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Showing papers on "Ab initio quantum chemistry methods published in 2004"


Journal ArticleDOI
TL;DR: The DFT‐D‐BLYP model seems to be even superior to standard MP2 treatments that systematically overbind, and the approach is suggested as a practical tool to describe the properties of many important van der Waals systems in chemistry.
Abstract: An empirical method to account for van der Waals interactions in practical calculations with the density functional theory (termed DFT-D) is tested for a wide variety of molecular complexes. As in previous schemes, the dispersive energy is described by damped interatomic potentials of the form C6R−6. The use of pure, gradient-corrected density functionals (BLYP and PBE), together with the resolution-of-the-identity (RI) approximation for the Coulomb operator, allows very efficient computations for large systems. Opposed to previous work, extended AO basis sets of polarized TZV or QZV quality are employed, which reduces the basis set superposition error to a negligible extend. By using a global scaling factor for the atomic C6 coefficients, the functional dependence of the results could be strongly reduced. The “double counting” of correlation effects for strongly bound complexes is found to be insignificant if steep damping functions are employed. The method is applied to a total of 29 complexes of atoms and small molecules (Ne, CH4, NH3, H2O, CH3F, N2, F2, formic acid, ethene, and ethine) with each other and with benzene, to benzene, naphthalene, pyrene, and coronene dimers, the naphthalene trimer, coronene · H2O and four H-bonded and stacked DNA base pairs (AT and GC). In almost all cases, very good agreement with reliable theoretical or experimental results for binding energies and intermolecular distances is obtained. For stacked aromatic systems and the important base pairs, the DFT-D-BLYP model seems to be even superior to standard MP2 treatments that systematically overbind. The good results obtained suggest the approach as a practical tool to describe the properties of many important van der Waals systems in chemistry. Furthermore, the DFT-D data may either be used to calibrate much simpler (e.g., force-field) potentials or the optimized structures can be used as input for more accurate ab initio calculations of the interaction energies. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1463–1473, 2004

4,332 citations


Journal ArticleDOI
TL;DR: In this article, the results of detailed calculations for bulk properties and the electronic structure of the cubic phase of the perovskite crystals with detailed optimization of basis set (BS) are discussed.

698 citations


Journal ArticleDOI
TL;DR: The results strongly indicate that even greater accuracy may be expected in reactions that preserve (either exactly or approximately) the number and types of chemical bonds.
Abstract: A theoretical model chemistry designed to achieve high accuracy for enthalpies of formation of atoms and small molecules is described. This approach is entirely independent of experimental data and contains no empirical scaling factors, and includes a treatment of electron correlation up to the full coupled-cluster singles, doubles, triples and quadruples approach. Energies are further augmented by anharmonic zero-point vibrational energies, a scalar relativistic correction, first-order spin-orbit coupling, and the diagonal Born-Oppenheimer correction. The accuracy of the approach is assessed by several means. Enthalpies of formation (at 0 K) calculated for a test suite of 31 atoms and molecules via direct calculation of the corresponding elemental formation reactions are within 1 kJ mol(-1) to experiment in all cases. Given the quite different bonding environments in the product and reactant sides of these reactions, the results strongly indicate that even greater accuracy may be expected in reactions that preserve (either exactly or approximately) the number and types of chemical bonds.

692 citations


Journal ArticleDOI
TL;DR: In this paper, a series of 20 ps ab initio molecular dynamics simulations of water at ambient density and temperatures ranging from 300 to 450 K are presented, where Car-Parrinello (CP) and Born-Oppenheimer (BO) molecular dynamics techniques are compared for systems containing 54 and 64 water molecules.
Abstract: A series of 20 ps ab initio molecular dynamics simulations of water at ambient density and temperatures ranging from 300 to 450 K are presented. Car-Parrinello (CP) and Born-Oppenheimer (BO) molecular dynamics techniques are compared for systems containing 54 and 64 water molecules. At 300 K, an excellent agreement is found between radial distribution functions (RDFs) obtained with BO and CP dynamics, provided an appropriately small value of the fictitious mass parameter is used in the CP simulation. However, we find that the diffusion coefficients computed from CP dynamics are approximately two times larger than those obtained with BO simulations for T>400 K, where statistically meaningful comparisons can be made. Overall, both BO and CP dynamics at 300 K yield overstructured RDFs and slow diffusion as compared to experiment. In order to understand these discrepancies, the effect of proton quantum motion is investigated with the use of empirical interaction potentials. We find that proton quantum effects...

