1
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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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Affiliation(s)
- Ramón L Panadés-Barrueta
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01069, Dresden, Germany
| | - Denis Duflot
- Univ. Lille, CNRS, UMR 8523, PhLAM - Physique des Lasers Atomes et Molécules, F-59000, Lille, France
| | - Juan Soto
- Departamento de Química Física, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Emilio Martínez-Núñez
- Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Daniel Peláez
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405, Orsay, France
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2
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Choe JC. Mechanism of Prebiotic Uracil Synthesis from Urea and HC 3O + in Space. ASTROBIOLOGY 2022; 22:1363-1369. [PMID: 36194055 DOI: 10.1089/ast.2022.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The potential energy surface for the formation of protonated uracil (UH+) from urea and HC3O+ was explored by performing quantum chemical complete basis set-QB3 calculations. A barrierless pathway was found for the formation of UH+, which was estimated to occur in the interstellar medium (ISM) much faster than the timescale of chemical revolution of typical dense interstellar clouds. Investigation of further reactions of UH+ formed through the obtained pathway led to the conclusion that uracil could be produced on icy grain surfaces but not in the gas phase of the ISM.
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Affiliation(s)
- Joong Chul Choe
- Department of Chemistry, Dongguk University-Seoul, Seoul, Korea
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3
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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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Affiliation(s)
- Diego Garay-Ruiz
- Institute
of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science & Technology (BIST), Avinguda Països Catalans,
16, 43007 Tarragona, Spain,Departament
de Química Física i Inorgànica, Universitat Rovira i Virgili (URV), Marcel·lí Domingo s/n, 43007 Tarragona, Spain
| | - Moises Álvarez-Moreno
- Institute
of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science & Technology (BIST), Avinguda Països Catalans,
16, 43007 Tarragona, Spain
| | - Carles Bo
- Institute
of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science & Technology (BIST), Avinguda Països Catalans,
16, 43007 Tarragona, Spain,Departament
de Química Física i Inorgànica, Universitat Rovira i Virgili (URV), Marcel·lí Domingo s/n, 43007 Tarragona, Spain,
| | - Emilio Martínez-Núñez
- Departmento
de Química Física, Facultade de Química, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain,
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4
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Cui Q, Peng J, Xu C, Lan Z. Automatic Approach to Explore the Multireaction Mechanism for Medium-Sized Bimolecular Reactions via Collision Dynamics Simulations and Transition State Searches. J Chem Theory Comput 2022; 18:910-924. [DOI: 10.1021/acs.jctc.1c00795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qinghai Cui
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Jiawei Peng
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Chao Xu
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education; School of Chemistry, South China Normal University, Guangzhou 510006, P. R. China
| | - Zhenggang Lan
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
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5
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Chiarinelli J, Barreiro-Lage D, Bolognesi P, RICHTER R, Zettergren H, Stockett MH, Díaz-Tendero S, Avaldi L. Electron and ion spectroscopy of the cyclo-alanine-alanine dipeptide. Phys Chem Chem Phys 2022; 24:5855-5867. [DOI: 10.1039/d1cp05811h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The VUV photoionisation and photofragmentation of cyclo-alanine-alanine (cAA) has been studiedin a joint experimental and theoretical work. The photoelectron spectrum and the photoelectron-photoion coincidence (PEPICO) measurements, which enable a control...
