Chirality and spin density: Ab initio and density functional approaches

The spin distribution in a stable nitroxide biradical that shows ferromagnetic interactions in the solid phase has been studied at three levels of theory: First, at the UHF level; then, including correlation effects in UMP 2 calculations; and finally, the results are compared with the spin density obtained using the local density functional (LDF ) approximation. It is shown that LDF spin densities are closer to UMP 2 than to UHF predictions; the difference between the UHF and the (UMP 2, LDF ) results points to a redistribution of the spin repartition between N and O due to electronic correlation. For planar conformations of the NO group, there is symmetric distribution (D_2d) of the spin density on the adamantane skeleton. For nonplanar nitroxides, the molecule is chiral (C₂), which results in a breakdown of the spin transmission on part of the adamantane cage. © 1993 John Wiley & Sons, Inc.     

Ab initio density functional theory applied to quasidegenerate problems

Ab initio density functional theory (DFT), previously applied primarily at the second-order many-body perturbation theory (MBPT) level, is generalized to selected infinite-order effects by using a new coupled-cluster perturbation theory (CCPT). This is accomplished by redefining the unperturbed Hamiltonian in ab initio DFT to correspond to the CCPT2 orbital dependent functional. These methods are applied to the Be-isoelectronic systems as an example of a quasidegenerate system. The CCPT2 variant shows better convergence to the exact quantum Monte Carlo correlation potential for Be than any prior attempt. When using MBPT2, the semicanonical choice of unperturbed Hamiltonian, plays a critical role in determining the quality of the obtained correlation potentials and obtaining convergence, while the usual Kohn-Sham choice invariably diverges. However, without the additional infinite-order effects, introduced by CCPT2, the final potentials and energies are not sufficiently accurate. The issue of the effects of the single excitations on the divergence in ordinary OEP2 is addressed, and it is shown that, whereas their individual values are small, their infinite-order summation is essential to the good convergence of ab initio DFT.     

Ab initio energetics of nonsubstituted monocyclic pyrones

The monocyclic nonsubstituted pyrones were studied computationally using state-of-the-art ab initio composite computational techniques. Combination of the accurate energies so obtained with conveniently chosen isodesmic or homodesmotic chemical reactions lead to very confident predictions of their corresponding standard enthalpy of formation. The internal consistency of the results obtained from a vast number of independent chemical schemes serves as a further support of the quality of our results, which are thus proposed to establish the energetics of α-pyrone and γ-pyrone.     

Ab initio and density functional theory based studies on collagen triplets

An understanding of the amino acid sequence dependent stability of polypeptides is of renowned interest to biophysicists and biochemists, in order to identify the nature of forces that stabilize the three-dimensional structure of proteins. In this study, the role of various collagen triplets influencing the stability of collagen has been addressed. It is found from this study that proline can stabilize the collagen triplet only when other residues are also in the polyproline II conformation. Solvation studies of various triplets indicate that the presence of polar residues increases the free energy of solvation. Especially the triplets containing arginine residues displays a higher solvation free energy. The chemical hardness of all the triplets in collagen-like conformation has been found to be higher than that in the extended conformation. Studies on Gly–X–Y, Gly–X–Hyp, and Gly–Pro–Y triplets confirm that there will be local variations in the stability of collagen along the entire sequence.     

Ab initio calculations on halogen-bonded complexes and comparison with density functional methods

A systematic theoretical investigation on a series of dimeric complexes formed between some halocarbon molecules and electron donors has been carried out by employing both ab initio and density functional methods. Full geometry optimizations are performed at the Moller-Plesset second-order perturbation (MP2) level of theory with the Dunning's correlation-consistent basis set, aug-cc-pVDZ. Binding energies are extrapolated to the complete basis set (CBS) limit by means of two most commonly used extrapolation methods and the aug-cc-pVXZ (X = D, T, Q) basis sets series. The coupled cluster with single, double, and noniterative triple excitations [CCSD(T)] correction term, determined as a difference between CCSD(T) and MP2 binding energies, is estimated with the aug-cc-pVDZ basis set. In general, the inclusion of higher-order electron correlation effects leads to a repulsive correction with respect to those predicted at the MP2 level. The calculations described herein have shown that the CCSD(T) CBS limits yield binding energies with a range of -0.89 to -4.38 kcal/mol for the halogen-bonded complexes under study. The performance of several density functional theory (DFT) methods has been evaluated comparing the results with those obtained from MP2 and CCSD(T). It is shown that PBEKCIS, B97-1, and MPWLYP functionals provide accuracies close to the computationally very expensive ab initio methods.     

