Neural Network Approach for a Rapid Prediction of Metal-Supported Borophene Properties.

We developed a high-dimensional neural network potential (NNP) to describe the structural and energetic properties of borophene deposited on silver. This NNP has the accuracy of density functional theory (DFT) calculations while achieving computational speedups of several orders of magnitude, allowing the study of extensive structures that may reveal intriguing moiré patterns or surface corrugations. We describe an efficient approach to constructing the training data set using an iterative technique known as the "adaptive learning approach". The developed NNP is able to produce, with excellent agreement, the structure, energy, and forces obtained at the DFT level. Finally, the calculated stability of various borophene polymorphs, including those not initially included in the training data set, shows better stabilization for ν ∼ 0.1 hole density, and in particular for the allotrope α (ν=1/9). The stability of borophene on the metal surface is shown to depend on its orientation, implying structural corrugation patterns that can be observed only from long-time simulations on extended systems. The NNP also demonstrates its ability to simulate vibrational densities of states and produce realistic structures with simulated STM images closely matching the experimental ones.

Conformational preferences of the flexible galactofuranose sugar in gas-phase.

In contrast with the predominant pyranose form of galactose, galactofuranose is known to be highly flexible. Such flexibility poses a remarkable challenge in terms of structural studies, thus hindering the in depth understanding of the structure/function relationship in this rare sugar. A thorough computational study based on molecular dynamics and density functional theory supported by vibrational spectroscopy in the gas phase was carried out to provide a better understanding of the instrinsic conformational preferences of galactofuranose. Based on energetic and spectroscopic criteria, we report a subtantially reduced conformational landscape: methyl α-D-galactofuranose adopts E2/1E conformations and methyl ß-D-galactofuranose adopts 1T2/1E conformations.

O-Acetylated sugars in the gas phase: stability, migration, positional isomers and conformation.

O-Acetylations are functional modifications which can be found on different hydroxyl groups of glycans and which contribute to the fine tuning of their biological activity. Localizing the acetyl modifications is notoriously challenging in glycoanalysis, in particular because of their mobility: loss or migration of the acetyl group may occur through the analytical workflow. Whereas migration conditions in the condensed phase have been rationalized, little is known about the suitability of Mass Spectrometry to retain and resolve the structure of O-acetylated glycan isomers. Here we used the resolving power of infrared ion spectroscopy in combination with ab initio calculations to assess the structure of O-acetylated monosaccharide ions in the gaseous environment of a mass analyzer. N-Acetyl glucosamines were synthetized with an O-acetyl group in positions 3 or 6, respectively. The protonated ions produced by electrospray ionization were observed by mass spectrometry and their vibrational fingerprints were recorded in the 3 µm range by IRMPD spectroscopy (InfraRed Multiple Photon Dissociation). Experimentally, the isomers show distinctive IR fingerprints. Additionally, ab initio calculations confirm the position of the O-acetylation and resolve their gas phase conformation. These findings demonstrate that the position of O-acetyl groups is retained through the transfer from solution to the gas phase, and can be identified by IRMPD spectroscopy.

Non long-range corrected density functionals incorrectly describe the intensity of the CH stretching band in polycyclic aromatic hydrocarbons.

We present a comprehensive study of the most relevant numerical aspects influencing frequencies and intensities in the infrared spectrum of isolated polycyclic aromatic hydrocarbons (PAHs) regarding the overestimate of the IR CH-stretching bands. We use naphthalene as benchmark and show the validity of our results to different members of the PAH family. Our analysis relies on widely employed density functional theory methods and second-order vibrational perturbational theory for the computation of vibrational eigenstates. We have focused on the elucidation of the origin of the systematic overestimate of the intensities in the CH-stretching region. To rule out nonfundamental numerical errors, we have initially considered the influence of the electronic basis set and various other parameters on the different stages of the vibrational analysis. In a second stage, we have benchmarked the results of different density functional theory functionals with respect to the aforementioned overestimate taken as the ratio between the most prominent features of the spectrum, the CH-bending and the CH-stretching bands. Our results unambiguously indicate that the long-range correction plays a major role in this spurious numerical issue. More specifically, this phenomenon is due to an incorrect description of the charge distribution (and hence dipole) within the symmetrically relevant CH bonds. Long-range correction specifically remedies this issue. It improves the description of the intensities in the stretching region while at the same time it does not perturb significantly the rest of the spectrum. With respect to the frequencies, we have observed an overall improvement when compared to noncorrected functionals.