585 citations


Journal ArticleDOI
02 Apr 2004-Science
TL;DR: Experimental evidence is presented for a very stable cluster corresponding to Al13I–, which features a structurally unperturbed Al13– core and a region of high charge density on the aluminum vertex opposite from the iodine atom.
Abstract: Al13- is a cluster known for the pronounced stability that arises from coincident closures of its geometric and electronic shells. We present experimental evidence for a very stable cluster corresponding to Al13I-. Ab initio calculations show that the cluster features a structurally unperturbed Al13- core and a region of high charge density on the aluminum vertex opposite from the iodine atom. This ionically bound magic cluster can be understood by considering that Al13 has an electronic structure reminiscent of a halogen atom. Comparisons to polyhalides provide a sound explanation for our chemical observations.

484 citations


Journal ArticleDOI
TL;DR: In this article, an all-atom force field for a class of room temperature ionic liquids of the 1-alkyl-3-methylimidazolium cation family was developed.
Abstract: An all-atom force field for a class of the room temperature ionic liquids of the 1-alkyl-3-methylimidazolium cation family was developed. The model is based on the AMBER force field with modifications on several parameters. The refinements include three aspects. (1) The force coefficients of the bond and angle parameters were adjusted to fit the vibrational frequency data, from both experiment and ab initio calculations. (2) The parameters for two types of torsions, which are absent in the original AMBER, were obtained by fitting the torsion energy profiles depending on dihedral angles. (3) The results of the minimum interaction energies and geometries for several ion pairs, calculated from ab initio and the force field, respectively, are compared. Then, the van der Waals (VDW) diameter of a type of hydrogen atom (H5) is adjusted. To validate the force field, we performed molecular dynamics (MD) simulations for five RTILs. The predicted densities are in better agreement than those reported from other simu...

479 citations


Journal ArticleDOI
TL;DR: In this article, the thermodynamic properties of Al, Ni, NiAl, and Ni3Al were studied using the first-principles approach using the ab initio plane wave pseudopotential method within the generalized gradient approximation.

441 citations


Journal ArticleDOI
TL;DR: In this paper, the Coulomb interaction is decomposed into long-range and short-range components, and the energy of a quantum electronic system is decomposed into long range and short range contributions.
Abstract: By splitting the Coulomb interaction into long-range and short-range components, we decompose the energy of a quantum electronic system into long-range and short-range contributions. We show that the long-range part of the energy can be efficiently calculated by traditional wave function methods, while the short-range part can be handled by a density functional. The analysis of this functional with respect to the range of the associated interaction reveals that, in the limit of a very short-range interaction, the short-range exchange-correlation energy can be expressed as a simple local functional of the on-top pair density and its first derivatives. This provides an explanation for the accuracy of the local density approximation (LDA) for the short-range functional. Moreover, this analysis leads also to new simple approximations for the short-range exchange and correlation energies improving the LDA.

434 citations


Journal ArticleDOI
TL;DR: The study presents reference ab initio structures and interaction energies of selected base pairs with binding energies ranging from -5 to -47 kcal/mol and indirectly supports the view that H-bonded base pairs are primarily stabilized by electrostatic interactions.
Abstract: Hydrogen-bonded nucleic acids base pairs substantially contribute to the structure and stability of nucleic acids. The study presents reference ab initio structures and interaction energies of selected base pairs with binding energies ranging from -5 to -47 kcal/mol. The molecular structures are obtained using the RI-MP2 (resolution of identity MP2) method with extended cc-pVTZ basis set of atomic orbitals. The RI-MP2 method provides results essentially identical with the standard MP2 method. The interaction energies are calculated using the Complete Basis Set (CBS) extrapolation at the RI-MP2 level. For some base pairs, Coupled-Cluster corrections with inclusion of noniterative triple contributions (CCSD(T)) are given. The calculations are compared with selected medium quality methods. The PW91 DFT functional with the 6-31G basis set matches well the RI-MP2/CBS absolute interaction energies and reproduces the relative values of base pairing energies with a maximum relative error of 2.6 kcal/mol when applied with Becke3LYP-optimized geometries. The Becke3LYP DFT functional underestimates the interaction energies by few kcal/mol with relative error of 2.2 kcal/mol. Very good performance of nonpolarizable Cornell et al. force field is confirmed and this indirectly supports the view that H-bonded base pairs are primarily stabilized by electrostatic interactions.

