Publications (20)75.89 Total impact
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Article: Ultrafast Damage Following Radiation-Induced Oxidation of Uracil in Aqueous Solution.
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ABSTRACT: Coulombic explosion of uracil: Ionizing radiation is used in cancer therapy to induce molecular damage in cells. Ab initio molecular dynamics were used to probe the early dissociation processes and ensuing chemical reactions following selective ionization of either uracil or the surrounding water molecules (see scheme, C gray, N blue, O red, H white).Angewandte Chemie International Edition 01/2013; · 13.45 Impact Factor -
Article: Collision induced dissociation of doubly-charged ions: Coulomb explosion vs. neutral loss in [Ca(urea)]2+ gas phase unimolecular reactivity via chemical dynamics simulations.
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ABSTRACT: In this paper we report different theoretical approaches to study the gas-phase unimolecular dissociation of the doubly-charged cation [Ca(urea)](2+), in order to rationalize recent experimental findings. Quantum mechanical plus molecular mechanical (QM/MM) direct chemical dynamics simulations were used to investigate collision induced dissociation (CID) and rotational-vibrational energy transfer for Ar + [Ca(urea)](2+) collisions. For the picosecond time-domain of the simulations, both neutral loss and Coulomb explosion reactions were found and the differences in their mechanisms elucidated. The loss of neutral urea subsequent to collision with Ar occurs via a shattering mechanism, while the formation of two singly-charged cations follows statistical (or almost statistical) dynamics. Vibrational-rotational energy transfer efficiencies obtained for trajectories that do not dissociate during the trajectory integration were used in conjunction with RRKM rate constants to approximate dissociation pathways assuming complete intramolecular vibrational energy redistribution (IVR) and statistical dynamics. This statistical limit predicts, as expected, that at long time the most stable species on the potential energy surface (PES) dominate. These results, coupled with experimental CID from which both neutral loss and Coulomb explosion products were obtained, show that the gas phase dissociation of this ion occurs by multiple mechanisms leading to different products and that reactivity on the complicated PES is dynamically complex.Physical Chemistry Chemical Physics 07/2012; 14(33):11724-36. · 3.57 Impact Factor -
Article: Structure and stability of charged clusters.
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ABSTRACT: When a cluster or nanodroplet bears charge, its structure and thermodynamics are altered and, if the charge exceeds a certain limit, the system becomes unstable with respect to fragmentation. Some of the key results in this area were derived by Rayleigh in the nineteenth century using a continuum model of liquid droplets. Here we revisit the topic using a simple particle-based description, presenting a systematic case study of how charge affects the physical properties of a Lennard-Jones cluster composed of 309 particles. We find that the ability of the cluster to sustain charge depends on the number of particles over which the charge is distributed-a parameter not included in Rayleigh's analysis. Furthermore, the cluster may fragment before the charge is strong enough to drive all charged particles to the surface. The charged particles in stable clusters are therefore likely to reside in the cluster's interior even without considering solvation effects.Journal of Physics Condensed Matter 07/2012; 24(28):284130. · 2.55 Impact Factor -
Article: Charge localization in multiply charged clusters and their electrical properties: some insights into electrospray droplets.
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ABSTRACT: The surface composition of charged Lennard-Jones clusters A(N) (n+), composed of N particles (55 ≤ N ≤ 1169) among which n are positively charged with charge q, thus having a net total charge Q = nq, is investigated by Monte Carlo with Parallel Tempering simulations. At finite temperature, the surface sites of these charged clusters are found to be preferentially occupied by charged particles carrying large charges, due to Coulombic repulsions, but the full occupancy of surface sites is rarely achieved for clusters below the stability limit defined in this work. Large clusters (N = 1169) follow the same trends, with a smaller propensity for positive particles to occupy the cluster surface at non-zero temperature. We show that these charged clusters rather behave as electrical spherical conductors for the smaller sizes (N ≤ 147) but as spheres uniformly charged in their volume for the larger sizes (N = 1169).The Journal of chemical physics 05/2012; 136(18):184503. · 3.09 Impact Factor -
Article: Environmental effects on vibrational properties of carotenoids: experiments and calculations on peridinin.