Ab initio dynamic correlation effects in density functional theories: a density based study for argon

In an attempt to get more insight into the links between the coverage of dynamic electron correlation effects defined in traditional wave function theories (WFT) by density functional theories (DFT) we have performed comprehensive studies for the Ar atom, for which the dynamic correlation effects play the dominant role. A density-based approach directly hinged on difference radial density (DRD) distributions defined with respect the Hartree-Fock radial density has been employed for analyzing the impact of dynamic correlation effects on the density. The DRD-distributions calculated by ab initio methods have been compared with their DFT counterparts generated for representatives of several generations of broadly used exchange-correlation functionals and for the recently developed orbital-dependent OEP2 exchange-correlation functional (Bartlett et al. in J Chem Phys 122:034104, 2005). For the local, generalized-gradient, and hybrid functionals it has been found that the dynamic WFT correlation effects on the density are to a significant extent accounted for by densities resulting from exchange-only calculations. It has been shown that the removal of self-interaction errors does not change this result. It has been demonstrated that the VWN5 and LYP correlation functionals do not represent any substantial dynamical correlation effects on the electron density, whereas these effects are well represented by the orbital-dependent OEP2 correlation functional. Critical comparison of the results of the present investigations with various published results obtained for more complex many-electron systems has been made. Attention has been paid to bringing into sharper relief the differences between the conclusions reached when using energy- or density-based criteria.     

Ab initio density functional theory investigation of Li-intercalated zinc oxide nanotube bundles

We have investigated the energetic, and geometric and electronic structure of Li-intercalated (5,5) zinc oxide nanotube (ZnONT) bundles via density functional theory as implemented in the code WIEN2k. Our results showed that the most prominent effect of Li intercalation on the electronic band structure is a shift of the Fermi energy which occurs as a result of charge transfer from lithium to the ZnONTs. All the Li-intercalated (5,5) ZnONT bundles are predicted to be metallic representing a substantial change in electronic properties relative to the undoped bundle, which is a wide band gap semiconductor. Both inside of the nanotube and the interstitial spaces are susceptible for intercalation. The present calculations suggest that the single-walled zinc oxide nanotube (SwZnONT) bundle is a promising candidate for the anode material in battery applications.     

Ab initio and density functional study of substituent effects in halogenated cations of alkenes

A theoretical study of the halogenated cations of mono-, di-, tri- and tetramethyl-substituted ethylenes, C₃H₆X⁺, C₄H₈X⁺, C₅H₁₀X⁺ and C₆H₁₂X⁺, X=F, Cl, Br, have been studied at the ab initio MP2 and density functional B3LYP levels of theory implementing 6-311++G(d,p) basis set. The potential energy surfaces of all molecules under investigation have been scanned and the ¹³C and ¹H NMR chemical shifts for all the bridged halonium ions studied have been calculated using the GIAO method at the B3LYP level. The calculated halogen binding energies in the halonium ions have been correlated with the experimental rates of chlorination and bromination of the corresponding alkenes. The computed hydride affinities and the NICS values for the bridged cations show that the bromo cations are more stable than the analogous chloro and fluoro cations.     

Ab initio and density functional calculations of mean-square amplitudes of vibration for benzene and cubane

Mean-square amplitudes of vibration were calculated using ab initio and density functional methods for benzene and cubane. Both 6-31G^* and 6-311G^** basis sets were employed. It was found that significant improvements were achieved when electron correlation was introduced, even if only at the local density functional level. The mean-square amplitudes calculated were not effected by the basis set used for benzene and slightly improved for the highly strained cubane molecule when the larger basis set was used. An attempt was also made to improve the calculated mean-square amplitudes by making use of scale factors found in the literature, which were developed to improve the calculated frequencies. It was found that only the SCF mean-square amplitudes were significantly improved.     

Ab initio dynamics with wave-packets and density matrices

Efficient methodologies to conduct simultaneous dynamics of electrons and nuclei are discussed. Particularly, attention is directed to a recent development that combines quantum dynamics with ab initio molecular dynamics. The two components of the methodology, namely, quantum dynamics and ab initio molecular dynamics, are harnessed together using a time-dependent self-consistent field-like coupling procedure. An approach to conduct quantum dynamics using an accurate banded, sparse and Toeplitz representation for the discrete free propagator is highlighted with suitable review of other related approaches. One notable feature of the method is that all important quantum dynamical effects including zero-point effects, tunneling as well as over-barrier reflections are accurately treated. Computational methodologies for improved efficiency of the quantum dynamics are also discussed. There exists a number of ways to carry out simultaneous ab initio molecular dynamics (such as Born–Oppenheimer dynamics and extended Lagrangian dynamics, Car–Parrinello dynamics being a prime example of the latter); our prime focus remains on atom-centered density-matrix propagation and Born–Oppenheimer dynamics. The electronic degrees of freedom are handled at accurate levels of density functional theory, using hybrid or gradient corrected approximations. Benchmark calculations are provided for a prototypical proton transfer system. Future generalizations and goals are discussed.     

