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year-2004

Publications during 2004

Article Reference A hybrid MP2/planewave-DFT scheme for large chemical systems: proton jumps in zeolites
We present an embedding scheme to introduce local corrections at post Hartree-Fock level to density functional theory (DFT) calculations. As a first application we study proton jump reactions in the zeolite HSSZ-13 and show that energy barriers and rate constants are significantly changed by second-order Møller-Plesset perturbation theory (MP2) corrections to plane wave based DFT calculations. Electronic energy barriers increase from 68 to 81 kJ/mol (dry zeolite), and from 22 to 30 kJ/mol (hydrated zeolite). The predicted heats of adsorption of one water molecule onto the Brønsted acidic sites O1 and O2 are 73 and 69 kJ/mol, respectively.
Article Reference A Photochemical Activation Scheme of Inert Dinitrogen by Dinuclear RuSUPFONT SIZE='-1'II/FONT/SUP and FeSUPFONT SIZE='-1'II/FONT/SUP Complexes
A general photochemical activation process of inert dinitrogen coordinated to two metal centers is presented on the basis of high-level DFT and ab initio calculations. The central feature of this activation process is the occupation of an antibonding pi* orbital upon electronic excitation from the singlet ground state S0 to the first excited singlet state S1. Populating the antibonding LUMO weakens the triple bond of dinitrogen. After a vertical excitation, the excited complex may structurally relax in the S1 state and approaches its minimum structure in the S1 state. This excited-state minimum structure features the dinitrogen bound in a diazenoid form, which exhibits a double bond and two lone pairs localized at the two nitrogen atoms, ready to be protonated. Reduction and de-excitation then yield the corresponding diazene complex; its generation represents the essential step in a nitrogen fixation and reduction protocol. The consecutive process of excitation, protonation, and reduction may be rearranged in any experimentally appropriate order. The protons needed for the reaction from dinitrogen to diazene can be provided by the ligand sphere of the complexes, which contains sulfur atoms acting as proton acceptors. These protonated thiolate functionalities bring protons close to the dinitrogen moiety. Because protonation does not change the pi*-antibonding character of the LUMO, the universal and well-directed character of the photochemical activation process makes it possible to protonate the dinitrogen complex before it is irradiated. The pi*-antibonding LUMO plays the central role in the activation process, since the diazenoid structure was obtained by excitation from various occupied orbitals as well as by a direct two-electron reduction (without photochemical activation) of the complex; that is, the important bending of N2 towards a diazenoid conformation can be achieved by populating the pi*-antibonding LUMO.
Article Reference A Proficient Enzyme: Insights on the Mechanism of Orotidine Monophosphate Decarboxylase from Computer Simulations
Decarboxylation of orotidine 5`-monophosphate (Omp) to uridine 5`-monophosphate by orotidine 5`-monophosphate decarboxylase (ODCase) is currently the object of vivid debate. Here, we clarify its enzymatic activity with long time scale classical molecular dynamics and hybrid ab initio CarParrinello/molecular mechanics simulations. The lack of structural (experimental) information on the ground state of ODCase/Omp complex is overcome by a careful construction of the model and the analysis of three different strains of the enzyme. We find that the ODCase/substrate complex is characterized by a very stable charged network OmpLysAspLysAsp, which is incompatible with the previously proposed direct decarboxylation driven by a ground-state destabilization. A direct decarboxylation induced by a transition-state electrostatic stabilization is consistent with our findings. The calculated activation free energy for the direct decarboxylation with the formation of a C6 carboanionic intermediate yields an overall rate enhancement by the enzyme (kcat/kwat = 3.5 1016) in agreement with experiments (kcat/kwat = 1.7 1017). The decarboxylation is accompanied by the movement of a fully conserved lysine residue toward the developing negative charge at the C6 position.
