Performance of recently developed kinetic energy density functionals for the calculation of hydrogen binding strengths and hydrogen-bonded structures

 The accuracy of predicted hydrogen binding energies and equilibrium structures for a benchmark set of molecules is compared for some recently developed density functionals, Becke's three parameter hybrid method with the Lee, Yang, and Parr (LYP) correlation functional (B3LYP), Becke's half and half functional combined with the LYP correlation functional (BHLYP), Perdew, Burke and Ernzerhof functional (PBE), Van Voorhis, Scuseria exchange correlation functional (VSXC), the hybrid Perdew, Burke and Ernzerhof functional (PBE1PBE), and meta-generalized gradient approximation (meta-GGA). Overall, the hybrid functionals which contain a portion of Hartree–Fock exchange (B3LYP, BHLYP, and PBE1PBE) yield the most accurate results. The kinetic-energy-density-dependent functionals, VSXC and meta-GGA, are significantly less accurate. Received: 10 December 1999 / Accepted: 5 March 2000 / Published online: 21 June 2000     

Long-range and short-range Coulomb correlation effects as simulated by Hartree–Fock,local density approximation,and generalized gradient approximation exchange functionals

 Exchange functionals used in density functional theory (DFT) are generally considered to simulate long-range electron correlation effects. It is shown that these effects can be traced back to the self-interaction error (SIE) of approximate exchange functionals. An analysis of the SIE with the help of the exchange hole reveals that both short-range (dynamic) and long-range (nondynamic) electron correlation effects are simulated by DFT exchange where the local density approximation (LDA) accounts for stronger effects than the generalized gradient expansion (GGA). This is a result of the fact that the GGA exchange hole describes the exact exchange hole close to the reference electron more accurately than the LDA hole does. The LDA hole is more diffuse, thus leading to an underestimation of exchange and stronger SIE effects, where the magnitude of the SIE energy is primarily due to the contribution of the core orbitals. The GGA exchange hole is more compact, which leads to an exaggeration of exchange in the bond and the nonbonding region and negative SIE contributions. Partitioning of the SIE into intra-/interelectronic and individual orbital contributions makes it possible to test the performance of a given exchange functional in different regions of the molecule. It is shown that Hartree–Fock exchange always covers some long-range effects via interelectronic exchange while self-interaction-corrected DFT is lacking these effects. Received: 25 May 2002 / Accepted: 7 October 2002 / Published online: 21 January 2003 Correspondence to: E. Kraka e-mail: kraka@theoc.gn.se Acknowledgements. This work was supported financially by the Swedish Natural Science Research Council (NFR). Calculations were done on the supercomputers of Nationellt Superdatorcentrum (NSC), Link?ping, Sweden. The authors thank the NSC for a generous allotment of computer time.     

Physical analysis of the diatomic “chemical” energy components

 The recent “chemical energy component analysis” permits the total energy of a molecule to be presented approximately but to good accuracy as a sum of atomic and diatomic energy contributions. Here the diatomic energy components are further decomposed into terms of different physical origin: electrostatics (in point-charge approximation and the distributed charge corrections), exchange effects, diatomic overlap and atomic basis extension terms. This analysis may provide us with a deeper insight into the factors influencing both the chemical bonds and the nonbonded interatomic interactions. Received: 6 May 2002 / Accepted: 13 November 2002 / Published online: 19 March 2003 Acknowledgements. The authors are indebted to the Hungarian Scientific Research Fund for partial financial support (grant no. OTKA T29716). Correspondence to: I. Mayer e-mail: mayer@chemres.hu     

Investigation of the S<Subscript>0</Subscript>S<Subscript>1</Subscript> excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid method

