Identification of active sites of biomolecules. 1. Methyl-alpha-mannopyranoside and Fe(III)

Car-Parrinello molecular dynamics (CPMD) simulations, DFT chemical reactivity index calculations, and mass spectrometric measurements are combined in an integrated effort to elucidate the details of the coordination of a transition-metal ion to a carbohydrate. The impact of the interaction with the FeIII ion on the glycosidic linkage conformation of methyl-alpha-d-mannopyranoside is studied by classical molecular dynamics (MD) and CPMD simulations. This study shows that FeIII interacts with specific hydroxyl oxygen atoms of the carbohydrate, affecting the ground state carbohydrate conformation. These conformational details are discussed in terms of a set of supporting experiments involving electrospray ionization mass spectrometry, and CPMD simulations clearly indicate that the specific conformational preference is due to intramolecular hydrogen bonding. Classical MD simulations proved insensitive to these important chemical properties. Thus, we demonstrate the importance of chemical reactivity calculations and CPMD simulations in predicting the active sites of biological molecules toward metal cations.     

Preferred conformation of the glycosidic linkage of methyl-beta-mannose

The conformational preference of the glycosidic linkage of methyl-beta-mannose was studied in the gas phase and in aqueous solution by ab initio calculations, and by molecular dynamics (MD) and Car-Parrinello molecular dynamics (CPMD) simulations. MD simulations were performed with various water potential functions to study the impact of the chosen water potential on the predicted conformational preference of the glycosidic linkage of the carbohydrate in solution. This study shows that the trans (t) orientation of the glycosidic linkage of methyl-beta-mannose is preferred over its gauche clockwise (g+) orientation in solution. CPMD simulations clearly indicate that this preference is due to intermolecular hydrogen bonding with surrounding water molecules, whereas no such information could be demonstrated by MD simulations. This study demonstrates the importance of ab initio molecular dynamics simulations in studying the structural properties of carbohydrate-water interactions.     

Solvation of Co(III)-cysteinato complexes in water: a DFT-based molecular dynamics study

Structural, dynamical, and vibrational properties of complexes made of metal cobalt(III) coordinated to different amounts of cysteine molecules were investigated with DFT-based Car-Parrinello molecular dynamics (CPMD) simulations in liquid water solution. The systems are composed of Co(III):3Cys and Co(III):2Cys immersed in liquid water which are modeled by about 110 explicit water molecules, thus one of the biggest molecular systems studied with ab initio molecular simulations so far. In such a way, we were able to investigate structural and dynamical properties of a model of a typical metal binding site used by several proteins. Cobalt, mainly a toxicological agent, can replace the natural binding metal and thus modify the biochemical activity. The structure of the surrounding solvent around the metal-ligands complexes is reported in detail, as well as the metal-ligands coordination bonds, using radial distribution functions and electronic analyses with Mayer bond orders. Structures of the Cocysteine complexes are found in very good agreement with EXAFS experimental data, stressing the importance of considering the surrounding solvent in the modeling. A vibrational analysis is also conducted and compared to experiment, which strengthens the reliability of the solvent interactions with the Cocysteine complexes from our molecular dynamics simulations, as well as the dynamics of the systems. From this preliminary analysis, we could suggest a vibrational fingerprint able to distinguish Co(III):2Cys from Co(III):3Cys. Our simulations also show the importance of considering a quantum explicit solvent, as solute-to-solvent proton transfer events have been observed.     

