Abdul-Rahman Allouche

Claude Bernard University Lyon 1 | UCBL · Département de physique

The interest in polycyclic aromatic hydrocarbons (PAH) spans numerous fields, and infrared (IR) spectroscopy is usually the method of choice to disentangle their molecular structure. In order to compute vibrational frequencies, numerous theoretical studies employ either quantum calculation methods, or empirical potentials, but it remains difficult...

Several methods are available to compute the anharmonicity in semi-rigid molecules. However, such methods are not routinely employed yet because of their large 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, thu...

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...

We have performed ab-initio calculations to investigate the van der Waals interaction between a Ca⁺ ion and a helium atom. We have focused on determining the low-lying electronic states of the Ca⁺−He ionic system using advanced theoretical methods, including RCCSD(T) and SA-CASSCF/MRCI , with the incorporation of Davidson and BSSE corrections. Furt...

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...

Group III-nitrides have acquired an important role in science and technology of compound semiconductors for fabricating the novel electronic and optical devices. AlN, InN, GaN and to a lesser extent BN and their alloys InGaN, AlGaN, and AlInN are of great interest for the high temperature electronics and optoelectronics applications. Recent growth...

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...

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...

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 t...

The azobenzene 1-arylazo-2-naphthol has been synthesized and characterized by elemental analysis, ¹H NMR, IR and UV–Vis spectroscopies using both experimental and theoretical methods. The MEP, NPA and FMOs have also been performed at the DFT/B3LYP-D3 level with different solvents in order to investigate the solvent's effect. The energetic behavior...

In this paper, Zn-phthalocyanine (ZnPc) with peripheral mono (ZnPcR1) and tetra quinoleinoxy (ZnPcR4) substituents of the phtalocyanine ring were theoretically studied for the adsorption of NO, CO2, CO, O2 and O3 gases using DFT/B3LYP-D3/6-311++ G (d, p) method. Data displayed a strong interaction between ZnPc, ZnPcR1 and ZnPcR4 and the studied gas...

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 fa...

The Interest in polycyclic aromatic hydrocarbons (PAHs) spans numerous fields and infrared spectroscopy is usually the method of choice to disentangle their molecular structure. In order to compute vibrational frequencies, numerous theoretical studies employ either quantum calculation methods, or empirical potentials, but it remains difficult to co...

In this study, we report the design and the synthesis of a Schiff base; Anil and its corresponding Boron Difluoride complexe; Boranil. The synthesis procedure was carried out adopting new, optimized reaction conditions. The Boranil dye presents the advantage to be emissive in solution. 1H and 19F NMR along with FTIR confirmed both compound's struct...

In this work, we present a thorough theoretical structure and spectroscopic study of the ground and low lying excited states of RbBa molecule. High-level ab-initio calculations are performed, using MCSCF/MRCI+Q level of method, based on the effective core potential (ECP) and core-polarization potential (CPP) approach. The potential energy curves, s...

Aluminum oxide nanoparticles are increasingly sought in numerous technological applications. However, as the nanoparticles grow during the synthesis, two phase transitions occur. At the nanoscale, numerical simulation of the stability of the alumina phases requires the use of empirical potentials that are reliable over a large range of system sizes...

The gas phase IR spectra of three protonated hexosamines are measured in the 3 μm range using IRMPD spectroscopy and compared with DFT simulation of the IR spectra to identify the ring conformations and the contributions of the α and β anomers to the experimental spectra. We propose an original approach for the deconvolution and quantification of h...

Full quantum mechanical calculations are performed to determine the broadening in the far wings of the cesium D1 and D2 line shapes arising from elastic collisions of Cs atom with inert helium atoms. The potential energy curves of the low-lying CsHe molecular states, as well as the related transition dipole moments, are carefully computed from ab i...

Several methods are available to compute the anharmonicity in semi-rigid molecules. However, such methods are not routinely employed yet because of their large 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, thu...

The novel compounds (E)‐2‐(((4‐hydroxyphenyl)imino)methyl)phenol, Tetraphenyl (hydroxyl) imidazole and their corresponding Boron difluoride complexes were synthesized and characterized by spectroscopic techniques. Density functional theory calculations at B3LYP‐D3/6–311++G (d, p) level of theory were performed for the geometric parameters. The MEP...

Aluminum oxide nanoparticles are increasingly sought in numerous technological applications. But, their structural properties can hardly be controlled during the synthesis because phase transitions occurs as the nanoparticle grows. Numerical simulation of such processes requires the use of empirical potentials that are reliable over a large range o...

This work focuses on new materials based on the addition of zinc as specifically metal centers for the capture of NO2 gas with DFT calculations. This study aims at the synthesis and the spectroscopic characterizations of the free base meso-tetrakis-,(3,4,5trimethoxyphenyl)porphyrin (H2TTMP) (I), meso tetrakis(3,4,5trimethoxyphenyl)porphyrinato)zinc...

Hexoses are mainly found in nature in the pyranose form (6-membered ring). Yet, furanose forms (5-membered ring) are observed in some rare polysaccharides.1 Using IRMPD spectroscopy (InfraRed Multiple Photon dissociation), we propose a straightforward diagnostic of the ring-size of N-acetyl galactosamine ions. The furanose form of N-acetyl galactos...

