Transition states from empirical force fields

 This is an overview of the use of empirical force fields in the study of reaction mechanisms. Empirical-valence-bond-type methods (including reactive force field and multiconfigurational molecular mechanics) produce full reaction surfaces by mixing, in the simplest case, known force fields describing reactants and products. The SEAM method instead locates approximate transition structures by energy minimization along the intersection of the component force fields. The transition-state force-field approach (including Q2MM) designs a new force field mimicking the transition structure as an energy minimum. The scope and applicability of the various methods are compared. Received: 17 April 2002 / Accepted: 26 July 2002 / Published online: 4 November 2002 Correspondence to: P.-O. Norrby e-mail: pon@kemi.dtu.dk     

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     

Density functional theory study of the mechanism of the proline-catalyzed intermolecular aldol reaction

Transition structures associated with the C-C bond-formation step of the proline-catalyzed intermolecular aldol reaction between acetone and isobutyraldehyde have been studies using density functional theory methods at the B3LYP/6-31G** computational level. A continuum model has been selected to represent solvent effects. For this step, which is the stereocontrolling and rate-determining step, four reactive channels corresponding to the syn and anti arrangement of the active methylene of the enamine relative to the carboxylic acid group of l-proline and the re and si attack modes to both faces of the aldehyde carbonyl group have been analyzed. The B3LYP/6-31G** energies are in good agreement with experiment, allowing us to explain the origin of the catalysis and stereoselectivity for these proline-catalyzed aldol reactions. Received: 2 April 2002 / Accepted: 18 July 2002 / Published online: 11 October 2002 Acknowledgements. This work was supported by research funds provided by the Ministerio de Educación y Cultura of the Spanish Government by DGICYT (project PB98–1429). All the calculations were performed on a Cray–Silicon Graphics Origin 2000 of the Servicio de Informática de la Universidad de Valencia. We are most indebted to this center for providing us with computer capabilities. Correspondence to: L. R. Domingo e-mail: domingo@utopia.uv.es     

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     

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     

Aconityl-derived polymers for biomedical applications. Modeling study of cis–trans isomerisation

 Soluble polymers have been prepared that are designed to undergo enhanced rates of hydrolysis at pH values less than that observed in blood circulation. The degradable element in the polymer mainchain is derived from cis-aconityl acid and is defined by a carboxylic acid pendent functionality (C-4) that is cis across a double bond to an amide at C-1 in the polymer mainchain. While degradation studies in vitro have confirmed these polymers do undergo enhanced rates of degradation at acidic pH values, there is also increasing evidence that during the degradation process the double bond isomerises to the trans configuration and thus prevents the full degradation of a polymer. From a molecular modelling perspective we are seeking to understand the propensity for this cis–trans isomerisation and the mechanism of this cis–trans isomerisation is discussed. Received: 29 April 2002 / Accepted: 6 September 2002 / Published online: 14 February 2003     

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     

The search for stationary points on a quantum mechanical/molecular mechanical potential-energy surface

 We propose a methodology to locate stationary points on a quantum mechanical/molecular mechanical potential-energy surface. This algorithm is based on a suitable approximation of an initial full Hessian matrix, either a modified Broyden–Fletcher–Goldfarg–Shanno or a Powell update formula for the location of, respectively, a minimum or a transition state, and the so-called rational function optimization. The latter avoids the Hessian matrix inversion required by a quasi-Newton–Raphson method. Some examples are presented and analyzed. Received: 16 July 2001 / Accepted: 9 October 2001 / Published online: 9 January 2002     

Dipole–reaction field interaction model for the solvent reorganization energy and its application to the benzoquinone–benzoquinone anion radical system

 Based on the spherical cavity approximation and the Onsager model, a dipole–reaction field interaction model has been proposed to elucidate the solvent reorganization energy of electron transfer (ET). This treatment only needs the cavity radius and the solute dipole moment in the evaluation of the solvent reorganization energy, and fits spherelike systems well. As an application, the ET reaction between p-benzoquinone and its anion radical has been investigated. The inner reorganization energy has been calculated at the level of MP2/6–31+G, and the solvent reorganization energies of different conformations have been evaluated by using the self-consistent reaction field approach at the HF/6–31+G level. Discussions have been made on the cavity radii and the values are found to be reasonable when compared with the experimental ones of some analogous intramolecular ET reactions. The ET matrix element has been determined on the basis of the two-state model. The fact that the value of the ET matrix element is about 10 times larger than RT indicates that this ET reaction can be treated as an adiabatic one. By invoking the classical Marcus ET model, a value of 4.9 × 10⁷M⁻¹s⁻¹ was obtained for the second-order rate constant, and it agrees quite well with the experimental one. Received: 19 October 2001 / Accepted: 17 January 2002 / Published online: 3 May 2002     

Density functional theory gas- and solution-phase study of nucleophilic substitution at di- and trisulfides