Article Reference Ab initio calculation of electrostatic multipoles with Wannier functions for large-scale biomolecular simulations
 
Article Reference Ab Initio Modeling of the Spatial, Electronic, and Vibrational Structure of Schiff Base Models for Visual Photoreceptors
We have assessed the relation between the spatial ground-state structure and the electronic and vibrational spectroscopic properties of neutral and protonated 11-cis-retinal Schiff base models within the density functional theory framework. For the neutral Schiff base model, a comprehensive model picture emerges, which is consistent with the available spectroscopic experimental data. For the protonated models, the calculations reveal a polaronic conjugation defect in the ground state in the Schiff base region. It is found that the C14C15 bond has enhanced double bond character, while the C13C14 and C15N bonds have reduced double bond character. This phenomenon affects the vibrational structure in an extended region of the spectrum. The CC, CC, and CN stretches in the fingerprint region and the ethylenic band are significantly delocalized. In the ab initio calculations, an enhanced coupling of the C14C15 and C15N stretching coordinates transpires, resulting in an asymmetric (C14C15N) stretching mode in the ethylenic region at 1639 cm-1. In addition, a coupled C14HC15H Au hydrogen-out-of-plane mode is found at 1019 cm-1. The calculated 13C NMR chemical shifts in the polyene chain are very sensitive to the perturbation of the bond length alternation pattern. The protonated models show a C13 response that is more deshielded than C15, supporting the presence of a polaronic charge effect in the protonated Schiff base and an accumulation of charge at C13, in line with all NMR spectroscopic data. Finally, we have resolved an essential difference between retinylidene iminium salts and rhodopsin. In contrast with rhodopsin, the delocalization of positive charge in these model compounds is intimately connected with the polarization effects from the counterion at the Schiff base. This supports recent inferences that the negative charge of the counterion in the rhodopsin protein is strongly delocalized around the polyene chain of the chromophore, and promotes accumulation of positive charge around the cis bond.
Article Reference Ab Initio Molecular Dynamics Simulations and g-Tensor Calculations of Aqueous Benzosemiquinone Radical Anion: Effects of Regular and “T-Stacked” Hydrogen Bonds
CarParrinello molecular dynamics (CP-MD) simulations of the benzosemiquinone radical anion in aqueous solution have been performed at ambient conditions. Analysis of the trajectory shows not only extensive hydrogen bonding to the carbonyl oxygen atoms (ca. 45.6 water molecules depending on distance criteria), but also relatively long-lived T-stacked hydrogen bonds to the semiquinone pi-system. These results are discussed in the context of recent findings on semiquinone-protein interactions in photosynthetic reaction centers, and of EPR and vibration spectroscopical data for the aqueous system. Snapshots from the CP-MD trajectory are used for the first quantum chemical analyses of dynamical effects on electronic g-tensors, using cluster models and a recently developed density functional method. In particular, the effects of intermolecular hydrogen-bond dynamics on the g-tensor components are examined, in comparison with recent EPR and ENDOR studies.
Article Reference Ab Initio Molecular Dynamics Study of Formate Ion Hydration
We perform ab initio molecular dynamics simulations of the aqueous formate ion. The mean number of water molecules in the first solvation shell, or the hydration number, of each formate oxygen is found to be consistent with recent experiments. Our ab initio pair correlation functions, however, differ significantly from many classical force field results and hybrid quantum mechanics/molecular mechanics predictions. They yield roughly one less hydrogen bond between each formate oxygen and water than force field or hybrid methods predict. Both the BLYP and PW91 exchange correlation functionals give qualitatively similar results. The time dependence of the hydration numbers are examined, and Wannier function techniques are used to analyze electronic configurations along the molecular dynamics trajectory.
Article Reference Ab Initio Molecular Dynamics Study of Uracil in Aqueous Solution
The hydrogen bonding of uracil in aqueous solution is investigated using density functional based ab initio molecular dynamics simulation (CarParrinello). During the 7 ps trajectory, the solute was observed to be coordinated by a first hydration shell composed of up to nine water molecules. Six water molecules are hydrogen-bonded to the amide and carbonyl groups and three further water molecules are located on either side of the uracil ring with a tendency to approach the ring through pi-hydrogen bonding. The hydrogen bonding is characterized by the computation of a number of structural and dynamical correlation functions. To highlight the importance of the finite temperature bulk solvent, these results are compared to structures obtained by a number of previous structural studies of ground-state hydrated clusters. The analysis presented here is the structural complement to an ab initio molecular dynamics determination of the infrared absorption spectrum of aqueous uracil that has appeared as a separate publication (J. Phys. Chem. B 2003, 107, 10344).
Article Reference Ab initio molecular-dynamics study of supercritical carbon dioxide
 
Article Reference An ab Initio Molecular Dynamics Study of the Aqueous Liquid-Vapor Interface
We present an ab initio molecular dynamics simulation of the aqueous liquid-vapor interface. Having successfully stabilized a region of bulk water in the center of a water slab, we were able to reproduce and further quantify the experimentally observed abundance of surface "acceptor-only"(19\%) and "single-donor"(66\%) moieties as well as substantial surface relaxation approaching the liquid-vapor interface. Examination of the orientational dynamics points to a faster relaxation in the interfacial region. Furthermore, the average value of the dipole decreases and the average value of the highest occupied molecular orbital for each water molecule increases approaching the liquid-vapor interface. Our results support the idea that the surface contains, on average, far more reactive states than the bulk.
