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1.
J Phys Chem A ; 125(46): 10006-10020, 2021 Nov 25.
Artigo em Inglês | MEDLINE | ID: mdl-34761946

RESUMO

Acetamide, a small organic compound containing a peptide bond, was observed in the interstellar medium, but reaction pathways leading to the formation of this prebiotic molecule remain uncertain. We investigated the possible formation of a peptide-like bond from the reaction between acetic acid (CH3-COOH) and methylamine (CH3-NH2) that were identified in the interstellar medium. From an experimental point of view, a quadrupole/octopole/quadrupole mass spectrometer was used in combination with synchrotron radiation as a tunable source of VUV photons for monitoring the reactivity of selected ions. Acetic acid was photoionized, and the reactivity of CH3COOH+• as well as COOH+ (produced from either acetic acid or formic acid) ions with neutral CH3NH2 was further studied. With no surprise, charge transfer, proton transfer, and concomitant dissociation processes were found to largely dominate the reactivity. However, a C(O)-N bond formation process between the two reactants was also evidenced, with a weak cross section reaction. From a theoretical point of view, results concerning reactivity and barrier heights were obtained using density functional theory, with the LC-ωPBE range-separated functional in combination with the 6-311++G(d,p) Pople basis set and are in perfect agreement with the experimental data.


Assuntos
Peptídeos , Prótons , Ácido Acético , Íons , Espectrometria de Massas
2.
Phys Chem Chem Phys ; 22(36): 20394-20408, 2020 Sep 23.
Artigo em Inglês | MEDLINE | ID: mdl-32914152

RESUMO

We present a combined theoretical and experimental investigation on the single photoionization and dissociative photoionization of gas-phase methyl ketene (MKE) and its neutral dimer (MKE2). The performed experiments entail the recording of photoelectron photoion coincidence (PEPICO) spectra and slow photoelectron spectra (SPES) in the energy regime 8.7-15.5 eV using linearly polarized synchrotron radiation. We observe both dimerization and trimerization of the monomer which brings about significantly complex and abstruse dissociative ionization patterns. These require the implementation of theoretical calculations to explore the potential energy surfaces of the monomer and dimer's neutral and ionized geometries. To this end, explicitly correlated quantum chemical methodologies involving the coupled cluster with single, double and perturbative triple excitations (R)CCSD(T)-F12 method, are utilized. An improvement in the adiabatic ionization energy of MKE is presented (AIE = 8.937 ± 0.020 eV) as well as appearance energies for multiple fragments formed through dissociative ionization of either the MKE monomer or dimer. In this regard, the synergy of experiment and theory is crucial to interpreting the obtained results. We discuss the potential astrochemical implications of this work in the context of recent advances in the field of astrochemistry and speculate on the potential presence and eventual fate of interstellar MKE molecules.

3.
J Phys Chem A ; 124(9): 1720-1734, 2020 Mar 05.
Artigo em Inglês | MEDLINE | ID: mdl-32049521

RESUMO

The presence of a carbonyl group in a molecule usually leads to the identification of a π-hole on the molecular electrostatic potential (MESP) of the species. How does this electrophilic site influence the formation of microhydrated complexes? To address this point, a panel of R2CO solutes with various MESPs was selected, and we identified the structures and properties of several complexes containing one, two, three and six water molecules. The following solutes were considered in the present study: H2CO, F2CO, Cl2CO,(NC)2CO and H2C═CO. Geometry optimizations and frequency calculations were carried out at the LC-ωPBE/6-311++G(d,p) level, with the GD3BJ empirical correction for dispersion. For a number of n water molecules around the R2CO solute, the structure and the features of the most stable (H2O)n:(R2CO) complexes are highly dependent on the MESP of the isolated R2CO solute. The formation of pi-hole bondings appears to play a decisive role in the initiation of a three-dimensional organization of water molecules around the solute.

