Dynamical properties of the water molecules in the hydration shells of Fe(II) and Fe(III) ions: ab initio QM/MM molecular dynamics simulations

Dynamical properties, librational and vibrational motions of water molecules in the first and second hydration shells of the Fe(II) and Fe(III) ion were evaluated by means of velocity autocorrelation functions obtained by combined quantum mechanical/molecular mechanical molecular dynamics (QM/MM-MD) simulations. The frequencies of rotation around three principal axes and the frequencies of intramolecular vibration of the water molecules in the first hydration shells obtained from the simulations are blue-shifted for both ions compared to those observed experimentally for liquid water. The intramolecular geometry of water molecules in the quantum mechanically treated region (ion plus first hydration shell) shows shorter O–H bonds and wider H–O–H angles than the bulk solvent.     

Speciation of the curium(III) ion in aqueous solution: a combined study by quantum chemistry and molecular dynamics simulation

The structures of aquo complexes of the curium(III) ion have been systematically studied using quantum chemical and molecular dynamics (MD) methods. The first hydration shell of the Cm3+ ion has been calculated using density functional theory (DFT), with and without inclusion of the conductor-like polarizable continuum medium (CPCM) model of solvation. The calculated results indicate that the primary hydration number of Cm3+ is nine, with a Cm-O bond distance of 2.47-2.48 A. The calculated bond distances and the hydration number are in excellent agreement with available experimental data. The inclusion of a complete second hydration shell of Cm3+ has been investigated using both DFT and MD methods. The presence of the second hydration shell has significant effects on the primary coordination sphere, suggesting that the explicit inclusion of second-shell effects is important for understanding the nature of the first shell. The calculated results indicate that 21 water molecules can be coordinated in the second hydration shell of the Cm3+ ion. MD simulations within the hydrated-ion model suggest that the second-shell water molecules exchange with the bulk solvent with a lifetime of 161 ps.     

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.     

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.     

Hydration shell structure and dynamics of curium(III) in aqueous solution: first principles and empirical studies

Results of ab initio molecular dynamics (AIMD), quantum mechanics/molecular mechanics (QM/MM), and classical molecular dynamics (CMD) simulations of Cm(3+) in liquid water at a temperature of 300 K are reported. The AIMD simulation was based on the Car-Parrinello MD scheme and GGA-PBE formulation of density functional theory. Two QM/MM simulations were performed by treating Cm(3+) and the water molecules in the first shell quantum mechanically using the PBE (QM/MM-PBE) and the hybrid PBE0 density functionals (QM/MM-PBE0). Two CMD simulations were carried out using ab initio derived pair plus three-body potentials (CMD-3B) and empirical Lennard-Jones pair potential (CMD-LJ). The AIMD and QM/MM-PBE simulations predict average first shell hydration numbers of 8, both of which disagree with recent experimental EXAFS and TRLFS value of 9. On the other hand, the average first shell hydration numbers obtained in the QM/MM-PBE0 and CMD simulations was 9, which agrees with experiment. All the simulations predicted an average first shell and second shell Cm-O bond distance of 2.49-2.53 ? and 4.67-4.75 ? respectively, both of which are in fair agreement with corresponding experimental values of 2.45-2.48 and 4.65 ?. The geometric arrangement of the 8-fold and 9-fold coordinated first shell structures corresponded to the square antiprism and tricapped trigonal prisms, respectively. The second shell hydration number for AIMD QM/MM-PBE, QM/MM-PBE0, CMD-3B, and CMD-LJ, were 15.8, 17.2, 17.7, 17.4, and 16.4 respectively, which indicates second hydration shell overcoordination compared to a recent EXAFS experimental value of 13. Save the EXAFS spectra CMD-LJ simulation, all the computed EXAFS spectra agree fairly well with experiment and a clear distinction could not be made between configurations with 8-fold and 9-fold coordinated first shells. The mechanisms responsible for the first shell associative and dissociative ligand exchange in the classical simulations have been analyzed. The first shell mean residence time was predicted to be on the nanosecond time scale. The computed diffusion constants of Cm(3+) and water are in good agreement with experimental data.     