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6
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Lucas K, Chen A, Schubmehl M, Kolonko KJ, Barnes GL. Exploring the Effects of Methylation on the CID of Protonated Lysine: A Combined Experimental and Computational Approach. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2675-2684. [PMID: 34677967 DOI: 10.1021/jasms.1c00225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We report the results of experiments, simulations, and DFT calculations that focus on describing the reaction dynamics observed within the collision-induced dissociation of l-lysine-H+ and its side-chain methylated analogues, Nε-methyl-l-lysine-H+ (Me1-lysine-H+), Nε,Nε-dimethyl-l-lysine-H+ (Me2-lysine-H+), and Nε,Nε,Nε-trimethyl-l-lysine-H+ (Me3-lysine-H+). The major pathways observed in the experimental measurements were m/z 130 and 84, with the former dominant at low collision energies and the latter at intermediate to high collision energies. The m/z 130 peak corresponds to loss of N(CH3)nH3-n, while m/z 84 has the additional loss of H2CO2 likely in the form of H2O + CO. Within the time frame of the direct dynamics simulations, m/z 130 and 101 were the most populous peaks, with the latter identified as an intermediate to m/z 84. The simulations allowed for the determination of several reaction pathways that result in these products. A graph theory analysis enabled the elucidation of the significant structures that compose each peak. Methylation results in the preferential loss of the side-chain amide group and a reduction of cyclic structures within the m/z 84 peak population in simulations.
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Affiliation(s)
- Kenneth Lucas
- Department of Chemistry and Biochemistry, Siena College, 515 Loudon Road, Loudonville, New York 12211, United States
| | - Amy Chen
- Department of Chemistry and Biochemistry, Siena College, 515 Loudon Road, Loudonville, New York 12211, United States
| | - Megan Schubmehl
- Department of Chemistry and Biochemistry, Siena College, 515 Loudon Road, Loudonville, New York 12211, United States
| | - Kristopher J Kolonko
- Stewart's Advanced Instrumentation and Technology (SAInT) Center, Siena College, 515 Loudon Road, Loudonville, New York 12211, United States
| | - George L Barnes
- Department of Chemistry and Biochemistry, Siena College, 515 Loudon Road, Loudonville, New York 12211, United States
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7
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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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Affiliation(s)
- Emilio Martínez-Núñez
- Department of Physical Chemistry, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - George L Barnes
- Department of Chemistry and Biochemistry, Siena College, Loudonville, New York, USA
| | - David R Glowacki
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Sabine Kopec
- Institut de Sciences Moléculaires d'Orsay, UMR 8214, Université Paris-Sud - Université Paris-Saclay, Orsay, France
| | - Daniel Peláez
- Institut de Sciences Moléculaires d'Orsay, UMR 8214, Université Paris-Sud - Université Paris-Saclay, Orsay, France
| | - Aurelio Rodríguez
- Galicia Supercomputing Center (CESGA), Santiago de Compostela, Spain
| | | | - Robin J Shannon
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | | | - Pablo G Tahoces
- Department of Electronics and Computer Science, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Saulo A Vazquez
- Department of Physical Chemistry, University of Santiago de Compostela, Santiago de Compostela, Spain
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8
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Collins SL, Koo I, Peters JM, Smith PB, Patterson AD. Current Challenges and Recent Developments in Mass Spectrometry-Based Metabolomics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:467-487. [PMID: 34314226 DOI: 10.1146/annurev-anchem-091620-015205] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
High-resolution mass spectrometry (MS) has advanced the study of metabolism in living systems by allowing many metabolites to be measured in a single experiment. Although improvements in mass detector sensitivity have facilitated the detection of greater numbers of analytes, compound identification strategies, feature reduction software, and data sharing have not kept up with the influx of MS data. Here, we discuss the ongoing challenges with MS-based metabolomics, including de novo metabolite identification from mass spectra, differentiation of metabolites from environmental contamination, chromatographic separation of isomers, and incomplete MS databases. Because of their popularity and sensitive detection of small molecules, this review focuses on the challenges of liquid chromatography-mass spectrometry-based methods. We then highlight important instrumentational, experimental, and computational tools that have been created to address these challenges and how they have enabled the advancement of metabolomics research.
