Publications by authors named "Jerome Cuny"

41 Publications

Venoarterial Extracorporeal Membrane Oxygenation in Severe Drug Intoxication: A Retrospective Comparison of Survivors and Nonsurvivors.

ASAIO J 2021 Sep 20. Epub 2021 Sep 20.

From the Department of Intensive Care, CHU Lille, Lille, France University of Lille, Inserm U1167, Institut Pasteur de Lille, Lille, France Department of Cardiovascular Surgery, CHU Lille, Lille, France Cardiovascular Intensive Care Unit, CHU Lille, Lille, France University of Lille, Inserm U1011, Institut Pasteur de Lille, EGID, Lille, France Emergency Department and SAMU, CHU Lille, Lille, France University of Lille, Inserm U1285, CNRS UMR 8576, Lille, France.

Selecting patients most likely to benefit from venoarterial extracorporeal membrane oxygenation (V-A ECMO) to treat refractory drug-induced cardiovascular shock remains a difficult challenge for physicians. This study reported short-term survival outcomes and factors associated with mortality in V-A ECMO-treated patients for poisoning. Twenty-two patients placed on V-A ECMO after drug intoxication from January 2014 to December 2020 were retrospectively analyzed. he primary endpoint of this study was survival at hospital discharge. Univariate descriptive analysis was performed to compare survivors and nonsurvivors during hospitalization. The overall survival at hospital discharge was 45.4% (n = 10/22). Survival rate tended to be higher in patients treated for refractory shock (n = 7/10) compared with those treated for refractory cardiac arrest (n = 3/12, p = 0.08). Low-flow duration and time from admission to ECMO cannulation were shorter in survivors (p = 0.02 and p = 0.03, respectively). Baseline characteristics before ECMO, including the class of drugs involved in the poisoning, between survivors and nonsurvivors were not statistically different except pH, bicarbonate, serum lactate, Sequential Organ Failure Assessment, and Survival After Veno-arterial-ECMO (SAVE) score. All patients with SAVE-score risk classes II/III survived whereas 85.7% (n = 12/14) of those with SAVE-score risk classes IV/V died. A lactic acid >9 mmol/L predicts mortality with a sensitivity/specificity ratio of 83.3%/100%. V-A ECMO for severe drug intoxication should be reserved for highly selected poisoned patients who do not respond to conventional therapies. Shortening the timing of V-A ECMO initiation should be a key priority in improving outcomes. Low-flow time >60min, lactic acid >9mmol/L, and SAVE-score may be good indicators of a worse prognosis.
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http://dx.doi.org/10.1097/MAT.0000000000001583DOI Listing
September 2021

Photoinduced Ligand Exchange Dynamics of a Polypyridyl Ruthenium Complex in Aqueous Solution.

J Phys Chem Lett 2021 Aug 29;12(30):7278-7284. Epub 2021 Jul 29.

Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, Laboratoire de Chimie et Physique Quantiques, 31062 Toulouse Cedex 9, France.

The understanding of photoinduced ligand exchange mechanisms in polypyridyl ruthenium(II) complexes operating in aqueous solution is of crucial importance to rationalize their photoreactivity. Herein, we demonstrate that a synergetic use of ab initio molecular dynamics simulations and static calculations, both conducted at the DFT level, can provide a full understanding of photosubstitution mechanisms of a monodentate ligand by a solvent water molecule in archetypal ruthenium complexes in explicit water. The simulations show that the photoinduced loss of a monodentate ligand generates an unreactive 16-electron species in a hitherto undescribed pentacoordinated triplet excited state that converts, via an easily accessible crossing point, to a reactive 16-electron singlet ground state, which combines with a solvent water molecule to yield the experimentally observed aqua complex in less than 10 ps. This work paves the way for the rational design of novel photoactive metal complexes relevant for biological applications.
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http://dx.doi.org/10.1021/acs.jpclett.1c01424DOI Listing
August 2021

Desymmetrised pentaporphyrinic gears mounted on metallo-organic anchors.

Chem Sci 2021 Feb 18;12(13):4709-4721. Epub 2021 Feb 18.

CEMES, Université de Toulouse, CNRS 29 Rue Marvig F-31055 Toulouse Cedex 4 France

Mastering intermolecular gearing is crucial for the emergence of complex functional nanoscale machineries. However, achieving correlated motion within trains of molecular gears remains highly challenging, due to the multiple degrees of freedom of each cogwheel. In this context, we designed and synthesised a series of star-shaped organometallic molecular gears incorporating a hydrotris(indazolyl)borate anchor to prevent diffusion on the surface, a central ruthenium atom as a fixed rotation axis, and an azimuthal pentaporphyrinic cyclopentadienyl cogwheel specifically labelled to monitor its motion by non-time-resolved Scanning Tunneling Microscopy (STM). Desymmetrisation of the cogwheels was first achieved sterically, . by introducing one tooth longer than the other four. For optimal mechanical interactions, chemical labelling was also investigated as a preferential way to induce local contrast in STM images, and the electronic properties of one single paddle were modulated by varying the porphyrinic scaffold or the nature of the central metal. To reach such a structural diversity, our modular synthetic approach relied on sequential cross-coupling reactions on a penta(-halogenophenyl)cyclopentadienyl ruthenium(ii) key building block, bearing a single pre-activated -iodophenyl group. Chemoselective Sonogashira or more challenging Suzuki-Miyaura reactions allowed the controlled introduction of the tagged porphyrinic tooth, and the subsequent four-fold cross-couplings yielded the prototypes of pentaporphyrinic molecular gears for on-surface studies, incorporating desymmetrised cogwheels over 5 nm in diameter.
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http://dx.doi.org/10.1039/d0sc06379gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8179540PMC
February 2021

Effect of intra-arrest trans-nasal evaporative cooling in out-of-hospital cardiac arrest: a pooled individual participant data analysis.