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ABSTRACT: Carotenoids are employed in light-harvesting complexes of dinoflagellates with the two-fold aim to extend the spectral range of the antenna and to protect it from radiation damage. We have studied the effect of the environment on the vibrational properties of the carotenoid peridinin in different solvents by means of vibrational spectroscopies and QM/MM molecular dynamics simulations. Three prototypical solvents were considered: cyclohexane (an apolar/aprotic solvent), deuterated acetonitrile (a polar/aprotic solvent) and methanol (a polar/protic solvent). Thanks to effective normal mode analysis, we were able to assign the experimental Raman and IR bands and to clarify the effect of the solvent on band shifts. In the 1500-1650 cm(-1) region, seven vibrational modes of the polyene chain were identified and assigned to specific molecular vibrations. In the 1700-1800 cm(-1) region a strong progressive down-shift of the lactonic carbonyl frequency is observed passing from cyclohexane to methanol solutions. This has been rationalized here in terms of solvent polarity and solute-solvent hydrogen bond interactions. On the basis of our data we propose a classification of non-equivalent peridinins in the Peridinin-Chlorophyll-Proteins, light-harvesting complexes of dinoflagellates.Physical Chemistry Chemical Physics 09/2011; 13(47):20954-64. · 3.57 Impact Factor -
Article: Modeling the infrared and circular dichroism spectroscopy of a bridged cyclic diamide.
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ABSTRACT: Density functional theory based molecular dynamics simulations are used to study the structure, infrared (IR) spectroscopy, circular dichroism (CD) spectroscopy, and coupling between the amide I vibrations of a bridged cyclic diamide in the gas phase and in aqueous solution. IR spectra computed via the dipole moment time correlation function show a large red-shift of 30 cm(-1) in the amide I vibration in solution compared to the gas phase, and are in good agreement with experiment. Conformationally averaged CD spectra computed using the CIS(D) method are highly sensitive to the structures used, and structures sampled in the aqueous phase simulation are required to obtain qualitatively correct CD spectra. Analysis of the coupling between the amide I modes shows that in the aqueous phase there is an increased localization of the vibrations on the individual peptide groups and a reduction in the mode coupling parameter compared to the gas phase. Overall, the results illustrate the significance of incorporating molecular dynamics in the simulation of IR and CD spectra.The Journal of Physical Chemistry B 02/2011; 115(18):5526-35. · 3.70 Impact Factor -
Article: Proton transfer from the inactive gas-phase nicotine structure to the bioactive aqueous-phase structure.
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ABSTRACT: The role of water in the structural change of nicotine from its inactive form in the gas phase to its bioactive form in aqueous solution has been investigated by two complementary theoretical approaches, i.e., geometry optimizations and molecular dynamics. Structures of the lowest-energy nicotineH(+)-(H(2)O)(n) complexes protonated either on the pyridine (inactive form) or pyrrolidine (active form) ring have been calculated, as well as the free-energy barriers for the proton-transfer tautomerization between the two cycles. These structures show chains of 2-4 water molecules bridging the two protonation sites. The room-temperature free-energy barrier to tautomerization along the minimum-energy path from the pyridine to the pyrrolidine cycle drops rapidly when the number of water molecules increases from 0 to 4, but still remains rather high (16 kJ/mol with four water molecules), indicating that the proton transfer is a rather difficult and rare event. We compare results obtained through this explicit water molecule approach to those obtained by means of continuum methods. Car-Parrinello molecular dynamics (CPMD) simulations of the proton-transfer process in bulk with explicit water molecules have been conducted at room temperature. No spontaneous proton transfers have been observed during the dynamics, and biased CPMD simulations have therefore been performed in order to measure the free-energy profile of the proton transfer in the aqueous phase and to reveal the proton-transfer mechanism through water bridges. The MD bias involves pulling the proton from the pyridine ring to the surrounding bulk. Dynamics show that this triggers the tautomerization toward the pyrrolidine ring, proceeding without energy barrier. The proton transfer is extremely fast, and protonation of the pyrrolidine ring was achieved within 0.5 ps. CPMD simulations confirmed the pivotal role played by the water molecules that bridge the two protonation sites of nicotine within the bulk of the surrounding water.Journal of the American Chemical Society 12/2010; 132(51):18067-77. · 9.91 Impact Factor -
Article: Infrared spectroscopy of the alanine dipeptide analog in liquid water with DFT-MD. Direct evidence for P(II)/beta conformations.
