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1.
J Chem Theory Comput ; 16(3): 1681-1689, 2020 Mar 10.
Artigo em Inglês | MEDLINE | ID: mdl-32003996

RESUMO

Several methods are available to compute the anharmonicity in semirigid molecules. However, such methods are not yet routinely employed because of their high computational cost, especially for large molecules. The potential energy surface is required and generally approximated by a quartic force field potential based on ab initio calculation, thus limiting this approach to medium-sized molecules. We developed a new, fast, and accurate hybrid quantum mechanics/machine learning (QM/ML) approach to reduce the computational time for large systems. With this novel approach, we evaluated anharmonic frequencies of 37 molecules, thus covering a broad range of vibrational modes and chemical environments. The obtained fundamental frequencies reproduce results obtained using B2PLYP/def2tzvpp with a root-mean-square deviation (RMSD) of 21 cm-1 and experimental results with a RMSD of 23 cm-1. Along with this very good accuracy, the computational time with our hybrid QM/ML approach scales linearly with N, while the traditional full ab initio method scales as N2, where N is the number of atoms.

2.
J Phys Chem Lett ; 10(9): 2300-2305, 2019 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-30999749

RESUMO

Understanding optical properties of molecular dyes is required to drive progress in molecular photonics. This requires a fundamental comprehension of the role of electronic structure, geometry, and interactions with the environment in order to guide molecular engineering strategies. In this context, we studied charged cyanine dye molecules in the gas phase with a controlled microenvironment to unravel the origin of the spectral tuning of this class of molecules. This was performed using a new approach combining femtosecond multiple-photon action spectroscopy of on-the-fly mass-selected molecular ions and high-level quantum calculations. While arguments based on molecular geometry are often used to design new polymethine dyes, we provide experimental evidence that electronic structure is of primary importance and hence the decisive criterion as suggested by recent theoretical investigations.

3.
J Mol Graph Model ; 88: 174-182, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30708284

RESUMO

Zinc-phthalocyanines ZnPc derivatives including quinoleinoxy groups have been studied through DFT calculations. The most stable geometries were characterized for the unsubstituted to the tetra substituted ZnPcs. The energy gap decreased from 2.146 eV for ZnPc to 2.050 eV for ZnPcR4, in agreement with the experimental trend, and indicating the reliability of the electrochemical evaluation of LUMO and HOMO energy levels. Optical transitions computed at the CAM-B3LYP-D3 with triple zeta basis sets were found to be in good agreement with experimental values for both the B and Q bands. Subsequently, structures were also characterized for NO2 adsorbed complexes, in order to assess the potential role of ZnPc as a NO2 sensor. A clear sigma bonding chemisorption of NO2 on Zn atom is observed for all derivatives, followed by a charge transfer from the π Pc conjugated system to the Zn-NO2 moiety. More importantly, after NO2 chemisorption on ZnPc derivative a remarkable red-shift is observed in the optical spectra, particularly for NO2/ZnPcR4 complex, thus offering a good index to detect the binding of NO2. The optical spectra and the vibrational spectra can therefore be used to detect the presence of NO2 and ZnPc derivatives show appropriate properties to constitute good NO2 sensors.

4.
Anal Chem ; 90(20): 11741-11745, 2018 10 16.
Artigo em Inglês | MEDLINE | ID: mdl-30152689

RESUMO

The vast array of molecular isomerisms which form the complex molecular structure of carbohydrates is the foundation of their biological versatility but defies the analytical chemist. Hyphenations of mass spectrometry with orthogonal structural characterization, such as ion mobility or ion spectroscopy, have recently shown great promise for distinction between closely related molecular structures. Yet, the lack of analytical strategies for identification of isomers present in mixtures remains a major obstacle to routine carbohydrate sequencing. In this context, an ideal workflow for glycomics would combine isomer separation and individual characterization of the molecular structure with atomistic resolution. Here we report the implementation of such a multidimensional analytical strategy, which consists of the first online coupling of high-performance liquid chromatography (HPLC)-MS and infrared multiple photon dissociation (IRMPD) spectroscopy. The performance of this novel workflow is exemplified in the case of monosaccharides (anomers) and disaccharides (regioisomers) standards. We report that the LC-MS-IRMPD approach offers a robust advanced MS diagnostic of mixtures of isomers, including carbohydrate anomers, which is critical for carbohydrate sequencing. Our results also explain the bimodal character generally observed in LC chromatograms of carbohydrates. More generally, this multidimensional analytical strategy opens the gateway to rapid identification of molecular isoforms with potential application in the "omics" fields.