Crit Care 2021 06 8;25(1):198. Epub 2021 Jun 8.

Department of Medicine Center for Resuscitation Science, Karolinska Institute, Solna, Sweden.

Background: Randomized trials have shown that trans-nasal evaporative cooling initiated during CPR (i.e. intra-arrest) effectively lower core body temperature in out-of-hospital cardiac arrest patients. However, these trials may have been underpowered to detect significant differences in neurologic outcome, especially in patients with initial shockable rhythm.

Methods: We conducted a post hoc pooled analysis of individual data from two randomized trials including 851 patients who eventually received the allocated intervention and with available outcome ("as-treated" analysis). Primary outcome was survival with favourable neurological outcome at hospital discharge (Cerebral Performance Category [CPC] of 1-2) according to the initial rhythm (shockable vs. non-shockable). Secondary outcomes included complete neurological recovery (CPC 1) at hospital discharge.

Results: Among the 325 patients with initial shockable rhythms, favourable neurological outcome was observed in 54/158 (34.2%) patients in the intervention and 40/167 (24.0%) in the control group (RR 1.43 [confidence intervals, CIs 1.01-2.02]). Complete neurological recovery was observed in 40/158 (25.3%) in the intervention and 27/167 (16.2%) in the control group (RR 1.57 [CIs 1.01-2.42]). Among the 526 patients with initial non-shockable rhythms, favourable neurological outcome was in 10/259 (3.8%) in the intervention and 13/267 (4.9%) in the control group (RR 0.88 [CIs 0.52-1.29]; p = 0.67); survival and complete neurological recovery were also similar between groups. No significant benefit was observed for the intervention in the entire population.

Conclusions: In this pooled analysis of individual data, intra-arrest cooling was associated with a significant increase in favourable neurological outcome in out-of-hospital cardiac arrest patients with initial shockable rhythms. Future studies are needed to confirm the potential benefits of this intervention in this subgroup of patients.
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http://dx.doi.org/10.1186/s13054-021-03583-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8188685PMC
June 2021

Density-functional tight-binding: basic concepts and applications to molecules and clusters.

Adv Phys X 2020 18;5(1):1710252. Epub 2020 Feb 18.

Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France.

The scope of this article is to present an overview of the Density Functional based Tight Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and its standard formulation up to second order. It also addresses methodological developments such as third order expansion, inclusion of non-covalent interactions, schemes to solve the self-interaction error, implementation of long-range short-range separation, treatment of excited states the time-dependent DFTB scheme, inclusion of DFTB in hybrid high-level/low level schemes (DFT/DFTB or DFTB/MM), fragment decomposition of large systems, large scale potential energy landscape exploration with molecular dynamics in ground or excited states, non-adiabatic dynamics. A number of applications are reviewed, focusing on -(i)- the variety of systems that have been studied such as small molecules, large molecules and biomolecules, bare orfunctionalized clusters, supported or embedded systems, and -(ii)- properties and processes, such as vibrational spectroscopy, collisions, fragmentation, thermodynamics or non-adiabatic dynamics. Finally outlines and perspectives are given.
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http://dx.doi.org/10.1080/23746149.2019.1710252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7116320PMC
February 2020

Simulation of Liquids with the Tight-Binding Density-Functional Approach and Improved Atomic Charges.

J Phys Chem B 2020 08 18;124(34):7421-7432. Epub 2020 Aug 18.

Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.

Theoretical description of liquids, especially liquid water, is an ongoing subject with important implications in various domains such as homogeneous catalysis; solvation of molecular, ionic, and biomolecular species; and reactivity. Various formalisms exist to describe liquids, each one displaying its own balance between accuracy and computational cost that defines its range of applications. The present article revisits the ability of the density-functional-based tight-binding (SCC-DFTB) approach to model liquids by focusing on liquid water and liquid benzene under ambient conditions. To do so, we benchmark a recent correction for the SCC-DFTB atomic charges that allows for a drastic improvement of the pair radial distribution functions of liquid water as compared to both experimental data and density-functional theory results performed in the generalized-gradient approximation. We also report the coupling of the deMonNano and i-PI codes to perform path-integral molecular dynamics. This allows us to rationalize the impact of nuclear quantum effects on the SCC-DFTB description of liquid water. This study evidences the rather good ability of SCC-DFTB to describe liquid water and liquid benzene. As the first example of application, we also present results for a benzene molecule solvated in water with the perspectives of further studies devoted to solvent/water interfaces.
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http://dx.doi.org/10.1021/acs.jpcb.0c04167DOI Listing
August 2020

Effect of Trans-Nasal Evaporative Intra-arrest Cooling on Functional Neurologic Outcome in Out-of-Hospital Cardiac Arrest: The PRINCESS Randomized Clinical Trial.

JAMA 2019 05;321(17):1677-1685

Department of Medicine, Center for Resuscitation Science, Karolinska Institute, Solna, Sweden.

Importance: Therapeutic hypothermia may increase survival with good neurologic outcome after cardiac arrest. Trans-nasal evaporative cooling is a method used to induce cooling, primarily of the brain, during cardiopulmonary resuscitation (ie, intra-arrest).

Objective: To determine whether prehospital trans-nasal evaporative intra-arrest cooling improves survival with good neurologic outcome compared with cooling initiated after hospital arrival.

