Evaluation of an ab initio quantum mechanical/molecular mechanical hybrid-potential link-atom method

 Hybrid potentials have become a common tool in the study of many condensed-phase processes and are the subject of much active research. An important aspect of the formulation of a hybrid potential concerns how to handle covalent bonds between atoms that are described with different potentials and, most notably, those at the interface of the quantum mechanical (QM) and molecular mechanical (MM) regions. Several methods have been proposed to deal with this problem, ranging from the simple link-atom method to more sophisticated hybrid-orbital techniques. Although it has been heavily criticized, the link-atom method has probably been the most widely used in applications, especially with hybrid potentials that use semiempirical QM methods. Our aim in this paper has been to evaluate the link-atom method for ab initio QM/MM hybrid potentials and to compare the results it gives with those of previously published studies. Given its simplicity and robustness, we find that the link-atom method can produce results of comparable accuracy to other methods as long as the charge distribution on the MM atoms at the interface is treated appropriately. Received: 27 September 2002 / Accepted: 21 October 2002 / Published online: 8 January 2003 Correspondence to: M. J. Field e-mail: mjfield@ibs.fr Acknowledgements. The authors thank the Institut de Biologie Structurale – Jean-Pierre Ebel, the Commissariat à l'Energie Atomique and the Centre National de la Recherche Scientifique for support of this work.     

De novo prediction of the ground state structure of transition metal complexes using semiempirical and ab initio quantum mechanics. Coordination isomerism

The ground state coordination isomers for 30 different trigonal bipyramidal transition metal complexes have been predicted using different levels of quantum mechanics: semiempirical (PM3(tm)), ab initio (MP2//HF), pure (BPW91) and hybrid (B3PW91) density functional theory (DFT) methods. For species where these methods failed to reproduce crystallographic data, hybrid quantum mechanics/molecular mechanics (QM/MM) methods were used to study more exact experimental models. Literature deficiencies regarding ground state multiplicity of these species were supplemented by spin predictions using previously tested PM3(tm) methods. Geometry optimization calculations were performed for each possible coordination isomer. The predicted ground state minima provided by the different methods are compared to each other and with crystallographic data. Pure DFT functionals outperformed hybrid functionals and MP2//HF. The very rapid PM3(tm) parameterization method provided accurate predictions in comparison to other levels of theory. An integrated MM/PM3(tm)/DFT de novo scheme accurately reproduced crystallographic data for species where the individual methods failed.     

A new method for modelling spectator chemical groups in ab initio calculations: effective group potentials

 A new method for an increased numerical efficiency of ab initio calculations is proposed. It is based on the assumption that in most cases chemical properties of functional groups in molecules are mainly controlled by a few electrons. This statement allows one to distinguish between two classes of nuclei and electrons: active and inactive ones. The effective group potential (EGP) method presupposes that the effect of inactive electrons in a functional chemical group can be described by a pseudopotential, in the same way that core electrons are replaced by effective core potentials in atoms. It is shown that EGPs are able to predict chemical and structural features of the active part of a molecule and at a fraction of the ordinary computational cost. The preliminary results reported here concern the determination of EGPs for ammonia, the methyl radical and the cyclopendadienyl ligand, which represent different types of bonding. Received: 15 September 1999 / Accepted: 3 February 2000 / Published online: 2 May 2000     

Internal rotation in squaramide and related compounds. A theoretical ab initio study

The structural and energetic changes associated with C–N bond rotation in a squaric acid derivative as well as in formamide, 3-aminoacrolein and vinylamine have been studied theoretically using ab initio molecular orbital methods. Geometry optimizations at the MP2(full)/6-31+G* level confirmed an increase in the C–N bond length and a smaller decrease in the C=O length on going from the equilibrium geometry to the twisted transition state. Other geometrical changes are also discussed. Energies calculated at the QCISD(T)/6-311+G** level, including zero-point-energy correction, show barrier heights decreasing in the order formamide, squaric acid derivative, 3-aminoacrolein and vinylamine. The origin of the barriers were examined using the atoms-in-molecules approach of Bader and the natural bond orbital population analysis. The calculations agree with Pauling's resonance model, and the main contributing factor of the barrier is assigned to the loss of conjugation on rotating the C–N bond. Finally, molecular interaction potential calculations were used to study the changes in the nucleophilicity of N and O (carbonyl) atoms upon C–N rotation, and to obtain a picture of the abilities of the molecules to act in nonbonded interactions, in particular hydrogen bonds. The molecular interaction potential results confirm the suitability of squaramide units for acting as binding units in host–guest chemistry. Received: 13 March 2002 / Accepted: 23 June 2002 / Published online: 21 August 2002     