4.
J Mol Model ; 25(12): 363, 2019 Nov 26.
Artigo em Inglês | MEDLINE | ID: mdl-31773281

RESUMO

Micro-hydrated trimethylamine oxide (TMAO) has been investigated using a range-separated-hybrid functional including empirical dispersion correction. Electrophilic and nucleophilic sites on TMAO and water clusters have been identified using the molecular electrostatic potential (MESP). The nature of the chemical bonding in the different isomers of the micro-hydrated complexes has been investigated with the topological analysis of the electron density (QTAIM) method. For complexes containing one to four water molecules, the strongest intermolecular interactions consist in hydrogen bonding between the oxygen atom of the TMAO and hydrogen atoms of water molecules. From five water molecules, interactions between water molecules become the main source of stabilization of the most stable isomer. From four stationary points corresponding to the 1:1 (TMAO:H2O) complex, we determined the minimum distances between water molecules and central TMAO allowing the latter molecule to be encapsulated within a water clathrate-type cage. Optimization of TMAO encapsulated within two water cages (512 and 51262) suggests that only in the case of the 512 62 water cage the insertion of TMAO, the preservation of the hydrogen bonding between water molecules is energetically favorable. The interaction energy between one inserted TMAO and the 512 62 water cage was calculated to be around 150 kJ/mol with respect to the ground state of two partners. This result suggests that a thorough investigation of mono-hydrated complexes may be particularly relevant to identify the most suitable water cage for encapsulating a given solute.

5.
Life (Basel) ; 9(4)2019 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-31717814

RESUMO

Space missions using probes to return dust samples are becoming more frequent. Dust collectors made of silica aerogel blocks are used to trap and bring back extraterrestrial particles for analysis. In this work, we show that it is possible to detect traces of adenine using surface-enhanced Raman spectroscopy (SERS). The method was first optimized using adenine deposition on glass slides and in glass wells. After this preliminary step, adenine solution was injected into the silica aerogel. Finally, gaseous adenine was successfully trapped in the aerogel. The presence of traces of adenine was monitored by SERS through its characteristic bands at 732, 1323, and 1458 cm-1 after the addition of the silver Creighton colloid. Such a method can be extended in the frame of Tanpopo missions for studying the interplanetary transfer of prebiotic organic compounds of biological interest.

6.
J Comput Chem ; 40(26): 2248-2283, 2019 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-31251411

RESUMO

The paper collects the answers of the authors to the following questions: Is the lack of precision in the definition of many chemical concepts one of the reasons for the coexistence of many partition schemes? Does the adoption of a given partition scheme imply a set of more precise definitions of the underlying chemical concepts? How can one use the results of a partition scheme to improve the clarity of definitions of concepts? Are partition schemes subject to scientific Darwinism? If so, what is the influence of a community's sociological pressure in the "natural selection" process? To what extent does/can/should investigated systems influence the choice of a particular partition scheme? Do we need more focused chemical validation of Energy Decomposition Analysis (EDA) methodology and descriptors/terms in general? Is there any interest in developing common benchmarks and test sets for cross-validation of methods? Is it possible to contemplate a unified partition scheme (let us call it the "standard model" of partitioning), that is proper for all applications in chemistry, in the foreseeable future or even in principle? In the end, science is about experiments and the real world. Can one, therefore, use any experiment or experimental data be used to favor one partition scheme over another? © 2019 Wiley Periodicals, Inc.


Assuntos
Teoria Quântica , Termodinâmica , Humanos
7.
Phys Chem Chem Phys ; 21(26): 14053-14062, 2019 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-30652173