5.
Nat Commun ; 8(1): 973, 2017 10 17.
Artigo em Inglês | MEDLINE | ID: mdl-29042546

RESUMO

Deciphering the carbohydrate alphabet is problematic due to its unique complexity among biomolecules. Strikingly, routine sequencing technologies-which are available for proteins and DNA and have revolutionised biology-do not exist for carbohydrates. This lack of structural tools is identified as a crucial bottleneck, limiting the full development of glycosciences and their considerable potential impact for the society. In this context, establishing generic carbohydrate sequencing methods is both a major scientific challenge and a strategic priority. Here we show that a hybrid analytical approach integrating molecular spectroscopy with mass spectrometry provides an adequate metric to resolve carbohydrate isomerisms, i.e the monosaccharide content, anomeric configuration, regiochemistry and stereochemistry of the glycosidic linkage. On the basis of the spectroscopic discrimination of MS fragments, we report the unexpected demonstration of the anomeric memory of the glycosidic bond upon fragmentation. This remarkable property is applied to de novo sequencing of underivatized oligosaccharides.Establishing generic carbohydrate sequencing methods is both a major scientific challenge and a strategic priority. Here the authors show a hybrid analytical approach integrating molecular spectroscopy and mass spectrometry to resolve carbohydrate isomerism, anomeric configuration, regiochemistry and stereochemistry.


Assuntos
Configuração de Carboidratos , Glicosídeos/química , Espectrometria de Massas/métodos , Oligossacarídeos/química , Análise de Sequência/métodos , Sequência de Carboidratos , Isomerismo
6.
J Phys Chem A ; 121(23): 4404-4411, 2017 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-28492322

RESUMO

It is demonstrated, using tandem mass spectrometry and radio frequency ion trap, that the adsorption of a H atom on the gold dimer cation, Au2H+, prevents its dissociation and allows for adsorption of CO. Reaction kinetics are measured by employing a radio frequency ion trap, where Au2+ and CO interact for a given reaction time. The effect of a hydrogen atom is evaluated by comparing reaction rate constants measured for Au2+ and Au2H+. The theoretical results for the adsorption of CO molecules and their reaction characteristics with Au2+ and Au2H+ are found to agree with the experimental findings. The joint investigations provide insights into hydrogen atom adsorption effects and consequent reaction mechanisms.

7.
Glycoconj J ; 34(3): 421-425, 2017 06.
Artigo em Inglês | MEDLINE | ID: mdl-27924423

RESUMO

We report an original MS-based hyphenated method for the elucidation of the epimerization in GAG fragments. It consists of measuring simultaneously the MS/MS spectrum and the gas phase IR spectrum to gain direct structural information. This is possible using a customized MS instrument, modified to allow injection of a tunable IR laser inside of the instrument for in situ spectroscopy of trapped ions. The proof of principle of this approach is performed in the case of a hyaluronic acid tetrasaccharide standard. In addition, we provide the reference IR fingerprint of glucuronic and Iduronic monosaccharide standards. Remarkably, we show that the gas phase IR fingerprint of reference hexuronic acid monosaccharides proves to be transposable to oligosaccharides. Therefore, the method presented here is predictive and allows structural elucidation of unknown GAG fragments, even in the absence of referenced standards.


Assuntos
Ácido Hialurônico/isolamento & purificação , Ácido Idurônico/isolamento & purificação , Espectrofotometria Infravermelho/métodos , Espectrometria de Massas em Tandem/métodos , Ácido Hialurônico/química , Ácido Idurônico/química , Monossacarídeos/química , Oligossacarídeos/química , Soluções , Espectrofotometria Infravermelho/instrumentação , Espectrofotometria Infravermelho/normas , Espectrometria de Massas em Tandem/normas
8.
J Mol Model ; 22(11): 285, 2016 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-27807714