Local-orbital-based correlated ab initio band structure calculations in insulating solids: LiF

 A local-orbital-based ab initio approach to calculate correlation effects on quasi-particle energies in insulating solids is presented. The use of localized Wannier-type Hartree–Fock orbitals allows correlation effects to be efficiently assessed. First a Green's function approach based on exact diagonalization is introduced and this is combined with an incremental scheme, while subsequently different levels of perturbative approximations are derived from the general procedure. With these methods the band structure of LiF is calculated and good agreement with experiment is found. By comparing the different approximations proposed, including the exact diagonalization procedure, their relative quality is established. Received: 25 June 2001 / Accepted: 31 August 2001 / Published online: 19 December 2001     

Direct ab initio dynamics calculations on the rate constants for the hydrogen-abstraction reaction of C2H5F with O (3P)

The hydrogen-abstraction reaction C₂H₅F+O → C₂H₄F+OH has been studied by a dual-level direct dynamics method. For the reaction, three reaction channels, one for α-abstraction and two for β-abstraction, have been identified. The potential-energy surface information is obtained at the MP2(full)/6-311G(d,p) and PMP2(full)/6-311G(3df,3pd) (single-point) levels. By canonical variational transition-state theory, rate constants for each reaction channel are calculated with a small-curvature tunneling correction. The total rate constant is calculated from the sum of the individual rate constants and the temperature dependence of the branching ratios is obtained over a wide range of temperatures from 300 to 5,000 K. The agreement of the rate constants with experiment is good in the experimental temperature range from 1,000 to 1,250 K. The calculated results indicate that at low temperatures α-abstraction is most likely to be the major reaction channel, while β-abstraction channels will significantly contribute to the whole reaction rate as the temperature increases. Received: 23 January 2002 / Accepted: 23 June 2002 / Published online: 20 September 2002     

Role of twisting and sliding on the solvation of a stacked cytosine dimer: an ab initio study

Ab initio calculations with inclusion of correlation effects at the MP2/6-31G* level have been used to predict the interaction energy of stacked cytosine dimer (C/C) as a function of twisting and sliding in the gas phase. Systematic calculations have also been carried out on the solvation free energies of various rotated and translated C/C dimers using a polarized continuum model approach at the HF/6-31G* level with a view to probe the role of various degrees of freedom on the free energy of solvation of the C/C dimer. The interaction energy of the C/C dimer decreases upon changing from a parallel to an antiparallel conformation in the gas phase. The 180°-rotated conformation has been found to be the most stable arrangement when compared to other rotated positions. The rotated and translated dimers exhibit lower solvation free energy than the parallel conformation. The decrease in the dipole moment upon rotation from the parallel to the antiparallel conformation indicates the cancellation of charge distribution upon rotation in the z direction of one cytosine base with respect to the other. The calculation reveals that the present approach could not yield association energy, ΔΔG _Asso, in a solvent medium. This may be due to the fact that in the case of floppy molecules the contribution from translational, rotational and vibrational free energies plays a significant role in the calculation of ΔΔG _Asso. Received: 13 December 2001 / Accepted: 25 March 2002 / Published online: 13 June 2002     

Parameterization of semiempirical methods to treat nucleophilic attacks to biological phosphates: AM1/d parameters for phosphorus

 This paper reports a new AM1/d model for phosphorus that can be used to model nucleophilic attack of phosphates relevant for biological phosphate hydrolysis reactions. The parameters were derived from a quantum dataset calculated with hybrid density-functional theory [B3LYP/6-311++G(3df,2p)//B3LYP/6-31++G(d,p)] of phosphates and phosphoranes in various charge states, and on transitions states for nucleophilic attacks. A suite of non-linear optimization methods is outlined for semiempirical parameter development based on integrated evolutionary (genetic), Monte Carlo simulated annealing and direction set minimization algorithms. The performance of the new AM1/d model and the standard AM1 and MNDO/d models are compared with the density-functional results. The results demonstrate that the strategy of developing semiempirical parameters specific for biological reactions offers considerable promise for application to large-scale biological problems. Received: 15 January 2002 / Accepted: 6 September 2002 / Published online: 28 March 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: D.M. York e-mail: york@chem.umn.edu Acknowledgements. D.M.Y. is grateful for financial support provided by the National Institutes of Health (grant 1R01-GM62248-01A1) and the Donors of The Petroleum Research Fund, administered by the American Chemical Society, and the Minnesota Supercomputing Institute through a 6-month research scholar award (X.L.). Computational resources were provided by the Minnesota Supercomputing Institute.     