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Affiliation(s)
- Stephanie L Collins
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Imhoi Koo
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Jeffrey M Peters
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
| | - Philip B Smith
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
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9
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Krettler CA, Thallinger GG. A map of mass spectrometry-based in silico fragmentation prediction and compound identification in metabolomics. Brief Bioinform 2021; 22:6184408. [PMID: 33758925 DOI: 10.1093/bib/bbab073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/29/2021] [Accepted: 02/12/2021] [Indexed: 12/27/2022] Open
Abstract
Metabolomics, the comprehensive study of the metabolome, and lipidomics-the large-scale study of pathways and networks of cellular lipids-are major driving forces in enabling personalized medicine. Complicated and error-prone data analysis still remains a bottleneck, however, especially for identifying novel metabolites. Comparing experimental mass spectra to curated databases containing reference spectra has been the gold standard for identification of compounds, but constructing such databases is a costly and time-demanding task. Many software applications try to circumvent this process by utilizing cutting-edge advances in computational methods-including quantum chemistry and machine learning-and simulate mass spectra by performing theoretical, so called in silico fragmentations of compounds. Other solutions concentrate directly on experimental spectra and try to identify structural properties by investigating reoccurring patterns and the relationships between them. The considerable progress made in the field allows recent approaches to provide valuable clues to expedite annotation of experimental mass spectra. This review sheds light on individual strengths and weaknesses of these tools, and attempts to evaluate them-especially in view of lipidomics, when considering complex mixtures found in biological samples as well as mass spectrometer inter-instrument variability.
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Affiliation(s)
- Christoph A Krettler
- Institute of Biomedical Informatics, Graz University of Technology, Stremayrgasse 16/I, 8010, Graz, Austria.,Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010, Graz, Austria
| | - Gerhard G Thallinger
- Institute of Biomedical Informatics, Graz University of Technology, Stremayrgasse 16/I, 8010, Graz, Austria.,Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010, Graz, Austria
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10
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Carrà A, Spezia R. In Silico
Tandem Mass Spectrometer: an Analytical and Fundamental Tool. ACTA ACUST UNITED AC 2021. [DOI: 10.1002/cmtd.202000071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Andrea Carrà
- Agilent Technologies Italia Via Piero Gobetti 2/C 20063 Cernusco SN, Milano Italy
| | - Riccardo Spezia
- Laboratoire de Chimie Théorique Sorbonne Université, UMR 7616 CNRS 4, Place Jussieu 75005 Paris France
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11
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Omidyan R, Abedini F, Shahrokh L, Azimi G. Excited State Deactivation Mechanism in Protonated Uracil: New Insights from Theoretical Studies. J Phys Chem A 2020; 124:5089-5097. [PMID: 32469520 DOI: 10.1021/acs.jpca.0c02284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We have conducted here a theoretical exploration, discussing the distinct excited state lifetimes reported experimentally for the two lowest lying protonated isomers of uracil. In this regard, the first-principal computational levels as well as the nonadiabatic surface hopping dynamics have been employed. It has been revealed that relaxation of the 1ππ* state of enol-enol form (EE+) to the ground is barrier-free via out-of-plane coordinates, resulting in an ultrashort S1 lifetime of this species. For the second most stable isomer (EK+), however, a significant barrier predicted in the CASPT2 S1 potential energy profile along the twisting coordinate has been proposed to explain the relevant long lifetime reported experimentally.
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Affiliation(s)
- Reza Omidyan
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| | - Fatemeh Abedini
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| | - Leila Shahrokh
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
| | - Gholamhassan Azimi
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran
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12
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Corinti D, Crestoni ME, Chiavarino B, Fornarini S, Scuderi D, Salpin JY. Insights into Cisplatin Binding to Uracil and Thiouracils from IRMPD Spectroscopy and Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:946-960. [PMID: 32233383 PMCID: PMC7997577 DOI: 10.1021/jasms.0c00006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The monofunctional primary complexes cis-[PtCl(NH3)2(L)]+, formed by the reaction of cisplatin, a major chemotherapeutic agent, with four nucleobases L, i.e., uracil (U), 2-thiouracil (2SU), 4-thiouracil (4SU), and 2,4-dithiouracil (24dSU), have been studied by a combination of infrared multiple photon dissociation (IRMPD) action spectroscopy in both the fingerprint (900-1900 cm-1) and the N-H/O-H stretching (3000-3800 cm-1) ranges, energy-resolved collision-induced dissociation (CID) mass spectrometry, and density functional calculations at the B3LYP/LACVP/6-311G** level. On the basis of the comparison across the experimental features and the linear IR spectra of conceivable structures, the cisplatin residue is found to promote a monodentate interaction preferentially with the O4(S4) atoms of the canonical forms of U, 4SU, and 24dSU and to the S2 atom of 2SU, yielding the most stable structures. Additional absorptions reveal the presence of minor, alternative tautomers in the sampled ion populations of 2SU and 24dSU, underlying the ability of cisplatin to increase the prospect of (therapeutically beneficial) nucleic acid strand disorder. Implication of these evidence may provide insights into drug mechanism and design.
