Hydrogen spillover mechanism on a Pd-doped Mg surface as revealed by ab initio density functional calculation

The hydrogenation kinetics of Mg is slow, impeding its application for mobile hydrogen storage. We demonstrate by ab initio density functional theory (DFT) calculations that the reaction path can be greatly modified by adding transition metal catalysts. Contrasting with Ti doping, a Pd dopant will result in a very small activation barrier for both dissociation of molecular hydrogen and diffusion of atomic H on the Mg surface. This new computational finding supports-for the first time by ab initio simulation-the proposed hydrogen spillover mechanism for rationalizing experimentally observed fast hydrogenation kinetics for Pd-capped Mg materials.     

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.     

Theory and range of modern semiempirical molecular orbital methods

Semiempirical molecular orbital methods have a long history. They serve to tackle large systems and complicated processes beyond the reach of ab initio or density functional methods. Although their setup is derived from Hartree–Fock theory, the design of approximate energy expressions and the empirical parameters are used to achieve higher accuracy than the underlying ab initio theory. In this way the effect of larger basis sets or correlation can be partially simulated. All widely used semiempirical methods establish their accuracy by error statistics for molecular properties with experimental and high-level ab initio or density functional theory calculations as a reference. Their computational efficiency makes them suitable for the study of biochemical systems and solid materials. The present review presents a variety of applications which demonstrate the need for and success of semiempirical methods.     

Theoretical study of photodetachment processes of anionic boron clusters. II. Dynamics

Photodetachment bands of anionic boron clusters, B(n) (n = 4,5) are theoretically examined here. The model Hamiltonians developed through extensive ab initio quantum chemistry calculations in Paper I are employed for the required nuclear dynamics study. While the precise location of vibronic lines and progression of vibrational modes within a given electronic band is derived from time-independent quantum mechanical studies, the broadband spectral envelopes and the nonradiative decay rate of electronic states are calculated by propagating wave packets in a time-dependent quantum mechanical framework. The theoretical results are in good accord with the experiment to a large extent. The discrepancies between the two can be partly attributed to the inadequate energy resolution of the experimental results and also to the neglect of dynamic spin-orbit interactions and computational difficulty related with detachment channels involving multi-electron transitions in the theoretical formalism.     

Tailoring approach for exploring electron densities and electrostatic potentials of molecular crystals

Experimental and theoretical studies of electron densities and the corresponding derived entities such as electrostatic potentials have been the primary means of understanding the chemical nature and electronic properties of crystalline substances. Conventional crystal calculation methods such as the embedded cluster models are capable of performing calculations on small and medium-sized molecules, while periodic ab initio methods can treat crystals with up to 200 atoms per unit cell. A linear scaling method, viz. the molecular tailoring approach, has recently been developed for obtaining ab initio quality one-electron properties. In the present study, the molecular tailoring approach is employed to generate electron density, electrostatic potential and interaction density maps with the ibuprofen crystal as a test case. The interaction density and electrostatic potential maps produced in the present work succinctly bring out the actual crystalline environment around a given reference molecule by including the interactions with atoms in its neighborhood. The results obtained from the molecular tailoring approach may thus be expected to enhance our understanding of the environment in the crystalline material with reasonably small computational effort.Contribution to the Jacopo Tomasi Honorary Issue     

Semiempirical and DFT computations of the influence of Tb(III) dopant on unit cell dimensions of cerium(III) fluoride

Several computational methods, both semiempirical and ab initio, were used to study the influence of the amount of dopant on crystal cell dimensions of CeF₃ doped with Tb³⁺ ions (CeF₃:Tb³⁺). AM1, RM1, PM3, PM6, and PM7 semiempirical parameterization models were used, while the Sparkle model was used to represent the lanthanide cations in all cases. Ab initio calculations were performed by means of GGA+U/PBE projector augmented wave density functional theory. The computational results agree well with the experimental data. According to both computation and experiment, the crystal cell parameters undergo a linear decrease with increasing amount of the dopant. The computations performed using Sparkle/PM3 and DFT methods resulted in the best agreement with the experiment with the average deviation of about 1% in both cases. Typical Sparkle/PM3 computation on a 2×2×2 supercell of CeF3:Tb3+ lasted about two orders of magnitude shorter than the DFT computation concerning a unit cell of this material. © 2014 Wiley Periodicals, Inc.     