 We have investigated the S₀ and S₁ electronic states in bacteriorhodopsin using a variety of QM/MM levels. The decomposition of the calculated excitation energies into electronic and electrostatic components shows that the interaction of the chromophore with the protein electric field increases the excitation energy, while polarization effects are negligible. Therefore, the experimentally observed reduction in excitation energy from solution phase to protein environment (the Opsin shift) does not come from the electrostatic interaction with the protein environment, but from either the interaction ofthe chromophore with the solvent or counter ion, or structural effects. Our high-level ONIOM(TD– B3LYP:Amber) calculation predicts the excitation energy within 8 kcal/mol from experiment, the discrepancy probably being caused by the neglect of polarization of the protein environment. In addition, we have shown that the level of optimization is extremely critical for the calculation of accurate excitation energies in bacteriorhodopsin. Received: 13 October 2001 / Accepted: 6 September 2002 / Published online: 3 February 2003 Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American Chemical Society, 2001 Correspondence to: K. Morokuma e-mail: morokuma@emory.edu     

Some thoughts about the stability and reliability of commonly used exchange–correlation functionals – coverage of dynamic and nondynamic correlation effects

 The self-interaction error (SIE) of commonly used density functional theory (DFT) exchange functionals mimics long-range (nondynamic) pair correlation effects in an unspecified way. Slater exchange suffers from a larger SIE and, therefore, covers more nondynamic correlation effects than Becke exchange, which is the reason why exchange–correlation (XC) functionals based on Slater exchange lead to stabler restricted DFT solutions than those based on Becke exchange. However, the stability of an XC functional does not guarantee higher accuracy. On the contrary, if system-specific nondynamic correlation effects have to be introduced via the form of the wave function, these will be suppressed by nondynamic correlation effects already covered by the exchange functional. Hybrid functionals suffer less from the SIE and, therefore, cover a smaller number of nondynamic electron correlation effects. Accordingly, they are better suited when nondynamic electron correlation has to be introduced by the form of the wave function. It is shown that, for example, broken-symmetry unrestricted DFT calculations are more accurate when carried out with B3LYP than BLYP contrary to claims made in the literature. Received: 8 November 2001 / Accepted: 30 January 2002 / Published online: 8 April 2002     

Rydberg character of the higher excited states of free-base porphin

 The Rydberg character of the excited states of free-base porphin (FBP) has been investigated by the ab initio configuration interaction singles (CIS) method and the state-averaged complete-active-space self-consistent-field method. Double-zeta basis sets augmented with s, p, and d Rydberg functions and d polarization functions have been employed. Two types of molecular orbitals sets, the restricted Hartree–Fock molecular orbitals obtained for the ground state (¹A _g ) and for the cation state (²A _u ), have been used in the CIS calculations. All the calculations show that Rydberg-type excitations play important roles especially in the N bands. In this article we propose applying the model of a perturbed Rydberg series to interpret the excited states of FBP. By using this model, we have succeeded in analyzing the characteristics of the excited states as well as the experimental oscillator strengths, which have considerable magnitude even in the higher excited states. Received: 27 November 2000 / Accepted: 11 April 2001 / Published online: 27 June 2001     

A comment on “Some fundamental problems with zero-flux partitioning of electron densities”

 It is shown that the statement made by Cassam-Chenai and Jayatilaka regarding the atoms of AIM to the effect that “In particular, we shall demonstrate that these atoms are not a consequence of the Schwinger variation principle, as has been claimed” is false. Received: 15 June 2001 / Accepted: 10 October 2001 / Published online: 19 June 2002     

Gradient of the ZAPT2 energy

 An explicit expression for the analytical first derivative of the Z-averaged perturbation theory taken to second order energy, due to Lee and Jayatilaka, is presented for application to high-spin systems described by a restricted open-shell Hartree–Fock wavefunction. The use of frozen core orbitals is incorporated into the derivation. Received: 23 April 2001 / Accepted: 31 August 2001 / Published online: 9 January 2002     