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Affiliation(s)
- Davide Corinti
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, P. le A. Moro 5, Roma 00185, Italy
| | - Maria Elisa Crestoni
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, P. le A. Moro 5, Roma 00185, Italy
| | - Barbara Chiavarino
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, P. le A. Moro 5, Roma 00185, Italy
| | - Simonetta Fornarini
- Dipartimento
di Chimica e Tecnologie del Farmaco, Università
di Roma “La Sapienza”, P. le A. Moro 5, Roma 00185, Italy
| | - Debora Scuderi
- Universite′
Paris-Saclay, CNRS, Institut de Chimie Physique
UMR8000, Orsay 91405, France
| | - Jean-Yves Salpin
- Université
Paris-Saclay, CNRS, Univ Evry,
LAMBE, Evry-Courcouronnes 91025, France
- CY
Cergy Paris Université, LAMBE, Evry-Courcouronnes 91025, France
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13
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Martin Somer A, Macaluso V, Barnes GL, Yang L, Pratihar S, Song K, Hase WL, Spezia R. Role of Chemical Dynamics Simulations in Mass Spectrometry Studies of Collision-Induced Dissociation and Collisions of Biological Ions with Organic Surfaces. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2-24. [PMID: 32881516 DOI: 10.1021/jasms.9b00062] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this article, a perspective is given of chemical dynamics simulations of collisions of biological ions with surfaces and of collision-induced dissociation (CID) of ions. The simulations provide an atomic-level understanding of the collisions and, overall, are in quite good agreement with experiment. An integral component of ion/surface collisions is energy transfer to the internal degrees of freedom of both the ion and the surface. The simulations reveal how this energy transfer depends on the collision energy, incident angle, biological ion, and surface. With energy transfer to the ion's vibration fragmentation may occur, i.e. surface-induced dissociation (SID), and the simulations discovered a new fragmentation mechanism, called shattering, for which the ion fragments as it collides with the surface. The simulations also provide insight into the atomistic dynamics of soft-landing and reactive-landing of ions on surfaces. The CID simulations compared activation by multiple "soft" collisions, resulting in random excitation, versus high energy single collisions and nonrandom excitation. These two activation methods may result in different fragment ions. Simulations provide fragmentation products in agreement with experiments and, hence, can provide additional information regarding the reaction mechanisms taking place in experiment. Such studies paved the way on using simulations as an independent and predictive tool in increasing fundamental understanding of CID and related processes.
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Affiliation(s)
- Ana Martin Somer
- Departamento de Química, Facultad de Ciencias, Módulo 13 Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco, 28049 Madrid, Spain
| | - Veronica Macaluso
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, 91025 Evry, France
| | - George L Barnes
- Department of Chemistry and Biochemistry, Siena College, Loudonville, New York 12211, United States
| | - Li Yang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P.R. China
| | - Subha Pratihar
- Department of Chemistry and Biochemistry Texas Tech University, Lubbock, Texas 79409, United States
| | - Kihyung Song
- Department of Chemistry, Korea National University of Education, Chungbuk 28644, Republic of Korea
| | - William L Hase
- Department of Chemistry and Biochemistry Texas Tech University, Lubbock, Texas 79409, United States
| | - Riccardo Spezia
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, LCT, 4, Place Jussieu, Paris, 75252 Cedex 05, France
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14
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Malik A, Angel LA, Spezia R, Hase WL. Collisional dynamics simulations revealing fragmentation properties of Zn(ii)-bound poly-peptide. Phys Chem Chem Phys 2020; 22:14551-14559. [DOI: 10.1039/d0cp02463e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Collisional simulations show how peptide fragmentation is modified by the presence of Zn(ii).