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ABSTRACT: Following our previous work [J. Phys. Chem. B. Lett., 2009, 113, 10059], DFT-based molecular dynamics (DFTMD) simulations of 2-Ala peptide (i.e. Ac-Ala-NHMe dialanine peptide analog with methyl group caps at the extremities) immersed in liquid water at room temperature are reported. Our goal here is the theoretical calculation of the infrared spectrum of aqueous 2-Ala, in order to provide a definitive understanding of the average conformation adopted by this peptide in the liquid phase, taking into account solute and solvent at the same theoretical level of representation. We find that the experimental Amide I-II band predominantly results from a mixture of partially unfolded P(II) and unfolded beta conformational equilibrium of aqueous 2-Ala at room temperature.Physical Chemistry Chemical Physics 09/2010; 12(35):10198-209. · 3.57 Impact Factor -
Article: Density functional theory based molecular dynamics study of hydration and electronic properties of aqueous La(3+).
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ABSTRACT: Structural and electronic properties of La(3+) immersed in bulk water have been assessed by means of density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations. Correct structural properties, i.e., La(III)-water distances and La(III) coordination number, can be obtained within the framework of Car-Parrinello simulations providing that both the La pseudopotential and conditions of the dynamics (fictitious mass and time step) are carefully set up. DFT-MD explicitly treats electronic densities and is shown here to provide a theoretical justification to the necessity of including polarization when studying highly charged cations such as lanthanoids(III) with classical MD. La(3+) was found to strongly polarize the water molecules located in the first shell, giving rise to dipole moments about 0.5 D larger than those of bulk water molecules. Finally, analyzing Kohn-Sham orbitals, we found La(3+) empty 4f orbitals extremely compact and to a great extent uncoupled from the water conduction band, while the 5d empty orbitals exhibit mixing with unoccupied states of water.The Journal of chemical physics 07/2010; 133(4):044509. · 3.09 Impact Factor -
Article: Theoretical spectroscopy of floppy peptides at room temperature. A DFTMD perspective: gas and aqueous phase.
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ABSTRACT: Theoretical spectroscopy is mandatory for a precise understanding and assignment of experimental spectra recorded at finite temperature. We review here room temperature DFT-based molecular dynamics simulations for the purpose of interpreting finite temperature infrared spectra of peptides of increasing size and complexity, in terms of temperature-dependent conformational dynamics and flexibility, and vibrational anharmonicities (potential energy surface anharmonicities, vibrational mode couplings and dipole anharmonicities). We take examples from our research projects in order to illustrate the main key-points and strengths of dynamical spectra modeling in that context. The calculations are presented in relation to room temperature gas phase IR-MPD experiments and room temperature liquid phase IR absorption experiments. These illustrations of floppy polypeptides have been chosen in order to convey the following ideas: temperature-dependent spectra modeling is pivotal for a precise understanding of gas phase spectra recorded at room temperature, including conformational dynamics and vibrational anharmonicities; harmonic spectroscopy (as commonly performed in the literature) can be misleading and even erroneous for a proper interpretation of spectra recorded at finite temperature; taking into account vibrational anharmonicities is pivotal for a proper interplay between theory and experiments; amide I-III bands are not necessarily the most relevant fingerprints for unraveling the local structures of peptides and more complex systems; liquid phase simulations have unraveled relationships between the zwitterionic properties of the peptide bonds and infrared signatures. The review presents a state-of-the-art account of the domain and offers perspectives and new developments for future still more challenging applications.Physical Chemistry Chemical Physics 04/2010; 12(14):3336-59. · 3.57 Impact Factor -
Article: DFT-MD and vibrational anharmonicities of a phosphorylated amino acid. Success and failure.