Ab initio density functional study of MgO (001) surface with topological defects

Magnesium oxide (MgO) is a useful material because of its catalytical properties. Moreover, surface defects have been found to play a crucial role in determining the activity and selectivity of catalytic surfaces. We present the results of a theoretical investigation of the electronic structure of the MgO (001) surface with three different topological defects. Our calculations are based on density functional theory (DFT) and the pseudopotential method. Slab geometry and periodic boundary conditions have been included with occupied orbitals expanded in plane waves. We compare the obtained results of the (001) MgO clean surface with those containing topological defects. The density of states DOS is analyzed in each case, as well as the chemical nature of the atoms belonging to the defects. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Ab initio and density functional theory calculations of molecular structure and vibrational spectrum of ethyl azidoacetate

Here we report ab initio and density functional results for molecular properties of ethyl azidoacetate (N₃CH₂COOC₂H₅) and for the corresponding singly ionized structure (N₃CH₂COOC₂H₅⁺). Ab initio ionization energies based on Koopmans’ theorem are in excellent agreement with the experimental data from ultraviolet photoelectron spectroscopy. DFT adiabatic energy differences between neutral and ionized structures are very sensitive to electronic correlation effects and are not in very good agreement with experiment. The results for the structure and vibrational frequencies are compared with the experimental data of related molecular structures.     

Ab initio and density functional theory evidence on the rate-limiting step in the Morita-Baylis-Hillman reaction

The first ab initio and DFT studies on the mechanism of the MBH reaction show that the rate-limiting step involves an intramolecular proton transfer in the zwitterionic intermediate generated by the addition of enolate to electrophile. The activation barrier for the C-C bond-formation is found to be 20.2 kcal/mol lower than the proton-transfer step for the MBH reaction between methyl vinyl ketone and benzaldehyde catalyzed by DABCO.     

Ab initio and density functional theory reinvestigation of gas-phase sulfuric acid monohydrate and ammonium hydrogen sulfate

We have calculated the thermochemical parameters for the reactions H(2)SO(4) + H(2)O <--> H(2)SO(4).H(2)O and H(2)SO(4) + NH(3) <--> H(2)SO(4).NH(3) using the B3LYP and PW91 functionals, MP2 perturbation theory and four different basis sets. Different methods and basis sets yield very different results with respect to, for example, the reaction free energies. A large part, but not all, of these differences are caused by basis set superposition error (BSSE), which is on the order of 1-3 kcal mol(-1) for most method/basis set combinations used in previous studies. Complete basis set extrapolation (CBS) calculations using the cc-pV(X+d)Z and aug-cc-pV(X+d)Z basis sets (with X = D, T, Q) at the B3LYP level indicate that if BSSE errors of less than 0.2 kcal mol(-1) are desired in uncorrected calculations, basis sets of at least aug-cc-pV(T+d)Z quality should be used. The use of additional augmented basis functions is also shown to be important, as the BSSE error is significant for the nonaugmented basis sets even at the quadruple-zeta level. The effect of anharmonic corrections to the zero-point energies and thermal contributions to the free energy are shown to be around 0.4 kcal mol(-1) for the H(2)SO(4).H(2)O cluster at 298 K. Single-point CCSD(T) calculations for the H(2)SO(4).H(2)O cluster also indicate that B3LYP and MP2 calculations reproduce the CCSD(T) energies well, whereas the PW91 results are significantly overbinding. However, basis-set limit extrapolations at the CCSD(T) level indicate that the B3LYP binding energies are too low by ca. 1-2 kcal/mol. This probably explains the difference of about 2 kcal mol(-1) for the free energy of the H(2)SO(4) + H(2)O <--> H(2)SO(4).H(2)O reaction between the counterpoise-corrected B3LYP calculations with large basis sets and the diffusion-based experimental values of S. M. Ball, D. R. Hanson, F. L Eisele and P. H. McMurry (J. Phys. Chem. A. 2000, 104, 1715). Topological analysis of the electronic charge density based on the quantum theory of atoms in molecules (QTAIM) shows that different method/basis set combinations lead to qualitatively different bonding patterns for the H(2)SO(4).NH(3) cluster. Using QTAIM analysis, we have also defined a proton transfer degree parameter which may be useful in further studies.     