Accuracy assessment of semiempirical molecular electrostatic potential of proteins

 Accurate electrostatic maps of proteins are of great importance in research of protein interaction with ligands, solvent media, drugs, and other biomolecules. The large size of real-life proteins imposes severe limitations on computational methods one can use for obtaining the electrostatic map. Well-known accurate second-order M?ller–Plesset and density functional theory methods are not routinely applicable to systems larger than several hundred atoms. Conventional semiempirical tools, as less resource demanding ones, could be an attractive solution but they do not yield sufficiently accurate calculation results with reference to protein systems, as our analysis demonstrates. The present work performs a thorough analysis of the accuracy issues of the modified neglect of differential overlap type semiempirical Hamiltonians AM1 and PM3 on example of the calculation of the molecular electrostatic potential and the dipole moment of natural amino acids. Real capabilities and limitations of these methods with application to protein modeling are discussed. Received: 26 April 2002 / Accepted: 19 September 2002 / Published online: 14 February 2003     

Gaussian-3 and related methods for accurate thermochemistry

In this paper, we present an overview of Gaussian-3 (G3) theory, a composite technique that employs a sequence of ab initio molecular orbital calculations to derive a total energy of a given molecular species. This method provides accurate energies of molecular systems for the calculation of enthalpies of formation, ionization potentials, electron affinities, proton affinities, etc. Also covered in this review are several variants of G3 theory including one based on scale factors (G3S) and an extended version (G3X) that uses improved geometries and larger Hartree-Fock basis sets. Finally, the G3/99 test set of accurate experimental data that is used for critical assessment is described. Overall, G3 theory has a mean absolute deviation from experiment of 1.07 kcal mol⁻¹ for the G3/99 test set and G3S theory has a similar accuracy of 1.08 kcal mol⁻¹. G3X theory is significantly more accurate with the mean absolute deviation from experiment decreasing from 1.07 kcal mol⁻¹ (G3) to 0.95 kcal mol⁻¹ (G3X). The scaled version of G3X theory shows a similar improvement. Received: 23 January 2002 / Accepted: 7 April 2002 / Published online: 4 July 2002     

NMR chemical shifts in the low–pH form of a-chymotrypsin. A QM/MM and ONIOM–NMR study

 The relationship between hydrogen bonding and NMR chemical shifts in the catalytic triad of low-pH α-chymotrypsin is investigated by combined use of the effective fragment potential [(2001) J Phys Chem A 105:293] and ONIOM–NMR [(2000) Chem Phys Lett 317:589] methods. Our study shows that while the His57 N^δ1−H bond is stretched by a relatively modest amount (to about 1.060 ?) this lengthening, combined with the polarization due to the molecular environment, is sufficient to explain the experimentally observed chemical shifts of 18.2 ppm. Furthermore, the unusual down-field shift of H^ɛ1 (9.2 ppm) observed experimentally is reproduced and shown to be induced by interactions with the C=O group of Ser214 as previously postulated. The free-energy cost of moving H^δ1 from His57 to Asp102 is predicted to be 5.5 kcal/mol. Received: 26 September 2001 / Accepted: 6 September 2002 / Published online: 21 January 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: J. H. Jensen e-mail: jan-jensen@uiowa.edu Acknowledgements. This work was supported by a Research Innovation Award from the Research Corporation and a type G starter grant from the Petroleum Research Fund. The calculations were performed on IBM RS/6000 workstations obtained through a CRIF grant from the NSF (CHE-9974502) and on supercomputers at the National Center for Supercomputer Applications at Urbana-Champaign. The authors are indebted to Visvaldas Kairys for help with the CHARMM program, and to Daniel Quinn for many helpful discussions.     

Partial Hessian vibrational analysis: the localization of the molecular vibrational energy and entropy

The partial Hessian vibrational analysis (PHVA), in which only a subblock of the Hesssian matrix is diagonalized to yield vibrational frequencies for partially optimized systems, is extended to the calculation of vibrational enthalpy and entropy changes for chemical reactions. The utility of this method is demonstrated for various deprotonation reactions by reproducing full HVA values to within 0.1–0.4 kcal/mol, depending on the number atoms included in the PHVA. When combined with the hybrid effective fragment potential method [Gordon MS, et al. (2001) J Phys Chem A 105:293–307], the PHVA method can provide (harmonic) free-energy changes for localized chemical reactions in very large systems. Received: 21 September 2001 / Accepted: 30 October 2001 / Published online: 22 March 2002     

Ab initio and density functional theory studies on the mechanism of nucleophilic vinylic substitution of 4<Emphasis Type="Italic">H</Emphasis>-pyran-4-one and 2-methyl-4<Emphasis Type="Italic">H</Emphasis>-pyran-4-one with ammonia

