, and statistical isomerization rates. Photoexcitation of selected isomers using an IMS-photo-IMS strategy shows that each geometric isomer photoisomerizes following absorption of near-infrared and visible light, with the EE isomer possessing a S1 ← S0 electronic transition with a band maximum near 680 nm and shorter wavelength S2 ← S0 electronic transition with a band maximum near 430 nm. The study demonstrates the utility of the IMS-photo-IMS strategy for providing fundamental gas-phase photochemical information on molecular systems with multiple isomerizable bonds.
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Pérez-Tabero S, Fernández B, Cabaleiro-Lago EM, Martínez-Núñez E, Vázquez SA. New Approach for Correcting Noncovalent Interactions in Semiempirical Quantum Mechanical Methods: The Importance of Multiple-Orientation Sampling. J Chem Theory Comput 2021; 17:5556-5567. [PMID: 34424696 PMCID: PMC8486165 DOI: 10.1021/acs.jctc.1c00365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
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. A set of small molecules
were selected as representative of various functional groups, and
intermolecular potential energy curves (IPECs) were evaluated for
the most relevant orientations of interacting molecular pairs. Then,
analytical corrections to PM6 were derived from fits to B3LYP-D3/def2-TZVP
reference–PM6 interaction energy differences. IPECs provided
by the B3LYP-D3/def2-TZVP combination of the electronic structure
method and basis set were chosen as the reference because they are
in excellent agreement with CCSD(T)/aug-cc-pVTZ curves for the studied
systems. The resulting method, called PM6-FGC (from functional group
corrections), significantly improves the performance of PM6 and shows
the importance of including a sufficient number of orientations of
the interacting molecules in the reference data set in order to obtain
well-balanced descriptions.
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Martínez-Núñez E, Barnes GL, Glowacki DR, Kopec S, Peláez D, Rodríguez A, Rodríguez-Fernández R, Shannon RJ, Stewart JJP, Tahoces PG, Vazquez SA. AutoMeKin2021: An open-source program for automated reaction discovery. J Comput Chem 2021; 42:2036-2048. [PMID: 34387374 DOI: 10.1002/jcc.26734] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/16/2021] [Accepted: 07/27/2021] [Indexed: 01/10/2023]
Abstract
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, use of chemical knowledge, a new search algorithm based on bond-order time series analysis, statistics of the chemical reaction networks, a web application to submit jobs, and other features. The source code, manual, installation instructions and the website link are available at: https://rxnkin.usc.es/index.php/AutoMeKin.
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Shannon RJ, Martínez-Núñez E, Shalashilin DV, Glowacki DR. ChemDyME: Kinetically Steered, Automated Mechanism Generation through Combined Molecular Dynamics and Master Equation Calculations. J Chem Theory Comput 2021; 17:4901-4912. [PMID: 34283599 DOI: 10.1021/acs.jctc.1c00335] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In many scientific fields, there is an interest in understanding the way in which 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, harnessing modern computing resources to automate mechanism discovery. In this work, we present a new approach to automated mechanism generation which couples molecular dynamics and statistical rate theory to automatically find kinetically important reactions and then solve the time evolution of the species in the evolving network. The key to this chemical network mapping through combined dynamics and ME simulation approach is the concept of "kinetic convergence", whereby the search for new reactions is constrained to those species which are kinetically favorable at the conditions of interest. We demonstrate the capability of the new approach for two systems, a well-studied combustion system and a multiple oxygen addition system relevant to atmospheric aerosol formation.