Design, Setting, And Participants: The PRINCESS trial was an investigator-initiated, randomized, clinical, international multicenter study with blinded assessment of the outcome, performed by emergency medical services in 7 European countries from July 2010 to January 2018, with final follow-up on April 29, 2018. In total, 677 patients with bystander-witnessed out-of-hospital cardiac arrest were enrolled.

Interventions: Patients were randomly assigned to receive trans-nasal evaporative intra-arrest cooling (n = 343) or standard care (n = 334). Patients admitted to the hospital in both groups received systemic therapeutic hypothermia at 32°C to 34°C for 24 hours.

Main Outcomes And Measures: The primary outcome was survival with good neurologic outcome, defined as Cerebral Performance Category (CPC) 1-2, at 90 days. Secondary outcomes were survival at 90 days and time to reach core body temperature less than 34°C.

Results: Among the 677 randomized patients (median age, 65 years; 172 [25%] women), 671 completed the trial. Median time to core temperature less than 34°C was 105 minutes in the intervention group vs 182 minutes in the control group (P < .001). The number of patients with CPC 1-2 at 90 days was 56 of 337 (16.6%) in the intervention cooling group vs 45 of 334 (13.5%) in the control group (difference, 3.1% [95% CI, -2.3% to 8.5%]; relative risk [RR], 1.23 [95% CI, 0.86-1.72]; P = .25). In the intervention group, 60 of 337 patients (17.8%) were alive at 90 days vs 52 of 334 (15.6%) in the control group (difference, 2.2% [95% CI, -3.4% to 7.9%]; RR, 1.14 [95% CI, 0.81-1.57]; P = .44). Minor nosebleed was the most common device-related adverse event, reported in 45 of 337 patients (13%) in the intervention group. The adverse event rate within 7 days was similar between groups.

Conclusions And Relevance: Among patients with out-of-hospital cardiac arrest, trans-nasal evaporative intra-arrest cooling compared with usual care did not result in a statistically significant improvement in survival with good neurologic outcome at 90 days.

Trial Registration: ClinicalTrials.gov Identifier: NCT01400373.
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http://dx.doi.org/10.1001/jama.2019.4149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6506882PMC
May 2019

Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review.

Molecules 2019 Apr 26;24(9). Epub 2019 Apr 26.

Programa de Doctorado en Nanociencias y Nanotecnología, CINVESTAV, Av. Instituto Politécnico Nacional, 2508, A.P. 14-740, Ciudad de México 07000, Mexico.

deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born-Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.
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http://dx.doi.org/10.3390/molecules24091653DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6539060PMC
April 2019

Size-dependent proton localization in hydrated uracil clusters: A joint experimental and theoretical study.

J Chem Phys 2019 Jan;150(1):014303

Laboratoire Collisions Agrégats Réactivité (LCAR/IRSAMC) UMR5589, Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.

A collision-induced dissociation study of hydrated protonated uracil (HO)UH clusters is reported. The mass-selected clusters collide with water molecules and rare gases at a controlled center of mass collision energy. From these measurements, absolute fragmentation cross sections and branching ratios are extracted as a function of the uracil hydration. For small clusters, up to n = 4, we observe that only neutral water molecules are evaporated upon collisions, whereas, for larger clusters, neutral uracil is also evaporated: this transition in the nature of the evaporation products is interpreted considering the lowest-energy isomers of each species that are obtained from a combination of density-functional based tight-binding and MP2 calculations. The simulations show that in (HO)UH the proton is located on the uracil molecule or on a water molecule strongly bound to uracil whereas, in larger clusters, the proton is bound to water molecules far from uracil. This correlation between the structure of the low-energy isomers and the experimental fragmentation channel suggests that dissociation may occur in a very short time after collisions so that energy has not enough time to be redistributed among all degrees of freedom and the ground-state geometry of the parent cluster partly determines the nature of the favored fragmentation channels. Of course, thermal dissociations originating from long lived, thus thermalized, collision complexes cannot be ruled out but they are not expected to play the major role since the experimental results can be satisfactorily accounted for by assuming that the fragmentation processes are mainly impulsive.
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http://dx.doi.org/10.1063/1.5044481DOI Listing
January 2019

The Ouzo effect to selectively assemble molybdenum clusters into nanomarbles or nanocapsules with increased HER activity.

Chem Commun (Camb) 2018 Nov;54(95):13387-13390

Univ Rennes, CNRS, ISCR-UMR6226, SCANMat-UMS2001, F-35000 Rennes, France.

Metal cluster nanoparticles are obtained by simple solvent shifting called the Ouzo effect. Remarkably, the assembly of [{Mo6Br8}L6]2- (L = Br- or NCS-) cluster units can be directed into nanomarbles or nanocapsules depending on the cluster chemistry. When deposited on electrodes, these nanoparticles show good activities in electrochemical water splitting under mild conditions.
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http://dx.doi.org/10.1039/c8cc07402jDOI Listing
November 2018

Metal Atom Clusters as Building Blocks for Multifunctional Proton-Conducting Materials: Theoretical and Experimental Characterization.

Inorg Chem 2018 Aug 30;57(16):9814-9825. Epub 2018 Jul 30.

Univ. Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes) - UMR 6226, F-35000 Rennes , France.

