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year-1997

Publications during 1997

Article Reference A density functional study of iron-porphyrin complexes
Equilibrium structures for oxygen and carbon monoxide complexes of iron porphyrin (FeP), computed with Car-Parrinello molecular dynamics, are in agreement with experimental data of heme models. In addition, we provide information on binding energies and spin-structure relationships, helping to understand the chemistry of the heme prosthetic group.
Article Reference A hybrid Gaussian and plane wave density functional scheme
 
Article Reference Ab initio infrared spectrum of liquid water
An ab initio calculation of the infrared spectrum of liquid water has been performed using Car-Parrinello molecular dynamics and evaluating the electronic polarization by means of the Berry phase formulation. The major features of the spectrum are in good agreement with experiments and are shown to arise from specific vibrational motions of the water molecules. The effect of quantum corrections to the spectrum is discussed.
Article Reference Ab initio molecular dynamics of ion solvation. The case of Be2+ in water
Structural aspects of the solvation behavior of Be2+ in liquid water are investigated with ab initio molecular dynamics based on a gradient-corrected density functional. The beryllium ion is shown to be fourfold coordinated, and the microscopic structure of the first hydration shell, especially the change of the intramolecular geometry of the complexating H2O molecules, is analyzed in detail. In particular, it is shown that the structure of the first hydration shell in solution cannot be determined reliably without taking into account its own solvation.
Article Reference Ab initio molecular dynamics simulation of liquid hydrogen fluoride
 
Article Reference Ab initio molecular dynamics simulation of methanol adsorbed in chabazite
Ab initio molecular dynamics simulations based on density functional theory together with a plane wave basis set and Vanderbilt pseudopotentials are performed to explore the potential energy surface of a methanol molecule interacting with the Brønsted site of zeolite chabazite. In agreement with a recent study a stationary point is located which corresponds to a chemisorbed methoxonium species. However, molecular dynamics simulations at 400 K show that configurations corresponding to this structure are of minor probability. Instead, the most stable structure is a physisorbed complex in which the strongly interacting Brønsted proton is significantly delocalized in the region between the methanol and the framework oxygen of the zeolite catalyst. A stationary point of the potential energy surface corresponding to such a structure proves to be more stable than the ion pair complex by about 18 kJ/mol.
Article Reference Ab initio molecular dynamics study of crystal hydrates of HCl including path integral results
 
Article Reference Ab initio molecular dynamics study of polyfluoride anions
 
Article Reference Chemical shifts of diamagnetic azafullerenes: (C59N)2 and C59HN
13C and 15N chemical shifts have been calculated for the azafullerenes (C59N)2 and C59HN using the GIAO (gauge including atomic orbitals)-SCF method based on the geometry obtained with the density functional theory BLYP scheme Our results are in good agreement with experimental data, in particular, for the "anomalous" shift of the saturated carbon. Combined with previous calculations of the structural stability and electronic as well as vibrational properties, the present findings confirm the calculated structures for both molecules and establish the [6,6]-closed configuration for the dimer.
Article Reference Condensed matter effects on the structure of crystalline glucose
By means of ab initio simulations based on the Car-Parrinello method, we have calculated the crystalline structures of [sigma]-D-glucose, [sigma]-D-glucose monohydrate and [beta]-D-glucose. The good agreement with the available experimental data gives us confidence in the applicability of the method to carbohydrates and opens the path towards the investigation of more complex problems, where a quantum mechanical description is essential. Condensed matter effects are discussed by comparing the structures of the glucose molecule in the crystalline and gas phases.
Article Reference Density functional study of structure and bonding in lithium clusters Li[sub n] and their oxides Li[sub n]O
 