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 relia...

Understanding optical properties of molecular dyes is compulsory to drive progresses 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 dyes molecules in t...

An ab initio approach based on effective core potentials (ECPs), core polarization potentials (CPPs) with three valence electrons and multireference configuration interaction (MRCI) level of calculation is used to determine the adiabatic potential energy curves, the spectroscopic constants and the permanent and transition electric dipole moments of...

Naphthalene dimer cations [C 10 H 8 ] 2⁺ have been produced by using an electron cyclotron resonance plasma ion source and stored in a compact electrostatic ion storage ring. We show that the radiative cooling of these cations is much slower than the isolated monomer naphthalene cations. We also report on photo-dissociation studies in the gas phase...

Although AlInN is originally a wurtzite structure, zincblende and rocksalt are other potential phases. It will be interesting to have a comparative study of the physical properties of this compound in various phases. A DFT-based study of wurtzite, zincblende and rocksalt phases of AlInN alloys is carried out. Structural (lattice parameter, bulk mod...

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 distin...

CdS nanoparticles have attracted much attention due to their important properties. To investigate their structural and optoelectronic properties and CdS-ligand interactions, we compare theoretical calculations and experimental results. In this paper, we determine the structures, vibrational frequencies, and electronic properties of CdS nanoparticle...

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...

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 since 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 a...

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...

The gas phase IR spectra of three protonated N-acetyl hexosamines and their methyl-blocked α and β anomers are measured in the 3 μm spectral range using IRMPD spectroscopy. Using molecular dynamics exploration of the conformational space followed by MP2 energy calculations and DFT simulation of the IR spectra, we propose energetic and spectroscopic...

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 the dissociation of gold dimer cation 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...

iGVPT2 is a program for computing anharmonic corrections to vibration frequencies, based on force field expansion of the potential energy surface in normal mode coordinates. It includes second order vibrational perturbation theory (VPT2) algorithm and its derived methods (VPT2+K, DCPT2, HDCPT2). iGVPT2 is interfaced with several computation chemist...

The lack of robust, high-throughput and sensitive analytical strategies that can conclusively map the structure of glycans has significantly hampered progress in fundamental and applied aspects of glycoscience. Resolution of the anomeric α/β glycan linkage within oligosaccharides remains a particular challenge. Here, we show that ‘memory’ of anomer...

Meso-tetraphenyl iron (III) porphyrin chloride dications (FeTPPCl²⁺)* were prepared in collisions with F⁺ and H⁺ at 3 keV. The dominant fragmentation channels were observed to involve the loss of the Cl atom and the successive loss of neutral phenyl groups for both collisional systems. The mass spectra in correlation with the deposited excitation e...

The formation of HNCO has been studied through DFT calculations in comparison with experimental IR measurements. Four different pathways starting from atomic nitrogen, water and carbon monoxide molecules were considered. Among them, the direct formation of NCO in the presence of water corresponds to the most favourable with a relative energy of 11....

IR spectroscopy of gas phase ions is proposed to resolve positional isomers of sulfated carbohydrates. Mass spectrometric fingerprints and gas phase vibrational spectra in the near and mid IR regions were obtained for sulfated monosaccharides, yielding unambiguous signatures of sulfated isomers. We report the first systematic exploration of the bio...

The direct photodissociation of trapped 85Rb_2^+ (rubidium) molecular ions by the cooling light for the 85Rb magneto-optical trap (MOT) is studied, both experimentally and theoretically. Vibrationally excited Rb2+ ions are created by photoionization of Rb2 molecules formed photoassociatively in the Rb MOT and are trapped in a modified spherical Pau...

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 va...

iGVPT2 is a program for computing anharmonic corrections to vibration frequencies, based on force field expansion of the potential energy surface in normal mode coordinates. It includes second order vibrational perturbation theory (VPT2) algorithm and its derived methods (VPT2+K, DCPT2, HDCPT2). iGVPT2 is interfaced with several computation chemist...

Fast radiative cooling of anthracene cations (C14H10)+ is studied with a compact electrostatic storage device, the Mini-Ring. The time evolution of the internal energy distribution of the stored ions is probed in a time range from 3 to 7 ms using laser-induced dissociation with 3.49-eV photons. The population decay rate due to radiative emission is...

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 irre...

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 since 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 a...

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 spectroscop...

Radiative cooling of polycyclic aromatic hydrocarbon (PAH) cations has been studied using a compact electrostatic ion storage ring, the Mini-Ring, in a time range up to 8 ms. The time evolution of the internal energy distribution of the ensemble of stored ions shows evidences of fast cooling which is attributed to the fluorescence from thermally ex...

Fast population decay of naphthalene cations (C10H8+) has been observed in a compact electrostatic storage ring, the Mini-Ring, up to 5 ms. Laser induced dissociation due to single-photon absorption was used to probe the internal energy distribution (IED) of the stored molecular ions as a function of the storage time. To determine the energy distri...

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 seventeen 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...

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...