The search for new multifunctional materials displaying proton-conducting properties is of paramount necessity for the development of electrochromic devices and supercapacitors as well as for energy conversion and storage. In the present study, proton conductivity is reported for the first time in three molybdenum cluster-based materials: (H)[MoBrS(OH)]-12HO and (H)[MoX(OH)]-12HO (X = Cl, Br). We show that the self-assembling of the luminescent [MoL(OH)] cluster units leads to both luminescence and proton conductivity (σ = 1.4 × 10 S·cm in (H)[MoCl(OH)]-12HO under wet conditions) in the three materials. The latter property results from the strong hydrogen-bond network that develops between the clusters and the water molecules and is magnified by the presence of protons that are statistically shared by apical hydroxyl groups between adjacent clusters. Their role in the proton conduction is highlighted at the molecular scale by ab initio molecular dynamics simulations that demonstrate that concerted proton transfers through the hydrogen-bond network are possible. Furthermore, thermogravimetric analysis also shows the ability of the compounds to accommodate more or less water molecules, which highlights that vehicular (or diffusion) transport probably occurs within the materials. An infrared fingerprint of the mobile protons is finally proposed based on both theoretical and experimental proofs. The present study relies on a synergic computational/experimental approach that can be extended to other proton-conducting materials. It thus paves the way to the design and understanding of new multifunctional proton-conducting materials displaying original and exciting properties.
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http://dx.doi.org/10.1021/acs.inorgchem.8b00340DOI Listing
August 2018

Evaluation of Gas-to-Liquid O Chemical Shift of Water: A Test Case for Molecular and Periodic Approaches.

J Chem Theory Comput 2018 Aug 6;14(8):4041-4051. Epub 2018 Aug 6.

LPCNO , Université Fédérale de Toulouse Midi-Pyrénées, INSA-CNRS-UPS , 135 avenue de Rangueil , 31077 Cedex 4 Toulouse , France.

Modeling liquid water features is a challenging and ongoing task that brings together a number of computational issues related to the description both of its electronic and geometrical structure. In order to go a step further in the understanding of this peculiar liquid, we present a thorough analysis of NMR gas-to-liquid O and H shifts of water using density functional theory based molecular dynamics. In order to be as consistent as possible, we consider the influence of basis sets, exchange-correlation functionals, and structural models, in both molecular and periodic schemes, to evaluate O and H nuclear shieldings. We show that strong error compensations between functional and basis-set expansion can be obtained in molecular approaches which artificially produces good O gas-to-liquid shifts with relatively small basis sets. We also demonstrate that, despite their ability to provide reliable liquid phase structures, generalized-gradient approximation based exchange-correlation functionals lead to strongly inconsistent values for O gas-to-liquid shift. This latter property is shown to be strongly influenced by intramolecular electronic delocalization, accentuated by the surrounded molecules. In contrast, H is less sensitive to this effect. By including a Hartree-Fock exchange term, through the use of hybrid functionals which partially correct the self-interaction error, better agreement with experimental values is obtained. The present study provides a detailed guideline to properly evaluate gas-to-liquid shifts in hydrogen bonded systems and emphasizes that, for nuclear shieldings, an accurate electronic structure evaluation prevails over the description of the liquid structure.
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http://dx.doi.org/10.1021/acs.jctc.8b00243DOI Listing
August 2018

Conformational Study and Chiroptical Properties of Chiral Dimethyl-Ethylenedithio-Tetrathiafulvalene (DM-EDT-TTF).

Chimia (Aarau) 2018 Jun;72(6):389-393

Laboratoire Moltech-Anjou, UMR 6200 CNRS-Université d'Angers, UFR Sciences, Bât. K 2 Bd. Lavoisier, 49045 Angers, France;, Email:

The enantiopure dimethyl-ethylenedithio-tetrathiafulvalene (DM-EDT-TTF) donor exists as biaxial (ax, ax) and biequatorial (eq, eq) conformers in equilibrium. DFT calculations combined with free energy surface (FES) analysis establish that the (ax, ax) form is more stable by ∼0.7 kcal·mol-1 than the (eq, eq) one and that the inter-conversion process involves a sequential conformational change through a boat type (ax, eq) conformer with an activation energy of ∼3 kcal.mol-1. TD-DFT calculations show similar, but opposite in sign, CD bands for the two conformers. A Boltzmann type average of the two CD curves, corresponding to a ratio of three (ax, ax) for one (eq, eq) conformers in equilibrium in solution, provides an excellent agreement with the experimental curve.
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http://dx.doi.org/10.2533/chimia.2018.389DOI Listing
June 2018

Density-functional tight-binding approach for metal clusters, nanoparticles, surfaces and bulk: application to silver and gold.

J Phys Condens Matter 2018 Aug 19;30(30):303001. Epub 2018 Jun 19.

Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.

Density-functional based tight-binding (DFTB) is an efficient quantum mechanical method that can describe a variety of systems, going from organic and inorganic compounds to metallic and hybrid materials. The present topical review addresses the ability and performance of DFTB to investigate energetic, structural, spectroscopic and dynamical properties of gold and silver materials. After a brief overview of the theoretical basis of DFTB, its parametrization and its transferability, we report its past and recent applications to gold and silver systems, including small clusters, nanoparticles, bulk and surfaces, bare and interacting with various organic and inorganic compounds. The range of applications covered by those studies goes from plasmonics and molecular electronics, to energy conversion and surface chemistry. Finally, perspectives of DFTB in the field of gold and silver surfaces and NPs are outlined.
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http://dx.doi.org/10.1088/1361-648X/aacd6cDOI Listing
August 2018

Molecular Dynamics Study of the Collision-Induced Reaction of H with CO on Small Water Clusters.

J Phys Chem A 2017 Dec 4;121(49):9485-9494. Epub 2017 Dec 4.

Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse (UPS) and CNRS , 118 Route de Narbonne, F-31062 Toulouse, France.