Article Reference Density Functional Theory-Based Molecular Dynamics Simulation of Acid-Catalyzed Chemical Reactions in Liquid Trioxane
Ab initio molecular dynamics simulation is used to investigate the kinetics and thermodynamics of some of the chemical reactions that occur during the induction phase of acid-catalyzed polymerization of 1,3,5-trioxane. In particular, the first ab initio calculation of a free-energy profile in a condensed-phase system is presented. The introduction of an H+ ion to a sample of trioxane liquid initiates the complete protolysis of several trioxane molecules in a rapid succession of picoseconds. Subsequently, the re-formation of small formaldehyde oligomers is observed, which break up again after 12 ps. The fast kinetics is found to be consistent with the results of a constrained ab initio molecular dynamics evaluation of the free-energy profile for the formation of a protonated dimer. In the trioxaneformaldehyde mixture, this reaction is found to be barrierless with a reaction free energy in the thermal range (10 kJ mol-1). Solvation of the chemically active carbocation by formaldehyde molecules reduces the binding energy compared to that in the gas phase by 1 order of magnitude.
Article Reference Electrical-conductivity calculation in ab initio simulations of metals:Application to liquid sodium
We describe a calculation of the electrical conductivity in ab initio simulations of liquid sodium, using the Kubo-Greenwood formula for the optical conductivity and the molecular-dynamics scheme based on finite-temperature density functional theory. The effect of different Brillouin-zone samplings and that of the finite size of the system have been extensively studied at different temperatures. Close to the melting point, even with an adequate sampling of the Brillouin zone, our results exhibit a large discrepancy between theory and experiment. This is much reduced at higher temperatures. The possible reasons for this behavior are discussed.
Article Reference Equilibrium Geometries and Electronic Structure of Iron−Porphyrin Complexes: A Density Functional Study
We have performed density functional theory (DFT) calculations of ironporphyrin (FeP) and its complexes with O2, CO, NO, and imidazole (Im). Our fully optimized structures agree well with the available experimental data for synthetic heme models. Comparison with crystallographic data for proteins highlights interesting features of carbon monoxymyoglobin. The diatomic molecule induces a 0.30.4 A displacement of the Fe atom out of the porphyrin nitrogen (Np) plane and a doming of the overall porphyrin ring. The energy of the irondiatomic bond increases in the order FeO2 (9 kcal/mol) FeCO (26 kcal/mol) FeNO (35 kcal/mol). The ground state of FeP(O2) is an open shell singlet. The bent FeO2 bond can be formally described as FeIIIO2-, and it is characterized by the anti-ferromagnetic coupling between one of the d electrons of Fe and one of the pi* electrons of O2. FeP(CO) is a closed shell singlet, with a linear FeCO bond. The complex with NO has a doublet ground state and a FeNO geometry intermediate between that of FeP(CO) and FeP(O2). The bending of the Fe(diatomic) angle requires a rather low energy for these three complexes, resulting in large-amplitude oscillations of the ligand even at room temperature. The addition of an imidazole ligand to FeP moves the Fe atom out of the porphyrin plane toward the imidazole and decreases significantly the energy differences among the spin states. Moreover, our calculations underline the potential role of the imidazole ligand in controlling the electronic structure of FeP by changing the out-of-planarity of the Fe atom. The presence of the imidazole increases the strength of the FeO2 and FeCO bonds (15 and 35 kcal/mol, respectively), but does not affect the energy of the FeNO bond, while the resulting FeP(Im)(NO) complex exhibits a longer and weaker FeIm bond.
Article Reference From silicon to RNA: The coming of age of ab initio molecular dynamics
Molecular dynamics is a very powerful tool for investigating the properties of complex many-body systems. Over the last ten years its scope has been greatly expanded by combining it with accurate first-principles calculations. This new methodology, which is called ab initio molecular dynamics, allows realistic simulations to be performed without adjustable parameters. This has led to enhanced reliability and predictive power and opened the way for the simulation of chemical processes in condensed phases. We describe here the principles on which ab initio molecular dynamics is based. We focus mainly on the more popular implementation, i.e. that based on density functional theory, plane wave expansion and pseudopotentials. We demonstrate its power by a survey of selected recent applications: a series of studies on the melting of silicon and on hydrogen-bonded systems, illustrative of two different fields, viz. materials science and physical chemistry.
Article Reference Infrared absorption in amorphous silicon from ab initio molecular dynamics
 
Article Reference Interaction of Alkene Radical Cations with Solvent Molecules As Described with Density Functional Theory
Structures and energetics of several distonic radical cations, in particular the adducts between ethylene radical cation and water, ammonia, and hydrogen fluoride, are investigated using various density functional and post HartreeFock methods. Both the structure and the energetics of the [CH2CH2.NH3]+ and [CH2CH2.HF]+ adducts with pronounced covalent and electrostatic bonding, respectively, are well described using the gradient-corrected BLYP functional. The intermediate bonding situation of [CH2CH2.OH2]+, in particular the structure, is not well described with BLYP, whereas the binding energy is in surprisingly close agreement with post HartreeFock methods. The reason for this behavior is analyzed in terms of the different contributions to the total energy, and it is shown that the deficiency is remedied when the nonlocal hybrid functional BHLYP is used. Finally, it is found that the performance of BLYP improves on inclusion of additional water molecules. Thus the weakness of BLYP to describe the structure of the [CH2CH2.OH2]+ radical cation is a specific exception rather than typical for the large class of distonic radical cations. One can therefore expect BLYP to provide a realistic description of alkene radical cations in aqueous solution.
Article Reference Lithium–aluminum contacts for organic light-emitting devices
 
Article Reference On the Quantum Nature of the Shared Proton in Hydrogen Bonds
 
Article Reference On-Ball Doping of Fullerenes: The Electronic Structure of C59N Dimers from Experiment and Theory
We present the first studies of the electronic structure of the heterofullerene (C59N)2 using electron energy-loss spectroscopy in transmission, photoemission spectroscopy, and density functional theory calculations. Both the C 1s excitation spectra and valence band photoemission show negligible occupation of the C-derived lowest unoccupied electronic states and indicate localization of the excess electrons at the N atoms. The experimental results, together with the detailed analysis of our theoretical data, provide compelling evidence for the chemical picture of a triply coordinated N atom with a lone pair in each heterofullerene unit, and confirm the theoretically predicted “6,6 closed” structure for the dimer.
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