433 citations


Journal ArticleDOI
TL;DR: In this paper, the trends in adsorption energy, geometry, vibrational properties, and other parameters derived from the electronic structure of the substrate were studied, and the influence of specific changes in their set-up, such as choice of the exchange correlation functional, the choice of pseudopotential, size of the basis set and substrate relaxation, has been carefully evaluated.
Abstract: We have studied the trends in CO adsorption on close-packed metal surfaces: Co, Ni, Cu from the 3d row, Ru, Rh, Pd, Ag from the 4d row and Ir, Pt, Au from the 5d row using density functional theory. In particular, we were concerned with the trends in adsorption energy, geometry, vibrational properties and other parameters derived from the electronic structure of the substrate. The influence of specific changes in our set-up, such as choice of the exchange correlation functional, the choice of pseudopotential, size of the basis set and substrate relaxation, has been carefully evaluated. We found that, while the geometrical and vibrational properties of the adsorbate–substrate complex are calculated with high accuracy, the adsorption energies calculated with the gradient-corrected Perdew–Wang exchange–correlation energies are overestimated. In addition, the calculations tend to favour adsorption sites with higher coordination, resulting in the prediction of the wrong adsorption sites for the Rh, Pt and Cu surfaces (hollow instead of top). The revised Perdew–Burke–Erzernhof functional (RPBE) leads to lower (i.e. more realistic) adsorption energies for transition metals, but to the wrong results for noble metals—for Ag and Au, endothermic adsorption is predicted. The site preference remains the same. We discuss trends in relation to the electronic structure of the substrate across the periodic table, summarizing the state-of-the-art of CO adsorption on close-packed metal surfaces.

402 citations


Journal ArticleDOI
TL;DR: In this paper, the trends in CO adsorption on close-packed metal surfaces were studied using density functional theory, and the effect of specific changes in the setup such as choice of the exchange correlation functional, the choice of pseudopotential and size of the basis set, substrate relaxation has been carefully evaluated.
Abstract: We have studied the trends in CO adsorption on close-packed metal surfaces: Co, Ni, Cu from the 3d row, Ru, Rh, Pd, Ag from the 4d row and Ir, Pt, Au from the 5d row using density functional theory. In particular, we were concerned with the trends in the adsorption energy, the geometry, the vibrational properties and other parameters derived from the electronic structure of the substrate. The influence of specific changes in our setup such as choice of the exchange correlation functional, the choice of pseudopotential and size of the basis set, substrate relaxation has been carefully evaluated. We found that while the geometrical and vibrational properties of the adsorbate-substrate complex are calculated with high accuracy, the adsorption energies calculated with the gradient-corrected Perdew-Wang exchange-correlation energies are overestimated. In addition, the calculations tend to favour adsorption sites with higher coordination, resulting in the prediction of wrong adsorption sites for the Rh, Pt and Cu surfaces (hollow instead of top). The revised Perdew-Burke-Erzernhof functional (RPBE) leads to lower (i.e. more realistic) adsorption energies for transition metals, but to wrong results for noble metals - for Ag and Au endothermic adsorption is predicted. The site preference remains the same. We discuss trends in relation to the electronic structure of the substrate across the Periodic Table, summarizing the state-of-the-art of CO adsorption on close-packed metal surfaces.