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Affiliation(s)
- Abdul Malik
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock
- USA
| | | | - Riccardo Spezia
- Laboratoire de Chimie Théorique
- Sorbonne Université
- UMR 7616 CNRS
- 75005 Paris
- France
| | - William L. Hase
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock
- USA
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15
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Jara‐Toro RA, Pino GA, Glowacki DR, Shannon RJ, Martínez‐Núñez E. Enhancing Automated Reaction Discovery with Boxed Molecular Dynamics in Energy Space. CHEMSYSTEMSCHEM 2019. [DOI: 10.1002/syst.201900024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Rafael A. Jara‐Toro
- INIFIQC (CONICET-UNC) Dpto. De Fisicoquímica-Facultad de Ciencias Químicas-Centro Láser de Ciencias MolecularesUniversidad de Córdoba Ciudad Universitaria X50000HUA Córdoba Argentina
| | - Gustavo A. Pino
- INIFIQC (CONICET-UNC) Dpto. De Fisicoquímica-Facultad de Ciencias Químicas-Centro Láser de Ciencias MolecularesUniversidad de Córdoba Ciudad Universitaria X50000HUA Córdoba Argentina
| | - David R. Glowacki
- Centre for Computational Chemistry School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Robin J. Shannon
- Centre for Computational Chemistry School of ChemistryUniversity of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Emilio Martínez‐Núñez
- Departmento de Química Física, Facultade de QuímicaUniversidade de Santiago de Compostela 15782 Santiago de Compostela Spain
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16
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Malik A, Lin YF, Pratihar S, Angel LA, Hase WL. Direct Dynamics Simulations of Fragmentation of a Zn(II)-2Cys-2His Oligopeptide. Comparison with Mass Spectrometry Collision-Induced Dissociation. J Phys Chem A 2019; 123:6868-6885. [DOI: 10.1021/acs.jpca.9b05218] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Abdul Malik
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061 United States
| | - Yu-Fu Lin
- Department of Chemistry Texas A&M University—Commerce, 2600 South Neal Street, Commerce, Texas 75428, United States
| | - Subha Pratihar
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061 United States
| | - Laurence A. Angel
- Department of Chemistry Texas A&M University—Commerce, 2600 South Neal Street, Commerce, Texas 75428, United States
| | - William L. Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061 United States
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17
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Braud I, Zamith S, Cuny J, Zheng L, L’Hermite JM. Size-dependent proton localization in hydrated uracil clusters: A joint experimental and theoretical study. J Chem Phys 2019; 150:014303. [DOI: 10.1063/1.5044481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Isabelle Braud
- Laboratoire Collisions Agrégats Réactivité (LCAR/IRSAMC) UMR5589, Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Sébastien Zamith
- Laboratoire Collisions Agrégats Réactivité (LCAR/IRSAMC) UMR5589, Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques (LCPQ/IRSAMC) UMR5626, Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Linjie Zheng
- Laboratoire de Chimie et Physique Quantiques (LCPQ/IRSAMC) UMR5626, Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Jean-Marc L’Hermite
- Laboratoire Collisions Agrégats Réactivité (LCAR/IRSAMC) UMR5589, Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
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18
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A Trajectory-Based Method to Explore Reaction Mechanisms. Molecules 2018; 23:molecules23123156. [PMID: 30513663 PMCID: PMC6321347 DOI: 10.3390/molecules23123156] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 11/23/2018] [Accepted: 11/29/2018] [Indexed: 12/02/2022] Open
Abstract
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 review, its application to solve mechanistic/kinetics problems in different research areas will be presented. Examples will be given of reactions involved in photodissociation dynamics, mass spectrometry, combustion chemistry and organometallic catalysis. Some planned improvements will also be described.