Glycosidic linkage conformation of methyl-alpha-mannopyranoside

We study the preferred conformation of the glycosidic linkage of methyl-alpha-mannopyranoside in the gas phase and in aqueous solution. Results obtained utilizing Car-Parrinello molecular dynamics (CPMD) simulations are compared to those obtained from classical molecular dynamics (MD) simulations. We describe classical simulations performed with various water potential functions to study the impact of the chosen water potential on the predicted conformational preference of the glycosidic linkage of the carbohydrate in aqueous solution. In agreement with our recent studies, we find that results obtained with CPMD simulations differ from those obtained from classical simulations. In particular, this study shows that the trans (t) orientation of the glycosidic linkage of methyl-alpha-mannopyranoside is preferred over its gauche anticlockwise (g-) orientation in aqueous solution. CPMD simulations indicate that this preference is due to intermolecular hydrogen bonding with surrounding water molecules, whereas no such information could be demonstrated by classical MD simulations. This study emphasizes the importance of ab initio MD simulations for studying the structural properties of carbohydrates in aqueous solution.     

Car-Parrinello MD simulations for the Na+ -phenylalanine complex in aqueous solution

Car-Parrinello molecular dynamics (CPMD) calculations are presented for a Na (+)(Phe) complex in aqueous solution and for various stable Na (+)(Phe) complexes and Na (+)(H 2O) n clusters in the gas phase (with up to six water molecules). The CPMD results are compared to available experimental and ab initio reference data, to DFT results obtained with various combinations of density functionals and basis sets, and to previous classical mechanics MD simulations. The agreement with the reference data in the gas phase validates the CPMD method, showing that it is a valid approach for studying these systems and that it describes correctly the competing Na (+)-Phe and Na (+)-H 2O interactions. Analysis of MD trajectories reveals that the Na (+)(Phe) complex in aqueous solution maintains a stable configuration in which the Na (+) cation hovers above the phenyl ring, at an average distance of 3.85 A from the ring center, while remaining strongly bound to one of the carboxylic oxygens of Phe. Constrained MD simulations indicate that the free energy barrier opposing dissociation of the complex exceeds 5.5 kcal/mol. We thus confirm that "cation- pi" interactions between alcali cations and the pi ring, combined with other kinds of interactions, may allow aromatic amino acids to overcome the competition with water in binding a cation.     

Density functional description of the early stages of the dioxygenation of [(MeC(CH2PPh2)3)M(catecholate)]+ complexes [M = Co(III), Ir(III)]: toward a rationalization of the catalytic mechanism of ring-opening dioxygenases

Density Functional Theory (DFT) has been applied to characterize the early stages of the reaction of dioxygenation of [(triphos)M(catecholate)]+ complexes [M = Co(III), Ir(III); triphos = MeC(CH2PPh2)3], which have been considered to be models of ring-opening dioxygenases. The structural features of the starting complexes and of the intermediate complexes formed by addition of O2 to the coordinated catecholato ion are well reproduced. The calculations showed that this preliminary stage can be obtained only when the oxygen molecule attacks the molecule on the catecholato site.     

Simulation of 59Co NMR chemical shifts in aqueous solution

59Co chemical shifts were computed at the GIAO-B3LYP level for [Co(CN)6]3-, [Co(H2O)6]3+, [Co(NH3)6]3+, and [Co(CO)4]- in water. The aqueous solutions were modeled by Car-Parrinello molecular dynamics (CPMD) simulations, or by propagation on a hybrid quantum-mechanical/molecular-mechanical Born-Oppenheimer surface (QM/MM-BOMD). Mean absolute deviations from experiment obtained with these methods are on the order of 400 and 600 ppm, respectively, over a total delta(59Co) range of about 18,000 ppm. The effect of the solvent on delta(59Co) is mostly indirect, resulting primarily from substantial metal-ligand bond contractions on going from the gas phase to the bulk. The simulated solvent effects on geometries and delta(59Co) values are well reproduced by using a polarizable continuum model (PCM), based on optimization and perturbational evaluation of quantum-mechanical zero-point corrections.     

Unusual temperature effects in propene polymerization using stereorigid zirconocene catalysts.