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ABSTRACT: Following our work on the phosphorylated deprotonated serine amino acid pSerH(-) [J. Chem. Theory Comput., 2009, 5, 2388], we investigate here the room temperature infrared spectroscopy of pSerH(+) (phosphorylated protonated serine) in the gas phase in relation with IR-MPD experiment. To that end, DFT-based Car-Parrinello molecular dynamics (DFTMD) are performed, giving a direct probe of vibrational anharmonicities. Agreement and disagreement with the experiment are explored in the light of DFT/functional, vibrational mode couplings and potential energy surface anharmonicities. Trends on the phosphate vibrational signatures in relation with its protonation state and environment are analysed, for the purpose of transferability into more complex phosphorylated peptide chains.Physical Chemistry Chemical Physics 04/2010; 12(14):3501-10. · 3.57 Impact Factor -
Article: Protonated urea collision-induced dissociation. Comparison of experiments and chemical dynamics simulations.
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ABSTRACT: Quantum mechanical plus molecular mechanical direct chemical dynamics were used, with electrospray tandem mass spectrometry experiments, potential energy surface calculations, and RRKM analyses, to study the gas-phase collision-induced dissociation (CID) of protonated urea. The direct dynamics were able to reproduce some of the experimental observations, in particular the presence of two fragmentation pathways, and, thus, to explain the dynamical origin of the two fragmentation ions observed in the CID spectra. A shattering dissociation mechanism takes place during the collision, and it becomes more important as the collision energy increases, thus explaining the linear increase of the high-energy reaction path (loss of ammonia) versus collision energy. By combining the different theoretical and experimental findings, a complete dynamical picture leading to the fragmentation was identified: (i) Oxygen-protonated urea, the most stable structure in the gas phase, must first isomerize to the nitrogen-protonated form. This can happen by multiple CID collisions or in the electrospray ionization process. (ii) Once the nitrogen-protonated isomer is formed, it can dissociate via two mechanisms: i.e, a slow, almost statistical, process forming a NH(4)(+)--NHCO intermediate that rapidly dissociates or a fast nonstatistical process which may lead to the high-energy products.The Journal of Physical Chemistry A 11/2009; 113(50):13853-62. · 2.95 Impact Factor -
Article: What first principles molecular dynamics can tell us about EXAFS spectroscopy of radioactive heavy metal cations in water
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ABSTRACT: In this paper we show how molecular dynamics simulation can improve comprehension of structure and dynamics of water solvent around heavy cations. In particular, metal-water radial distribution function obtained from molecular dynamics can be used into EXAFS equation to improve the experimental signal fitting. Here we show results on structure and dynamics of Co<sup>2+</sup>, that is a radiocontaminant cation in its isotopic form <sup>60</sup>Co, and lanthanoids(III) that are the chemical analogues of actinides(III) in aqueous solution.Radiochimica Acta. 07/2009; 97(7):339-346. -
Article: Time-dependent density functional theory molecular dynamics simulations of liquid water radiolysis.
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ABSTRACT: The early stages of the Coulomb explosion of a doubly ionized water molecule immersed in liquid water are investigated with time-dependent density functional theory molecular dynamics (TD-DFT MD) simulations. Our aim is to verify that the double ionization of one target water molecule leads to the formation of atomic oxygen as a direct consequence of the Coulomb explosion of the molecule. To that end, we used TD-DFT MD simulations in which effective molecular orbitals are propagated in time. These molecular orbitals are constructed as a unitary transformation of maximally localized Wannier orbitals, and the ionization process was obtained by removing two electrons from the molecular orbitals with symmetry 1B(1), 3A(1), 1B(2) and 2A(1) in turn. We show that the doubly charged H(2)O(2+) molecule explodes into its three atomic fragments in less than 4 fs, which leads to the formation of one isolated oxygen atom whatever the ionized molecular orbital. This process is followed by the ultrafast transfer of an electron to the ionized molecule in the first femtosecond. A faster dissociation pattern can be observed when the electrons are removed from the molecular orbitals of the innermost shell. A Bader analysis of the charges carried by the molecules during the dissociation trajectories is also reported.ChemPhysChem 10/2008; 9(14):2099-103. · 3.41 Impact Factor -
Article: Solvation of Co(III)-cysteinato complexes in water: a DFT-based molecular dynamics study.
