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Publications during 2012

Article Reference A density-functional theory investigation of the structural and spin properties of (PO2)4(WO3)8 model bronzes
Plane-wave density-functional theory calculations of P4W8O32 mono-phosphate tungsten bronzes with pentagonal tunnels demonstrate that (1) these materials possess a ground (singlet) state structure of orthorombic symmetry, as observed by X-ray diffraction crystallography at room temperature; (2) open-shell states lie very close in energy to the ground state and are significantly populated at room temperature; and (3) these low-lying states are likely to be implicated in the formation of a superstructure due to the tilting of WO6 octahedra (Peierls-like structural transformations) upon temperature decrease. The latter finding is consistent with the existence of a low-temperature incommensurate structure, as evidenced by the satellite peaks observed in X-ray diffraction patterns.
Article Reference A first principles DFT study of novel 1,3,5-triphenyl-2-pyrazolines
The structures, energetics, and global reactivity descriptors of some novel 1,3,5-triphenyl-2-pyrazolines, in both neutral and charged states, are investigated using density-functional theory, by using the Becke-Lee-Yang-Parr (BLYP) generalized gradient corrections to the local spin density approximation exchange and correlation energy, norm-conserving pseudopotentials, and a plane-wave expansion of the Kohn-Sham orbitals.
Article Reference A first principles molecular dynamics study of the solvation structure and migration kinetics of an excess proton and a hydroxide ion in binary water-ammonia mixtures
We have investigated the solvation structure and migration kinetics of an excess proton and a hydroxide ion in water-ammonia mixed liquids of varying composition by means of ab initio molecular dynamics simulations. The excess proton is always found to be attached to an ammonia molecule to form the ammonium ion. Migration of the excess proton is found to occur very occasionally from one ammonia to the other but no proton transfer to a water molecule is observed during the entire simulations. Also, when the ammonium ion is solvated in water only, its hydrogen bond dynamics and rotation are found to occur at a faster rate than those in water-ammonia mixtures. For water-ammonia mixtures containing a proton less, the defect is found to stay like the hydroxide ion. For these systems, occasional proton transfer is found to occur only through the hydrogen bonded chains of water molecules in these water-ammonia mixtures. No proton transfer is found to take place from an ammonia molecule. The presence of ammonia molecules makes the realization of proper presolvated state of the hydroxide ion to accept a proton a more difficult process and, as a result, the rate of proton transfer and migration kinetics of the hydroxide ion in water-ammonia mixtures are found to be slower than that in liquid water and these rates are found to slow down further with increase of ammonia concentration.
Article Reference A first principles molecular dynamics study of vibrational spectral diffusion and hydrogen bond dynamics in liquid methanol
We present a first principles theoretical study of vibrational spectral diffusion and hydrogen bond dynamics in liquid methanol at room temperature. The dynamics of spectral diffusion of OD modes of deuterated methanol reveals two times scales: a short time scale of about 120 fs and a longer time scale of about 3.2 ps. A damped oscillation is also found at around 120–180 fs. Calculations of power spectrum of relative velocities and hydrogen bond correlation functions reveal that the short time dynamics originates from intermolecular motion of hydrogen bonded methanol pairs while the long time relaxation corresponds to the breaking dynamics of hydrogen bonds. The quantitative details of the time constants are found to depend on the frequency of tagged OD bonds.
Article Reference A New Piece in the Puzzle of Lithium/Air Batteries: Computational Study on the Chemical Stability of Propylene Carbonate in the Presence of Lithium Peroxide
The electrolyte role in non-aqueous lithium/air batteries is attracting a lot of attention in several research groups, because of its fundamental importance in producing the appropriate reversible electrochemical reduction. While recent published works identify the lithium superoxide as the main degrading agent for propylene carbonate (PC), there is no clear experimental evidence that the oxygen at the cathode interface layer does not reduce further to peroxide before reacting with PC. Here, we investigate the reactivity of lithium peroxide versus propylene carbonate and find that Li2O2 irreversibly decomposes the carbonate solvent, leading to alkyl carbonates. We also show that, compared with a single Li2O2 unit in PC, a crystalline surface of Li2O2 exhibits an enhanced reactivity. Our findings support the possibility that in lithium/air cells, oxygen may still be reduced to peroxide, with the formation of solid Li2O2, which degrades by decomposing PC.