RESUMO

We have developed and tested a new time-effective and accurate hybrid QM//MM generalized second-order vibrational perturbation theory (GVPT2) approach. In this approach, two different levels of theory were used, a high level one (DFT) for computing the harmonic spectrum and a lower fast one (Molecular Mechanic) for the anharmonic corrections. To validate our approach, we used B2PLYP/def2-TZVPP as the high-level method, and the MMFF94 method for the anharmonic corrections as the low-level method. The calculations were carried out on 28 molecules (containing from 2 to 47 atoms) covering a broad range of vibrational modes present in organic molecules. We find that this fast hybrid method reproduces the experimental frequencies with a very good accuracy for organic and bio-molecules. The root-mean-square deviation (RMSD) is about 27 cm -1 while the full B3LYP/SNSD simulation reproduces the experimental values with a RMSD of about 41 cm -1. Concerning the computational time, the hybrid B2PLYP//MMFF94 approach considerably outperforms the full B3LYP/SNSD: for the larger molecule of our set (a dipeptide containing 47 atoms), the anharmonic corrections are 2300 times faster using hybrid MMFF94 rather than full B3LYP, which represents an additional computation time to the harmonic calculation of merely 9 %, instead of 32100 % with the full B3LYP approach. This time-effective and accurate alternative to the traditional GVPT2 approach will allow the spectroscopy community to explore anharmonic effects in larger biomolecules, which are generally unaffordable.

9.
J Chem Phys ; 143(4): 044308, 2015 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-26233130

RESUMO

Two-colour polarization labelling experiments have been used to explore the excitation spectrum of the rubidium dimer in the region 25,500-27,000 cm(-1), probing two mutually interacting states, identified from ab initio calculations as the 5(1)Σu(+) and 5(1)Πu states whose atomic dissociation products are Rb(5s) + Rb(5d). Treating the rather irregular progressions observed in the excitation spectra as transitions to single states with (numerous) local perturbations, we propose spectroscopic parameters and potential energy curves to describe the investigated levels. Observations cover more than 20 vibrational levels in the inner minima of both the 5(1)Πu and 5(1)Σu(+) states. Analysis was guided by ab initio calculations performed to describe the (1,3)Λg,u electronic states of Rb2 up to the Rb(5s) + Rb(5f) atomic asymptote. The theoretical potential energy curves are given in ASCII format in an electronic supplement to this paper.

10.
J Phys Chem A ; 119(33): 8944-9, 2015 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-26214730

RESUMO

A predictive model for nanoparticle nucleation has not yet been successfully achieved. Classical nucleation theory fails because the atomistic nature of the seed has to be considered. Indeed, geometrical structure as well as stoichiometry do not always match the bulk values. We present a fully microscopic approach based on a first-principle study of aluminum oxide clusters. We calculated stable structures of AlxOy and their associated thermodynamic properties. From these data, the chemical composition of a gas composed of aluminum and oxygen atoms can be calculated as a function of temperature, pressure, and aluminum to oxygen ratio. We demonstrate the accuracy of this approach in reproducing experimental results obtained with time-resolved spectroscopy of a laser-induced plasma from an Al2O3 target. We thus extended the calculation to lower temperatures, i.e., longer time scales, to propose a scenario of composition gas evolution leading to the first alumina seeds.

11.
Phys Chem Chem Phys ; 17(39): 25705-13, 2015 Oct 21.
Artigo em Inglês | MEDLINE | ID: mdl-26119005

RESUMO

Mid-infrared spectroscopy coupled with mass spectrometry is an appealing tool for the sequencing and structural elucidation of functional modifications in biopolymers, as it offers direct spectroscopic identification of the functionality where the traditional mass spectrometric approach is insufficient. Whereas the gas phase vibrational spectroscopy of peptides (and to a lesser extent saccharides) has been widely investigated, sulfation has attracted much less attention, despite its prevalence in natural polymers. The simulation of the vibrational spectra of such functionalized compounds is however notoriously challenging, which impairs the interpretation of spectroscopic data in terms of structure. Driven by a striking case of such a failure for a sulfated glycosaminoglycan fragment, we elaborate on an original hybrid GVPT2 anharmonic approach. This strategy offers a significantly improved accuracy in the description of the sulfate modes, without the recourse to empirical scaling factors, and with a greatly reduced computational cost which is otherwise prohibitive for molecules of this size. Alternatively, we propose a selection of reasonably accurate harmonic methods with adequate scaling factors optimized on a set of benchmark compounds.