Free Car-Parrinello molecular dynamics (CPMD) simulations of four diastereomers of the zirconium-propene complexes [{iPr(3-iPr-CpFlu)}ZriBu(C3H6)]+ (Cp=cyclopentadienyl; Flu=fluorenyl) provide valuable insight into the mechanism and stereocontrol of propene polymerization with stereorigid metallocenes. Spontaneous insertion of propene into the zirconium-isobutyl bond is not observed, and propene is found to be weakly bound and to rotate relatively freely around the C--C bond to be formed. Large-amplitude rotation of the isopropyl substituent around the Cp--iPr bond may play a role in triggering dissociation of propene. Three of the four diastereomers eliminate propene during the course of the simulations, which makes dissociation the dominating event on a 20-ps timescale. The CPMD simulations thus support the validity of the assumption, fundamental to statistical propagation models, that each insertion is independent of the preceding insertions. Using insertion barriers from static density functional calculations, the statistical model predicts the polypropene microstructure in good agreement with experiment at low polymerization temperatures for the catalysts {iPr(3-R-CpFlu)}ZrCl2 (R=H, iPr, tBu). The predictions become less accurate at higher temperatures, probably due to the onset of the competing back-skip reaction, which is not included in the model.     

Car-Parrinello molecular dynamics simulation of Fe 3+ (aq)

The optimized geometry and energetic properties of Fe(D2O)n 3+ clusters, with n = 4 and 6, have been studied with density-functional theory calculations and the BLYP functional, and the hydration of a single Fe 3+ ion in a periodic box with 32 water molecules at room temperature has been studied with Car-Parrinello molecular dynamics and the same functional. We have compared the results from the CPMD simulation with classical MD simulations, using a flexible SPC-based water model and the same number of water molecules, to evaluate the relative strengths and weaknesses of the two MD methods. The classical MD simulations and the CPMD simulations both give Fe-water distances in good agreement with experiment, but for the intramolecular vibrations, the classical MD yields considerably better absolute frequencies and ion-induced frequency shifts. On the other hand, the CPMD method performs considerably better than the classical MD in describing the intramolecular geometry of the water molecule in the first hydration shell and the average first shell...second shell hydrogen-bond distance. Differences between the two methods are also found with respect to the second-shell water orientations. The effect of the small box size (32 vs 512 water molecules) was evaluated by comparing results from classical simulations using different box sizes; non-negligible effects are found for the ion-water distance and the tilt angles of the water molecules in the second hydration shell and for the O-D stretching vibrational frequencies of the water molecules in the first hydration shell.     

Elucidating the vibrational spectra of hydrogen-bonded aggregates in solution: electronic structure calculations with implicit solvent and first-principles molecular dynamics simulations with explicit solvent for 1-hexanol in n-hexane

Fourier transform infrared spectroscopy is a popular method for the experimental investigation of hydrogen-bonded aggregates, but linking spectral information to microscopic information on aggregate size distribution and aggregate architecture is an arduous task. Static electronic structure calculations with an implicit solvent model, Car-Parrinello molecular dynamics (CPMD) using the Becke-Lee-Yang-Parr (BLYP) exchange and correlation energy functionals and classical molecular dynamics simulations for the all-atom version of the optimized parameters for liquid simulations (OPLS-AA) force field were carried out for an ensemble of 1-hexanol aggregates solvated in n-hexane. The initial configurations for these calculations were size-selected from a distribution of aggregates obtained from a large-scale Monte Carlo simulation. The vibrational spectra computed from the static electronic structure calculations for monomers and dimers and from the CPMD simulations for aggregates up to pentamers demonstrate the extent of the contribution of dangling or nondonating hydroxyl groups found in linear and branched aggregates to the "monomeric" peak. Furthermore, the computed spectra show that there is no simple relationship between peak shift and aggregate size nor architecture, but the effect of hydrogen-bond cooperativity is shown to differentiate polymer-like (cooperative) and dimer-like (noncooperative) hydrogen bonds in the vibrational spectrum. In contrast to the static electronic structure calculations and the CPMD simulations, the classical molecular dynamics simulations greatly underestimate the vibrational peak shift due to hydrogen bonding.     

