Structure and dynamics of La(III) in aqueous solution – An ab initio QM/MM MD approach

Ab initio QM/MM MD simulations have allowed to clarify some of the ambiguities arising from various studies on the hydrated La(III) ion. Both nine- and ten-coordinated hydrates co-exist and interchange in a dissociative process on the nano- or even subnanosecond scale, and thus much faster than any other trivalent main group or transition metal ions. The weak ion–ligand bond (53 N/m) supplies a reasonable explanation for it. The simulation results for La(III) are also compared to those for the isoelectronic ions Cs(I) and Ba(II) obtained by the same ab initio MD procedure, leading to conclusions on the influence of central ion charge on structural and dynamic properties of hydrate complexes.     

One- and three-parameter density functional theory and high level ab initio theory study of the CH+CH disproportionation reaction

Complete basis set (CBS) ab initio computational studies were performed with the target being to explore the CH+CH potential energy surface. Several closed and open shell intermediates were located on the potential energy surface. Computed enthalpies for the branching reactions, as well as heats of formation are in excellent agreement. Although CBS computed energies are of high quality, this computational study is not capable of predicting the branching product ratio due to fact that neither the MP2 nor the 6-311G(2d,2p) basis set are sufficient to locate the reactant complexes and the transition state structures for the hydrogen and carbon transfer reactions in the reaction complexes. To properly explore the CH+CH potential energy surface a much higher ab initio theory level is required.     

High level of ab initio and density functional theory computational study of structural and energetic properties of tetrafluorhydrazine rotamers

The HF, MP2, MP3, MP4, and QCISD ab initio methods were compared with local, hybrid, and gradient-corrected density functional theory (DFT) methods for computing structures and energies of N2F4 rotamers. In all DFT calculations 6-311 + G(2d) basis set was used. The generated structures energies of trans- and gauche-N₂F₄ rotamers, and their dissociation energies to nitrogen difluoride were compared with experimental data. Suitable hybrid and gradient-corrected DFT methods for determining structures and energies for these and similar molecular systems were discussed.     

QM/MM connection atoms for the multistate treatment of organic and biological molecules

We present an extension of our semiempirical floating occupation MO-CI approach for the determination of ground and excited state potential energy surfaces of interest in photochemistry. The QM/MM variant of the method, which allows for electrostatic and van der Waals interactions between the QM and MM subsystems, is supplemented with a treatment of covalent interactions based on Antes and Thiels connection atom approach. We concentrate on the correct treatment of electrostatic interactions concerning the connection atom, on the specific requirements for the representation of excited states, and on the transferability of the optimal parameters. We show the viability of the method with four examples of connection atoms: S in a thioether bridge, acylic C, aliphatic C, and N in a peptide. The results obtained with the QM/MM treatment compare well with all-QM results of the same level.     

Transition state structure invariance to model system size and calculation levels: a QM/MM study of the carboxylation step catalyzed by Rubisco

The present study elucidates structural features related to the molecular mechanism in the carboxylation step of the reaction catalyzed by Rubisco. Starting from the initial X-ray Protein Data Bank structure of a Rubisco monomer, the reactive subsystem in vacuo is subjected to quantum chemical semiempirical and ab initio studies, while the effects of the protein environments are included by means of a hybrid quantum mechanical/molecular mechanical (QM/MM) approach. The QM/MM is used to characterize the transition structure for carboxylation inside the protein. The calculations were made with the AM1/CHARMM/GRACE scheme. Comparisons between the in vacuo and in situ transition structures show remarkable invariance with respect to geometric parameters, index and transition vector amplitudes. The transition state couples the carbon dioxide attack to the C2 center of the substrate in its dienol form with a simultaneous intramolecular hydrogen transfer from the C2 atom to the hydroxyl group linked to the C3 center. This study suggests that carboxylation may be simultaneously coupled to the activation of the C3 center in the enzyme. Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 10 December 1998     