Journal ArticleDOI
TL;DR: A new approach that combines electronic structure methods and molecular dynamics simulations to investigate the infrared spectroscopy of condensed phase systems is presented, and the methods presented are simple, and transferable to more complicated systems.
Abstract: We present a new approach that combines electronic structure methods and molecular dynamics simulations to investigate the infrared spectroscopy of condensed phase systems. This approach is applied to the OH stretch band of dilute HOD in liquid D2O and the OD stretch band of dilute HOD in liquid H2O for two commonly employed models of water, TIP4P and SPC/E. Ab initio OH and OD anharmonic transition frequencies are calculated for 100 HOD x (D2O)n and HOD x(H2O)n (n = 4-9) clusters randomly selected from liquid water simulations. A linear empirical relationship between the ab initio frequencies and the component of the electric field from the solvent along the bond of interest is developed. This relationship is used in a molecular dynamics simulation to compute frequency fluctuation time-correlation functions and infrared absorption line shapes. The normalized frequency fluctuation time-correlation functions are in good agreement with the results of previous theoretical approaches. Their long-time decay times are 0.5 ps for the TIP4P model and 0.9 ps for the SPC/E model, both of which appear to be somewhat too fast compared to recent experiments. The calculated line shapes are in good agreement with experiment, and improve upon the results of previous theoretical approaches. The methods presented are simple, and transferable to more complicated systems.

Journal ArticleDOI
30 Jan 2004-Science
TL;DR: The results support the idea that the surface contains, on average, far more reactive states than the bulk, and the average value of the dipole decreases and the highest occupied molecular orbital for each water molecule increases approaching the liquid-vapor interface.
Abstract: 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.

Journal ArticleDOI
03 Dec 2004-Science
TL;DR: Experimental and theoretical evidence is presented for an excited-state deactivation mechanism specific to hydrogen-bonded aromatic dimers, which may account, in part, for the photostability of the Watson-Crick base pairs in DNA.
Abstract: We present experimental and theoretical evidence for an excited-state deactivation mechanism specific to hydrogen-bonded aromatic dimers, which may account, in part, for the photostability of the Watson-Crick base pairs in DNA. Femtosecond time-resolved mass spectroscopy of 2-aminopyridine clusters reveals an excited-state lifetime of 65 ± 10 picoseconds for the near-planar hydrogen-bonded dimer, which is significantly shorter than the lifetime of either the monomer or the 3- and 4-membered nonplanar clusters. Ab initio calculations of reaction pathways and potential-energy profiles identify the mechanism of the enhanced excited-state decay of the dimer: Conical intersections connect the locally excited 1 ππ* state and the electronic ground state with a 1 ππ* charge-transfer state that is strongly stabilized by the transfer of a proton.

Journal ArticleDOI
TL;DR: It is demonstrated that the CR-EOMCCSD(T) approaches provide a highly accurate description of excited states dominated by double excitations, excited states displaying a manifestly multireference character, and PESs of exciting states along bond breaking coordinates with the ease of the ground-state CCSD(T).
Abstract: The single-reference ab initio methods for high accuracy calculations of potential energy surfaces (PESs) of excited electronic states, termed the completely renormalized equation-of-motion coupled-cluster approaches with singles, doubles, and noniterative triples [CR-EOMCCSD(T)], are developed. In the CR-EOMCCSD(T) methods, which are based on the formalism of the method of moments of coupled-cluster equations, the suitably designed corrections due to triple excitations are added, in a state-selective manner, to the excited-state energies obtained in the standard equation-of-motion coupled-cluster calculations with singles and doubles (EOMCCSD). It is demonstrated that the CR-EOMCCSD(T) approaches, which can be regarded as the excited-state analogs of the ground-state CR-CCSD(T) theory, provide a highly accurate description of excited states dominated by double excitations, excited states displaying a manifestly multireference character, and PESs of excited states along bond breaking coordinates with the ease of the ground-state CCSD(T) or CR-CCSD(T) calculations. The performance of the CR-EOMCCSD(T) methods is illustrated by the results of calculations for the excited states of CH+, HF, N2, C2, and ozone.