Assuntos
Glucosamina/química , Espectrofotometria Infravermelho , Simulação por Computador , Dimetil Sulfóxido/química , Modelos Moleculares , Teoria Quântica , Espectrofotometria Infravermelho/métodos , Sulfatos/química , Sulfonas/química , Dióxido de Enxofre/química
12.
J Phys Chem A ; 118(46): 11033-46, 2014 Nov 20.
Artigo em Inglês | MEDLINE | ID: mdl-25350349

RESUMO

Using LR-TDDFT, we calculated the 0-0 energies of 15 small radicals for which the experimental values in gas phase are available. We used 17 functionals. It turned out that B3LYP, M06-2X, ωB97X-D, CAM-B3LYP, and HSE06 functionals are the most effective functionals in terms of root-mean-square and average unsigned deviation. Using the standard value (0.47 a0(-1)) of the attenuation parameter ω, the long-range-corrected LC-GGA functionals give poor results. However, the LC-PBE with ω = 0.25 a0(-1) give a performance similar to that of B3LYP. Taking into account zero-point correction improves the results, but the contribution of adiabatic correction is more important than that due to the vibration. The vertical approximation is certainly not recommended. An adiabatic calculation seems to give a good compromise between computing time (and resources) and reliability of the results for most of molecules investigated in this work.

13.
Phys Chem Chem Phys ; 16(40): 22131-8, 2014 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-25211353

RESUMO

An original application of the coupling of mass spectrometry with vibrational spectroscopy, used for the first time to discriminate isobaric bioactive saccharides with sulfate and phosphate functional modifications, is presented. Whereas their nominal masses and fragmentation patterns are undifferentiated by sole mass spectrometry, their distinctive OH stretching modes at 3595 cm(-1) and 3666 cm(-1), respectively, provide a reliable spectroscopic diagnostic for distinguishing their sulfate or phosphate functionalization. A detailed analysis of the 6-sulfated and 6-phosphated d-glucosamine conformations is presented, together with theoretical scaled harmonic spectra and anharmonic spectra (VPT2 and DFT-based molecular dynamics simulations). Strong anharmonic effects are observed in the case of the phosphated species, resulting in a dramatic enhancement of its phosphate diagnostic mode.


Assuntos
Glucosamina/análogos & derivados , Glucosamina/química , Glucose-6-Fosfato/análogos & derivados , Gases/química , Glucose-6-Fosfato/química , Espectrometria de Massas , Conformação Molecular , Teoria Quântica , Espectrofotometria Infravermelho
14.
J Am Soc Mass Spectrom ; 24(8): 1271-9, 2013 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-23722725

RESUMO

We studied the optical properties of gas-phase polysaccharides (maltose, maltotetraose, and maltohexaose) ions by action spectroscopy using the coupling between a quadrupole ion trap and a vacuum ultraviolet (VUV) beamline at the SOLEIL synchrotron radiation facility (France) in the 7 to 18 eV range. The spectra provide unique benchmarks for evaluation of theoretical data on electronic transitions of model carbohydrates in the VUV range. The effects of the nature of the charge held by polysaccharide ions on the relaxation processes were also explored. Finally the effect of isomerization of polysaccharides (with melezitose and raffinose) on their photofragmentation with VUV photons is presented.


Assuntos
Polissacarídeos/análise , Sequência de Carboidratos , Glicosídeos/química , Isomerismo , Dados de Sequência Molecular , Fotoquímica , Espectrofotometria Ultravioleta , Síncrotrons , Vácuo
15.
J Chem Phys ; 136(11): 114302, 2012 Mar 21.
Artigo em Inglês | MEDLINE | ID: mdl-22443759

RESUMO

For the Rb(2) and Cs(2) molecules, the adiabatic potential-energy curves and the transition dipole moments of the 43 Ω((+∕-)) (g,u) low-lying states dissociating adiabatically to the limits up to ns+(n-1)d (n = 5,6 for Rb(2) and Cs(2), respectively), have been computed as a function of the internuclear distance R for a large and dense grid. Each molecule was treated as a two-electron system. We used an ab initio approach involving a relativistic non-empirical pseudo-potential for Rb and Cs cores, core-valence polarization potentials, and full valence configuration interaction calculations for the two valence electrons. Spin-orbit effects were taken into account through semi-empirical spin-orbit pseudopotentials. Equilibrium distances, transition energies, rotational constants, and harmonic frequencies as well as depths of wells and heights of barriers are reported for all the molecular states investigated in Hund's cases (a) and (c). Extensive tables of energy values and transition dipole moments are given in an auxiliary (EPAPS) files as a database for future studies on Rb(2) and Cs(2).