QM/MM calculation of solvent effects on absorption spectra of guanine

Electronic spectra of guanine in the gas phase and in water were studied by quantum mechanical/molecular mechanical (QM/MM) methods. Geometries for the excited‐state calculations were extracted from ground‐state molecular dynamics (MD) simulations using the self‐consistent‐charge density functional tight binding (SCC‐DFTB) method for the QM region and the TIP3P force field for the water environment. Theoretical absorption spectra were generated from excitation energies and oscillator strengths calculated for 50 to 500 MD snapshots of guanine in the gas phase (QM) and in solution (QM/MM). The excited‐state calculations used time‐dependent density functional theory (TDDFT) and the DFT‐based multireference configuration interaction (DFT/MRCI) method of Grimme and Waletzke, in combination with two basis sets. Our investigation covered keto‐N7H and keto‐N9H guanine, with particular focus on solvent effects in the low‐energy spectrum of the keto‐N9H tautomer. When compared with the vertical excitation energies of gas‐phase guanine at the optimized DFT (B3LYP/TZVP) geometry, the maxima in the computed solution spectra are shifted by several tenths of an eV. Three effects contribute: the use of SCC‐DFTB‐based rather than B3LYP‐based geometries in the MD snapshots (red shift of ca. 0.1 eV), explicit inclusion of nuclear motion through the MD snapshots (red shift of ca. 0.1 eV), and intrinsic solvent effects (differences in the absorption maxima in the computed gas‐phase and solution spectra, typically ca. 0.1–0.3 eV). A detailed analysis of the results indicates that the intrinsic solvent effects arise both from solvent‐induced structural changes and from electrostatic solute–solvent interactions, the latter being dominant. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Density functional theory (DFT) and ab initio investigations of the electronic and molecular structures of the monomer and the dimer of trimethylaluminium

The electronic and molecular structures of the monomer and dimer of trimethylalu-minium have been studied using density functional theory and ab initio MP2 method. The optimized geometry of the monomer Al(CH3)3 is of C3h symmetry, whereas that of the dimer [A1(CH3)3]2 contains a carbon-bridged four-membered ring structure with C2h symmetry. The hydrogen-bridged six-membered ring structure is found to be unstable. The calculated dimerization energy for the four-membered ring structure is 78 kJ/mol, in close proximity to the experimental value of 85.27 kJ/mol.     

Geometry optimization with QM/MM,ONIOM, and other combined methods. I. Microiterations and constraints

Hybrid energy methods such as QM/MM and ONIOM, that combine different levels of theory into one calculation, have been very successful in describing large systems. Geometry optimization methods can take advantage of the partitioning of these calculations into a region treated at a quantum mechanical (QM) level of theory and the larger, remaining region treated by an inexpensive method such as molecular mechanics (MM). A series of microiterations can be employed to fully optimize the MM region for each optimization step in the QM region. Cartesian coordinates are used for the MM region and are chosen so that the internal coordinates of the QM region remain constant during the microiterations. The coordinates of the MM region are augmented to permit rigid body translation and rotation of the QM region. This is essential if any atoms in the MM region are constrained, but it also improves the efficiency of unconstrained optimizations. Because of the microiterations, special care is needed for the optimization step in the QM region so that the system remains in the same local valley during the course of the optimization. The optimization methodology with microiterations, constraints, and step-size control are illustrated by calculations on bacteriorhodopsin and other systems.     

Accurate ab initio prediction of propagation rate coefficients in free-radical polymerization: Acrylonitrile and vinyl chloride

A systematic methodology for calculating accurate propagation rate coefficients in free-radical polymerization was designed and tested for vinyl chloride and acrylonitrile polymerization. For small to medium-sized polymer systems, theoretical reaction barriers are calculated using G3(MP2)-RAD. For larger systems, G3(MP2)-RAD barriers can be approximated (to within 1 kJ mol⁻¹) via an ONIOM-based approach in which the core is studied at G3(MP2)-RAD and the substituent effects are modeled with ROMP2/6-311+G(3df,2p). DFT methods (including BLYP, B3LYP, MPWB195, BB1K and MPWB1K) failed to reproduce the correct trends in the reaction barriers and enthalpies with molecular size, though KMLYP showed some promise as a low cost option for very large systems. Reaction rates are calculated via standard transition state theory in conjunction with the one-dimensional hindered rotor model. The harmonic oscillator approximation was shown to introduce an error of a factor of 2–3, and would be suitable for “order-of-magnitude” estimates. A systematic study of chain length effects indicated that rate coefficients had largely converged to their long chain limit at the dimer radical stage, and the inclusion of the primary substituent of the penultimate unit was sufficient for practical purposes. Solvent effects, as calculated using the COSMO model, were found to be relatively minor. The overall methodology reproduced the available experimental data for both of these monomers within a factor of 2.     