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ABSTRACT: Structural, dynamical, and vibrational properties of complexes made of metal cobalt(III) coordinated to different amounts of cysteine molecules were investigated with DFT-based Car-Parrinello molecular dynamics (CPMD) simulations in liquid water solution. The systems are composed of Co(III):3Cys and Co(III):2Cys immersed in liquid water which are modeled by about 110 explicit water molecules, thus one of the biggest molecular systems studied with ab initio molecular simulations so far. In such a way, we were able to investigate structural and dynamical properties of a model of a typical metal binding site used by several proteins. Cobalt, mainly a toxicological agent, can replace the natural binding metal and thus modify the biochemical activity. The structure of the surrounding solvent around the metal-ligands complexes is reported in detail, as well as the metal-ligands coordination bonds, using radial distribution functions and electronic analyses with Mayer bond orders. Structures of the Cocysteine complexes are found in very good agreement with EXAFS experimental data, stressing the importance of considering the surrounding solvent in the modeling. A vibrational analysis is also conducted and compared to experiment, which strengthens the reliability of the solvent interactions with the Cocysteine complexes from our molecular dynamics simulations, as well as the dynamics of the systems. From this preliminary analysis, we could suggest a vibrational fingerprint able to distinguish Co(III):2Cys from Co(III):3Cys. Our simulations also show the importance of considering a quantum explicit solvent, as solute-to-solvent proton transfer events have been observed.The Journal of Physical Chemistry B 06/2008; 112(20):6490-9. · 3.70 Impact Factor -
Article: A coupled Car-Parrinello molecular dynamics and EXAFS data analysis investigation of aqueous Co(2+).
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ABSTRACT: We have studied the microscopic solvation structure of Co(2+) in liquid water by means of density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations and extended X-ray absorption fine structure (EXAFS) data analysis. The effect of the number of explicit water molecules in the simulation box on the first and second hydration shell structures has been considered. Classical molecular dynamics simulations, using an effective two-body potential for Co(2+)-water interactions, were also performed to show box size effects in a larger range. We have found that the number of explicit solvent molecules has a marginal role on the first solvation shell structural parameters, whereas larger boxes may be necessary to provide a better description of the second solvation shell. Car-Parrinello simulations were determined to provide a reliable description of structural and dynamical properties of Co(2+) in liquid water. In particular, they seem to describe both the first and second hydration shells correctly. The EXAFS signal was reconstructed from Car-Parrinello simulations. Good agreement between the theoretical and experimental signals was observed, thus strengthening the microscopic picture of the Co(2+) solvation properties obtained using first-principle simulations.The Journal of Physical Chemistry A 01/2007; 110(48):13081-8. · 2.95 Impact Factor -
Article: Toward a DFT-based molecular dynamics description of Co(II) binding in sulfur-rich peptides.
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ABSTRACT: In this paper, we investigated the reliability of a Car-Parrinello molecular dynamics (CPMD) approach to characterize the binding of Co(II) metal cation to peptide molecules containing cysteine. To this end, we compared pseudo-potentials and DFT plane wave expansion, which are used as key ingredients in the CPMD method, with standard all-electron Gaussian basis set DFT calculations. The simulations presented here are the first attempts to characterize interactions and dynamics of Co(II) metal with the building blocks of phytochelatin peptide molecules. Benchmark calculations are performed on [Co(Cys-H)]+ and [Co(Glutathione-H)]+ complexes, since they are the main fragments of the Co(II)-Cys and Co(II)-glutathione systems found in gas phase electrospray ionisation mass spectrometry (ESI-MS) experiments done in our laboratory. We also present benchmark calculations on the [Co(H2O)6)]2+ cluster with direct comparisons to highly correlated ab initio calculations and experiments. In particular, we investigated the dissociation path of one water molecule from the first hydration shell of Co(II) with CPMD. Overall, our molecular dynamics simulations shed some light on the nature of the Co(II) interaction and reactivity in Co(II)-phytochelatin building block systems related to the biological and environmental activity of the metal, either in the gas or liquid phase.Physical Chemistry Chemical Physics 06/2006; 8(17):2040-50. · 3.57 Impact Factor -
Article: Differentiation of the fucoidan sulfated L-fucose isomers constituents by CE-ESIMS and molecular modeling.