Journal ArticleDOI
07 May 2004-Langmuir
TL;DR: This multitechnique and multiscale approach demonstrates the compatibility of bond-valence models of surface oxygen proton affinities and Stern-based models of the EDL structure, with the actual molecular interfacial distributions observed experimentally, revealing new insight into EDL properties including specific binding sites and hydration states of sorbed ions, interfacial solvent properties, and the effect of solution ionic strength.
Abstract: A comprehensive picture of the interface between aqueous solutions and the (110) surface of rutile (α-TiO2) is being developed by combining molecular-scale and macroscopic approaches, including experimental measurements, quantum calculations, molecular simulations, and Gouy−Chapman−Stern models. In situ X-ray reflectivity and X-ray standing-wave measurements are used to define the atomic arrangement of adsorbed ions, the coordination of interfacial water molecules, and substrate surface termination and structure. Ab initio calculations and molecular dynamics simulations, validated through direct comparison with the X-ray results, are used to predict ion distributions not measured experimentally. Potentiometric titration and ion adsorption results for rutile powders having predominant (110) surface expression provide macroscopic constraints of electrical double layer (EDL) properties (e.g., proton release) which are evaluated by comparison with a three-layer EDL model including surface oxygen proton affini...

Journal ArticleDOI
TL;DR: The internal consistency and convergence behavior of the data suggests accuracies of +/-0.2 kcal mol(-1) in these predictions, except perhaps in the HCNO case, and the need for CCSDTQ [full coupled cluster through quadruple excitations] computations to eliminate remaining uncertainties is apparent.
Abstract: In continuing pursuit of thermochemical accuracy to the level of 0.1 kcal mol−1, the heats of formation of NCO, HNCO, HOCN, HCNO, and HONC have been rigorously determined using state-of-the-art ab initio electronic structure theory, including conventional coupled cluster methods [coupled cluster singles and doubles (CCSD), CCSD with perturbative triples (CCSD(T)), and full coupled cluster through triple excitations (CCSDT)] with large basis sets, conjoined in cases with explicitly correlated MP2-R12/A computations. Limits of valence and all-electron correlation energies were extrapolated via focal point analysis using correlation consistent basis sets of the form cc-pVXZ (X=2–6) and cc-pCVXZ (X=2–5), respectively. In order to reach subchemical accuracy targets, core correlation, spin-orbit coupling, special relativity, the diagonal Born–Oppenheimer correction, and anharmonicity in zero-point vibrational energies were accounted for. Various coupled cluster schemes for partially including connected quadrupl...

Journal ArticleDOI
TL;DR: In this article, a force field for interactions of water molecules with the (110) surface of rutile (α-TiO2) has been generalized for atomistically detailed molecular dynamics simulations of the interfacial structure of the uncharged mineral surface in contact with liquid SPC/E water at 298 K and 1 atm.
Abstract: A recently developed force field for interactions of water molecules with the (110) surface of rutile (α-TiO2) has been generalized for atomistically detailed molecular dynamics simulations of the interfacial structure of the uncharged mineral surface in contact with liquid SPC/E water at 298 K and 1 atm and for negatively charged surfaces in contact with SPC/E water containing dissolved electrolyte ions (Rb+, Sr2+, Zn2+, Na+, Ca2+, Cl-). Both hydroxylated (dissociative) and nonhydroxylated (associative) surfaces are simulated, since both types of water−surface interactions have been postulated from ab initio calculations and spectroscopic studies under near-vacuum conditions. The positions of water molecules at the interface were found to be very similar for both hydroxylated and nonhydroxylated surfaces, with either terminal hydroxyl groups or associated water molecules occupying the site above each terminal titanium atom. Beyond these surface oxygens, a single additional layer of adsorbed water molecul...

Journal ArticleDOI
TL;DR: An automatic procedure for the generation of potential energy surfaces based on high level ab initio calculations is described, which allows us to determine the vibrational wave functions for molecules of up to ten atoms.
Abstract: An automatic procedure for the generation of potential energy surfaces based on high level ab initio calculations is described. It allows us to determine the vibrational wave functions for molecules of up to ten atoms. Speedups in computer time of about four orders of magnitude in comparison to standard implementations were achieved. Effects due to introduced approximations—within the computation of the potential—on fundamental modes obtained from vibrational self-consistent field and vibrational configuration interaction calculations are discussed. Benchmark calculations are provided for formaldehyde and 1,2,5-oxadiazole (furazan).