The successive hydrogenation of CO is supposed to be the main mechanism leading to the formation of complex oxygenated species in the interstellar medium, possibly mediated by ice layers or ice grains. In order to simulate the dynamical influence of a water environment on the first step of the hydrogenation process, we perform molecular dynamics simulations of the reactive collision of H with CO adsorbed on water clusters in the framework of the self-consistent-charge density functional based tight-binding approach (SCC-DFTB) to calculate potential energy surfaces. The reaction probabilities and the reactive cross sections are determined for water cluster sizes up to ten water molecules. The collision results are analyzed in terms of different reaction pathways: reactive or nonreactive, sticking or desorption of the products or reactants. We show that the HCO radical, although potentially formed as an intermediate regardless of the size of the water cluster, is significantly stabilized for cluster sizes larger than one water molecule and may remain adsorbed on water clusters with more than three molecules. This behavior is shown to be linked with the dissipation of the collision energy into vibrational excitation of the water cluster.
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http://dx.doi.org/10.1021/acs.jpca.7b09217DOI Listing
December 2017

Theoretical investigation of the solid-liquid phase transition in protonated water clusters.

Phys Chem Chem Phys 2017 Oct;19(40):27288-27298

Laboratoire de Chimie et Physique Quantiques (LCPQ/IRSAMC), Université de Toulouse and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.

Protonated water clusters have received a lot of attention as they offer tools to bridge the gap between molecular and bulk scales of water. However, their properties are still not fully understood and deserve further theoretical and experimental investigations. In this work, we simulate the caloric curves of protonated water clusters (HO)H (n = 20-23). These curves, which have recently been measured experimentally, are characteristic of the phase changes occurring in the aggregates with respect to temperature. The present simulations are achieved by combining parallel-tempering molecular dynamics and the self-consistent-charge density-functional based tight-binding approach and are focused on a restricted size range around (HO)H which presents singular properties. The shape of the experimental caloric curves and their size dependence are satisfactorily reproduced by the simulations which allows us to further provide a description of the phase transition in terms of structural modifications, dynamics of water molecules and proton mobility. Similar to the experiments, we observe that (HO)H exhibits a sharper phase transition than the neighbouring size clusters, which can be traced back to both structural and dynamic peculiarities.
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http://dx.doi.org/10.1039/c7cp04863gDOI Listing
October 2017

Keto-polymethines: a versatile class of dyes with outstanding spectroscopic properties for and two-photon microscopy imaging.

Chem Sci 2017 Jan 3;8(1):381-394. Epub 2016 Aug 3.

ENS Lyon , Université de Lyon 1 , CNRS Laboratoire de chimie de l'ENS Lyon , UMR 5182 CNRS, 46 allée d'Italie , 69364 Lyon , France . Email: ; Email:

The synthesis of keto-heptamethine derivatives has been expanded to various new symmetrical and asymmetrical structures, including an unprecedented di-anionic keto-polymethine. The spectroscopic behavior of these new dyes has been systematically and thoroughly investigated, revealing that the formation of hydrogen bond interactions with protic solvents is responsible for a dramatic enhancement of the fluorescence quantum yield in the far-red spectral region. The existence of these strong hydrogen-bond interactions was further confirmed by molecular dynamics simulations. These bis-dipolar polymethines exhibit large two-photon absorption (TPA) cross-sections ( in GM) in the near-infrared, making them ideal candidates for NIR-to-NIR two-photon microscopy imaging applications. We demonstrate that the molecular engineering of the hydrophilic/hydrophobic balance enables targeting of different cellular components, such as cytoplasm or cell membranes. Addition of appropriate substituents provides the molecule with high-water-solubility, affording efficient two-photon probes for angiography.
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http://dx.doi.org/10.1039/c6sc02488bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5365052PMC
January 2017

Metadynamics combined with auxiliary density functional and density functional tight-binding methods: alanine dipeptide as a case study.

J Mol Model 2017 Mar 15;23(3):72. Epub 2017 Feb 15.

UMR 5253 CNRS/ENSCM/UM, MACS, Institut Charles Gerhardt Montpellier, 8 rue de l'Ecole Normale, 34296, Montpellier cedex 5, France.

Application of ab initio molecular dynamics to study free energy surfaces (FES) is still not commonly performed because of the extensive sampling required. Indeed, it generally necessitates computationally costly simulations of more than several hundreds of picoseconds. To achieve such studies, efficient density functional theory (DFT) formalisms, based on various levels of approximate computational schemes, have been developed, and provide a good alternative to commonly used DFT implementations. We report benchmark results on the conformational change FES of alanine dipeptide obtained with auxiliary density functional theory (ADFT) and second- and third-order density functional tight-binding (DFTB) methods coupled to metadynamics simulations. The influence of an explicit water solvent is also studied with DFTB, which was made possible by its lower computational cost compared to ADFT. Simulations lengths of 2.1 and 15 ns were achieved with ADFT and DFTB, respectively, in a reasonably short computational time. ADFT leads to a free energy difference (ΔF ) of ∼ -3 kcal mol between the two low energy conformers, C and C, which is lower by only 1.5 kcal mol than the ΔF computed with DFTB. The two minima in ADFT FES are separated by an energy barrier of 9 kcal mol, which is higher than the DFTB barriers by 2-4 kcal mol. Despite these small quantitative differences, the DFTB method reveals FES shapes, confor-mation geometries and energies of the stationary points in good agreement with these found with ADFT. This validates the promising applicability of DFTB to FES of reactions occurring in larger-size systems placed in complex environments.
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http://dx.doi.org/10.1007/s00894-017-3265-4DOI Listing
March 2017

Structural Characterization of Sulfur-Containing Water Clusters Using a Density-Functional Based Tight-Binding Approach.