The evaluation of bond dissociation energies for simple sulphur containing molecules using ab initio and density functional methods

The S–H and C–S bond dissociation energies for simple alkylthiols and dialkylsulphides, along with the S–S bond dissociation energy for dimethyl disulphide, compounds which have been used in the metal–organic chemical vapour deposition (MOCVD) growth of wide band gap II–VI (12–16) Zn- and Cd-based compound semiconductors, have been computed using the ab initio (ROHF and MP2) and density functional theory (DFT) methods (BHandH, BHandHLYP, B3LYP, B3P86, B3PW91, BLYP and BP86) with the 6-311+G(2d,p) basis set along with high accuracy complete basis set, CBS-4 and CBS-Q energy computations. The computed energies are compared with experimental results and the suitability of the DFT methods, for the computational study of these systems, is discussed.     

QM/MM: what have we learned,where are we,and where do we go from here?

This paper briefly reviews the current status of the most popular methods for combined quantum mechanical/molecular mechanical (QM/MM) calculations, including their advantages and disadvantages. There is a special emphasis on very general link-atom methods and various ways to treat the charge near the boundary. Mechanical and electric embedding are contrasted. We consider methods applicable to gas-phase organic chemistry, liquid-phase organic and organometallic chemistry, biochemistry, and solid-state chemistry. Then we review some recent tests of QM/MM methods and summarize what we learn about QM/MM from these studies. We also discuss some available software. Finally, we present a few comments about future directions of research in this exciting area, where we focus on more intimate blends of QM with MM. Contribution to the Proceedings of the 10th Electronic Computational Chemistry Conference     

Density functional theory and quadratic complete basis set ab initio studies of the HNSi to HSiN isomerization and hydrogen insertion reactions with further isomerizations of the insertion products

Ab initio and density functional theory (DFT) computational studies were performed in order to determine the potential energy profiles for the inter-conversions of the small silicon–nitrogen built chemical systems: HSiN, HNSi, HSiNH₂, and HNSiH₂. Three hybrid DFT methods demonstrated high reliability in computing structures and potential energy profiles for these chemical transformations. The stability of some of these molecular systems and their interconversions was discussed and computational results were compared with experimental observations when available.     

Theoretical molecular structures for partially bonded complexes of trimethylamine with SO2 and SO3: ab initio and density functional theory calculations

The self-consistent reaction field (SCRF) method based on Onsager's reaction field theory is applied to investigate the effect of polar media on molecular structures of complexes of trimethylamime (TMA) with SO_x (x=2,3). The calculated SCRF N–S bond lengths at the MPW1PW91/6-311+G(3df) level are in satisfactory agreement with the experimental N–S bond lengths for the TMA–SO_x upon crystallization. The results are enough to demonstrate the usefulness of the reaction field theory in providing qualitative understanding of the medium effect on the partially bonded system such as TMA–SO_x.     

Energy bands and bond alternation potential in poly(para-phenylene vinylene): a comparative ab initio quantum chemical and density functional theory study

We present calculations of the total energy per unit cell for different bond alternations of the C-C bonds bridging the distance between two aromatic rings in poly(para-phenylene vinylene) (PPV), using two different parametrizations of the energy functional in the local density approximation (LDA) and the ab initio Hartree-Fock (HF) method. For the application of correlation corrections to the HF results the system is already too large. We find that even simple LDA methods are reliable alternatives to the ab initio HF method for the calculation of potential surfaces in polymers with large unit cells. The results in turn can be used to determine parameters for model Hamiltonians necessary for theoretical studies of the dynamics of nonlinear quasiparticles in the polymers. We further present the LDA band structures of PPV together with their HF and correlation (many body perturbation theory of 2^nd order in Møller-Plesset partitioning, MP2) corrected counterparts. We find that the fundamental gap obtained is too large both with HF and with the correlation corrected band structure compared to experiment. However, we use only a modest correlation method and a small basis set, which already brings us to the limits of the computers available to us. The LDA gaps on the other hand are too small which, however, could be corrected with the help of self interaction corrections. None of the latter methods would lead to exceedingly large computation times.     