Journal ArticleDOI
TL;DR: In this paper, the authors investigated the low-lying excited singlet states of the guanine-cytosine base pair with multi-reference ab initio methods (complete-active-space self-consistent field (CASSCF) method and second-order perturbation theory based on the CASPT2).
Abstract: The low-lying excited singlet states of the Watson–Crick form of the guanine–cytosine base pair have been investigated with multi-reference ab initio methods (complete-active-space self-consistent-field (CASSCF) method and second-order perturbation theory based on the CASSCF reference (CASPT2)). The reaction paths and energy profiles for single proton transfer from guanine to cytosine in the 1ππ* guanine-to-cytosine charge-transfer state and for twisting of the CC double bond of the cytosine ring in the locally excited 1ππ* state of cytosine have been explored by excited-state geometry optimization using the configuration-interaction-with-singles (CIS) method and single-point energy calculations at the CASPT2 level. Avoided crossings of the 1ππ* potential-energy functions with the electronic ground-state potential-energy function have been identified along both reaction paths. The results suggest the existence of low-lying conical intersections of the 1ππ* potential-energy surface with the S0 surface which become accessible by possibly barrierless single proton transfer as well as out-of-plane deformation of cytosine and may trigger an ultrafast radiationless decay to the ground state. The relevance of these results for the rationalization of the photostability of the genetic code is briefly discussed.

Journal ArticleDOI
TL;DR: In this paper, an ab initio gradient embedded genetic algorithm program was used to detect the linear global minima for NaCl(2) (-) and Na2)Cl(3) (-), and three-dimensional structures for the larger species.
Abstract: The application of the ab initio genetic algorithm with an embedded gradient has been carried out for the elucidation of global minimum structures of a series of anionic sodium chloride clusters, Na(x)Cl(x+1) (-) (x=1-4), produced in the gas phase using electrospray ionization and studied by photoelectron spectroscopy. These are all superhalogen species with extremely high electron binding energies. The vertical electron detachment energies for Na(x)Cl(x+1) (-) were measured to be 5.6, 6.46, 6.3, and 7.0 eV, for x=1-4, respectively. Our ab initio gradient embedded genetic algorithm program detected the linear global minima for NaCl(2) (-) and Na(2)Cl(3) (-) and three-dimensional structures for the larger species. Na(3)Cl(4) (-) was found to have C(3v) symmetry, which can be viewed as a Na(4)Cl(4) cube missing a corner Na(+) cation, whereas Na(4)Cl(5) (-) was found to have C(4v) symmetry, close to a 3x3 planar structure. Excellent agreement between the theoretically calculated and the experimental spectra was observed, confirming the obtained structures and demonstrating the power of the developed genetic algorithm technique.

Journal ArticleDOI
TL;DR: For the water system, the electric field method is superior to the potential approach, as judged by comparison with experiments for the absorption line shape, and for the N-methylacetamide system the two methods are comparable.
Abstract: Kwac and Cho [J. Chem. Phys. 119, 2247 (2003)] have recently developed a combined electronic structure/molecular dynamics approach to vibrational spectroscopy in liquids. The method involves fitting ab initio vibrational frequencies for a solute in a cluster of solvent molecules to a linear combination of the electrostatic potentials on the solute atoms due to the charges on the solvent molecules. These authors applied their method to the N-methylacetamide-D/D(2)O system. We (S. A. Corcelli, C. P. Lawrence, and J. L. Skinner, [J. Chem. Phys. 120, 8107 (2004)]) have recently explored a closely related method, where instead of the electrostatic potential, the solute vibrational frequencies are fit to the components of the electric fields on the solute atoms due to the solvent molecules. We applied our method to the HOD/D(2)O and HOD/H(2)O systems. In order to make a direct comparison of these two approaches, in this paper we apply their method to the water system, and our method to the N-methylacetamide system. For the water system we find that the electric field method is superior to the potential approach, as judged by comparison with experiments for the absorption line shape. For the N-methylacetamide system the two methods are comparable.