Quantum mechanical/molecular mechanical simulations of the Tl(III) ion in water

Classical molecular dynamics (MD) and combined quantum mechanical/molecular mechanical (QM/MM) MD simulations have been performed to investigate the structural and dynamical properties of the Tl(III) ion in water. A six-coordinate hydration structure with a maximum probability of the Tl-O distance at 2.21 A was observed, which is in good agreement with X-ray data. The librational and vibrational spectra of water molecules in the first hydration shell are blue-shifted compared with those of pure liquid water, and the Tl-O stretching force constant was evaluated as 148 Nm(-1). Both structural and dynamical properties show a distortion of the first solvation shell structure. The second shell ligands' mean residence time was determined as 12.8 ps. The Tl(III) ion can be classified as "structure forming" ion; the calculated hydration energy of -986 +/- 9 kcal mol agrees well with the experimental value of -986 kcal mol.     

应用L-J(12/6)势能模型对Fe2+水化作用的分子动力学模拟

本文首先优化出Fe²⁺和水分子相互作用的Lennard-Jones(12/6)势能模型中的2个参数：ε_IW=0.180 kcal·mol^-1和σ_IW=0.2885 nm。然后在298.15 K和573 K 温度条件下，用这个势能模型去运行Fe²⁺极稀水溶液系统的分子动力学模拟。模拟的结果显示，Fe²⁺的第一和第二水化壳层的结构和动力学性质与实验的，以及其他势能模型模拟出的结果一致。模拟的同时获得了关于RWK2水分子模型内部结构变化的新信息。此外，模拟揭示了温度变化对Fe²⁺水化结构和动力学性质的影响。     

Be(II) in aqueous solution--an extended ab initio QM/MM MD study

An ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulation at double-zeta restricted Hartree-Fock (RHF) level was performed at 293.15 K, including first and second hydration shell in the QM region to study the structural and dynamical properties of the Be(II)-hydrate in aqueous solution. The first tetrahedrally arranged hydration shell, with the four water molecules located at a mean Be-O distance of 1.61 A, is highly inert with respect to ligand exchange processes. The second shell, however, consisting in average of approximately 9.2 water ligands at a mean Be-O distance of 3.7 A and the third shell at a mean Be-O distance of 5.4 A with approximately 19 ligands rapidly exchange water molecules between them and with the bulk, respectively. Other structural parameters such as radial and angular distribution functions (RDF and ADF) and tilt- and theta-angle distributions were also evaluated. The dynamics of the hydrate were studied in terms of ligand mean residence times (MRTs) and librational and vibrational frequencies. The mean residence times for second shell and third shell ligands were determined as 4.8 and 3.2 ps, respectively. The Be-O stretching frequency of 658 cm(-1), associated with a force constant of 147 N m(-1) could be overestimated but it certainly reflects the exceptional stability of the ion-ligand bond in the first hydration shell.     

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.     

Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching

A novel least-squares fitting approach is presented to obtain classical force fields from trajectory and force databases produced by ab initio (e.g., Car-Parrinello) molecular dynamics (MD) simulations. The method was applied to derive effective nonpolarizable three-site force fields for liquid water at ambient conditions from Car-Parrinello MD simulations in the Becke-Lee-Yang-Parr approximation to the electronic density functional theory. The force-matching procedure includes a fit of short-ranged nonbonded forces, bonded forces, and atomic partial charges. The various parameterizations of the water force field differ by an enforced smooth cut-off applied to the short-ranged interaction term. These were obtained by fitting to the trajectory and force data produced by Car-Parrinello MD simulations of systems of 32 and 64 H(2)O molecules. The new water force fields were developed assuming both flexible or rigid molecular geometry. The simulated structural and self-diffusion properties of liquid water using the fitted force fields are in close agreement with those observed in the underlying Car-Parrinello MD simulations. The resulting empirical models compare to experiment much better than many conventional simple point charge (SPC) models. The fitted potential is also shown to combine well with more sophisticated intramolecular potentials. Importantly, the computational cost of the new models is comparable to that for SPC-like potentials.     

Using MD snapshots in ab initio and DFT calculations: OH vibrations in the first hydration shell around Li+(aq)

The average OH stretching vibrational frequency for the water molecules in the first hydration shell around a Li(+) ion in a dilute aqueous solution was calculated by a hybrid molecular dynamics + quantum-mechanical ("MD + QM") approach. Using geometry configurations from a series of snapshots from an MD simulation, the anharmonic, uncoupled OH stretching frequencies were calculated for 100 first-shell OH oscillators at the B3LYP and HF/6-31G(d,p) levels of theory, explicitly including the first shell and the relevant second shell water molecules into charge-embedded supermolecular QM calculations. Infrared intensity-weighting of the density-of-states (DOS) distributions by means of the squared dipole moment derivatives (which vary by a factor of 20 over the OH stretching frequency band at the B3LYP level), changes the downshift from approximately -205 to -275 cm(-1) at the B3LYP level. Explicit inclusion of relevant third-shell water molecules in the supermolecular cluster leads to a further downshift by approximately -30 cm(-1). Our final estimated average downshift is approximately -305 cm(-1). The experimental value lies somewhere in the range between -290 and -420 cm(-1). Also, the absolute nu(OH) frequency is well reproduced in our calculations. "In-liquid" instantaneous correlation curves between nu(OH) and various typical H-bond strength parameters such as R(O...O), R(H...O), the intramolecular OH bond length, and the IR intensity are presented. Some of these correlations are robust and persist also for the rather distorted instantaneous geometries in the liquid; others are less so.     