 Nucleophilic vinylic substitutions of 4H-pyran-4-one and 2-methyl-4H-pyran-4-one with ammonia were calculated by the B3LYP method using the 6-31G(d,p) basis set. Bulk solvent effects of aqueous solution were estimated by the polarized continuum and Poisson–Boltzmann self-consistent reaction field models using the 6-311+G(d,p) basis set. In the gas phase different mechanisms were found for the two reaction systems calculated. The reaction of 4H-pyran-4-one proceeds through enol, whereas a feasible path for the less reactive 2-methyl-4H-pyran-4-one is the mechanism through a keto intermediate. Addition of ammonia in concert with proton transfer is the rate-determining step ofthe reaction. The mechanism proceeding either by a bimolecular nucleophilic substitution (S_N2) or by one involving a tetrahedral zwitterionic intermediate is shown to be unlikely in the gas phase or nonpolar solution. The effects of bulk solvent not only consist in a reduction of the various activation barriers by about 25–40 kJ mol⁻¹ but also in a change in the reaction mechanism. Received 26 May 2002 / Accepted 26 July 2002 / Published online: 14 February 2003     

Ab initio study of rate constants of the reaction: HCN + OH → CN + H2O

A method applying ab initio direct dynamics has been utilized in studying the hydrogen abstraction reaction HCN + OH → CN + H₂O. The geometries of the reactants, products, and the transition state have been optimized at the QCISD/6-311G(d, p) level. Single-point energies were further evaluated at the QCISD(T)/6-311+G(2df, 2p)//QCISD/6-311G(d, p) level. The barrier heights for the forward and reverse reactions were predicted to be 15.95 and 7.51 kcal mol⁻¹ at the QCISD(T)/6-311 + G(2df, 2p)//QCISD/6-311G(d, p) level, respectively. The reaction rate constants were calculated in the temperature range from 298 to 4,000 K using the canonical variational transition-state theory with a small-curvature tunneling correction. The results of the calculation show that the theoretical rate constants are in good agreement with experimental data over the measured temperature range of 400–2,600 K. Received: 18 August 2002 / Accepted: 30 August 2002 / Published online: 20 November 2002 Acknowledgements. Our thanks are due to D.G. Truhlar for providing the POLYRATE 8.2 program. This work was supported by the National Science Foundation of China. We also thank D.C. Fang and Y. M. Xie for their valuable help, and P.R. Yan for reading our paper. Correspondence to: Q. S. Li e-mail: qsli@mh.bit.edu.cn     

Comparison of algorithms for conical intersection optimisation using semiempirical methods

We present a comparison of three previously published algorithms for optimising the minimum energy crossing point between two Born–Oppenheimer electronic states. The algorithms are implemented in a development version of the MNDO electronic structure package for use with semiempirical configuration interaction methods. The penalty function method requires only the energies and gradients of the states involved, whereas the gradient projection and Lagrange–Newton methods also require the calculation of non-adiabatic coupling terms. The performance of the algorithms is measured against a set of well-known small molecule conical intersections. The Lagrange–Newton method is found to be the most efficient, with the projected gradient method also competitive. The penalty function method can only be recommended for situations where non-adiabatic coupling terms cannot be calculated. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Heteroelectrocyclic reactions of 3-acyl-4-azido heterocycles: ab initio and density functional calculations on 3-azido-propenal as a model system

 Concerted as well as stepwise reaction pathways for cyclization of 3-azido-propenal to isoxazole have been investigated by density functional (B3LYP) and ab initio methods up to CCSD(T)/cc-pVQZ methods. These calculations clearly establish the pathway with concerted albeit asynchronous nitrogen extrusion and ring closure as the most feasible mechanism. Barriers for cyclization increase in the order Hartree–Fock<B3LYP<ACPF<CCSD(T). According to the geometrical parameters and the electronic structure of the TS as evidenced by natural bond order analysis this cyclization can be interpreted as a pseudopericyclic (heteroelectrocyclic) reaction. Received: 26 May 2002 / Accepted: 18 June 2002 / Published online: 14 February 2003     

Modeling the H5+ potential-energy surface: a first attempt

 Ab initio molecular electronic structure calculations are performed for H₅ ⁺ at the QCISD(T) level of theory, using a correlation-consistent quadruple-zeta basis set. Structures, vibrational frequencies and thermochemical properties are evaluated for ten stationary points of the H₅ ⁺ hypersurface and are compared with previous calculations. The features of the H₃ ⁺…H₂ interaction at intermediate and large intermolecular distances are also investigated. Furthermore, an analytical functional form for the potential-energy surface of H₅ ⁺ is derived using a first-order diatomics-in-molecule perturbation theory approach. Its topology is found to be qualitatively correct for the short-range interaction region. Received: 15 March 2001 / Accepted: 5 July 2001 / Published online: 11 October 2001