Journal ArticleDOI
TL;DR: In this article, the authors used ab initio calculations and a continuum model to study the mechanism for formation of carbamate from CO2 and alkanolamines, and concluded that a single-step, third-order reaction is the most likely.
Abstract: Ab initio calculations and a continuum model have been used to study the mechanism for formation of carbamate from CO2 and alkanolamines. The molecules studied are ethanolamine and diethanolamine. A brief review is also made of published experimental observations relevant to the reaction mechanism. The ab inito results suggest that a single-step, third-order reaction is the most likely. It would seem unlikely that a zwitterion intermediate with a significant lifetime is present in the system. A single-step mechanism also seems to be in good agreement with the experimental data.

Journal ArticleDOI
TL;DR: These reconstructions lead to the opening of an optical gap without the aid of passivating ligands, thus "self-healing" the surface electronic structure of CdSe nanoparticles.
Abstract: Ab initio calculations of the structural, electronic, and optical properties of CdSe nanoparticles are presented. The atomic structures of the clusters are relaxed both in vacuum and in the presence of surfactant ligands. In both cases, we predict significant geometrical rearrangements of the nanoparticle surface while the wurtzite core is maintained. These reconstructions lead to the opening of an optical gap without the aid of passivating ligands, thus ``self-healing'' the surface electronic structure. Our calculations also predict the existence of a midgap state responsible for recently observed subband emission.

Journal ArticleDOI
TL;DR: The authors' calculations allow direct comparison with experiments and demonstrate that a small amount of dopants can drastically modify the electronic transport properties of the tube, which is certainly a key effect feature for envisioning nanoelectronics.
Abstract: Electronic quantum transport is investigated in boron- and nitrogen-doped carbon nanotubes using tight-binding methods correlated to ab initio calculations The present technique accurately accounts for both effects of dopants, namely, charge transfer and elastic scattering Generic transport properties such as conduction mechanisms, mean-free paths, and conductance scalings are derived for various concentration of randomly distributed boron and nitrogen dopants Our calculations allow direct comparison with experiments and demonstrate that a small amount of dopants (<05%) can drastically modify the electronic transport properties of the tube, which is certainly a key effect feature for envisioning nanoelectronics

Journal ArticleDOI
TL;DR: An analysis of the energetic parameters of the local minima suggests that rare AT base pair conformation is not populated due to the shallowness of this minimum, which completely disappears from the Gibbs free energy surface.
Abstract: The results of a comprehensive study on the double-proton transfer in Adenine−Thymine (AT) and Guanine−Cytosine (GC) base pairs at room temperature in gas phase and with the inclusion of environmental effects are obtained. The double-proton-transfer process has been investigated in the AT and GC base pairs at the B3LYP/6-31G(d) and MP2/6-31G(d) levels of theory. It has been predicted that the hydrogen-bonded bases possess nonplanar geometries due to sp3 hybridization of nitrogen atoms and because of the soft intermolecular vibrations in the molecular complexes. An analysis of the energetic parameters of the local minima suggests that rare AT base pair conformation is not populated due to the shallowness of this minimum, which completely disappears from the Gibbs free energy surface. The stabilization of canonic or rare forms of the DNA bases by water molecules and metal cations has been predicted by calculating the optimal configuration of charges (using differential product/transition state stabilization...

Journal ArticleDOI
TL;DR: The vibrational spectra confirm the existence of NH3(+) in glycinium oxalate and indicates the presence of peculiar intermolecular C-H...O hydrogen bonding interaction producing "blue shift" of C- H stretching frequency.