RESUMO

Propynal (HCCCHO) is a complex organic compound (COM) of astrochemical and astrobiological interest. We present a combined theoretical and experimental investigation on the single photon ionization of gas-phase propynal, in the 10 to 15.75 eV energy range. Fragmentation pathways of the resulting cation were investigated both theoretically and experimentally. The adiabatic ionization energy (AIE) has been measured to be AIEexp = 10.715 ± 0.005 eV using tunable VUV synchrotron radiation coupled with a double imaging photoelectron photoion coincidence (i2PEPICO) spectrometer. In the energy range under study, three fragments formed by dissociative photoionization were identified experimentally: HC3O+, HCO+ and C2H2+, and their respective appearance energies (AE) were found to be AE = 11.26 ± 0.03, 13.4 ± 0.3 and 11.15 ± 0.03 eV, respectively. Using explicitly correlated coupled cluster calculations and after inclusion of the zero point vibrational energy, core-valence and scalar relativistic effects, the AIE is calculated to be AIEcalc = 10.717 eV, in excellent agreement with the experimental finding. The appearance energies of the fragments were calculated using a similar methodological approach. To further interpret the observed vibrational structure, anharmonic frequencies were calculated for the fundamental electronic state of the propynal cation. Moreover, MRCI calculations were carried out to understand the population of excited states of the cationic species. This combined experimental and theoretical study will help to understand the presence and chemical evolution of propynal in the external parts of interstellar clouds where it has been observed.

8.
Phys Chem Chem Phys ; 20(23): 15687-15695, 2018 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-29846373

RESUMO

More than ten years ago, Manners and coworkers published the first experimental study on the efficiency of titanocene to catalyze the dehydrocoupling of dimethylamine borane (DMAB, T. Clark, C. Russell and I. Manners, J. Am. Chem. Soc., 2006, 128, 9582-9583). Several experimental investigations have shown that a two-step mechanism leads to the formation of a cyclic diborazane (Me2N-BH2)2via the linear diborazane (HNMe2-BH2-NMe2-BH3). This finding stood in contradiction to the following theoretical investigations of the reaction pathway. Herein, using dispersion-corrected density functional theory (DFT-D), we propose an energetically favored reaction mechanism in perfect agreement with the experimental findings. It is shown that van der Waals interactions play a prominent role in the reaction pathway. The formation of 3-center 2-electron interactions, classical dihydrogen bonds, and non-classical dihydrogen bonds was identified with the help of topological and localized orbital approaches.

9.
Chemistry ; 23(27): 6504-6508, 2017 May 11.
Artigo em Inglês | MEDLINE | ID: mdl-28324628

RESUMO

Transamination of [Co{N(SiMe3 )2 }2 ]2 with C6 H4 (NHSiiPr3 )2 gave the centrosymmetric trinuclear [{Coter N(SiMe3 )2 (µ-η-[o-C6 H4 (κNSiiPr3 )2 ])}2 Coint ] (1) (Coter , Coint =terminal, internal Co, respectively), with 3-coordinate Coter , and Coint "sandwiched" between the o-phenylenes of the two ligands; experimental and computational data support CoII centres and ditopic o-amido-imino-cyclohexen-allyl ligands; magnetic studies reveal intermetallic ferromagnetic interactions and single-molecule magnet (SMM) character. One-electron reduction of 1 yielded the salt [K(18-crown-6)(THF)2 ][{Coter N(SiMe3 )2 (µ-η-[o-C6 H4 (κNSiiPr3 )2 ])}2 Coint ] (4) with the anion isostructural to 1. The centrosymmetric Fe complex [{Feter N(SiMe3 )2 (µ-η-[o-C6 H4 (κNSiiPr3 )2 ])}2 Feint ] (5), analogous to 1, was also obtained.

