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     

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     

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     

A priori rate constants for kinetic modeling

The advent of computer-aided methods for constructing detailed kinetic models of multicomponent reacting systems provides fresh motivation for the development of efficient and accurate methods for estimating rate constants. There is now the real likelihood that a priori rate estimates, formerly of primarily academic interest, could directly impact major public policy and business decisions. This opportunity brings many challenges. The process of building a computer model for a real-world system can require hundreds of thousands of rate estimates, making most existing rate calculation techniques impractical. Also, the demands for tight error bars on model predictions used to make major decisions often imply levels of accuracy unachievable with existing rate calculation techniques. Past and recent progress towards developing fast and accurate rate estimates is selectively reviewed, and our methodology is outlined. New rate estimates for several types of reactions involving O and HO₂ are presented. Several technical issues requiring further work by the theoretical chemistry community are highlighted. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00214-002-0368-4. Received: 6 February 2002 / Accepted: 2 June 2002 / Published online: 2 October 2002 Acknowledgements. This work was partially supported by the National Computational Science Alliance under Grant CTS010006 N and utilized the Origin 2000 High-performance Computing and UniTree Mass Storage systems. We are grateful for financial support from the EPA Center for Airborne Organics, the NSF CAREER program, Alstom Power, Dow Chemical, and the Office of Basic Energy Science, U.S. Department of Energy through grant DE-FG02-98ER14914. The authors acknowledge the contribution of Hans-Heinrich Carstensen in the initial stages of this work. Correspondence to: W.H. Green Jr. e-mail: whgreen@mit.edu Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00214-002-0368-4     

Study of the dynamics of protein folding through minimalistic models

 Starting with the Levinthal paradox, a brief introduction to the protein folding problem is presented. The existing theories of protein folding, including the folding funnel scenario, are discussed. After briefly discussing different simulation studies of model proteins, we discuss our recent work on the dynamics of folding of the model HP-36 (the chicken villin headpiece) protein by using a simplified hydropathy scale. Special attention has been paid to the statics and dynamics of contact formation among the hydrophobic residues. The results obtained from this simple model appear to be surprisingly similar to several features observed in the folding of real proteins. The account concludes with a discussion of future problems. Received: 28 April 2002 / Accepted: 11 August 2002 / Published online: 13 November 2002 Correspondence to: B. Bagchi e-mail: bbagchi@sscu.iisc.ernet.in Acknowledgements. We thank Samir Pal and Arnab Mukherjee for many discussions and Arun Yethiraj for helpful suggestions. The financial support from DST, India, is gratefully acknowledged. G. S. thanks CSIR for a research fellowship.     

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     

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     

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.     

The fundamental nature and role of the electrostatic potential in atoms and molecules

 A variety of atomic and molecular properties can be expressed in terms of the electrostatic potential. These include energies, covalent and anionic radii, electronegativities (chemical potentials) and a variety of properties that depend upon noncovalent interactons. We present a survey of such relationships, which may be exact or approximate; they may involve the potential in three-dimensional space, along the axes between bonded atoms, at nuclei or on molecular surfaces. Thus, the electrostatic potential, which is rigorously related to the electronic density by Poisson's equation, can be regarded as, effectively, another fundamental determinant of atomic and molecular properties. Received: 6 March 2002 / Accepted: 15 May 2002 / Published online: 29 July 2002     

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.     

Quantum mechanics and mixed quantum mechanics/molecular mechanics simulations of model nerve agents with acetylcholinesterase

 The accurate modeling of biological processes presents major computational difficulties owing to the inherent complexity of the macromolecular systems of interest. Simulations of biochemical reactivity tend to require highly computationally intensive quantum mechanical methods, but localized chemical effects tend to depend significantly on properties of the extended biological environment – a regime far more readily examined with lower-level classical empirical models. Mixed quantum/classical techniques are gaining in popularity as a means of bridging these competing requirements. Here we present results comparing two quantum mechanics/molecular mechanics implementations (the SIMOMM technique of Gordon et al. as implemented in GAMESS, and the ONIOM technique of Morokuma et al. found in Gaussian 98) as performed on the enzyme acetylcholinesterase and model nerve agents. This work represents part of the initial phase of a DoD HPCMP Challenge project in which we are attempting to reliably characterize the biochemical processes responsible for nerve agent activity and inhibition, thereby allowing predictions on compounds unrelated to those already studied. Received: 10 October 2001 / Accepted: 13 November 2002 / Published online: 1 April 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: M. M. Hurley e-mail: hurley@arl.army.mil     

Semiempirical QM/MM potential with simple valence bond (SVB) for enzyme reactions. Application to the nucleophilic addition reaction in haloalkane dehalogenase

 We present a method for the correction of errors in combined QM/MM calculations using a semiempirical Hamiltonian for enzyme reactions. Since semiempirical models can provide a reasonable representation of the general shape of the potential energy surface for chemical reactions, we introduce a simple valence bond-like (SVB) term to correct the energies at critical points on the potential energy surface. The present SVB term is not a stand-alone potential energy function, but it is used purely for introducing small energy corrections to the semiempirical Hamiltonian to achieve the accuracy needed for modeling enzymatic reactions. We show that the present coupled QM-SVB/MM approach can be parameterized to reproduce experimental and ab initio results for model reactions, and have applied the PM3-SVB/MM potential to the nucleophilic addition reaction in haloalkane dehalogenase. In a preliminary energy minimization study, the PM3-SVB/MM results are reasonable, suggesting that it may be used in free energy simulations to assess enzymatic reaction mechanism. Received: 1 November 2001 / Accepted: 6 September 2002 / Published online: 19 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: Lakshmi S. Devi-Kesavan e-mail: kesavan@chem.umn.edu Acknowledgments. The work is partially supported by the NIH and the NSF.     