Journal ArticleDOI
TL;DR: In this article, the electronic structure and chemical bonding of B7- and B7 have been investigated using photoelectron spectroscopy and ab initio calculations, and two almost degenerate pyramidal structures I (C6v, 3A1), and II (C2v, 1A1) were the most stable for B7-, the triplet structure-I is slightly more stable than the singlet structure at our highest level of theory[RCCSD(T)/6-311+G(2df)] by 0.7 kcal/mol only
Abstract: The electronic structure and chemical bonding of B7- and B7 have been investigated using photoelectron spectroscopy and ab initio calculations. Complicated, but well-resolved, photoelectron spectra were obtained for B7- at several photon energies and were shown distinctly to contain contributions from different B7- isomers. The structures of the global minima and low-lying isomers were identified using extensive ab initio calculations. Two almost degenerate pyramidal structures I (C6v, 3A1) and II (C2v, 1A1) were the most stable for B7-. The triplet structure-I is slightly more stable than the singlet structure at our highest level of theory[RCCSD(T)/6-311+G(2df)] by 0.7 kcal/mol only. The next lowest singlet structure V (C2v, 1A1) was perfectly planar and was 7.8 kcal/mol higher in energy at RCCSD(T)/6-311+G(2df) level. The observed photoelectron spectra can only be explained when contributions from all these three low-lying isomers were considered; the observed spectral feature s were in good agreement with the calculated detachment transitions from the three isomers. Analyses of the molecular orbitals and chemical bonding revealed evidence that the triplet pyramidal C6V structure-I has a twofold ( and ) aromaticity, the singlet pyramidal C2V structure-II has -aromaticity and -antiaromaticity, and the singlet planar C2V structure V has a twofold ( andmore » ) antiaromaticity.« less

Journal ArticleDOI
TL;DR: In this paper, the authors used ab initio molecular dynamics (AIMD), following the Born-Oppenheimer forces obtained from density-functional theory (DFT), and obtained diffusivities that are substantially lower than the experimental values.
Abstract: Motivated by the very low diffusivity recently found in ab initio simulations of liquid water, we have studied its dependence with temperature, system size, and duration of the simulations. We use ab initio molecular dynamics (AIMD), following the Born-Oppenheimer forces obtained from density-functional theory (DFT). The linear-scaling capability of our method allows the consideration of larger system sizes (up to 128 molecules in this study), even if the main emphasis of this work is in the time scale. We obtain diffusivities that are substantially lower than the experimental values, in agreement with recent findings using similar methods. A fairly good agreement with D(T) experiments is obtained if the simulation temperature is scaled down by approximately 20%. It is still an open question whether the deviation is due to the limited accuracy of present density functionals or to quantum fluctuations, but neither technical approximations (basis set, localization for linear scaling) nor the system size (down to 32 molecules) deteriorate the DFT description in an appreciable way. We find that the need for long equilibration times is consequence of the slow process of rearranging the H-bond network (at least 20 ps at AIMDs room temperature). The diffusivity is observed to be very directly linked to network imperfection. This link does not appear an artifact of the simulations, but a genuine property of liquid water.

Journal ArticleDOI
TL;DR: In this article, the properties of low-index Pt surfaces were investigated using periodic density functional theory and the results of the calculations were discussed in the context of the mechanism of oxygen reduction.
Abstract: Properties of the oxygen molecule, atomic oxygen, and intermediate products of its reduction, OH, OOH, H 2 O 2 on (111), (100), and (110) Pt surfaces have been investigated using periodic density functional theory. The Pt surfaces are modeled as four-layer slabs. Adsorption energies and geometries, as well as the charge-transfer properties are calculated. Computed characteristics of the adsorbed oxygen reduction intermediates supply known tendencies of the low index Pt surface activities under different experimental conditions. Electric field dependencies of the properties of all species adsorbed on a Pt 9 (111) cluster have been also studied. Lowering the field causes an increase of the O-O bond length of O 2ads , attracting the molecule to the Pt surface and increasing the charge transfer from Pt to 2π* orbitals of the oxygen molecule. The weakening of the O-O bond is evidenced by a decrease of the O-O stretching frequency. The charge-transfer from the Pt 9 cluster to the adsorbates is observed for all species. In our calculations hydrogen peroxide was unstable on all three low-index Pt surfaces and dissociated into two hydroxyls or a water molecule and atomic oxygen. The results of the calculations are discussed in the context of the mechanism of oxygen reduction.