Article Reference A Simple AIMD Approach to Derive Atomic Charges for Condensed Phase Simulation of Ionic Liquids
The atomic charges for two ionic liquids (ILs), 1-n-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) and 1-ethyl-3-methylimidazolium hexafluorophosphate ([EMIM][PF6]), were derived from periodic crystal phase calculations with density functional theory (DFT) and plane wave basis sets (denoted as ?AIMD-c charge?). For both ILs, the total charge was found to be ±0.8 e for the cation and anion, respectively, due to the charge transfer between ions and polarization caused by the environment. These atomic charges were used in a force field developed within the general Amber force field framework. Using this force field, static, dynamic, and thermodynamic properties were computed for the two ILs using molecular dynamics simulation. The results were compared against results obtained using the same Amber force field but four different sets of partial charges, denoted as full charge, scaled charge, AIMD-l charge, and AIMD-b charge, respectively. The full charge was derived from quantum chemistry calculation of isolated ions in a vacuum and resulted in a total charge of unity on each ion. The scaled charge was obtained by uniformly scaling the full charge by 0.8. AIMD-l and AIMD-b charges were derived from liquid phase ab initio molecular dynamics simulations. The scaled charges have the same total charge on the ions as the AIMD-c charge but different distributions. It was found that simulation results not only depend on the total charge of each ion, but they are also sensitive to the charge distribution within an ion, especially for dynamic and thermodynamic properties. Overall, for the two ILs under study, the AIMD-c charge was found to predict experimental results better than the other four sets of charges, indicating that fitting charges from crystal phase DFT calculations, instead of extensive sampling of the liquid phase configurations, is a simple and reliable way to derive atomic charges for condensed phase ionic liquid simulations.
Article Reference A simple model of molecular imaging with noncontact atomic force microscopy
Article Reference A transferable ab initio based force field for aqueous ions
We present a new polarizable force field for aqueous ions (Li+, Na+, K+, Rb+, Cs+, Mg2 +, Ca2 +, Sr2 +, and Cl−) derived from condensed phase ab initio calculations. We use maximally localized Wannier functions together with a generalized force and dipole-matching procedure to determine the whole set of parameters. Experimental data are then used only for validation purposes and a good agreement is obtained for structural, dynamic, and thermodynamic properties. The same procedure applied to crystalline phases allows to parametrize the interaction between cations and the chloride anion. Finally, we illustrate the good transferability of the force field to other thermodynamic conditions by investigating concentrated solutions.
Article Reference Ab Initio Calculations of X-ray Spectra: Atomic Multiplet and Molecular Orbital Effects in a Multiconfigurational SCF Approach to the L-Edge Spectra of Transition Metal Complexes
A new ab initio approach to the calculation of X-ray spectra is demonstrated. It combines a high-level quantum chemical description of the chemical interactions and local atomic multiplet effects. We show here calculated L-edge X-ray absorption (XA) and resonant inelastic X-ray scattering spectra for aqueous Ni2+ and XA spectra for a polypyridyl iron complex. Our quantum chemical calculations on a high level of accuracy in a post-Hartree?Fock framework give excellent agreement with experiment. This opens the door to reliable and detailed information on chemical interactions and the valence electronic structure in 3d transition-metal complexes also in transient excited electronic states. As we combine a molecular-orbital description with a proper treatment of local atomic electron correlation effects, our calculations uniquely allow, in particular, identifying the influence of interatomic chemical interactions versus intra-atomic correlations in the L-edge X-ray spectra.