Ab initio calculation of the dipole polarizabilities of unsaturated hydrocarbons

Finite-field SCF MO calculations of polarizability are reported for ethene, benzene and naphthalene using three good gaussian basis sets Double-zeta wavefunctions yield values of α_LL and α_MM in agreement with experiment but the calculated α_NN is half the experimental value. Polarization functions when present preferentially improve α_NN. (L,M) and N refer to the molecular long, medium and normal axes, respectively.) STO-4G results are given for benzene, naphthalene, azulene, anthracene and phenanthrene, and the agreement with the experiment is reasonable after scaling the calculated α_LL and α_MM by a constant factor. The calculated α_MM are an order of magnitude too low.     

Ab initio and coupled-perturbed density functional theory estimation of zero-field splittings in MnII transition metal complexes

The paper presents a method comparison for the prediction of zero-field splitting (ZFS) parameters in a series of Mn (II) coordination complexes. The test set consists of Mn (II) complexes that are experimentally well-characterized by X-ray diffraction and high-field electron paramagnetic resonance. Their ZFS parameters have been calculated using density functional theory (DFT) as well as complete active space self-consistent field (CASSCF) methods. It is shown that the recently introduced coupled-perturbed spin-orbit coupling (CP-SOC) approach [ Neese, F. J. Chem. Phys. 2007, 127, 164112 ] together with hybrid-DFT functionals leads to a slope of the correlation line (plot of experimental vs calculated D values) that is essentially unity provided that the direct spin-spin interaction is properly included in the treatment. This is different from our previous DFT study on the same series of complexes where a severe overestimation of the D parameter has been found [ Zein, S. ; Duboc, C. ; Lubitz, W. ; Neese, F. Inorg. Chem. 2008, 47, 134 ]. CASSCF methods have been used to evaluate the ZFS in an "ab initio ligand-field" type treatment. The study demonstrates that a substantial part of the relevant physics is lost in such a treatment since only excitations within the manganese d-manifold are accounted for. Thus, a severe underestimation of the D parameter has been found. Because the CASSCF calculations in combination with quasidegenerate perturbation theory treats the SOC to all orders, we have nevertheless verified that second-order perturbation theory is an adequate approximation in the case of the high-spin d (5) configuration.     

The bonding character of AlSO isomers in quartet excited states: Ab initio and density functional theory studies

The geometries and the bonding properties have been predicted for four isomers of AlSO species in the quartet state at density functional theory and coupled cluster [CCSD(T)] all‐electron correlation levels with a large 6‐311+G(3df) basis set. Results have indicated that for the AlSO species in quartet state the lowest state is ⁴A″ state which corresponds to a cyclic structure; the other three isomers (cyclic, bent, and linear) are higher than the lowest state by 26.9 kcal/mol (cyclic ⁴A′), 19.4 kcal/mol (⁴A″), and 28.3 kcal/mol (linear AlSO ⁴Σ), respectively. The calculated dissociation energies for the lowest quartet state species (AlSO: ⁴A″) are 27.3 kcal/mol for the radical mechanism [M(²P)+SO(³Σ^?)] and 154.7 kcal/mol for the mechanism [M(²P)+S(³P)+O(³P)]. Inspection of the bonding character indicates that the cyclic AlSO species in the lowest quartet state (⁴A″) should be classified as thiodioxide (similar to disulfide or dioxide), and the cyclic ⁴A′ state should be classified as thiosuperoxide. The bent Al? SO(⁴A″) species has some thiosuperoxide character, while the linear Al? SO(⁴Σ) structure should be classified as a molecular complex with a weak interaction bonding. However, this thiosuperoxide is not as ionic as LiO₂ and LiSO and is also less ionic than the cyclic AlO₂. In addition, the combinations of Al with SO species exhibit the amphoteric character of Al. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2002     

Ab initio molecular dynamics using hybrid density functionals

Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.     

Tautomerism and isomerism of guanine–cytosine DNA base pair: Ab initio and density functional theory approaches

The relative stabilities of guanine–cytosine (G–C) DNA base pairs are theoretically investigated with a focus on the keto–enol tautomerism as well as on the cis–trans enol isomerism by using both ab initio method and the density functional theory. The G–C pairs of the keto tautomers turn out to be in general more stable than those of the enol tautomers, 9H-guanine pair, 9KK (see the notation below), being the most stable one. The stability of the G–C pairs appears to be affected by various factors including the keto–enol tautomerization, cis–trans enol isomerization, and the steric hindrance between two tautomeric pairs. Although the B3LYP calculations tend to underestimate the binding energies, in addition, it is shown that the binding energy of G–C pairs interacting through hydrogen bonds can be reasonably calculated with the DFT method, contrary to the base pairs with stacked configurations.