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Marques JMC, Martínez-Núñez E, Hase WL. Editorial: Application of Optimization Algorithms in Chemistry. Front Chem 2020; 8:198. [PMID: 32266215 PMCID: PMC7101079 DOI: 10.3389/fchem.2020.00198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
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Murillo-Sánchez ML, González-Vázquez J, Corrales ME, de Nalda R, Martínez-Núñez E, García-Vela A, Bañares L. Femtochemistry under scrutiny: Clocking state-resolved channels in the photodissociation of CH3I in the A-band. J Chem Phys 2020; 152:014304. [DOI: 10.1063/1.5134473] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Panadés-Barrueta RL, Martínez-Núñez E, Peláez D. Specific Reaction Parameter Multigrid POTFIT (SRP-MGPF): Automatic Generation of Sum-of-Products Form Potential Energy Surfaces for Quantum Dynamical Calculations. Front Chem 2019; 7:576. [PMID: 31475138 PMCID: PMC6702682 DOI: 10.3389/fchem.2019.00576] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/30/2019] [Indexed: 11/13/2022] Open
Abstract
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 topographical characterization of a (intermolecular) PES based on the Transition State Search Using Chemical Dynamical Simulations (TSSCDS) family of methods;i (ii) the global optimization of the parameters of a semiempirical Hamiltonian in order to reproduce a given level of electronic structure theory; and (iii) a tensor decomposition algorithm which turns the resulting SRP-PES into sum of products (Tucker) form with the Multigrid POTFIT algorithm. The latter is necessary for quantum dynamical studies within the Multiconfiguration Time-Dependent Hartree (MCTDH) quantum dynamics method. To demonstrate our approach, we have applied our methodology to the cis-trans isomerization reaction in HONO in full dimensionality (6D). The resulting SRP-PES has been validated through the computation of classical on-the-fly dynamical calculations as well as calculations of the lowest vibrational eigenstates of HONO as well as high-energy wavepacket propagations.
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Ferro-Costas D, Martínez-Núñez E, Rodríguez-Otero J, Cabaleiro-Lago E, Estévez CM, Fernández B, Fernández-Ramos A, Vázquez SA. Influence of Multiple Conformations and Paths on Rate Constants and Product Branching Ratios. Thermal Decomposition of 1-Propanol Radicals. J Phys Chem A 2018; 122:4790-4800. [DOI: 10.1021/acs.jpca.8b02949] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Siebrand W, Smedarchina Z, Ferro-Costas D, Martínez-Núñez E, Fernández-Ramos A. Reply to the 'Comment on "Methanol dimer formation drastically enhances hydrogen abstraction from methanol by OH at low temperature"' by D. Heard, R. Shannon, J. Gomez Martin, R. Caravan, M. Blitz, J. Plane, M. Antiñolo, M. Agundez, E. Jimenez, B. Ballesteros, A. Canosa, G. El Dib, J. Albaladejo and J. Cernicharo, Phys. Chem. Chem. Phys., 2018, 20, DOI: 10.1039/C7CP04561A. Phys Chem Chem Phys 2018; 20:8355-8357. [PMID: 29498727 DOI: 10.1039/c8cp00519b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
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 higher than the values of the Comment, which confirm the conclusions of the original article that dimers can be present in a small amount. The second argument based on the dependence of the pseudo-first order rates on the methanol concentration was already explained in detail in the Supporting Information of the original article.
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Siebrand W, Smedarchina Z, Martínez-Núñez E, Fernández-Ramos A. Methanol dimer formation drastically enhances hydrogen abstraction from methanol by OH at low temperature. Phys Chem Chem Phys 2018; 18:22712-8. [PMID: 27479134 DOI: 10.1039/c6cp04173f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
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 calculations. These calculations also show that methanol dimers are much more reactive to hydroxyl than monomers and imply that a dimer concentration of about 30% of the equilibrium concentration can account quantitatively for the observed rates. The assumed presence of dimers is supported by the observation of cluster formation in these and other cold beams of molecules subject to hydrogen bonding. The calculations imply an important caveat with respect to the use of cold expansion beams for the study of interstellar chemistry.
