Density Functional Theory Molecular Mechanics Research Articles

Photolytic Cleavage of Co-C Bond in Coenzyme B12-Dependent Glutamate Mutase.

Glutamate mutase (GLM) is a coenzyme B12-dependent enzyme that catalyzes the conversion of S-glutamate to (2 S,3 S)-3-methyl aspartate. The initial step in the catalytic process is the homolytic cleavage of the coenzyme's Co-C bond upon binding of a substrate. Alternatively, the Co-C bond can be cleaved using light. To investigate the photolytic cleavage of the Co-C bond in GLM, we applied a combined density functional theory/molecular mechanics (DFT/MM) and time-dependent-DFT/MM method to scrutinize the ground and the low-lying excited states. Potential energy surfaces (PESs) were generated as a function of axial bond lengths to describe the photodissociation mechanism. The S1 PES was characterized as the crossing of two electronic states, metal-to-ligand charge transfer (MLCT), and ligand field (LF). In GLM, radical pairs generate from the LF state. Two pathways, path A and path B, were identified as possible channels to connect the MLCT and LF electronic states. The S1 PES in GLM was compared with the S1 PES for coenzyme B12-dependent ethanolamine ammonia lyase as well as the isolated AdoCbl cofactor. Finally, the theoretical insights related to the photodissociation mechanism were compared with transient absorption spectroscopy, electron paramagnetic resonance, and resonance Raman spectroscopy.

Effect of Ge/Si substitutions on the local geometry of Si framework sites in zeolites: A combined high resolution 29Si MAS NMR and DFT/MM study on zeolite Beta polymorph C (BEC)

We employed density functional theory/molecular mechanics (DFT/MM) calculations and 29Si magic-angle spinning (MAS) NMR spectroscopy to investigate the effect of single and multiple Ge/Si substitutions on the 29Si NMR parameters as well as the local geometry of SiO4 tetrahedra of the nearest (Ge-O-Si) and next-nearest (Ge-O-Si-O-Si) neighboring Si atoms. The influences of the Ge/Si substitutions are compared with the effects of the corresponding Al/Si substitutions (i.e., Al-O-Si and Al-O-Si-O-Si, respectively). Zeolite Beta polymorph C (BEC), containing double four-membered rings (D4Rs) and exhibiting three distinguishable T sites in the framework, was chosen for this study as a model of germanium containing zeolites. Our computations give a systematic downshift of the 29Si chemical shift of Si by 1–6 ppm for Ge-O-Si sequences. Furthermore, the contributions of two, three, and four Ge atoms as the nearest neighbors to the downshift of Si are not additive and the calculated downshifts lie in the intervals from 2 to 6 ppm, from 1 to 9 ppm, and from 5 to 11 ppm, respectively. Conversely, the contributions of two, three, and four Al atoms as the nearest neighbors are approximately additive. The downshifts caused by Ge nearest neighbors are less than half compared with the corresponding downshifts caused by Al. Moreover, our calculations show that there are no systematic contributions of Ge and Al as next-nearest neighbors (i.e., Ge-O-Si-O-Si and Al-O-Si-O-Si, respectively) to the 29Si chemical shift of Si, and not even the direction (sign) can be predicted without calculating the corresponding sequence.

Optical properties of pyridine and methyl-pyridinium in water using DFT/MM

Molecular properties such as excitation energies, polarisabilities and two-photon absorption cross-sections of pyridine and N-methyl-pyridinium embedded in a solvent of water are studied using density functional theory/molecular mechanics (DFT/MM) calculations. The purpose of this study is to study how well the differences between a cationic and a neutral specie can be predicted with water as the solvent. In order to answer this question, the DFT/MM method used is benchmarked in terms of convergence profiles, e.g. how many calculations are needed in order to obtain a statistically converged result. Quantification of for example how many water molecules needs to be included in the quantum mechanics system in the calculations before a converged molecular property is obtained which is also benchmarked. The latter will serve as valuable information in further calculations of larger organic molecules, where more experimental data are available. In this work, the calculated excitation energies are compared to experimentally determined ultraviolet/visible (UV/VIS) spectra of both pyridine and N-methyl-pyridinium and a reasonable agreement is found.