Hydration of simple amides. FTIR spectra of HDO and theoretical studies

The hydration of formamide (F), N-methylformamide (NMF), N,N-dimethylformamide (DMF), acetamide (A), N-methylacetamide (NMA), and N,N-dimethylacetamide (DMA) has been studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H2O. The difference spectra procedure has been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. To facilitate the interpretation of obtained spectral results, DFT calculations of aqueous amide clusters were performed. Molecular dynamics (MD) simulation for the cis and trans forms of NMA was also carried out for the SPC model of water. Infrared spectra reveal that only two to three water molecules from the surrounding of the amides are statistically affected, from among ca. 30 molecules present in the first hydration sphere. The structural-energetic characteristic of these solute-affected water molecules differs only slightly from that in the bulk and corresponds to the clathrate-like hydrogen-bonded cage typical for hydrophobic hydration, with the possible exception of F. MD simulations confirm such organization of water molecules in the first hydration sphere of NMA and indicate a practical lack of orientation and energetic effects beyond this sphere. The geometry of hydrogen-bonded water molecules in the first hydration sphere is very similar to that in the bulk phase, but MD simulations have affirmed subtle differences recognized by the spectral method and enabled their understanding. The spectral data and simulations results are highly compatible. In the case of F, NMF, and A, there is a visible spectral effect of water interactions with N-H groups, which have destabilizing influence on the amides hydration shell. There is no spectral sign of such interaction for NMA as the solute. The energetic stability of water H-bonds in the amide hydration sphere and in the bulk fulfills the order: NMA > DMA > A > NMF > bulk > DMF > F. Microscopic parameters of water organization around the amides obtained from the spectra, which have been used in the hydration model based on volumetric data, confirm the more hydrophobic character of the first three amides in this sequence. The increased stability of the hydration sphere of NMA relative to DMA and of NMF relative to DMF seems to have its origin in different geometries, and so the stability, of water cages containing the amides.     

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.     

Structure and dynamics of high-spin Ru in aqueous solution: Ab initio QM/MM molecular dynamics simulation

The structural and dynamical properties of high-spin Ru²⁺ in aqueous solution have been theoretically studied using molecular dynamics (MD) simulations. The conventional MD simulation based on pair potentials gives the overestimated average first shell coordination number of 9, whereas the value of 5.9 was observed when the three-body corrected function was included. A combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation has been performed to take into account the many-body effects on the hydration shell structure of Ru²⁺. The most important region, the first hydration shell, was treated by ab initio quantum mechanics at UHF level using the SBKJC VDZ ECP basis set for Ru²⁺ and the 6-31G^∗ basis sets for water. An exact coordination number of 6 for the first hydration shell was obtained from the QM/MM simulation. The QM/MM simulation predicts the average Ru²⁺–O distance of 2.42 Å for the first hydration shell, whereas the values of 2.34 and 2.46 Å are resulted from the pair potentials without and with the three-body corrected simulations, respectively. Several other structural properties representing position and orientation of the solvate molecules were evaluated for describing the hydration shell structure of the Ru²⁺ ion in dilute aqueous solution. A mean residence time of 7.1 ps was obtained for water ligands residing in the second hydration shell.     

Structure and dynamics of phosphate ion in aqueous solution: an ab initio QMCF MD study

A simulation of phosphate in aqueous solution was carried out employing the new QMCF MD approach which offers the possibility to investigate composite systems with the accuracy of a QMMM method but without the time consuming creation of solute-solvent potential functions. The data of the simulations give a clear picture of the hydration shells of the phosphate anion. The first shell consists of 13 water molecules and each oxygen of the phosphate forms in average three hydrogens bonds to different solvent molecules. Several structural parameters such as radial distribution functions and coordination number distributions allow to fully characterize the embedding of the highly charged phosphate ion in the solvent water. The dynamics of the hydration structure of phosphate are described by mean residence times of the solvent molecules in the first hydration shell and the water exchange rate.