Modeling electrochemical interfaces from ab initio molecular dynamics: water adsorption on metal surfaces at potential of zero charge

The origin of the potential difference between the potential of zero charge of a metal/water interface and the work function of the metal is a recurring issue because it is related to how water interacts with metal surface in the absence of surface charge. Recently ab initio molecular dynamics method has been used to model electrochemical interfaces to study interfacial potential and the structure of interface water. Here, we will first introduce the computational standard hydrogen electrode method, which allows for ab initio determination of electrode potentials that can be directly compared with experiment. Then, we will review the recent progress from ab initio molecular dynamics simulation in understanding the interaction between water and metal and its impact on interfacial potential. Finally, we will give our perspective for future development of ab initio computational electrochemistry.     

Modeling mechanisms of unusual benzene imine n6 adduct formation in carcinogenic reactions of arylnitrenium ions with adenosine

Reaction mechanisms of the unusual benzene imine N6 adduct formation in carcinogenic reactions of arylnitrenium ions with adenosine have been investigated with density functional theory (DFT) and high-level ab initio methods. The DFT calculations indicate that the reaction pathways initiated by attack of adenine at the ortho C site of 4-biphenylylnitrenium ion are favored. However, high-level MP2 and QCISD calculations provide a contrary conclusion, that is the reaction pathways initiated by attack of adenine at the para C site of 4-biphenylylnitrenium ion are more feasible. Comparing with experimental results, the conclusion from high-level ab initio calculations is ultimately supported. The present study makes a theoretical prediction on the final products in the studied reaction, which is in agreement with experimental observations. In addition, this study provides some inspirations to the attacks of arylnitrenium ions at amino group of purines and pyrimidines in similar carcinogenic reactions.     

Linewidths of C2H2 perturbed by H2: experiments and calculations from an ab initio potential

In this work we present a theoretical and experimental study of the acetylene-hydrogen system. A potential surface considering rigid monomers has been obtained by ab initio quantum chemistry methods. This 4-dimensional potential is further employed to compute, using the close-coupling approach and the coupled-states approximation, pressure broadening coefficients of C(2)H(2) isotropic Raman Q lines over a temperature range of 77 to 2000 K. Experimental data for the acetylene nu(2) Raman lines broadened by molecular hydrogen are obtained using stimulated Raman spectroscopy. The comparison of theoretical values with experimental data at 143 K is promising. Approximations to increase the computational efficiency are proposed.     

Electron binding energies of hydrated H3O+ and OH-: photoelectron spectroscopy of aqueous acid and base solutions combined with electronic structure calculations

The electronic structure of hydrated H3O+ and OH- is probed in a water jet by photoelectron spectroscopy employing 100 eV photons. The first ionization potential for OH- at 9.2 eV and the second ionization potential for H3O+ at 20 eV are resolved, corresponding to the removal of an electron from the 2ppi highest occupied molecular orbital and from the 1e orbital, respectively. These assignments are supported by present computational results based on a combination of molecular dynamics and ab initio calculations.     

A full quantum embedded cluster study of proton siting in chabazite

We propose a computational strategy within the full quantum embedded cluster methodology for modeling reactivity in extended systems. This method takes advantages of the embedded cluster methodology for treating interactions in the active region accurately while allowing interactions with the remaining crystal framework to be treated fully quantum mechanically by using the ab initio tight-binding theory. We have applied this method to study proton siting in chabazite. We found that our calculated relative stability of proton at four different oxygen sites agree well with those from previously periodic calculations, though the computational demand for the present approach is much less.     

Comments on the electronic structure of dimeric copper,as calculated with the hartree—fock—slater method

The first-principles numerical discrete variational method was employed to study the electronic structure of Cu₂, using the Xα approximation for the exchange interaction. One-electron eigenvalues and ionization potentials are given. Results are discussed in the framework of the approximations used, and compared with published ab initio results.     