Article Reference BPA-PC on a Ni(111) Surface: The Interplay between Adsorption Energy and Conformational Entropy for Different Chain-End Modifications
We extend a previous dual scale modeling approach for the behavior of polymers near a metal surface to a variety of end groups. Our approach combines a coarse-grained polymer model with ab initio DFT calculations. Such a procedure was applied to a melt of phenolic-like terminated Bisphenol A-polycarbonate (BPA-PC) interacting with a (111) nickel surface (Delle Site, L.; Abrams, C. F.; Alavi, A.; Kremer, K. Phys. Rev. Lett. 2002, 89, 156103. Abrams, C. F.; Delle Site, L.; Kremer, K. Phys. Rev. E 2003, 67, 021807). This work extends this study to different chain-end modifications of BPA-PC, p-tert-butylphenolic, p-tetramethylpropylphenolic, and p-cumylphenolic. We show how the interplay between adsorption energies and conformational entropy selects different morphologies for the various melts at the interface. Implications of these results for realistic technical materials are finally discussed.
Article Reference Car-Parrinello molecular dynamics simulation of base-catalyzed amide hydrolysis in aqueous solution
The base catalyzed hydrolysis of N-methylacetamide is elucidated by means of Car-Parrinello simulation. The process is investigated in aqueous solution, including a quantum treatment of all electronic degrees of freedom. The rate-determining step is the attack of a hydroxide ion on the amide carbon atom. This is followed by protonation of the nitrogen atom. The final dissociation may occur via two different pathways: (i) dissociation into an amine and a carboxylic acid and (ii) oxygen deprotonation and dissociation into an amine and a carboxyl anion. The later pathway was found to be strongly favored.
Article Reference Charge separation and polymerization of hydrocarbons at an ultrahigh pressure
Ab initio molecular dynamics simulations have been performed as a function of density for a disordered sample of butadiene (CH2=CH−CH=CH2) at ambient temperature. At high density the system spontaneously reacts, in the ground state, with an ionic mechanism to mainly produce trans poly-butadiene chains. The reaction mechanism has been characterized. The pressure strongly modifies the molecular dipole generating cooperative phenomena in the sample.
Article Reference Cisplatin Binding to DNA Oligomers from Hybrid Car-Parrinello/Molecular Dynamics Simulations
The structure and binding of cisplatin to DNA in aqueous solution are investigated via a QM/MM methodology. In our approach, the platinated moiety is treated at the density functional level and the biomolecular frame with the AMBER force field. The calculations are based on X-ray structures of platinated DNA in the free form (cispt-d(CCTCTG*G*TCTCC)-d(GGAGACCAGAGG) [Takahara, et al. Nature 1995, 377, 649652]1) and in complex with HMG protein domain A (cispt-d(CCUCTCTG*G*ACCTTCC)-d(GGAGAGACCTGGAAGG) [Ohndorf et al. Nature 1999, 399, 708712]2 as well as on a cisplatin docked DNA model. During the QM/MM simulation, the structure of the platinated DNA dodecamer rearranges significantly toward structural determinants of the solution structure as obtained by NMR spectroscopy [Gelasco et al. Biochemistry 1998, 37, 92309239].3 The calculated 195Pt chemical shifts of the QM/MM structure relative to cisplatin in aqueous solution are in qualitative agreement with the experimental data [Bancroft et al. J. Am. Chem. Soc. 1990, 112, 68606871. Miller et al. Inorg. Chem. 1985, 24, 24212425].4,5 The QM/MM structure of the platinated/DNA HMG complex, on the other hand, remains rather similar to the X-ray structure, consistent with its relatively low flexibility. Docking of Pt(NH3)22+ onto DNA in its canonical B-conformation causes a large axis bend and a rearrangement of DNA as experimentally observed in the platinated adducts, with NMR chemical shifts in qualitative agreement with the values in aqueous solution.4,5
Article Reference CO bonded to platinum: effects of semi-core polarization
The CO-platinum bond is systematically investigated with respect to metal semi-core polarization for platinum carbonyls and CO bonded to Pt(1 1 1). This is an issue of renewed interest owing to the recent observation [J. Phys. Chem. B 105 (2001) 4018] that several implementations of the density functional theory predict a three-fold hollow site to be the preferred adsorption site of CO on Pt(1 1 1), whereas experimental low coverage data show that atop is the stable adsorption site. The present calculations reveal clear effects of semi-core polarization in structural, energetic and vibrational properties. In general, the effects are more pronounced in atop compared with bridge and hollow configurations. For the carbonyls, fair agreement with experimental gas phase data is obtained if semi-core polarization effects are taken into account. Allowing for 5s5p relaxation, reduces the atop site preference from ˊ0.2 to ˊ0.1 eV for CO/Pt(1 1 1).