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.     

Computational study of the interaction of proflavine with d(ATATATATAT)2 and d(GCGCGCGCGC)2

The interaction of proflavine (PR) with two B-DNA decamers of alternating AT and GC sequence, called [deca(dG-dC)]₂ and [deca(dA-dT)]₂, respectively, was computationally investigated by the ONIOM method, exploiting a three-layer QM/QM/MM hybrid approach. The highest level QM method was applied to the model system, which comprises the intercalation site (5th and 6th base pairs) and the inserted PR molecule. The connecting sugar phosphate backbone was added in the medium layer region. Both higher and medium level layers, differing in the size of the basis set used, were treated by the DFT MPWB1K functional. The full system in the lower layer was described by the empirical AMBER force field. The calculated values of the interaction energy of PR with [deca(dG-dC)]₂ and [deca(dA-dT)]₂, as well as with the dinucleotides d(GpC)₂, and d(ApT)₂, the latter considered either in vacuo and in the mimicked water solvent, support for a static higher affinity toward G-C compared to the A-T DNA base sequences, in agreement with structural results from crystallographic studies. Furthermore, the different structural characteristics of the [deca(dG-dC)]₂/PR complex compared to those of the [deca(dA-dT)]₂/PR, furnish a possible interpretation of apparently controversial experimental thermodynamic data, explained in terms of two possible modes of non-covalent binding of ligands with DNA, namely intercalation and external binding, respectively.     

Microwave spectroscopic and ab initio studies of pyrolysis products of 2-nitrosopropene (syn form) and its pyrolysis mechanism

The pyrolysis products of CH₂=C(CH₃)---NO (syn form) have been determined by microwave spectroscopy. The pyrolysis products of CH₂=C(CH₃)---NO (syn form) and its ¹⁵N isotopic species were found to be CH₂=O, CH₃CN, and CH₃C¹⁵N. The produce of formaldehyde and methyl cyanide suggests that the C=C and N=O double bonds of CH₂=C(CH₃)---N=O (syn form) were broken. To explain the generation of the two molecules, a four-membered ring molecule (9) as an intermediate, is proposed. The four-membered ring molecule as an intermediate is also supported by ab initio MO calculation. Applying the pyrolysis mechanism obtained for 2-nitrosopropene (syn form) to that of 1,1,2-trichloronitrosoethane, one of its complicated pyrolysis mechanisms was explained. The rotational constants and geometrical parameters of two intermediates, 9 and CH₂=CCl---NO (13), were obtained by ab initio MO calculation (MP2/6-31G**) to predict their microwave spectra.     

Ab initio and density function theory computational studies of the CH4 + H → CH3 + H2 reaction

The activation barrier for the CH₄ + H → CH₃ + H₂ reaction was evaluated with traditional ab initio and Density Functional Theory (DFT) methods. None of the applied ab initio and DFT methods was able to reproduce the experimental activation barrier of 11.0-12.0 kcal/mol. All ab initio methods (HF, MP2, MP3, MP4, QCISD, QCISD(T), G1, G2, and G2MP2) overestimated the activation energy. The best results were obtained with the G2 and G2MP2 ab initio computational approaches. The zero-point corrected energy was 14.4 kcal mol⁻¹. Some of the exchange DFT methods (HFB) computed energies which were similar to the highly accurate ab initio methods, while the B3LYP hybrid DFT methods underestimated the activation barrier by 3 kcal mol⁻¹. Gradient-corrected DFT methods underestimated the barrier even more. The gradient-corrected DFT method that incorporated the PW91 correlational functional even generated a negative reaction barrier. The suitability of some computational methods for accurately predicting the potential energy surface for this hydrogen radical abstraction reaction was discussed.