Article Reference Ab Initio Dynamics of Cellulose Pyrolysis: Nascent Decomposition Pathways at 327 and 600 °C
We modeled nascent decomposition processes in cellulose pyrolysis at 327 and 600 °C using Car?Parrinello molecular dynamics (CPMD) simulations with rare events accelerated with the metadynamics method. We used a simulation cell comprised of two unit cells of cellulose I? periodically repeated in three dimensions to mimic the solid cellulose. To obtain initial conditions at reasonable densities, we extracted coordinates from larger classical NPT simulations at the target temperatures. CPMD-metadynamics implemented with various sets of collective variables, such as coordination numbers of the glycosidic oxygen, yielded a variety of chemical reactions such as depolymerization, fragmentation, ring opening, and ring contraction. These reactions yielded precursors to levoglucosan (LGA)?the major product of pyrolysis?and also to minor products such as 5-hydroxy-methylfurfural (HMF) and formic acid. At 327 °C, we found that depolymerization via ring contraction of the glucopyranose ring to the glucofuranose ring occurs with the lowest free-energy barrier (20 kcal/mol). We suggest that this process is key for formation of liquid intermediate cellulose, observed experimentally above 260 °C. At 600 °C, we found that a precursor to LGA (pre-LGA) forms with a free-energy barrier of 36 kcal/mol via an intermediate/transition state stabilized by anchimeric assistance and hydrogen bonding. Conformational freedom provided by expansion of the cellulose matrix at 600 °C was found to be crucial for formation of pre-LGA. We performed several comparison calculations to gauge the accuracy of CPMD-metadynamics barriers with respect to basis set and level of theory. We found that free-energy barriers at 600 °C are in the order pre-LGA pre-HMF formic acid, explaining why LGA is the kinetically favored product of fast cellulose pyrolysis.
Article Reference Ab Initio Molecular Dynamics Study of the Very Short O–H···O Hydrogen Bonds in the Condensed Phases
In this paper are presented the results of theoretical studies of the structure and proton motion in very short O···O intramolecular hydrogen bonds in two molecular crystals. A comparison was conducted between 3-cyano-2,4-pentanedione (I) and 4-cyano-2,2,6,6-tetramethyl-3,5-heptanedione (II) in the solid state. The dynamics of proton motion in the O?H···O hydrogen bond were investigated in he NVT ensemble at 298 and 50 K, respectively, for crystals I and II using Car?Parrinello and path integral molecular dynamics. Very large delocalization of the bridging proton was noted especially in the path integral simulation where quantum effects are taken into account. The infrared spectrum was calculated, and a comparative vibrational analysis was performed. CPMD vibrational results appear to be in qualitative agreement with the experimental ones.
Article Reference Ab initio prediction of equilibrium boron isotope fractionation between minerals and aqueous fluids at high P and T
Over the last decade experimental studies have shown a large B isotope fractionation between materials carrying boron incorporated in trigonally and tetrahedrally coordinated sites, but the mechanisms responsible for producing the observed isotopic signatures are poorly known. In order to understand the boron isotope fractionation processes and to obtain a better interpretation of the experimental data and isotopic signatures observed in natural samples, we use first principles calculations based on density functional theory in conjunction with ab initio molecular dynamics and a new pseudofrequency analysis method to investigate the B isotope fractionation between B-bearing minerals (such as tourmaline and micas) and aqueous fluids containing H 3 BO 3 and H 4 BO 4 - species. We confirm the experimental finding that the isotope fractionation is mainly driven by the coordination of the fractionating boron atoms and have found in addition that the strength of the produced isotopic signature is strongly correlated with the BO bond length. We also demonstrate the ability of our computational scheme to predict the isotopic signatures of fluids at extreme pressures by showing the consistency of computed pressure-dependent β factors with the measured pressure shifts of the BO vibrational frequencies of H 3 BO 3 and H 4 BO 4 - in aqueous fluid. The comparison of the predicted with measured fractionation factors between boromuscovite and neutral fluid confirms the existence of the admixture of tetrahedral boron species in neutral fluid at high P and T found experimentally, which also explains the inconsistency between the various measurements on the tourmaline–mica system reported in the literature. Our investigation shows that the calculated equilibrium isotope fractionation factors have an accuracy comparable to the experiments and give unique and valuable insight into the processes governing the isotope fractionation mechanisms on the atomic scale.