J Phys Chem A 2016 Nov 3;120(45):9089-9100. Epub 2016 Nov 3.

Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS , 118 Route de Narbonne, F-31062 Toulouse, France.

A global optimization search of low-energy isomers is carried out to investigate the structural and stability properties of sulfur-containing water clusters, including both (HO)SO and (HO)HSO aggregates. The systematic optimization algorithm involves a combination of parallel-tempering molecular dynamics and periodic gradient-driven quenches with energy and energy-gradient calculations performed using the Self-Consistent-Charge Density-Functional based Tight-Binding (SCC-DFTB) scheme. Comparisons with new MP2 and DFT calculations on the smallest systems and previous ab initio investigations of the literature show that the SCC-DFTB approach provides a fairly accurate description of both neutral and ionic species, comparable to that of DFT. Structural and stability features of larger sulfur-containing clusters, with up to 20 water molecules, are also determined using the SCC-DFTB scheme. The interest of this work is 2-fold: (i) the benchmark on small species demonstrates the ability of SCC-DFTB to describe complex potential energy landscapes involving hydrogen-bonds and proton transfers; (ii) it opens the way to the study of large clusters that can hardly be performed within ab initio approaches.
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http://dx.doi.org/10.1021/acs.jpca.6b08251DOI Listing
November 2016

Benchmarking Density Functional Based Tight-Binding for Silver and Gold Materials: From Small Clusters to Bulk.

J Phys Chem A 2016 Oct 13;120(42):8469-8483. Epub 2016 Oct 13.

CEMES CNRS UPR 8011 , 29 rue Jeanne Marvig, BP 94347, 31055 Toulouse Cedex 4, France.

We benchmark existing and improved self-consistent-charge density functional based tight-binding (SCC-DFTB) parameters for silver and gold clusters as well as for bulk materials. In the former case, our benchmarks focus on both the structural and energetic properties of small-size Ag and Au clusters (N from 2 to 13), medium-size clusters with N = 20 and 55, and finally larger nanoparticles with N = 147, 309, and 561. For bulk materials, structural, energetics and elastic properties are discussed. We show that SCC-DFTB is quite satisfactory in reproducing essential differences between silver and gold aggregates, in particular their 2D-3D structural transitions, and their dependency upon cluster charge. SCC-DFTB is also in agreement with DFT and experiments in the medium-size regime regarding the energetic ordering of the different low-energy isomers and allows for an overall satisfactory treatment of bulk properties. A consistent convergence between the cohesive energies of the largest investigated nanoparticles and the bulk's is obtained. On the basis of our results for nanoparticles of increasing size, a two-parameter analytical extrapolation of the cohesive energy is proposed. This formula takes into account the reduction of the cohesive energy for undercoordinated surface sites and converges properly to the bulk cohesive energy. Values for the surface sites cohesive energies are also proposed.
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http://dx.doi.org/10.1021/acs.jpca.6b09292DOI Listing
October 2016

Ab Initio Quality NMR Parameters in Solid-State Materials Using a High-Dimensional Neural-Network Representation.

J Chem Theory Comput 2016 Feb 19;12(2):765-73. Epub 2016 Jan 19.

Condensed Matter Physics Section, The Abdus Salaam International Center for Theoretical Physics , Strada Costiera 11, I-34151 Trieste, Trieste, Italy.

Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful experimental tools to probe the local atomic order of a wide range of solid-state compounds. However, due to the complexity of the related spectra, in particular for amorphous materials, their interpretation in terms of structural information is often challenging. These difficulties can be overcome by combining molecular dynamics simulations to generate realistic structural models with an ab initio evaluation of the corresponding chemical shift and quadrupolar coupling tensors. However, due to computational constraints, this approach is limited to relatively small system sizes which, for amorphous materials, prevents an adequate statistical sampling of the distribution of the local environments that is required to quantitatively describe the system. In this work, we present an approach to efficiently and accurately predict the NMR parameters of very large systems. This is achieved by using a high-dimensional neural-network representation of NMR parameters that are calculated using an ab initio formalism. To illustrate the potential of this approach, we applied this neural-network NMR (NN-NMR) method on the (17)O and (29)Si quadrupolar coupling and chemical shift parameters of various crystalline silica polymorphs and silica glasses. This approach is, in principal, general and has the potential to be applied to predict the NMR properties of various materials.
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http://dx.doi.org/10.1021/acs.jctc.5b01006DOI Listing
February 2016

Cationic Methylene-Pyrene Isomers and Isomerization Pathways: Finite Temperature Theoretical Studies.

J Phys Chem A 2015 Dec 11;119(51):12845-54. Epub 2015 Dec 11.

Université de Toulouse, UPS-OMP, IRAP , 31400 Toulouse, France.