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Varela JA, Vázquez SA, Martínez-Núñez E. An automated method to find reaction mechanisms and solve the kinetics in organometallic catalysis. Chem Sci 2017; 8:3843-3851. [PMID: 28966776 PMCID: PMC5577717 DOI: 10.1039/c7sc00549k] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/07/2017] [Indexed: 12/19/2022] Open
Abstract
A novel computational method is proposed in this work for use in discovering reaction mechanisms and solving the kinetics of transition metal-catalyzed reactions. The method does not rely on either chemical intuition or assumed a priori mechanisms, and it works in a fully automated fashion. Its core is a procedure, recently developed by one of the authors, that combines accelerated direct dynamics with an efficient geometry-based post-processing algorithm to find transition states (Martinez-Nunez, E., J. Comput. Chem.2015, 36, 222-234). In the present work, several auxiliary tools have been added to deal with the specific features of transition metal catalytic reactions. As a test case, we chose the cobalt-catalyzed hydroformylation of ethylene because of its well-established mechanism, and the fact that it has already been used in previous automated computational studies. Besides the generally accepted mechanism of Heck and Breslow, several side reactions, such as hydrogenation of the alkene, emerged from our calculations. Additionally, the calculated rate law for the hydroformylation reaction agrees reasonably well with those obtained in previous experimental and theoretical studies.
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Romero MJ, Suárez V, Fernández-Fariña S, Maneiro M, Martínez-Núñez E, Zaragoza G, González-Noya AM, Pedrido R. Effect of the Metal Ion on the Enantioselectivity and Linkage Isomerization of Thiosemicarbazone Helicates. Chemistry 2017; 23:4884-4892. [PMID: 28207181 DOI: 10.1002/chem.201700195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Indexed: 11/11/2022]
Abstract
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 chirally pure cobalt helicates, and the ΛΛ isomer of a single enantiomer has been crystallized as only product for the cobalt methyl-substituted thiosemicarbazone helicate. Interestingly linkage isomers have been formed from zinc ethyl-substituted thiosemicarbazone helicate enantiomers for the first time. The co-existence of these isomers has been evaluated from the point of view of both experimental results and computational calculations.
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Pérez-Soto R, Vázquez SA, Martínez-Núñez E. Photodissociation of acryloyl chloride at 193 nm: interpretation of the product energy distributions, and new elimination pathways. Phys Chem Chem Phys 2016; 18:5019-26. [DOI: 10.1039/c5cp07759a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The use of an automated TS search method leads to the finding of novel HCl elimination pathways.
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Rossich Molina E, Salpin JY, Spezia R, Martínez-Núñez E. On the gas phase fragmentation of protonated uracil: a statistical perspective. Phys Chem Chem Phys 2016; 18:14980-90. [DOI: 10.1039/c6cp01657j] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The major fragmentation pathways of protonated uracil calculated in this work using statistical methods agree with mass spectrometry experiments.
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Vázquez SA, Martínez-Núñez E. HCN elimination from vinyl cyanide: product energy partitioning, the role of hydrogen–deuterium exchange reactions and a new pathway. Phys Chem Chem Phys 2015; 17:6948-55. [DOI: 10.1039/c4cp05626d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A schematic diagram of HCN elimination channels from vinyl cyanide including a new CCdiss pathway.
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Martínez-Núñez E. An automated transition state search using classical trajectories initialized at multiple minima. Phys Chem Chem Phys 2015; 17:14912-21. [DOI: 10.1039/c5cp02175h] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
TS finding using iterative TSSCDS with trajectories initialized at different minima.
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Martínez-Núñez E. An automated method to find transition states using chemical dynamics simulations. J Comput Chem 2014; 36:222-34. [DOI: 10.1002/jcc.23790] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 11/05/2014] [Indexed: 02/01/2023]
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Rodríguez-Fernández R, Vázquez SA, Martínez-Núñez E. Collision-induced dissociation mechanisms of [Li(uracil)]+. Phys Chem Chem Phys 2013; 15:7628-37. [DOI: 10.1039/c3cp50564b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Nogueira JJ, Sánchez-Coronilla A, Marques JM, Hase WL, Martínez-Núñez E, Vázquez SA. Intermolecular potentials for simulations of collisions of SiNCS+ and (CH3)2SiNCS+ ions with fluorinated self-assembled monolayers. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.02.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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