Molecular and electronic structures of bis(pyridine-2,6-diimine)metal complexes [ML2](PF6)n (n = 0, 1, 2, 3; M = Mn, Fe, Co, Ni, Cu, Zn)

A series of mononuclear, octahedral first-row transition metal ion complexes mer-[M(II)L0(2)](PF6)2 containing the tridentate neutral ligand 2,6-bis[1-(4-methoxyphenylimino)ethyl]pyridine (L0) and a Mn(II), Fe(II), Co(II), Ni(II), Cu(II), or Zn(II) ion have been synthesized and characterized by X-ray crystallography. Cyclic voltammetry and controlled potential coulometry show that each dication (except those of Cu(II) and Zn(II)) can be reversibly one-electron-oxidized, yielding the respective trications [M(III)L0(2)]3+, and in addition, they can be reversibly reduced to the corresponding monocations [ML2]+ and the neutral species [ML2]0 by two successive one-electron processes. [MnL2]PF6 and [CoL2]PF6 have been isolated and characterized by X-ray crystallography; their electronic structures are described as [Mn(III)L1(2)]PF6 and [Co(I)L0(2)]PF6 where (L1)1- represents the one-electron-reduced radical form of L0. The electronic structures of the tri-, di-, and monocations and of the neutral species have been elucidated in detail by a combination of spectroscopies: UV-vis, NMR, X-band EPR, Mossbauer, temperature-dependent magnetochemistry. It is shown that pyridine-2,6-diimine ligands are noninnocent ligands that can be coordinated to transition metal ions as neutral L0 or, alternatively, as monoanionic radical (L1)1-. All trications are of the type [M(III)L0(2)]3+, and the dications are [M(II)L0(2)]2+. The monocations are described as [Mn(III)L1(2)]+ (S = 0), [Fe(II)L0L1]+ (S = 1/2), [Co(I)L0(2)]+ (S = 1), [Ni(I)L0(2)]+ (S = 1/2), [Cu(I)L0(2)]+ (S = 0), [Zn(II)L1L0]+ (S = 1/2) where the Mn(II) and Fe(II) ions are low-spin-configurated. The neutral species are described as [Mn(II)L1(2)]0, [Fe(II)L1(2)]0, [Co(I)L0L1]0, [Ni(I)L0L1]0, and [Zn(II)L1(2)]0; their electronic ground states have not been determined.     

Crucial role of Cu-S bonding for structural changes accompanying the reversible CuI/CuII transition in an unrestrained Cu(N[symbol: see text]S)2 coordination arrangement. An experimental and DFT study

The structure of reversibly oxidizable [Cu(mmb)2](BF4) with 1-methyl-2-(methylthiomethyl)-1H-benzimidazole (mmb) as bidentate N,S-donor ligand has been determined and compared with that of the copper(II) species [Cu(mmb)2(eta 1-ClO4)](ClO4). In the complex ions of the equilibrium [CuI(mmb)2](+) + ClO4- reversible e- + [CuII(mmb)2-(eta 1-ClO4)]+ the almost linear N-Cu-N backbone is invariant whereas the bonds to the thioether sulfur centers and especially the changing S-Cu-S angle (145.18(5) degrees for the CuII species, 109.33(3) degrees for the CuI form) reflect the metal oxidation state. In contrast to the perchlorate coordinating copper(II) species, [CuI(mmb)2](BF4) contains a cation with a very large vacant site at the metal center, resulting in elliptical channels within the crystal. DFT calculations on [CuI(mb)2]+, [CuII(mb)2]2+, and [CuII(mb)2(OClO3)]+ with mb = 2-methylthiomethyl-1H-benzimidazole confirm the essential role of the metal-sulfur bonds in responding to the reversible CuI/II electron transfer process, even in the absence of electronically stronger interacting thiolate sulfur centers or sophisticated oligodentate ligands.     