Nickel(ii), copper(ii) and zinc(ii) metallo-intercalators: structural details of the DNA-binding by a combined experimental and computational investigation

We present a thorough characterization of the interaction of novel nickel(II) (1), copper(II) (2) and zinc(II) (3) Schiff base complexes with native calf thymus DNA (ct-DNA), in buffered aqueous solution at pH 7.5. UV-vis absorption, circular dichroism (CD) and viscometry titrations provided clear evidence of the intercalative mechanism of the three square-planar metal complexes, allowing us to determine the intrinsic DNA-binding constants (K(b)), equal to 1.3 × 10(7), 2.9 × 10(6), and 6.2 × 10(5) M(-1) for 1, 2 and 3, respectively. Preferential affinity, of one order of magnitude, toward AT compared to GC base pair sequences was detected by UV-vis absorption titrations of 1 with [poly(dG-dC)]2 and [poly(dA-dT)]2. Structural details of the intercalation site of the three metal complexes within [dodeca(dA-dT)]2 were obtained by molecular dynamics (MD) simulations followed by density functional theory/molecular mechanics (DFT/MM) calculations. The calculations revealed that three major intermolecular interactions contribute to the strong affinity between DNA and the three metal complexes: (1) the electrostatic attraction between the two positively charged triethylammoniummethyl groups of the metal complexes and the negatively charged phosphate groups of the DNA backbone; (2) the intercalation of the naphthalene moiety within the four nitrogen bases of the intercalation site; (3) the metal coordination by exocyclic donor atoms of the bases, specifically the carbonyl oxygen and amine nitrogen atoms. Remarkably, the Gibbs formation free energy calculated for the intercalation complexes of 1, 2 and 3 with [dodeca(dA-dT)]2 in the implicit water solution is in agreement with the experimental Gibbs free energy values obtained from the DNA-binding constants as ΔG° = -RT ln(K(b)). In particular, the DNA-binding affinity trend, 1 > 2 > 3, is reproduced. Finally, the first shell coordination distances calculated for the intercalation complex 3/[dodeca(dA-dT)]2 are in excellent agreement with the experimental distances extracted from the extended X-ray absorption fine structure (EXAFS) spectrum of the corresponding 3/ct-DNA solutions. The latter results provided the first evidence of metal ion coordination by native DNA in aqueous solution.

Metal complex–DNA binding: Insights from molecular dynamics and DFT/MM calculations

Molecular dynamics (MD) simulations, followed by density functional theory/molecular mechanics (DFT/MM) calculations, provided a detailed structure of the binding site between the cationic metallointercalator (dipyrido [3,2-a:2′,3′-c]phenazine)(glycinato)copper(II), [Cu(gly)(dppz)]+, and the two dodeca-deoxynucleotide duplexes [dodeca(dG-dC)]2 and [dodeca(dA-dT)]2. Three simultaneous DNA binding types were detected in the fully optimized DFT/MM structures: 1) metal coordination through exocyclic oxygen atoms of nitrogen bases; 2) intercalation of the dppz chromophore between stacked Watson–Crick AT–AT and GC–GC bases; and 3) hydrogen bonding between the glycinato ligand and amine groups or heterocyclic nitrogen atoms of DNA bases. Standard enthalpy and Gibbs free energy values were used to evaluate, in vacuo and in solution, the formation energy of both [Cu(gly)(dppz)]/dodecanucleotide complexes. The latter were in excellent agreement with the recently reported value of the experimental DNA-binding constant, providing a physical interpretation of the enthalpy, entropy and solvent contributions in the binding mechanism.

Hybrid density functional–molecular mechanics calculations for core-electron binding energies of glycine in water solution

We report hybrid density functional theory-molecular mechanics (DFT/MM) calculations performed for glycine in water solution at different pH values. In this paper, we discuss several aspects of the quantum mechanics-molecular mechanics (QM/MM) simulations where the dynamics and spectral binding energy shifts are computed sequentially, and where the latter are evaluated over a set of configurations generated by molecular or Car-Parrinello dynamics simulations. In the used model, core ionization takes place in glycine as a quantum mechanical (QM) system modeled with DFT, and the solution is described with expedient force fields in a large molecular mechanical (MM) volume of water molecules. The contribution to the core electronic binding energy from all interactions within and between the two (DFT and MM) parts is accounted for, except charge transfer and dispersion. While the obtained results were found to be in qualitative agreement with experiment, their precision must be qualified with respect to the problem of counter ions, charge transfer and optimal division of QM and MM parts of the system. Results are compared to those of a recent study [Ottoson et al., J. Am. Chem. Soc., 2011, 133, 3120].

Transition metal catalysis by density functional theory and density functional theory/molecular mechanics

AbstractDensity functional theory (DFT) and density functional theory/molecular mechanics (DFT/MM) methods are useful tools in modern homogeneous catalysis. Calculation, with its ability to characterize otherwise hardly accessible intermediates and transition states, is a key complement to experiment for the full characterization of the often intricate reaction mechanisms involved in transition metal catalysis. DFT and DFT/MM techniques have been applied to the characterization of full catalytic cycles, as those in cross‐coupling; to the systematic analysis of single reaction steps common to several catalytic cycles, such as CH activation; to the elucidation of processes involving different spin states, such as the rebound mechanism for CH activation; to the identification of transient intermediates with key mechanistic roles, such as those in oxygen‐evolving complexes; to the analysis of the catalytic keys to polymerization control, as in olefin polymerization; and to reproduction and rationalization of experimentally reported enantioselectvities, as in the case of olefin dihydroxylation. The currently available techniques provide sufficient accuracy to offer chemical insight into the systems involved in experiment, as proved by the growing body of successful applications in the field. © 2012 John Wiley & Sons, Ltd.This article is categorized under: Structure and Mechanism > Molecular Structures