A hierarchical construction scheme for accurate potential energy surface generation: an application to the F+H2 reaction

We present a hierarchical construction scheme for accurate ab initio potential energy surface generation. The scheme is based on the observation that when molecular configuration changes, the variation in the potential energy difference between different ab initio methods is much smaller than the variation for potential energy itself. This means that it is easier to numerically represent energy difference to achieve a desired accuracy. Because the computational cost for ab initio calculations increases very rapidly with the accuracy, one can gain substantial saving in computational time by constructing a high accurate potential energy surface as a sum of a low accurate surface based on extensive ab initio data points and an energy difference surface for high and low accuracy ab initio methods based on much fewer data points. The new scheme was applied to construct an accurate ground potential energy surface for the FH(2) system using the coupled-cluster method and a very large basis set. The constructed potential energy surface is found to be more accurate on describing the resonance states in the FH(2) and FHD systems than the existing surfaces.     

Kernel energy method: Basis functions and quantum methods

The kernel energy method (KEM) has been illustrated with peptides and has been shown to reduce the computational difficulty associated with obtaining ab initio quality quantum chemistry results for large biological compounds. In a recent paper, the method was illustrated by application to 15 different peptides, ranging in size from 4 to 19 amino acid residues, and was found to deliver accurate Hartree–Fock (HF) molecular energies within the model, using Slater‐type orbital (STO)‐3G basis functions. A question arises concerning whether the results obtained from the use of KEM are wholly dependent on the STO‐3G basis functions that were employed, because of their relative simplicity, in the first applications. In the present work, it is shown that the accuracy of KEM does not depend on a particular choice of basis functions. This is done by calculating the ground‐state energy of a representative peptide, ADPGV7B, containing seven amino acid residues, using seven different commonly employed basis function sets, ranging in size from small to medium to large. It is shown that the accuracy of the KEM does not vary in any systematic way with the size or mathematical completeness of the basis set used, and good accuracy is maintained over the entire variety of basis sets that have been tested. Both approximate HF and density functional theory (DFT) calculations are made. We conclude that the accuracy inherent in the KEM is not dependent on a particular choice of basis functions. The first application, to 15 different peptides mentioned above, employed only HF calculations. A second question that arises is whether the results obtained with the use of KEM will be accurate only within the HF approximation. Therefore, in the present work we also study whether KEM is applicable across a variety of quantum computational methods, characterized by differing levels of accuracy. The peptide, Zaib4, containing 74 atoms, was used to calculate its energy at seven different levels of accuracy. These include the semi‐empirical methods, AM1 and PM5, a DFT B3LYP model, and ab initio HF, MP2, CID, and CCSD calculations. KEM was found to be widely applicable across the spectrum of quantum methods tested. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Proton and carbon-13 chemical shifts: Comparison between theory and experiment

A series of ab initio ¹H and ¹³C NMR chemical shifts are presented for all molecules for which gas-phase experimental measurements exist. Quantitative agreement with this large set of data is achieved by the use of gauge-invariant atomic orbitals in an SCF perturbation theory approach. The effect of basis set completeness on these ¹H and ¹³C chemical shifts is also examined. The 4-31G basis set is found to provide internally consistent results and give satisfactory agreement with gas-phase experimental data. Errors within 6% for ¹H shifts and 3% for ¹³C shifts result. Increasing the basis set to the 6-31G^* level does not significantly improve the agreement. For ¹H shifts only, the 3-21G basis set is adequate. The validity of the particular computational approach employed here is further substantiated by comparison to another ab initio magnetic shielding method.     

The ab initio model potential method and the optimized orbitals for the multiconfiguration self-consistent field-configuration interaction approach

A computational scheme is proposed for generating effective orbital sets for electron groups within the framework of the multiconfiguration self-consistent field-configuration interaction (MCSCF-CI) approach in the ab initio model potential method. © 1996 John Wiley & Sons, Inc.     

Charge Transport Properties of Molecular Junctions Built from Dithiol Polyenes

We present a study of the charge transmission behavior of a series of dithiol polyenes in the context of molecular junctions. Using the Landauer theory and zero voltage approximation the Green’s functions of the inserted molecules are calculated from a fully ab initio wave function based procedure. Various possibilities in approximating the correlation space are explored and quantitatively evaluated. Our results show that the transmission behavior of a molecular junction is not a monotonic function of the length of the employed molecule. Moreover, we introduce the analytic solution of a suitable model system to countercheck the ab initio results and find a remarkable degree of correspondence.     