This paper provides spectral characterizations of the two isomers of the 1-methylenepyrene cation, namely, the 1-pyrenemethylium and a pyrene-like isomer owing a tropylium cycle. Both are possible photodissociation products of the 1-methylpyrene cation and were proposed as potential contributors to the diffuse interstellar bands. In that respect, vibrational and electronic spectra are computed for the optimized structures at the density functional theory (DFT) and time-dependent (TD-)DFT levels. Finite temperature effects on these spectra are estimated from molecular dynamics simulations within the density functional-based tight-binding (DFTB) and TD-DFTB frameworks, these methods being first benchmarked against DFT and TD-DFT calculations. The computed spectra allow discrimination of the two isomers. When the temperature increases, bands are observed to redshift and merge. The isomerization mechanism is investigated with the metadynamics technique, a biased dynamics scheme allowing to probe reaction mechanisms with high energy barriers by investigating the free energy surface at various temperatures. Four pathways with similar barrier heights (3.5-4 eV) are found, showing that the interconversion process would only occur in interstellar clouds under photoactivation. The present study opens the way to simulations on larger methyl- and methylenePAHs of astrophysical interest and their experimental investigation.
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http://dx.doi.org/10.1021/acs.jpca.5b09494DOI Listing
December 2015

Evaluation of (95)Mo Nuclear Shielding and Chemical Shift of [Mo6X14](2-) Clusters in the Liquid Phase.

Inorg Chem 2015 Aug 24;54(16):7673-83. Epub 2015 Jul 24.

†Institut des Sciences Chimiques de Rennes, UMR 6226 CNRS-Université de Rennes 1-Ecole Nationale Supérieure de Chimie de Rennes, 11 Allée de Beaulieu, 35708 Rennes, France.

[Mo6X14](2-) octahedral molybdenum clusters are the main building blocks of a large range of materials. Although (95)Mo nuclear magnetic resonance was proposed to be a powerful tool to characterize their structural and dynamical properties in solution, these measurements have never been complemented by theoretical studies which can limit their interpretation for complex systems. In this Article, we use quantum chemical calculations to evaluate the (95)Mo chemical shift of three clusters: [Mo6Cl14](2-), [Mo6Br14](2-), and [Mo6I14](2-). In particular, we test various computational parameters influencing the quality of the results: size of the basis set, treatment of relativistic and solvent effects. Furthermore, to provide quantum chemical calculations that are directly comparable with experimental data, we evaluate for the first time the (95)Mo nuclear magnetic shielding of the experimental reference, namely, MoO4(2-) in aqueous solution. This is achieved by combining ab initio molecular dynamics simulations with a periodic approach to evaluate the (95)Mo nuclear shieldings. The results demonstrate that, despite the difficulty to obtain accurate (95)Mo chemical shifts, relative values for a cluster series can be fairly well-reproduced by DFT calculations. We also show that performing an explicit solvent treatment for the reference compound improves by ∼50 ppm the agreement between theory and experiment. Finally, the standard deviation of ∼70 ppm that we calculate for the (95)Mo nuclear shielding of the reference provides an estimation of the accuracy we can achieve for the calculation of the (95)Mo chemical shifts using a static approach. These results demonstrate the growing ability of quantum chemical calculations to complement and interpret complex experimental measurements.
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http://dx.doi.org/10.1021/acs.inorgchem.5b00396DOI Listing
August 2015

Phase changes of the water hexamer and octamer in the gas phase and adsorbed on polycyclic aromatic hydrocarbons.

Phys Chem Chem Phys 2015 Jul;17(26):17079-89

Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.

We investigate thermodynamic properties of small water clusters adsorbed on polycyclic aromatic hydrocarbons (PAHs), which are relevant systems in the context of astrophysical and atmospheric chemistry. We present heat capacity curves computed from parallel-tempering molecular dynamics and Monte Carlo simulations that were performed using the self-consistent-charge density-functional based tight-binding method. These curves are characteristic of the phase changes occurring in the aggregates and provide useful information on the evolution of the interaction between the water molecules and the PAHs as a function of temperature. After benchmarking our approach on the water hexamer and octamer in the gas phase, we present some results for these same clusters adsorbed on coronene and circumcoronene. When compared to the curves obtained for the isolated water clusters, the phase change temperature significantly decreases for the (H2O)8-PAH clusters whereas it depends on the nature of the PAH in the case of the hexamer. We analyse these differences as connected to the relative energies of the optimized characteristic isomers and to their dynamical behavior. We also evidence the population changes of the various cluster isomers as a function of temperature.
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http://dx.doi.org/10.1039/c5cp02099aDOI Listing
July 2015

Ab initio molecular dynamics study of the mechanism of proton recombination with a weak base.

J Phys Chem B 2014 Dec 21;118(48):13903-12. Epub 2014 Nov 21.

Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS , 118 Route de Narbonne, F-31062 Toulouse, France.

Despite its fundamental nature, many of the microscopic features of acid–base recombination remain poorly understood. In this work, we use ab initio molecular dynamics simulations to study the recombination of the proton with a weak base, the carbonate ion CO3(2–). Our simulations elucidate the network structure around CO3(2–) that provides a distribution of pathways over which recombination can occur. We observe that the penultimate neutralization step involves a correlated behavior of the transferred protons that is mediated by the water wires decorating the carbonate. These concerted proton transfers are coupled to collective compressions of these water wires. We show further that these processes are dynamically coupled to the reorganization of the water molecules hydrating the CO3(2–) ion. The insights from these simulations help to bridge the structural and dynamical complexity of the microscopic mechanisms with those of phenomenological models invoked by experiments in this field.
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http://dx.doi.org/10.1021/jp507246eDOI Listing
December 2014

Aqueous solutions: state of the art in ab initio molecular dynamics.

Philos Trans A Math Phys Eng Sci 2014 Mar 10;372(2011):20120482. Epub 2014 Feb 10.

Department of Chemistry and Applied Biosciences, ETH Zurich and Università della Svizzera Italiana, , via G. Buffi 13, 6900 Lugano, Switzerland.