Article Reference Competition between Water and Hydrogen Peroxide at Ti Center in Titanium Zeolites. An ab Initio Study
A combined CarParrinello molecular dynamics blue moon sampling approach has been adopted to study the competitive attack of H2O and H2O2 at a tetracoordinated Titanium site in a Tizeolite. The results indicate that, although the attack of water to form a trigonal bipyramidal center is thermodynamically more stable, the attack of hydrogen peroxide to form a similar adduct is kinetically favored. In both cases, solvent cooperation is effective in the formation of the adducts. The relevance of such a result in relation to the catalytic properties of Tizeolites is discussed.
Article Reference Computational Approaches to Activity in Rhodium-Catalysed Hydroformylation
In this theoretical study on rhodium-catalysed hydroformylation we examine an unmodified hydridorhodium(I) carbonyl system a together with three variants modified by the model phosphane ligands PF3 (system b), PH3 (system c) and PMe3 (system d), which show increasing basicity on the Tolman chi parameter scale. The olefinic substrate for all systems is ethene. Based on the dissociative hydroformylation mechanism, static and dynamic quantum-mechanical approaches are made for preequilibria and the whole catalytic cycle. Agreement with experimental results was achieved with regard to the predominance of phosphane monocoordination in systems b-d, different sensitivity of unmodified and modified systems towards hydrogen pressure and the early location of the rate-determining step. Neither the catalytic cycle as a whole nor olefin insertion as an important selectivity-determining step gives a clear picture of activity differences among a-d. However, the crucial first catalytic step, association of ethene to the active species [HRhL3] (L=CO, PR3), may play the key role in the experimentally observed higher activity of a and systems with less basic phosphane ligands modelled by b.
Article Reference Controlling the Conformation of Arylamides: Computational Studies of Intramolecular Hydrogen Bonds between Amides and Ethers or Thioethers
The role of an ortho-alkylthioether group in controlling the conformation around the ring&bond;N bonds of meta-connected arylamide oligomers is studied. Density functional theory (DFT) geometries of model compounds, including acetanilide, an ether acetanilide, and a thioether acetanilide, and their corresponding diamides, show that for either monoamide or diamide the alkyl side chain of the thioether should be perpendicular to the aryl plane, whereas for the ether monoamide, the alkyl side chain is in the aryl plane. DFT ring&bond;N torsional potentials and constrained geometries of the model compounds demonstrate that carbonyl&bond;S repulsion leads to a high torsional barrier and that intramolecular N&bond;HsdotsdotsdotS and C&bond;HsdotsdotsdotO hydrogen bonds and ring-amide conjugation lead to N&bond;H having a preferred orientation in the benzene plane pointing towards S. The N&bond;H bond lengthens and the ortho-ring C&bond;H bond shortens in a regular pattern in the approach to the preferred orientation. Calculated IR frequencies for the N&bond;H stretch show a clear red shift between model compounds without and with the thioether side chain.
Article Reference Density-functional theory characterization of acid sites in chabazite
The nature of the acid sites in zeolites and the factors contributing to enhanced catalytic activity have been the subject of much study in the literature. In particular, the issue of whether all of the acid sites in a particular zeolite are homogeneous or heterogeneous in acid strength requires the development of a systematic way to quantify acidity. To address this, we performed a detailed density-functional theory (DFT) investigation of the reactivity of the acid sites in the zeolite chabazite. We calculated energies of adsorption of bases, deprotonation energies, and vibrational frequencies on a periodic chabazite (SSZ-13) model with various loadings of acid sites per unit cell, and with various structural framework defects. We found that the four acidic oxygens at the aluminum T site all have roughly the same proton affinity, and the deprotonation energy is not correlated to the OH bond length or vibrational stretch frequency. Furthermore, we found that the adsorption energy of various bases at each acid site oxygen is roughly the same and correlated only to the gas-phase proton affinity of the base; it does not vary significantly with acid-site concentration or framework defects near the acid site. Given the range of local chemical structure that we investigated, our results suggest that the strength of the acid sites in chabazite is not influenced significantly by chemical or structural variations in the framework near the acid site.
Article Reference Density-functional theory-based molecular simulation study of liquid methanol
 
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