Online Separation and Identification of Isomers Using Infrared Multiple Photon Dissociation Ion Spectroscopy Coupled to Liquid Chromatography: Application to the Analysis of Disaccharides Regio-Isomers and Monosaccharide Anomers.

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.

MS/IR, a new MS-based hyphenated method for analysis of hexuronic acid epimers in glycosaminoglycans.

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.

Hydrogen-Induced Adsorption of Carbon Monoxide on the Gold Dimer Cation: A Joint Experimental and DFT Investigation.

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.

Anharmonic simulations of the vibrational spectrum of sulfated compounds: application to the glycosaminoglycan fragment glucosamine 6-sulfate.

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.

Atomistic Mechanisms for the Nucleation of Aluminum Oxide Nanoparticles.

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.

High-lying electronic states of the rubidium dimer-Ab initio predictions and experimental observation of the 5(1)Σu(+) and 5(1)Πu states of Rb2 by polarization labelling spectroscopy.

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.

Distinguishing isobaric phosphated and sulfated carbohydrates by coupling of mass spectrometry with gas phase vibrational spectroscopy.

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.

TDDFT assessment of functionals for optical 0-0 transitions in small radicals.

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.

Transition dipole moments between the low-lying Ω(g,u)(+∕-) states of the Rb2 and Cs2 molecules.

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).

On-the-fly investigation of XUV excited large molecular ions using a high harmonic generation light source.

We present experiments where extreme ultraviolet femtosecond light pulses are used to photoexcite large molecular ions at high internal energy. This is done by combining an electrospray ionization source and a mass spectrometer with a pulsed light source based on high harmonic generation. This allows one to study the interaction between high energy photons and mass selected ions in conditions that are accessible on large-scale facilities. We show that even without an ion trapping device, systems as large as a protein can be studied. We observe light induced dissociative ionization and proton migration in model systems such as reserpine, insulin and cytochrome c. These results offer new perspectives to perform time-resolved experiments with ultrashort pulses at the heart of the emerging field of attosecond chemistry.

Gabedit--a graphical user interface for computational chemistry softwares.

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/.

Gas phase photo-formation and vacuum UV photofragmentation spectroscopy of tryptophan and tyrosine radical-containing peptides.

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.

Controlled ultrafast ππ*-πσ* dynamics in tryptophan-based peptides with tailored micro-environment.

Ultrafast charge, energy and structural dynamics in molecules are driven by the topology of the multidimensional potential energy surfaces that determines the coordinated electronic and nuclear motion. These processes are also strongly influenced by the interaction with the molecular environment, making very challenging a general understanding of these dynamics on a microscopic level. Here we use electrospray and mass spectrometry technologies to produce isolated molecular ions with a controlled micro-environment. We measure ultrafast photo-induced ππ*-πσ* dynamics in tryptophan species in the presence of a single, charged adduct. A striking increase of the timescale by more than one order of magnitude is observed when changing the added adduct atom. A model is proposed to rationalize the results, based on the localized and delocalized effects of the adduct on the electronic structure of the molecule. These results offer perspectives to control ultrafast molecular processes by designing the micro-environment on the Angström length scale.

Photodetachment of tryptophan anion: an optical probe of remote electron.

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.

Combining Quantum Mechanics and Machine-Learning Calculations for Anharmonic Corrections to Vibrational Frequencies.

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.

Optical properties of isolated hormone oxytocin dianions: ionization, reduction, and copper complexation effects.

Trapped oxytocin (OT) peptide dianions and copper-oxytocin complex dianions are subjected to electron detachment when irradiated by a UV light. Electron photodetachment experiments as a function of the laser wavelength were performed on the native disulfide-containing ring oxytocin, the reduced dithiol oxytocin, and the Cu(II)-oxytocin complex. The electron detachment yield was used to monitor the excited electronic spectrum of the trapped ions. The spectra can be used as a fingerprint of the ionization state of the tyrosine chromophore under different structural environments. In gas-phase oxytocin dianion [OT-2H](2-), the tyrosine is deprotonated while it is neutral for the reduced form of oxytocin [OT(SH)-2H](2-). Optical spectra for the copper complex dianion [OT-4H+Cu](2-) are in favor of a neutral tyrosine in the complex. A structure with the metal cation chelated to four deprotonated amide groups is proposed for this complex.