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19
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Rodríguez A, Rodríguez‐Fernández R, A. Vázquez S, L. Barnes G, J. P. Stewart J, Martínez‐Núñez E. tsscds2018: A code for automated discovery of chemical reaction mechanisms and solving the kinetics. J Comput Chem 2018; 39:1922-1930. [DOI: 10.1002/jcc.25370] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/03/2018] [Accepted: 05/11/2018] [Indexed: 01/13/2023]
Affiliation(s)
| | - Roberto Rodríguez‐Fernández
- Departamento de Química Física, Facultade de QuímicaCampus Vida, Universidade de Santiago de Compostela Santiago de Compostela 15782 Spain
| | - Saulo A. Vázquez
- Departamento de Química Física, Facultade de QuímicaCampus Vida, Universidade de Santiago de Compostela Santiago de Compostela 15782 Spain
| | - George L. Barnes
- Department of Chemistry and BiochemistrySiena College 515 Loudon Road, Loudonville New York
| | - James J. P. Stewart
- Stewart Computational Chemistry 15210 Paddington Circle, Colorado Springs Colorado 80921
| | - Emilio Martínez‐Núñez
- Departamento de Química Física, Facultade de QuímicaCampus Vida, Universidade de Santiago de Compostela Santiago de Compostela 15782 Spain
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20
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Homayoon Z, Macaluso V, Martin-Somer A, Muniz MCNB, Borges I, Hase WL, Spezia R. Chemical dynamics simulations of CID of peptide ions: comparisons between TIK(H +) 2 and TLK(H +) 2 fragmentation dynamics, and with thermal simulations. Phys Chem Chem Phys 2018; 20:3614-3629. [PMID: 29340378 DOI: 10.1039/c7cp06818b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gas phase unimolecular fragmentation of the two model doubly protonated tripeptides threonine-isoleucine-lysine (TIK) and threonine-leucine-lysine (TLK) is studied using chemical dynamics simulations. Attention is focused on different aspects of collision induced dissociation (CID): fragmentation pathways, energy transfer, theoretical mass spectra, fragmentation mechanisms, and the possibility of distinguishing isoleucine (I) and leucine (L). Furthermore, discussion is given regarding the differences between single collision CID activation, which results from a localized impact between the ions and a colliding molecule N2, and previous thermal activation simulation results; Z. Homayoon, S. Pratihar, E. Dratz, R. Snider, R. Spezia, G. L. Barnes, V. Macaluso, A. Martin-Somer and W. L. Hase, J. Phys. Chem. A, 2016, 120, 8211-8227. Upon thermal activation unimolecular fragmentation is statistical and in accord with RRKM unimolecular rate theory. Simulations show that in collisional activation some non-statistical fragmentation occurs, including shattering, which is not present when the ions dissociate statistically. Products formed by non-statistical shattering mechanisms may be related to characteristic mass spectrometry peaks which distinguish the two isomers I and L.
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Affiliation(s)
- Zahra Homayoon
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061 USA.
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21
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Martin-Somer A, Martens J, Grzetic J, Hase WL, Oomens J, Spezia R. Unimolecular Fragmentation of Deprotonated Diproline [Pro2-H]− Studied by Chemical Dynamics Simulations and IRMPD Spectroscopy. J Phys Chem A 2018; 122:2612-2625. [DOI: 10.1021/acs.jpca.7b11873] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ana Martin-Somer
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, CEA-CNRS, Université Paris Saclay, Evry 91025, France
- Departamento de Química, Facultad de Ciencias, Módulo
13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Jonathan Martens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Josipa Grzetic
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - William L. Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
- van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 908, 1098XH Amsterdam, The Netherlands
| | - Riccardo Spezia
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, CEA-CNRS, Université Paris Saclay, Evry 91025, France
- Laboratoire de Chimie Théorique, LCT, Sorbonne Université, CNRS, F. 75005 Paris, France
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22
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Jeanvoine Y, Largo A, Hase WL, Spezia R. Gas Phase Synthesis of Protonated Glycine by Chemical Dynamics Simulations. J Phys Chem A 2018; 122:869-877. [DOI: 10.1021/acs.jpca.7b11622] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yannick Jeanvoine
- LAMBE,
Univ Evry, CNRS, CEA, Université Paris-Saclay, 91025 Evry, France
| | - Antonio Largo
- Computational
Chemistry Group, Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Valladolid, Valladolid 47011, Spain
| | - William L. Hase
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Riccardo Spezia
- LAMBE,
Univ Evry, CNRS, CEA, Université Paris-Saclay, 91025 Evry, France
- Laboratoire
de Chimie Théorique, Sorbonne Universités, UPMC Univ Paris 06, UMR-CNRS 7616, 75252 Paris, France
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23
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Macaluso V, Homayoon Z, Spezia R, Hase WL. Threshold for shattering fragmentation in collision-induced dissociation of the doubly protonated tripeptide TIK(H+)2. Phys Chem Chem Phys 2018; 20:19744-19749. [DOI: 10.1039/c8cp02577k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Determination of shattering threshold for unimolecular dissociation of a model tripeptide.