 Density functional calculations indicate that nucleophilic substitution in the thiolate–disulfide and thiolate–trisulfide exchange reactions proceeds by an addition–elimination pathway. Solution calculations were performed using B3LYP/6-31+G* and the polarized continuum method. These solution-phase calculations indicate that for the reactions where the sulfur under attack bears a hydrogen atom, the substitution proceeds via an addition–elimination mechanism; however, when a methyl group is attached to the sulfur under attack, the S_N2 mechanism is predicted. Received: 12 October 2001 / Accepted: 28 November 2001 / Published online: 8 April 2002     

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     

Action of HCl on 3-hydroxypyrazolo(iso)quinolines to give 1-chloropyrazoles: evidence for an addition–elimination mechanism by ab initio calculations in gas phase and water

 Addition–elimination reactions involving a nucleophile and a remote leaving group [S^H _N(AE)^tele] are well-known under basic conditions, especially amongst electron-poor six-membered heterocycles, but are less commonly encountered for five-membered heterocycles and are rare under acidic conditions. Concentrated HCl converts 1-hydroxy-1H-pyrazolo[3,4-c] isoquinoline and 1-hydroxy-1H-pyrazolo[3,4-c]quinoline into 3-chloro-1H-pyrazolo[3,4-c]isoquinoline and 3-chloro-1H-pyrazolo[3,4-c]quinoline, respectively. However, apparently neither the isomeric 1-hydroxy-1H-pyrazolo[4,3-c](iso)-quinolines nor the parent 1-hydroxypyrazole undergo this reaction. Additionally, all these systems are refractory under basic conditions. We present a plausible mechanism for the reaction, involving the 3-addition of Cl^- to the diprotonated heterocycle, followed by the elimination of water. Calculations of the initial transition states and intermediates, using optimisation at B3LYP/6-311+G(d,p), including thermochemistry [HF/6-31+G(d)], and single-point Poisson–Boltzmann self-consistent reaction field determination of the free energy of solvation (Jaguar Poisson–Boltzmann self-consistent reaction field), support this mechanism and reproduce the observed order of reactivity, the addition step being 2–4 kcal less favourable for the isomeric 1-hydroxy-1H-pyrazolo[4,3-c](iso)quinolines and provide a rationalisation for the role of strong acid. Received: 27 June 2002 / Accepted: 6 September 2002 / Published online: 14 February 2003     

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     

Multireference perturbation configuration interaction V. Third-order energy contributions in the Møller–Plesset and Epstein–Nesbet partitions

 A simple implementation of third-order perturbation theory applied to a multireference zero-order wavefunction is presented. Two different partitions of the Hamiltonian (M?ller–Plesset baricentric and Epstein–Nesbet) are considered. Two test cases, CH₂ and N₂, are examined. The third-order results are shown to be in good agreement in either partition and are generally an improvement with respect to the second-order results. The phenomenon of intruder states, absent in Epstein–Nesbet, appears to be magnified in the M?ller–Plesset partition. Received: 22 November 2001 / Accepted: 22 February 2002 / Published online: 3 May 2002     

A charge-scaling method to treat solvent in QM/MM simulations

 We present a method to treat the solvent efficiently in hybrid quantum mechanical/molecular mechanical simulations of chemical reactions in enzymes. The method is an adaptation of an approach developed for molecular-mechanical free-energy simulations. The charges of each of the exposed ionizable groups are scaled, and the system is simulated in the presence of a limited number of explicit solvent molecules to obtain a reasonable set of structures. Continuum electrostatics methods are then used to correct the energies. Variations in the procedure are discussed with an emphasis on modifications from the original protocol. We illustrate the method by applying it to the study of a hydrolysis reaction in a highly charged system comprising a complex between the base excision repair enzyme uracil-DNA glycosylase and double-stranded DNA. The resulting adiabatic reaction profile is in good agreement with experiment, in contrast to that obtained without scaling the charges. Received: 5 October 2001 / Accepted: 6 September 2002 / Published online: 28 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: M. Karplus e-mail: marci@tammy.harvard.edu     

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     

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     

An overlap criterion for selection of core orbitals

 An overlap criterion is defined that connects the identification of core orbitals in a molecular system, which can be problematic, to that in isolated atoms, which is well defined. This approach has been tested on a variety of troublesome systems that have been identified in the literature, including molecules containing third-row main-group elements, and is shown to remove errors of up to 100 kcal/mol arising from an inconsistent treatment of core orbitals at different locations on a potential-energy surface. For some systems and choices of core orbitals, errors as large as 19 kcal/mol can be introduced even when consistent sets of orbitals are frozen, and the new method is shown to identify these cases of substantial core–valence mixing. Finally, even when there is limited core–valence mixing, the frozen-core approximation can introduce errors of more than 5 kcal/mol, which is much larger than the presumed accuracy of models such as G2 and CBS-QB3. The source of these errors includes interatomic core–core and core–valence dispersion forces. Received: 31 August 2001 / Accepted: 11 October 2001 / Published online: 9 January 2002