10.
J Mol Model ; 22(12): 294, 2016 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-27888405

RESUMO

For over a decade, amine-borane has been considered as a potential chemical hydrogen vector in the context of a search for cleaner energy sources. When catalyzed by organometallic complexes, the reaction mechanisms currently considered involve the formation of ß-BH agostic intermediates. A thorough understanding of these intermediates may constitute a crucial step toward the identification of ideal catalysts. Topological approaches such as QTAIM and ELF revealed to be particularly suitable for the description of ß-agostic interactions. When studying model catalysts, accurate theoretical calculations may be carried out. However, for a comparison with experimental data, calculations should also be carried out on large organo-metallic species, often including transition metals belonging to the second or the third row. In such a case, DFT methods are particularly attractive. Unfortunately, triple-ζ all electrons basis sets are not easily available for heavy transition metal elements. Thus, a subtle balance should be reached between the affordable level of calculations and the required accuracy of the electronic description of the systems. Herein we propose the use of B3LYP functional in combination with the LanL2DZ pseudopotential for the metal atom and 6-311++G(2d,2p) basis set for the other atoms, followed by a single point using the DKH2 relativistic Hamiltonian in combination with the B3LYP/DZP-DKH level, as a "minimum level of theory" leading to a consistent topological description of the interaction within the ELF and QTAIM framework, in the context of isolated (gas-phase) group 4 metallocene catalysts.

11.
Chemistry ; 22(44): 15834-15846, 2016 Oct 24.
Artigo em Inglês | MEDLINE | ID: mdl-27624284

RESUMO

Understanding ribose reactivity is a crucial step in the "RNA world" scenario because this molecule is a component of all extant nucleotides that make up RNA. In solution, ribose is unstable and susceptible to thermal destruction. We examined how ribose behaves upon thermal activation when adsorbed on silica, either alone or with the coadsorption of inorganic salts (MgCl2 , CaCl2 , SrCl2 , CuCl2 , FeCl2 , FeCl3 , ZnCl2 ). A combination of 13 C NMR, in situ IR, and TGA analyses revealed a variety of phenomena. When adsorbed alone, ribose remains stable up to 150 °C, at which point ring opening is observed, together with minor oxidation to a lactone. All the metal salts studied showed specific interactions with ribose after dehydration, resulting in the formation of polydentate metal ion complexes. Anomeric equilibria were affected, generally favoring ribofuranoses. Zn2+ stabilized ribose up to higher temperatures than bare silica (180 to 200 °C). Most other cations had an adverse effect on ribose stability, with ring opening already upon drying at 70 °C. In addition, alkaline earth cations catalyzed the dehydration of ribose to furfural and, to variable degrees, its further decarbonylation to furan. Transition-metal ions with open d-shells took part in redox reactions with ribose, either as reagents or as catalysts. These results allow the likelihood of prebiotic chemistry scenarios to be evaluated, and may also be of interest for the valorization of biomass-derived carbohydrates by heterogeneous catalysis.


Assuntos
Metais/química , Prebióticos , RNA/química , Ribose/química , Sais/química , Dióxido de Silício/química , Catálise
12.
J Phys Chem A ; 120(27): 5041-52, 2016 Jul 14.
Artigo em Inglês | MEDLINE | ID: mdl-26890990

RESUMO

Experimental and theoretical studies have been carried out to demonstrate the selective generation of two different C2H3N(+) isomers, namely, the acetonitrile [CH3CN](•+) and the ketenimine [CH2CNH](•+) radical cations. Photoionization and dissociative photoionization experiments from different neutral precursors (acetonitrile and butanenitrile) have been performed using vacuum ultraviolet (VUV) synchrotron radiation in the 10-15 eV energy range, delivered by the DESIRS beamline at the SOLEIL storage ring. For butanenitrile (CH3CH2CH2CN) an experimental ionization threshold of 11.29 ± 0.05 eV is obtained, whereas the appearance energy for the formation of [CH2CNH](•+) fragments is 11.52 ± 0.05 eV. Experimental findings are fully supported by theoretical calculations at the G4 level of theory (ZPVE corrected energies at 0 K), giving a value of 11.33 eV for the adiabatic ionization energy of butanenitrile and an exothermicity of 0.49 for fragmentation into [CH2CNH](•+) plus C2H4, hampered by an energy barrier of 0.29 eV. The energy difference between [CH3CN](•+) and [CH2CNH](•+) is 2.28 eV (with the latter being the lowest energy isomer), and the isomerization barrier is 0.84 eV. Reactive monitoring experiments of the [CH3CN](•+) and [CH2CNH](•+) isomers with C2H4 have been performed using the CERISES guided ion beam tandem mass spectrometer and exploiting the selectivity of ethylene that gives exothermic charge exchange and proton transfer reactions with [CH3CN](•+) but not with [CH2CNH](•+) isomers. In addition, minor reactive channels are observed leading to the formation of new C-C bonds upon reaction of [CH3CN](•+) with C2H4, and their astrochemical implications are briefly discussed.