Mechanism and control of molecular energy flow: a modeling perspective

 Vibrational energy flow in organic molecules occurs by a multiple-time-scale mechanism that can be modeled by a single exponential only in its initial stages. The mechanism is a consequence of the hierarchical structure of the vibrational Hamiltonian, which leads to diffusion of vibrational wavepackets on a manifold with far fewer than the 3N−6 dimensions of the full vibrational state space. The dynamics are controlled by a local density of states, which does not keep increasing with molecular size. In addition, the number of vibrational coordinates severely perturbed during chemical reaction is small, leading to preservation of the hierarchical structure at chemically interesting energies. This regularity opens up the possibility of controlling chemical reactions by controlling the vibrational energy flow. Computationally, laser control of intramolecular vibrational energy redistribution can be modeled by quantum-classical, or by purely quantum-mechanical models of the molecule and control field. Received: 26 July 2002 / Accepted: 30 September 2002 / Published online: 2 December 2002 Electronic Supplementary Material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00214-002-0394-2. Acknowledgements. This work was supported by NSF grant CHE 9986670. Correspondence to: M. Gruebele e-mail: gruebele@scs.uiuc.edu     

Evaluation of the Coulomb energy in relativistic self-consistent-field theory

 Computational schemes are presented with which to evaluate the electrostatic Coulomb energy in relativistic molecular electronic structure calculations using a basis of four-component Dirac spinor amplitudes. We demonstrate that algorithms may be constructed and implemented which differ only in minor details from those in common use in nonrelativistic quantum chemistry, and that the four-component formalism is neither as complicated nor as expensive as has been suggested recently in the literature. Spherically symmetrical atomic basis sets are presented which indicate that accurate representations of the Coulomb energy may be obtained using modest expansions of the electronic density in a scalar auxiliary basis set of spherical harmonic Gaussian-type functions. Received: 15 April 2002 / Accepted: 15 May 2002 / Published online: 29 July 2002     

Comments on “Some fundamental problem with zero flux partitioning of electron densities”

 The article by P. Cassam-Chena? and D. Jayatilaka (Theor Chem Acc (2001) 105: 213) is critically analyzed. Received: 18 April 2001 / Accepted: 9 September 2001 / Published online: 3 June 2002     

Ab initio structure and vibrational frequencies of lithium aromatic sulfonyl imide salts

The structure and vibrational frequencies of an aromatic lithium sulfonyl imide, i.e., lithium bis(4-nitrophenylsulfonyl)imide (LiNPSI) has been studied using self-consistent ab initio Hartree–Fock and hybrid density functional methods. These calculations engender two linkage isomers, which correspond to the local minima on the potential-energy surface. In the lowest-energy isomer, the ligand binds to the metal ion through two oxygens, one from each of the different SO₂ groups on the central nitrogen and forms a six-membered ring. Another LiNPSI isomer, wherein the anion coordinates through oxygen and nitrogen atoms and which is 55.9 kJmol⁻¹ higher in energy, has also been obtained. The S–N–S bond angle in the free anion as well as in the LiNPSI complex turns out to be nearly 121°. A comparison of the vibrational spectra of the free NPSI anion and that of the LiNPSI complex reveals that the SO₂ stretching vibrations at 1,239 and 1,205 cm⁻¹ can be used to differentiate between the two linkage isomers of the complex. The stronger complexation ability of the NPSI anion, compared to that for (CF₃SO₂)₂N⁻ has been explained in terms of the charge density within the molecular electrostatic potential isosurface encompassing both SO₂ groups of the anion. Received: 20 February 2002 / Accepted: 25 March 2002 / Published online: 3 June 2002     

The performance of the rapid estimation of basis set error and correlation energy from partial charges method on new molecules of the G3/99 test set

Experimental enthalpies of formation have been approximated using single-point Hartree–Fock (HF)–self-consistent-field (SCF) total energies plus the rapid estimation of basis set error and correlation energy from partial charges (REBECEP) energy corrections. The energy corrections are calculated from the HF–SCF partial atomic charges and optimized atomic energy parameters. The performance of the method was tested on 51 closed-shell neutral molecules (50 molecules from the G3/99 thermochemistry database plus urea, composed of H, C, N, O, and F atoms). The predictive force of the method is demonstrated, because these larger molecules were not used for the optimization of the atomic parameters. We used the earlier RECEP-3 [HF/6-311+G(2d,p)] and REBECEP [HF/6-31G(d)] atomic parameter sets obtained from the G2/97 thermochemistry database (containing small molecules) together with natural population analysis and Mulliken partial charges. The best results were obtained using the natural population analysis charges, although the Mulliken charges also provide useful results. The root-mean-square deviations from the experimental enthalpies of formation for the selected 51 molecules are 1.15, 3.96, and 2.92 kcal/mol for Gaussian-3, B3LYP/6-11+G(3df,2p), and REBECEP (natural population analysis) enthalpies of formation, respectively (the corresponding average absolute deviations are 0.94, 7.09, and 2.27 kcal/mol, respectively). The REBECEP method performs considerably better for the 51 test molecules with a moderate 6-31G(d) basis set than the B3LYP method with a large 6-311+G(3df,2p) basis set. Received: 10 March 2001 / Accepted: 5 July 2001 / Published online: 11 October 2001     