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Affiliation(s)
| | - Zahra Homayoon
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock
- USA
| | | | - William L. Hase
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock
- USA
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24
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Rossich Molina E, Eizaguirre A, Haldys V, Urban D, Doisneau G, Bourdreux Y, Beau J, Salpin J, Spezia R. Characterization of Protonated Model Disaccharides from Tandem Mass Spectrometry and Chemical Dynamics Simulations. Chemphyschem 2017; 18:2812-2823. [DOI: 10.1002/cphc.201700202] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/09/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Estefania Rossich Molina
- LAMBE, Univ Evry, CEA, CNRSUniversité Paris-Saclay F-91025 Evry France
- LAMBE, Université Cergy-PontoiseUniversité Paris-Seine F-91025 Evry France
| | - Ane Eizaguirre
- LAMBE, Univ Evry, CEA, CNRSUniversité Paris-Saclay F-91025 Evry France
- LAMBE, Université Cergy-PontoiseUniversité Paris-Seine F-91025 Evry France
| | - Violette Haldys
- LAMBE, Univ Evry, CEA, CNRSUniversité Paris-Saclay F-91025 Evry France
- LAMBE, Université Cergy-PontoiseUniversité Paris-Seine F-91025 Evry France
| | - Dominique Urban
- ICMMO—SM2B, Univ Paris-SudUniversité Paris-Saclay and CNRS F-91405 Orsay France
| | - Gilles Doisneau
- ICMMO—SM2B, Univ Paris-SudUniversité Paris-Saclay and CNRS F-91405 Orsay France
| | - Yann Bourdreux
- ICMMO—SM2B, Univ Paris-SudUniversité Paris-Saclay and CNRS F-91405 Orsay France
| | - Jean‐Marie Beau
- ICMMO—SM2B, Univ Paris-SudUniversité Paris-Saclay and CNRS F-91405 Orsay France
| | - Jean‐Yves Salpin
- LAMBE, Univ Evry, CEA, CNRSUniversité Paris-Saclay F-91025 Evry France
- LAMBE, Université Cergy-PontoiseUniversité Paris-Seine F-91025 Evry France
| | - Riccardo Spezia
- LAMBE, Univ Evry, CEA, CNRSUniversité Paris-Saclay F-91025 Evry France
- LAMBE, Université Cergy-PontoiseUniversité Paris-Seine F-91025 Evry France
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25
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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: 69] [Impact Index Per Article: 9.9] [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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Affiliation(s)
- J A Varela
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidad de Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - S A Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Física , Universidad de Santiago de Compostela , 15782 Santiago de Compostela , Spain .
| | - E Martínez-Núñez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Física , Universidad de Santiago de Compostela , 15782 Santiago de Compostela , Spain .