13.
Phys Chem Chem Phys ; 17(14): 9258-81, 2015 Apr 14.
Artigo em Inglês | MEDLINE | ID: mdl-25760795

RESUMO

Agostic bonding is of paramount importance in C-H bond activation processes. The reactivity of the σ C-H bond thus activated will depend on the nature of the metallic center, the nature of the ligand involved in the interaction and co-ligands, as well as on geometric parameters. Because of their importance in organometallic chemistry, a qualitative classification of agostic bonding could be very much helpful. Herein we propose descriptors of the agostic character of bonding based on the electron localization function (ELF) and Quantum Theory of Atoms in Molecules (QTAIM) topological analysis. A set of 31 metallic complexes taken, or derived, from the literature was chosen to illustrate our methodology. First, some criteria should prove that an interaction between a metallic center and a σ X-H bond can indeed be described as "agostic" bonding. Then, the contribution of the metallic center in the protonated agostic basin, in the ELF topological description, may be used to evaluate the agostic character of bonding. A σ X-H bond is in agostic interaction with a metal center when the protonated X-H basin is a trisynaptic basin with a metal contribution strictly larger than the numerical uncertainty, i.e. 0.01 e. In addition, it was shown that the weakening of the electron density at the X-Hagostic bond critical point with respect to that of X-Hfree well correlates with the lengthening of the agostic X-H bond distance as well as with the shift of the vibrational frequency associated with the νX-H stretching mode. Furthermore, the use of a normalized parameter that takes into account the total population of the protonated basin, allows the comparison of the agostic character of bonding involved in different complexes.

14.
J Org Chem ; 80(6): 3280-8, 2015 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-25695186

RESUMO

A new route to Martin's spirosilanes has been devised. The original synthesis does not allow diversely substituted spirosilane derivatives to be synthesized, and thus their corresponding silicates. In this report, Martin's spirosilanes bearing alkyl, aryl, halogen, alkoxy, and trifluoromethyl substituents on the aryl ring have been prepared through a versatile four-step route. Addition of fluoride onto these Lewis acids as a prototypical reaction with a nucleophile yielded a library of stable fluorosilicates. Both sets of compounds have been characterized by X-ray crystallography.

15.
Phys Chem Chem Phys ; 17(4): 2804-13, 2015 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-25501292

RESUMO

As a simple molecule containing the four main atoms essential for life as we know it, isocyanic acid can be considered as a prebiotic molecule. As such, the understanding of reaction mechanisms leading to its formation is fundamental. Isocyanic acid is present in different physical environments in the medium. Previous studies have suggested that, in water-containing ices, on the surface of dust grains, HNCO may be formed from N and CO in their fundamental states. To further investigate the reaction process, herein we investigate this reaction by means of the matrix-isolation technique.

16.
J Am Soc Mass Spectrom ; 24(3): 365-80, 2013 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-23389479

RESUMO

The kinetic method is a widely used approach for the determination of thermochemical data such as proton affinities (PA) and gas-phase acidities (ΔH° acid ). These data are easily obtained from decompositions of noncovalent heterodimers if care is taken in the choice of the method, references used, and experimental conditions. Previously, several papers have focused on theoretical considerations concerning the nature of the references. Few investigations have been devoted to conditions required to validate the quality of the experimental results. In the present work, we are interested in rationalizing the origin of nonlinear effects that can be obtained with the kinetic method. It is shown that such deviations result from intrinsic properties of the systems investigated but can also be enhanced by artifacts resulting from experimental issues. Overall, it is shown that orthogonal distance regression (ODR) analysis of kinetic method data provides the optimum way of acquiring accurate thermodynamic information.