A density functional theory study of a concerted mechanism for proton exchange between amino acid side chains and water

 A concerted mechanism for proton exchange between water and the amino acid side chains of cysteine, serine, arginine and glutamic acid has been investigated with hybrid density functional theory. The models used include, besides the amino acid side chain, a number of water molecules ranging from one to five in some cases. The modeling of the amino acids without their backbones is shown to be an excellent approximation. Long-range polarization effects were incorporated through a dielectric cavity method allowing a better comparison to existing measurements for free amino acids in water. The barriers converge rather fast with the number of water molecules for all the present amino acids and the converged values are in reasonable agreement with experiments with discrepancies in the range 2–6 kcal/mol. The dielectric effects were found to be small for all systems except cysteine, where there is a lowering of the barrier by 3–5 kcal/mol. The transition states for these concerted pathways form rings in which the separated charges can be stabilized. Received: 25 October 1999 / Accepted: 5 April 2000 / Published online: 21 June 2000     

Computational structural determination and energy landscape analysis of the hepatic carcinogen 2-(acetylamino)fluorene

 2-(Acetylamino)fluorene (AAF), a potent mutagen and a prototypical example of the mutagenic aromatic amines, forms covalent adducts to DNA after metabolic activation in the liver. A benchmark study of AAF is presented using a number of the most widely used molecular mechanics and semiempirical computational methods and models. The results are compared to higher-level quantum calculations and to experimentally obtained crystal structures. Hydrogen bonding between AAF molecules in the crystal phase complicates the direct comparison of gas-phase theoretical calculations with experiment, so Hartree–Fock (HF) and Becke–Perdew (BP) density functional theory (DFT) calculations are used as benchmarks for the semiempirical and molecular mechanics results. Systematic conformer searches and dihedral energy landscapes were carried out for AAF using the SYBYL and MMFF94 molecular mechanics force fields; the AM1, PM3 and MNDO semiempirical quantum mechanics methods; HF using the 3-21G*and 6-31G* basis sets; and DFT using the nonlocal BP functional and double numerical polarization basis sets. MMFF94, AM1, HF and DFT calculations all predict the same planar structures, whereas SYBYL, MNDO and PM3 all predict various nonplanar geometries. The AM1 energy landscape is in substantial agreement with HF and DFT predictions; MMFF94 is qualitatively similar to HF and DFT; and the MNDO, PM3 and SYBYL results are qualitatively different from the HF and DFT results and from each other. These results are attributed to deficiencies in MNDO, PM3 and SYBYL. The MNDO, PM3 and SYBYL models may be unreliable for compounds in which an amide group is immediately adjacent to an aromatic ring. Received: 26 May 2002 / Accepted: 12 December 2002 / Published online: 14 February 2003     

The calculation of electron localization and delocalization indices at the Hartree–Fock, density functional and post-Hartree–Fock levels of theory