17.
J Phys Chem A ; 115(32): 8933-9, 2011 Aug 18.
Artigo em Inglês | MEDLINE | ID: mdl-21744817

RESUMO

Tryptophan (Trp(•)) and tyrosyl (Tyr(•)) radical containing peptides were produced by UV laser-induced electron detachment from a suitable precursor. Vacuum ultraviolet (VUV) action spectra of these radical peptides were recorded with synchrotron radiation in the 4.5-16 eV range, from which fragmentation pathways and yields are measured as a function of the VUV photon energy. An enhancement in photofragmentation yields of radical species by 1 order of magnitude with respect to nonradical peptides is demonstrated here for the first time. Photofragmentation spectra are compared with absorption spectra for model chromophores calculated in the frame of the time-dependent density functional theory (TDDFT). A qualitative agreement in the position of bands in the 6-8 eV region is observed between experimental photofragmentation and calculated absorption spectra. Photofragmentation spectra of peptide radicals can be useful to better assess the complex deactivation pathways that occur following the absorption of a VUV photon in biomolecular radical anions.


Assuntos
Radicais Livres/química , Peptídeos/química , Espectroscopia Fotoeletrônica/métodos , Fotólise , Triptofano/química , Tirosina/química , Absorção , Gases/química , Fótons , Síncrotrons , Raios Ultravioleta , Vácuo
18.
J Comput Chem ; 32(1): 174-82, 2011 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-20607691

RESUMO

Gabedit is a freeware graphical user interface, offering preprocessing and postprocessing adapted (to date) to nine computational chemistry software packages. It includes tools for editing, displaying, analyzing, converting, and animating molecular systems. A conformational search tool is implemented using a molecular mechanics or a semiempirical potential. Input files can be generated for the computational chemistry software supported by Gabedit. Some molecular properties of interest are processed directly from the output of the computational chemistry programs; others are calculated by Gabedit before display. Molecular orbitals, electron density, electrostatic potential, nuclear magnetic resonance shielding density, and any other volumetric data properties can be displayed. It can display electronic circular dichroism, UV-visible, infrared, and Raman-computed spectra after a convolution. Gabedit can generate a Povray file for geometry, surfaces, contours, and color-coded planes. Output can be exported to a selection of popular image and vector graphics file formats; the program can also generate a series of pictures for animation. Quantum mechanical electrostatic potentials can be calculated using the partial charges on atoms, or by solving the Poisson equation using the multigrid method. The atoms in molecule charges can also be calculated. Gabedit is platform independent. The code is distributed under free open source X11 style license and is available at http://gabedit.sourceforge.net/.

19.
J Phys Chem B ; 114(49): 16388-92, 2010 Dec 16.
Artigo em Inglês | MEDLINE | ID: mdl-21086975

RESUMO

We present a new model to predict chemical shifts for biological molecules. It is simple, fast, and involves a limited number of parameters. It is particularly adapted to be used in molecular dynamics studies with a molecular mechanic potential. We test the model for polyamines, which are rather small molecules, as well as for proteins for which a lot of NMR chemical shifts are available. The tests show that our simple and fast model is competitive, by its accuracy, with sophisticated models specifically developed for proteins. It was also seen to be successful for polyamines.


Assuntos
Modelos Biológicos , DNA/química , Espectroscopia de Ressonância Magnética , Proteínas/química , RNA/química , Fatores de Tempo
20.
Phys Chem Chem Phys ; 12(14): 3399-403, 2010 Apr 14.
Artigo em Inglês | MEDLINE | ID: mdl-20352677

RESUMO

The UV photoexcitation spectrum of deprotonated tryptophan anion is presented. Singly deprotonated amino-acid tryptophan has been produced in an electrospray ionization source, isolated in a quadrupole ion trap and photoexcited with a UV tunable laser, resulting in the photodetachment of the excess electron. Whereas no influence of the proton on the UV spectrum of tryptophan was previously reported (Phys. Chem. Chem. Phys., 2004, 6, 2633; J. Chem. Phys., 2005, 122, 074310), we observe a strong bathochromism due to the presence of the negatively charged group in the vicinity of the chromophore. An excellent agreement with TD-DFT (time dependent density functional theory) predictions for the absorption spectrum of the lowest energy conformer is found. The sensitivity of the tryptophan chromophore to the presence of a remote negative charge offers new perspectives for charge mapping in large biomolecules.


Assuntos
Triptofano/química , Ânions , Elétrons , Fotoquímica , Espectrometria de Massas por Ionização por Electrospray
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