Mobility of O+ in He and interaction potential of HeO+

New experimental measurements are reported for the mobility of O(+) ions in He gas at 300 K. The accuracy of these new values is estimated as +/-2.5%, which allows them to serve as a stringent test of a new ab initio potential that we have calculated using the RCCSD(T) method. We employed the aug-cc-pV5Z basis set with counterpoise corrections and took spin-orbit coupling into account. The present experimental values lie below the calculated ones, but the difference becomes statistically significant only at moderate and high values of the ratio of the electric field strength to the gas number density; even there they are only marginally significant.     

Cis-->trans, trans-->cis isomerizations and N-O bond dissociation of nitrous acid (HONO) on an ab initio potential surface obtained by novelty sampling and feed-forward neural network fitting

The isomerization and dissociation dynamics of HONO are investigated on an ab initio potential surface obtained by fitting the results of electronic structure calculations at 21 584 configurations by using previously described novelty sampling and feed-forward neural network (NN) methods. The electronic structure calculations are executed by using GAUSSIAN 98 with a 6-311G(d) basis set at the MP4(SDQ) level of accuracy. The average absolute error of the NN fits varies from 0.012 eV (1.22 kJ mol(-1)) to 0.017 eV (1.64 kJ mol(-1)). The average computation time for a HONO trajectory using a single NN surface is approximately 4.8 s. These computation times compare very favorably with those required by other methods primarily because the NN fitting needs to be executed only one time rather than at every integration point. If the average result obtained from a committee of NNs is employed at each point rather than a single NN, increased fitting accuracy can be achieved at the expense of increased computational requirements. In the present investigation, we find that a committee comprising five NN potentials reduces the average absolute interpolation error to 0.0111 eV (1.07 kJ mol(-1)). Cis-trans isomerization rates with total energy of 1.70 eV (including zero point energy) have been computed for a variety of different initial distributions of the internal energy. In contrast to results previously reported by using an empirical potential, where cis-->trans to trans-->cis rate coefficient ratios at 1.70 eV total energy were found to lie in the range of 2.0-12.9 depending on the vibration mode excited, these ratios on the ab initio NN potential lie in the range of 0.63-1.94. It is suggested that this result is a reflection of much larger intramode coupling terms present in the ab initio potential surface. A direct consequence of this increased coupling is a significant decrease in the mode specific rate enhancement when compared to results obtained by using empirical surfaces. All isomerizations are found to be first order in accordance with the results reported by using empirical potentials. The dissociation rate to NO+OH has been investigated at internal HONO energies of 3.10 and 3.30 eV for different distributions of this energy among the six vibrational modes of HONO. These dissociations are also found to be first order. The computed dissociation rate coefficients exhibit only modest mode specific rate enhancement that is significantly smaller than that obtained on an empirical surface because of the much larger mode couplings present on the ab initio surface.     

Multi‐frequency (S,X, Q and W‐band) EPR and ENDOR Study of Vanadium(IV) Incorporation in the Aluminium Metal–Organic Framework MIL‐53

Doping the well‐known metal–organic framework MIL‐53(Al) with vanadium(IV) ions leads to significant changes in the breathing behaviour and might have repercussions on the catalytic behaviour as well. To understand the properties of such a doped framework, it is necessary to determine where dopant ions are actually incorporated. Electron paramagnetic resonance (EPR) and electron–nuclear double resonance (ENDOR) are applied to reveal the nearest environment of the paramagnetic vanadium(IV) dopant ions. EPR spectra of as‐synthesised vanadium‐doped MIL‐53 are recorded at S‐, X‐, Q‐ and W‐band microwave frequencies. The EPR spectra suggest that at low dopant concentrations (1.0–2.6 mol %) the vanadium(IV) ions are well dispersed in the matrix. Varying the vanadium dopant concentration within this range or the dopant salt leads to the same dominant EPR component. In the ENDOR spectra, hyperfine (HF) interactions with ¹H, ²⁷Al and ⁵¹V nuclei are observed. The HF parameters extracted from simulations strongly suggest that the vanadium(IV) ions substitute Al in the framework.