The simulation of liquids by ab initio molecular dynamics (AIMD) has been a subject of intense activity over the last two decades. The significant increase in computational resources as well as the development of new and efficient algorithms has elevated this method to the status of a standard quantum mechanical tool that is used by both experimentalists and theoreticians. As AIMD computes the electronic structure from first principles, it is free of ad hoc parametrizations and has thus been applied to a large variety of physical and chemical problems. In particular, AIMD has provided microscopic insight into the structural and dynamical properties of aqueous solutions which are often challenging to probe experimentally. In this review, after a brief theoretical description of the Born-Oppenheimer and Car-Parrinello molecular dynamics formalisms, we show how AIMD has enhanced our understanding of the properties of liquid water and its constituent ions: the proton and the hydroxide ion. Thereafter, a broad overview of the application of AIMD to other aqueous systems, such as solvated organic molecules and inorganic ions, is presented. We also briefly describe the latest theoretical developments made in AIMD, such as methods for enhanced sampling and the inclusion of nuclear quantum effects.
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http://dx.doi.org/10.1098/rsta.2012.0482DOI Listing
March 2014

Nuclear quantum effects and hydrogen bond fluctuations in water.

Proc Natl Acad Sci U S A 2013 Sep 6;110(39):15591-6. Epub 2013 Sep 6.

Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, United Kingdom.

The hydrogen bond (HB) is central to our understanding of the properties of water. However, despite intense theoretical and experimental study, it continues to hold some surprises. Here, we show from an analysis of ab initio simulations that take proper account of nuclear quantum effects that the hydrogen-bonded protons in liquid water experience significant excursions in the direction of the acceptor oxygen atoms. This generates a small but nonnegligible fraction of transient autoprotolysis events that are not seen in simulations with classical nuclei. These events are associated with major rearrangements of the electronic density, as revealed by an analysis of the computed Wannier centers and (1)H chemical shifts. We also show that the quantum fluctuations exhibit significant correlations across neighboring HBs, consistent with an ephemeral shuttling of protons along water wires. We end by suggesting possible implications for our understanding of how perturbations (solvated ions, interfaces, and confinement) might affect the HB network in water.
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http://dx.doi.org/10.1073/pnas.1308560110DOI Listing
September 2013

Proton transfer through the water gossamer.

Proc Natl Acad Sci U S A 2013 Aug 18;110(34):13723-8. Epub 2013 Jul 18.

Department of Chemistry and Applied Biosciences, Eidgenössiche Technische Hochschule Zurich and Università della Svizzera Italiana, CH-6900 Lugano, Switzerland.

The diffusion of protons through water is understood within the framework of the Grotthuss mechanism, which requires that they undergo structural diffusion in a stepwise manner throughout the water network. Despite long study, this picture oversimplifies and neglects the complexity of the supramolecular structure of water. We use first-principles simulations and demonstrate that the currently accepted picture of proton diffusion is in need of revision. We show that proton and hydroxide diffusion occurs through periods of intense activity involving concerted proton hopping followed by periods of rest. The picture that emerges is that proton transfer is a multiscale and multidynamical process involving a broader distribution of pathways and timescales than currently assumed. To rationalize these phenomena, we look at the 3D water network as a distribution of closed directed rings, which reveals the presence of medium-range directional correlations in the liquid. One of the natural consequences of this feature is that both the hydronium and hydroxide ion are decorated with proton wires. These wires serve as conduits for long proton jumps over several hydrogen bonds.
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http://dx.doi.org/10.1073/pnas.1306642110DOI Listing
August 2013

Shape modulation of octanuclear Cu(I) or Ag(I) dichalcogeno template clusters with respect to the nature of their encapsulated anions: a combined theoretical and experimental investigation.

Inorg Chem 2013 Jul 10;52(13):7752-65. Epub 2013 Jun 10.

Institut des Sciences Chimiques de Rennes, UMR 6226 CNRS, Université de Rennes 1, Ecole Nationale Supérieure de Chimie de Rennes, Avenue du Général Leclerc, 35042 Rennes, France.

M8L6 clusters (M = Cu(I), Ag(I); L = dichalcogeno ligand) are known for their ability to encapsulate various kinds of saturated atomic anions. Calculations on the models [M8(E2PH2)6](2+) (M = Cu(I), Ag(I); E = S, Se) and the ionic or neutral [M8(X)(E2PH2)6](q) (X = H, F, Cl, Br, O, S, Se, N, P, C) indicate that the cubic M8L6 cage adapts its shape for maximizing the host-guest bonding interaction. The interplay between size, covalent and ionic bonding favors either a cubic, tetracapped tetrahedral, or bicapped octahedral structure of the metal framework. Whereas the large third- and fourth-row main group anions maintain the cubic shape, a distortion toward a tetracapped tetrahedral arrangement of the metals occurs in the case of hydride, fluoride, and oxide. The distortion is strong in the case of hydride, weak in the case of fluoride, and intermediate in the case of oxide. Density functional theory (DFT) calculations predict a bicapped octahedral architecture in the case of nitride and carbide. These computational results are supported by X-ray structures, including those of new fluorine- and oxygen-containing compounds. It is suggested that other oxygen-containing as well as so far unknown nitride-containing clusters should be feasible. For the first time, the dynamical behavior of the encapsulated hydride has been investigated by metadynamics simulations. Our results clearly demonstrate that the interconversion mechanism between two identical tetracapped tetrahedral configurations occurs through a succession of M-H bonds breaking and forming which present very low activation energies and which involve a rather large number of intermediate structures. This mechanism is full in accordance with (109)Ag and (1)H state NMR measurements.
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http://dx.doi.org/10.1021/ic400959aDOI Listing
July 2013
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