 Localization, λ(A), and delocalization indices, δ(A,B), as defined in the atoms in molecules theory, are a convenient tool for the analysis of molecular electronic structure from an electron-pair perspective. These indices can be calculated at any level of theory, provided that first- and second-order electron densities are available. In particular, calculations at the Hartree–Fock (HF) and configuration interaction (CI) levels have been previously reported for many molecules. However, λ(A) and δ(A,B) cannot be calculated exactly in the framework of Kohn–Sham (KS) density functional theory (DFT), where the electron-pair density is not defined. As a practical workaround, one can derive a HF-like electron-pair density from the KS orbitals and calculate approximate localization and delocalization indices at the DFT level. Recently, several calculations using this approach have been reported. Here we present HF, CI and approximate DFT calculations of λ(A) and δ(A,B) values for a number of molecules. Furthermore, we also perform approximate CI calculations using the HF formalism to obtain the electron-pair density. In general, the approximate DFT and CI results are closer to the HF results than to the CI ones. Indeed, the approximate calculations take into account Coulomb electron correlation effects on the first-order electron density but not on the electron-pair density. In summary, approximate DFT and CI localization and delocalization indices are easy to calculate and can be useful in the analysis of molecular electronic structure; however, one should take into account that this approximation increases systematically the delocalization between covalently bonded atoms, with respect to the exact CI results. Received: 13 February 2002 / Accepted: 24 April 2002 / Published online: 18 June 2002     

Orbital-band interactions and the reactivity of molecules on oxide surfaces: from explanations to predictions

 The surface chemistry of oxides is relevant for many technological applications: catalysis, photoelectrolysis, electronic-device fabrication, prevention of corrosion, sensor development, etc. This article reviews recent theoretical works that deal with the surface chemistry of oxides. The account begins with a discussion of results for the adsorption of CO and NO on oxides, systems which have been extensively studied in the literature and constitute an ideal benchmark for testing the quality of different levels of theory. Then, systematic studies concerned with the behavior of adsorbied alkali metals and sulfur-containing molecules are presented. Finally, a correlation between the electronic and chemical properties of mixed-metal oxides is analyzed and basic principles for designing chemically active oxides are introduced. Advances in theoretical methods and computer capabilities have made possible a fundamental understanding of many phenomena associated with the chemistry of molecules on oxide surfaces. Still many problems in this area remain as a challenge, and the approximate nature of most theoretical methods makes necessary a close coupling between theory and experiment. Following this multidisciplinary approach, the importance of band-orbital interactions for the reactivity of oxide surfaces has become clear. Simple models based on band-orbital mixing can explain trends found for the interaction of many adsorbates with oxide surfaces. These simple models provide a conceptual framework for modifying or controlling the chemical activity of pure oxides and for engineering mixed-metal oxides. In this respect, theoretical calculations can be very useful for predicting the best ways for enhancing the reactivity of oxide systems and reducing the waste of time, energy and materials characteristic of an empirical design. Received: 21 June 2001 / Accepted: 8 October 2001 / Published online: 1 February 2002     

Squaramido-based receptors: applicability of molecular interaction potential to molecular recognition of polyalkylammonium compounds

 A computational study of the mechanism of host–guest complexation between quaternary ammonium compounds and squaramido-based tripodal receptors has been carried out. Semiempirical molecular orbital calculations, which are in qualitative agreement with experimental results have been performed using the PM3 Hamiltonian. Molecular interaction potential (MIP) maps were used to analyze the suitability of both host and guest binding units for a high-affinity recognition process. MIP calculations were computed from PM3 wavefunctions of the corresponding ammonium cations and dimethyl squaramide as a model compound for the hydrogen-bond-acceptor unit of the receptors. MIP analyses are helpful for understanding the host–guest process from the point of view of the double-complementarity principle. Received: 23 June 1999 / Accepted: 22 September 1999 / Published online: 17 January 2000     

A proposed modification of CBS-4M model chemistry for application to molecules of increasing molecular size

 In order to calculate more accurately the enthalpies of formation, ΔH _f°(298 K), for large molecules using the CBS-4M method, a new formulation of the empirical higher-level correction to the energy is proposed: ΔE=a|S|² _{i i} I _{i i} +b(n _α+n _β)+cΔ<S ²>+Σn _i d _{i .} The new methodology (CBS-4MB) applied to a set of 114 molecules of different size significantly decreases the mean absolute deviation from 3.78 to 2.06 kcal/mol. Received: 7 February 2001 / Accepted: 5 April 2001 / Published online: 13 June 2001