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ABSTRACT: Alpha-L-fucose, the monosaccharide component of fucoidan, is found in the polysaccharide mainly as its sulfated form where sulfate groups are in position 2 and/or 4 and/or 3. The correlation between biological activities and structure of fucoidan requires the determination of the sulfation pattern of the fucose residues. Therefore, it is of importance to discriminate between the isobaric sulfated fucose isomers. For this purpose, the three isomers 2-O-, 3-O-, and 4-O-sulfated fucose have been analyzed using electrospray ion trap mass spectrometry and capillary electrophoresis. The results reported herein show that it is possible to differentiate between these three positional isomers of sulfated fucose based on their fragmentation pattern upon MS/MS experiments. 3-O-Sulfated fucose was characterized by the loss of the hydrogenosulfate anion HSO4- as the main fragmentation product, while the two other isomers 2-O-, and 4-O-sulfated fucose exhibited cross-ring fragmentation yielding to distinctive (0,2)X and (0,2)A daughter ion, respectively. A computational study of the conformation of the sulfated fucose isomers was carried out providing an understanding of the fragmentation pattern with respect to the position of the sulfate group.Carbohydrate Research 05/2006; 341(5):598-609. · 2.33 Impact Factor -
Article: Density-functional theory-based molecular simulation study of liquid methanol.
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ABSTRACT: We present a density-functional theory based molecular dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare well with recent neutron diffraction data. We observe that, in line with infrared spectroscopic data, the hydroxyl-stretching mode is significantly redshifted in the liquid, whereas the hydroxyl bending mode shows a blueshift. A substantial enhancement of the molecular dipole moment is accompanied by significant fluctuations due to thermal motion. We compute a value of 32 for the relative permittivity, almost identical to the experimental value of 33. Our results provide valuable data for improvement of empirical potentials.The Journal of Chemical Physics 12/2004; 121(20):10111-9. · 3.33 Impact Factor -
Article: Molecular Dynamics and Room Temperature Vibrational Properties of Deprotonated Phosphorylated Serine
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ABSTRACT: The local structure of phosphorylated residues in peptides and proteins may have a decisive role on their functional properties. Recent IRMPD experiments have started to provide spectroscopic signatures of such structural details; however, a proper modeling of these signatures beyond the harmonic approximation, taking into account temperature and entropic effects, is still lacking. In order to bridge this gap, DFT-based Car-Parrinello molecular dynamics simulations have been carried out for the first time on a phosphorylated amino acid, gaseous deprotonated phosphoserine. It is found that all vibrational signatures are successfully reproduced, and new deconvolution techniques enable the assignment of the vibrational spectrum directly from the dynamics results and the comparison of vibrational modes at several temperatures. The lowest energy structure is found to involve a strong hydrogen bond between the deprotonated phosphate and the acid with relatively small free energy barriers to proton transfer; however, we find that proton shuttling between the two sites does not occur frequently. Anharmonicities turn out to be important to reproduce the frequencies and shapes of several experimental bands. Comparison of room temperature and 13 K, effectively harmonic dynamics, allows insight to be obtained into vibrational anharmonicities. In particular, a significant blue-shift and broadening of the C=O stretching frequency from 13 to 300 K can be ascribed to intrinsic anharmonicity rather than to anharmonic coupling to other modes. On the other hand, significant couplings are found for the stretching motions of the hydrogen bonded P-O bond and of the free P-OH bond, mainly with modes within the phosphate group.Journal of Chemical Theory and Computation.
Top co-authors
Top Journals
Institutions
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2012
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Université de Reims Champagne-Ardennes
Reims, Champagne-Ardenne, France -
University of Cambridge
Cambridge, ENG, United Kingdom
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2006–2011
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Université d'Évry-Val-d'Essonne
Évry, Ile-de-France, France
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2004
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Universiteit van Amsterdam
- Van 't Hoff Institute for Molecular Sciences
Amsterdam, North Holland, Netherlands
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