Incollection Reference Ab-initio Calculations of the Vibrational Properties of Nanostructures
Article Reference Ab-initio study of intermolecular interaction and structure of liquid cyclopentasilane
We report on an ab initio calculation study of intermolecular interactions between cyclopentasilane (CPS) molecules in liquid CPS. Our calculations show that the SiH bonds that are oriented toward the center of the ring of a CPS molecule play a significant role in the interaction between CPS molecules. This interaction results in the formation of special bonds between CPS molecules, which resemble hydrogen bonds. These hydrogen bonds cause a red shift of IR absorption peaks corresponding to the SiH stretch vibration. The formation of hydrogen bonds in the liquid phase of CPS was further confirmed by ab-initio molecular dynamics simulations. The analysis of pair correlation functions has shown a significant contribution of hydrogen bonds to the structure of the CPS liquid system.
Book Reference Advances in Chemical Physics
The Advances in Chemical Physics series—the cutting edge of research in chemical physicsThe Advances in Chemical Physics series provides the chemical physics and physical chemistry fields with a forum for critical, authoritative evaluations of advances in every area of the discipline. Filled with cutting-edge research reported in a cohesive manner not found elsewhere in the literature, each volume of the Advances in Chemical Physics series offers contributions from internationally renowned chemists and serves as the perfect supplement to any advanced graduate class devoted to the study of chemical physics.This volume explores:Hydrogen Bond Topology and Proton Ordering in Ice and Water Clusters (Sherwin J. Singer and Chris Knight)Molecular Inner-Shell Spectroscopy, Arpis Technique and Its Applications (Eiji Shigemasa and Nobuhiro Kosugi)Geometric Optimal Control of Simple Quantum Systems: Geometric Optimal Control Theory (Dominique Sugny)Density Matrix Equation for a Bathed Small System and its Application to Molecular Magnets (D. A. Garanin)A Fractional Langevin Equation Approach to Diffusion Magnetic Resonance Imaging (Jennie Cooke)
Article Reference Amorphous Ge 15 Te 85 : density functional, high-energy x-ray and neutron diffraction study
Article Reference Anharmonic transitions in nearly dry l-cysteine I
Article Reference Atomic Force Microscopy Reveals Bistable Configurations of Dibenzo[a,h]thianthrene and their Interconversion Pathway
We investigated dibenzo[a,h]thianthrene molecules adsorbed on ultrathin layers of NaCl using a combined low-temperature scanning tunneling and atomic force microscope. Two stable configurations exist corresponding to different isomers of free nonplanar molecules. By means of excitations from inelastic electron tunneling we can switch between both configurations. Atomic force microscopy with submolecular resolution allows unambiguous determination of the molecular geometry, and the pathway of the interconversion of the isomers. Our investigations also shed new light on contrast mechanisms in scanning tunneling microscopy.
Article Reference Atomic scale structures of interfaces between kaolinite edges and water
This paper reports the atomic scale structures of kaolinite edge surfaces in contact with water. The commonly occurring edge surfaces are investigated (i.e. (0 1 0) and (1 1 0)) by using first principles molecular dynamics (FPMD) technique. For (1 1 0)-type edge surface, there are two different surface topologies (denoted as (1 1 0)-1 and (1 1 0)-2) and they are considered separately. By using constrained FPMD technique, the free-energy changes for the leaving processes of water ligands of O-sheet Al cations have been calculated and thus, the coordination states of those Al cations are determined. The results show that for (0 1 0) and (1 1 0)-2 edges, both the 5 and 6-fold coordination states are possible whereas for (1 1 0)-1 edges, only the 6-fold states are stable. Based on the analyses of H-bonding structures at the interfaces, the surface acid/base reactive sites are illustrated. (1) T-sheet groups are Si–OH, behaving as both proton donors and acceptors. (2) Bridging oxygen At (0 1 0) and (1 1 0)-2 edges, these sites are inaccessible from the water and thus, they are not effective reactive sites. At (1 1 0)-1 edges, the bridging oxygen atoms are proton accepting sites. (3) O–sheet groups At (0 1 0) and (1 1 0)-2 edges, for 6-fold Al cases, the active surface groups are Al–(OH)(OH2) and for the 5-fold Al cases, the active surface groups are Al–(OH). At (1 1 0)-1 edges, the active site is Al–OH2. This study provides fundamental structural properties for understanding the interface chemistry of widely occurring 1:1 type phyllosilicates.
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