Effect of Al/Si Substitutions and Silanol Nests on the Local Geometry of Si and Al Framework Sites in Silicone-Rich Zeolites: A Combined High Resolution27Al and29Si NMR and Density Functional Theory/Molecular Mechanics Study

We employed 29Si and 27Al (3Q) magic-angle spinning (MAS) NMR spectroscopy and density functional theory/molecular mechanics (DFT/MM) calculations to investigate the effect of Al/Si substitutions and the presence of silanol nests on the 29Si and 27Al NMR parameters as well as the local geometry of SiO4 and AlO4− tetrahedra of the nearest and next-nearest neighboring Si and Al atoms. The silicon-rich zeolite of the chabazite structure (Si/Al 38) was chosen for this study as a representative model of silicon-rich zeolites since it exhibits a low number of distinguishable T sites. Our computational results show the following: (I) Al atoms can occupy three different crystallographic T sites in the framework of chabazite (Si/Al 38). This result is in agreement with two observed 27Al NMR resonances. (II) An Al/Si substitution causes a downshift of the 29Si chemical shift of the nearest neighboring Si atoms (Al−O−Si) by 4−11 ppm. (III) The effect of a more distant Al/Si substitution (Al−O−Si−O−Si) is significant...

Modelling spectroscopic properties of large molecular systems. The combined Density Functional Theory/Molecular Mechanics approach

In this presentation we review some theoretical aspects of the combined Density Functional Theory/Molecular Mechanics (DFT/MM) approach designed to describe large molecular systems in an effective and efficient manner. We will introduce the concept of (polarizable) DFT/MM response theory thereby enabling calculation of a variety of molecular properties. Here we will focus on spectroscopic properties described by linear response with respect to the applied magnetic or electric field. Of special interest will be UV and NMR properties since these are ideal probes for extracting important information concerning the nature of the intermolecular interactions between a solute and the solvent. The methods developed will be applied to acetone and pyridine in aqueous solution. In all cases we find, upon comparison to experimental data, the DFT/MM scheme to be accurate and at the same time cost-effective.

Effects of Vanadium Substitution on the Structure and Photocatalytic Behavior of ETS-10

A combination of experimental and computational methods has been used to investigate the effects of vanadium doping in ETS-10. Near edge X-ray absorption fine structure (NEXAFS) spectra reveal octahedrally coordinated VIV and VV species within V-doped ETS-10 materials, confirming substitution for TiIV sites only. Computational models, using hybrid density functional theory/molecular mechanics (DFT/MM) methods, have been developed that contain varying concentrations of VIV and VV within the O−M−O (M = Ti, V) chain. Geometry optimizations indicate that VV substitution leads to larger changes in the local chain geometry than VIV substitution. Substitution energetics for VIV and VV in different sites have been calculated to determine preferred locations of the two species, suggesting that long chains of VV are not stable and demonstrating the need for both VV and VIV within V-substituted materials. Wavefunctions for systems with an electron added or removed are used to identify electron and hole trapping site...

A visible light photocatalyst: effects of vanadium substitution on ETS-10

Hybrid density functional theory/molecular mechanics (DFT/MM) methods have been used to investigate the effects of vanadium substitution in ETS-10. Models have been developed to contain varying concentrations of V(IV) and V(V) within the O-M-O (M = Ti, V) chain. Most of the V-substituted models have a localized mid-gap state. The occupation of this localized state depends upon the dopant oxidation state, leading to the addition of multiple low energy transitions. A linear correlation has been identified between band gap energies estimated using ground state orbital energies and those calculated using the more accurate and computationally demanding time-dependent DFT (TDDFT) method for a variety of transition metal substituted models of ETS-10. Consistent with experimental data for V substitution, our models predict a decrease in the optical band gap with increasing [V], due to a lowering of the delocalized d-orbital states at the bottom of the conduction band with increasing V d-orbital character. This effect is more pronounced in the case of V(V) substitution than V(IV). Excitation energies for the V-doped models, calculated with TDDFT methods correlate well with experimental data, allowing for the assignment of specific optical transitions to experimental UV-Vis spectra. The electronic structure of V-substituted ETS-10 at high V concentration demonstrates band gap energies within the visible range of the spectrum. Additionally, at high [V] the band gap energy and presence of low energy electron traps can be controlled by the relative concentration of V(IV) and V(V) along the O-M-O chain, establishing V-substituted ETS-10 as a promising visible light photocatalyst.