A theoretical investigation of the mechanism for the reaction between a quebrachitol derivative and N3−

The reaction between a mesylated compound and sodium azide was previously studied experimentally at a temperature of 140 °C using dimethylformamide as a solvent. The product was assigned on the basis of the analysis of the NMR spectra. In this work semiempirical (AM1 and PM3), ab initio (Hartree–Fock and MP2) and density functional theory (BLYP functional) quantum mechanical calculations, using continuum models for describing the solvent effect, were carried out for this process to better understand the reaction mechanism. Three distinct mechanisms involving a carbocation and epoxide intermediates, and a transition-state structure for direct attack of the N₃ ⁻ species to the reactant were investigated. The theoretically calculated preferred reaction pathway passing through an epoxide intermediate agrees nicely with the experimental proposal, providing a good example of where theoretical calculations can be of great help to definitively elucidate the reaction mechanism. Received: 10 July 2001 / Accepted: 20 December 2001 / Published online: 8 April 2002     

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     

A density functional theory study of bridging and terminal oxotitanium(IV) oligomeric and polymeric linear titanoxanes

 This work deals with theoretical investigations on the oxygen–transition metal bond in systems containing linear chains of Ti–O units. From an experimental point of view, in the recent past a number of systems containing linearly arranged Ti–O units were synthesized, in which the Ti atom is complexed with Schiff bases such as acacen and salen. The theoretical study presented here has been carried out applying the density functional theory to model compounds of these systems, in order to shed light on the interactions between the transition metal and oxygen. Calculations have been performed on Ti–O oligomers (dimers, trimers and tetramers) by means of density functional theory at the gradient-corrected level of theory, optimizing the molecular geometries. Calculations have also been performed on linear polymers of the same systems, applying periodic boundary conditions, in order to compare the results with those of oligomeric analogues. Received: 12 January 2002 / Accepted: 16 April 2002 / Published online: 5 July 2002     

Recent applications of density functional theory calculations to biomolecules

The purpose of this overview is to highlight the broad scope and utility of current applications of density functional theory (DFT) methods for the study of the properties and reactions of biomolecules. This is illustrated using examples selected from research carried out within our research group and in collaboration with others. The examples include the hyperfine coupling constants of amino acid radicals, the use of an amino acid as a chiral catalyst for the formation of carbon–carbon bonds in the aldol reaction, hydrogen-bond mediated catalysis of an aminolysis reaction, radiation-induced protein–DNA cross-links, and the mechanism by which an antitumor drug cleaves DNA. We demonstrate that DFT-based methods can be applied successfully to a broad range of problems that remain beyond the scope of conventional electron-correlation methods. Furthermore, we show that contemporary computational quantum chemistry complements experiment in the study of biological systems. Received: 19 December 2001 / Accepted: 8 April 2002 / Published online: 4 July 2002     

Prediction of the Raman spectrum of the aqueous formate anion by a combined density functional theory and self-consistent-reaction-field study

Formate, HCOO⁻, is a small ion that can be used as a convenient model to represent general carboxylic acids as well as the terminal side chains of glutamic and aspartic amino acids in biological systems. Several ab initio techniques (Hartree–Fock and density functional theory methods) were used to study the formate anion in aqueous solution, where the solvent was treated as an electrostatic influence by means of a self-consistent-reaction-field (SCRF) method. The comparison of calculated frequencies with Raman experimental data constitutes a good test for the solvation model employed in this work. The results showed that the application of a SCRF method not only produced smaller errors but also improved the linear correlation between predicted and experimental values. This latter characteristic enables a more efficient application of a linear scaling factor, λ, which corrects the calculated frequencies. In fact, the application of λ to the values calculated for the continuum, when compared to those obtained for a vacuum, resulted in smaller root-mean-square errors of the deviations from the experimental data. Received: 15 May 2000 / Accepted: 19 June 2000 / Published online: 11 September 2000     

Computational insight into the effect of C(19) substituents on [1,7]-hydrogen shift in previtamin D

 B3LYP calculations in conjunction with natural bond orbital population analysis have been performed for a previtamin D model and corresponding transition structures for the [1,7]-hydrogen migration. In addition the 19,19-difluoro, 19-methoxy and 19-fluoro substituted analogs were investigated. The calculated activation barriers decrease in the following order: CHF₂>CH₃>CH₂OCH₃ (24.8, 23.5 and 20.1 kcal/mol). This is in qualitative agreement with experiments. It has been suggested that a decrease of the barrier by a 19-methoxy substituent and its increase by a 19,19-difluoro substituent are phenomena of different origin. In the case of 19-methoxy substitution, the effect is due to the charge redistribution in the triene system and the decrease of the C(19)–H bond energy. The effect of two fluorine substituents at C-19 on the activation barrier is suggested to originate from the combination and balance of several factors: electrostatic repulsion between the negative fluorine atom and the π-electron cloud over the conjugated system, an increase of the HOMO–LUMO gap, and geminal difluoro substitution affecting C–F and C–C bond energies. Received: 17 May 2002 / Accepted: 11 September 2002 / Published online: 14 February 2003