New insights into alpha-GalNAc-Ser motif: influence of hydrogen bonding versus solvent interactions on the preferred conformation

The structural features of the mucin-type simplest model, namely, the glycopeptide alpha-O-GalNAc-l-Ser diamide, have been investigated by combining NMR spectroscopy, molecular dynamics simulations, and DFT calculations. In contrast to previous reports, the study reveals that intramolecular hydrogen bonds between sugar and peptide residues are very weak and, as a consequence, not strong enough to maintain the well-defined conformation of this type of molecule. In fact, the observed conformation of this model glycopeptide can be satisfactorily explained by the presence of water pockets/bridges between the sugar and the peptide moieties. Additionally, DFT calculations reveal that not only the bridging water molecules but also the surrounding water molecules in the first hydration shell are essential to keep the existing conformation.     

Oxidation of methanol by FeO2+ in water: DFT calculations in the gas phase and ab initio MD simulations in water solution

We investigate the mechanism of methanol oxidation to formaldehyde by ironoxido ([Fe(IV)O]2+), the alleged active intermediate in the Fenton reaction. The most likely reaction mechanisms are explored with density functional theory (DFT) calculations on microsolvated clusters in the gas phase and, for a selected set of mechanisms, with constrained Car-Parrinello molecular dynamics (CPMD) simulations in water solution. Helmholtz free energy differences are calculated using thermodynamic integration in a simulation box with 31 water molecules at 300 K. The mechanism of the reaction is investigated with an emphasis on whether FeO2+ attacks methanol at a C-H bond or at the O-H bond. We conclude that the most likely mechanism is attack by the oxido oxygen at the C-H bond ("direct CH mechanism"). We calculate an upper bound for the reaction Helmholtz free energy barrier in solution of 50 kJ/mol for the C-H hydrogen transfer, after which transfer of the O-H hydrogen proceeds spontaneously. An alternative mechanism, starting with coordination of methanol directly to Fe ("coordination OH mechanism"), cannot be ruled out, as it involves a reaction Helmholtz free energy barrier in solution of 44 +/- 10 kJ/mol. However, this coordination mechanism has the disadvantage of requiring a prior ligand substitution reaction, to replace a water ligand by methanol. Because of the strong acidity of [FeO(H2O)5]2+, we also investigate the effect of deprotonation of a first-shell water molecule. However, this is found to increase the barriers for all mechanisms.     

Investigations into conformational transitions and solvation structure of a 7-piperidino-5,9-methanobenzo[8] annulene in water

Solvation shell structure of a 7-piperidino-5,9-methanobenzo[8] annulene (PMA) in water has been investigated in ambient conditions using both molecular dynamics (MD) and Car-Parrinello molecular dynamics (CPMD) calculations. From the MD calculations, we find that this molecule exists in three major conformational states out of which two are in twist-boat forms and one in chair form. Due to the limited time scale accessible in CPMD simulations, we have studied all the three conformational states separately using CPMD. The molecular geometry, electronic charge distribution and solvation structure for all three forms are investigated. The stability order of the chair and twist-boat conformations in water solvent has been reversed when compared to the gaseous phase results and in the case of polar aprotic solvents (J. Org. Chem., 1999, 61, 5979). From the radial distribution function, we find that the solvent density around the chair form is significantly lower, which has to be directly related to the smaller solvent accessible area for this conformation and this is in complete agreement with earlier reports. Among the findings are that the solvation shell structure around the nitrogen atom in the chair form of PMA is considerably different from the open conformational forms or the twist-boat forms. The dipole moment for the closed form is found to be significantly larger when compared to the twist-boat forms.     

Theoretical calculations: Can Gibbs free energy for intermolecular complexes be predicted efficiently and accurately?