17.
J Phys Chem A ; 116(50): 12357-63, 2012 Dec 20.
Artigo em Inglês | MEDLINE | ID: mdl-23190040

RESUMO

Reactions between dilute methane and nonenergetic hydroxyl radicals were carried out at 3.5 K. The temperature was kept low in order to characterize the stepwise reaction and prevent parasitic side reactions. The hydroxyl radicals originate from discharged H(2)O/He mixtures. The reactions were monitored in situ using a Fourier transform infrared spectrometer. The formation of CH(3) radicals was confirmed simultaneously with the formation of water ice. Subsequent recombination reactions lead to the formation of ethane (C(2)H(6)). Production of ethane and water ice occur preferentially to the formation of methanol.

18.
J Am Soc Mass Spectrom ; 23(12): 2167-77, 2012 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-23055074

RESUMO

Numerous studies have highlighted the role of the proton donor characteristics of the phenol group of 17ß-estradiol (E(2)) in its association with the estrogen receptor alpha (ERα). Since the substitutions at position C((11)) have been reported to modulate this association, we hypothesized that such substitutions may modify the phenol acidity. Hence, phenol gas-phase acidity of nine C((11))-substituted E(2)-derivatives were evaluated using the extended Cooks' kinetic method, which is a method widely used to determine thermochemical properties by mass spectrometry. To enhance accuracy in data collection we recorded data from several instruments, including quadrupole ion trap, triple quadrupole, and hybrid QqTOF. Indeed, we report for the first time the use of the QqTOF instrument to provide a novel means to improve data accuracy by giving access to an intermediate effective temperature range. All experimental gas-phase acidity values were supported by theoretical calculations. Our results confirmed the ability of distant substituents at C((11)) to modulate the phenol acidity through electrostatic interactions, electron withdrawing inductive effects, and mesomeric effects. However, no relationship was found between the phenol gas-phase acidity of investigated steroids and their binding affinity for ERα assessed in solution. Thus, our results highlight that the intrinsic properties of the hormone do not influence sufficiently the stabilization of the hormone/ERα complex. It is more likely that such stabilization would be more related to factors depending on the environment within the binding pocket such as hydrophobic, steric as well as direct intermolecular electrostatic effects between ERα residues and the substituted steroidal estrogens.


Assuntos
Estradiol/análogos & derivados , Espectrometria de Massas/instrumentação , Espectrometria de Massas/métodos , Estradiol/química , Receptor alfa de Estrogênio/metabolismo , Gases/química , Humanos , Concentração de Íons de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Cinética , Modelos Moleculares , Ligação Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Eletricidade Estática , Temperatura
20.
Chemphyschem ; 13(11): 2688-98, 2012 Aug 06.
Artigo em Inglês | MEDLINE | ID: mdl-22693155

RESUMO

Even in the highly diluted gas phase, rather than electron transfer the benzene dication C(6)H(6)(2+) undergoes association with dinitrogen to form a transient C(6)H(6)N(2)(2+) dication which is best described as a ring-protonated phenyl diazonium ion. Isotopic labeling studies, photoionization experiments using synchrotron radiation, and quantum chemical computations fully support the formation of protonated diazonium, which is in turn a prototype species of superacidic chemistry in solution. Additionally, reactions of C(6)H(6)(2+) with background water involve the transient formation of diprotonated phenol and, among other things, afford a long-lived C(6)H(6)OH(2)(2+) dication, which is attributed to the hydration product of Hogeveen's elusive pyramidal structure of C(6)H(6)(2+), as the global minimum of doubly ionized benzene. Nitrogen is essential for the formation of the C(6)H(6)OH(2)(2+) dication in that it mediates the formation of the water adduct, while the bimolecular encounter of the C(6)H(6)(2+) dication with water only leads to (dissociative) electron transfer.

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