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26
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Pratihar S, Ma X, Homayoon Z, Barnes GL, Hase WL. Direct Chemical Dynamics Simulations. J Am Chem Soc 2017; 139:3570-3590. [DOI: 10.1021/jacs.6b12017] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Subha Pratihar
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Xinyou Ma
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Zahra Homayoon
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - George L. Barnes
- Department
of Chemistry and Biochemistry, Siena College, Loudonville, New York 12211, United States
| | - William L. Hase
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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27
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Latrous L, Salpin JY, Haldys V, Léon E, Correia C, Lamsabhi AM. Gas-phase interactions of organotin compounds with cysteine. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:1006-1015. [PMID: 27428725 DOI: 10.1002/jms.3812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/02/2016] [Accepted: 07/12/2016] [Indexed: 06/06/2023]
Abstract
The gas-phase interactions of cysteine with di-organotin and tri-organotin compounds have been studied by mass spectrometry experiments and quantum calculations. Positive-ion electrospray spectra show that the interaction of di- and tri-organotins with cysteine results in the formation of [(R)2 Sn(Cys-H)]+ and [(R)3 Sn(Cys)]+ ions, respectively. MS/MS spectra of [(R)2 Sn(Cys-H)]+ complexes are characterized by numerous fragmentation processes, notably associated with elimination of NH3 and (C,H2 ,O2 ). Several dissociation routes are characteristic of each given organic species. Upon collision, both the [(R)3 Sn(Gly)]+ and [(R)3 Sn(Cys)]+ complexes are associated with elimination of the intact amino acid, leading to the formation of [(R)3 Sn]+ cation. But for the latter complex, two additional fragmentation processes are observed, associated with the elimination of NH3 and C3 H4 O2 S. Calculations indicate that the interaction between organotins and cysteine is predominantly electrostatic but also exhibits a considerable covalent character, which is slightly more pronounced in tri-organotin complexes. A preferred bidentate interaction of the type -η2 -S-NH2 , with sulfur and the amino group, is observed. As for the [(R)3 Sn(Cys)]+ complexes, their stability is due to the combination of the hydrogen bond taking place between the amino group and the sulfur lone pair and the interaction between the carboxylic oxygen atom and the metal. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Latifa Latrous
- Laboratoire de Chimie Analytique et Electrochimie Campus Universitaire, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092, Tunis, Tunisia.
| | - Jean-Yves Salpin
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, Bâtiment Maupertuis-Boulevard François Mitterrand, 91025, Evry, France
- CNRS-UMR 8587, Evry, France
| | - Violette Haldys
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, Bâtiment Maupertuis-Boulevard François Mitterrand, 91025, Evry, France
- CNRS-UMR 8587, Evry, France
| | - Emmanuelle Léon
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, Bâtiment Maupertuis-Boulevard François Mitterrand, 91025, Evry, France
- CNRS-UMR 8587, Evry, France
| | - Catarina Correia
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonne, Bâtiment Maupertuis-Boulevard François Mitterrand, 91025, Evry, France
- CNRS-UMR 8587, Evry, France
| | - Al Mokhtar Lamsabhi
- Departamento de Química, Ciencias, M-13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC Cantoblanco, 28049, Madrid, Spain
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28
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Homayoon Z, Pratihar S, Dratz E, Snider R, Spezia R, Barnes GL, Macaluso V, Martin Somer A, Hase WL. Model Simulations of the Thermal Dissociation of the TIK(H+)2 Tripeptide: Mechanisms and Kinetic Parameters. J Phys Chem A 2016; 120:8211-8227. [DOI: 10.1021/acs.jpca.6b05884] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zahra Homayoon
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Subha Pratihar
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | | | | | - Riccardo Spezia
- Laboratoire
Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne UMR 8587 CNRS-CEA-UEVE, Bd. F. Mitterrand, 91025 Evry Cedex, France
| | - George L. Barnes
- Department
of Chemistry and Biochemistry, Siena College, Loudonville, New York 12211, United States
| | - Veronica Macaluso
- Laboratoire
Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne UMR 8587 CNRS-CEA-UEVE, Bd. F. Mitterrand, 91025 Evry Cedex, France
| | - Ana Martin Somer
- Laboratoire
Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne UMR 8587 CNRS-CEA-UEVE, Bd. F. Mitterrand, 91025 Evry Cedex, France
| | - William L. Hase
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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