The theoretical study has been performed to refine the procedure for calculations of Gibbs free energy with a relative accuracy of less than 1 kcal/mol. Three benchmark intermolecular complexes are examined via several quantum-chemical methods, including the second-order Moller-Plesset perturbation (MP2), coupled cluster (CCSD(T)), and density functional (BLYP, B3LYP) theories augmented by Dunnings correlation-consistent basis sets. The effects of electron correlation, basis set size, and anharmonicity are systematically analyzed, and the results are compared with available experimental data. The results of the calculations suggest that experimental accuracy can be reached only by extrapolation of MP2 and CCSD(T) total energies to the complete basis set. The contribution of anharmonicity to the zero point energy and TDeltaSint values is fairly small. The new, economic way to reach chemical accuracy in the calculations of the thermodynamic parameters of intermolecular interactions is proposed. In addition, interaction energy (De) and free energy change (DeltaA) for considered species have been evaluated by Carr-Parrinello molecular dynamics (CPMD) simulations and static BLYP-plane wave calculations. The free energy change along the reaction paths were determined by the thermodynamic integration/"Blue Moon Ensemble" technique. Comparison between obtained values, and available experimental and conventional ab initio results has been made. We found that the accuracy of CPMD simulations is affected by several factors, including statistical uncertainty and convergence of constrained forces (TD integration), and the nature of DFT (density functional theory) functional. The results show that CPMD technique is capable of reproducing interaction and free energy with an accuracy of 1 kcal/mol and 2-3 kcal/mol respectively.     

Targeted proton delivery in the catalyzed reduction of oxygen to water by bimetallic pacman porphyrins

A combined experimental and theoretical investigation of the role of proton delivery in determining O2 reduction pathways catalyzed by cofacial bisporphyrins is presented. A homologous family of dicobalt(II) Pacman porphyrins anchored by xanthene [Co2(DPX) (1) and Co2(DPXM) (3)] and dibenzofuran [Co2(DPD) (2) and Co2(DPDM) (4)] have been synthesized, characterized, and evaluated as catalysts for the direct four-proton, four-electron reduction of O2 to H2O. Structural analysis of the intramolecular diiron(III) mu-oxo complex Fe2O(DPXM) (5) and electrochemical measurements of 1-4 establish that Pacman derivatives bearing an aryl group trans to the spacer possess structural flexibilities and redox properties similar to those of their parent counterparts; however, these trans-aryl catalysts exhibit markedly reduced selectivities for the direct reduction of O2 to H2O over the two-proton, two-electron pathway to H2O2. Density functional theory calculations reveal that trans-aryl substitution results in inefficient proton delivery to O2-bound catalysts compared to unsubstituted congeners. In particular, the HOMO of [Co2(DPXM)(O2)]+ disfavors proton transfer to the bound oxygen species, funneling the O-O activation pathway to single-electron chemistry and the production of H2O2, whereas the HOMO of [Co2(DPX)(O2)]+ directs protonation to the [Co2O2] core to facilitate subsequent multielectron O-O bond activation to generate two molecules of H2O. Our findings highlight the importance of controlling both proton and electron inventories for specific O-O bond activation and offer a unified model for O-O bond activation within the clefts of bimetallic porphyrins.     

Simulation of 59Co NMR Chemical Shifts in Aqueous Solution

⁵⁹Co chemical shifts were computed at the GIAO‐B3LYP level for [Co(CN)₆]^3?, [Co(H₂O)₆]³⁺, [Co(NH₃)₆]³⁺, and [Co(CO)₄]^? in water. The aqueous solutions were modeled by Car–Parrinello molecular dynamics (CPMD) simulations, or by propagation on a hybrid quantum‐mechanical/molecular‐mechanical Born–Oppenheimer surface (QM/MM‐BOMD). Mean absolute deviations from experiment obtained with these methods are on the order of 400 and 600 ppm, respectively, over a total δ(⁵⁹Co) range of about 18 000 ppm. The effect of the solvent on δ(⁵⁹Co) is mostly indirect, resulting primarily from substantial metal–ligand bond contractions on going from the gas phase to the bulk. The simulated solvent effects on geometries and δ(⁵⁹Co) values are well reproduced by using a polarizable continuum model (PCM), based on optimization and perturbational evaluation of quantum‐mechanical zero‐point corrections.