Structure and dynamics of the CrIII ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation

Structural and dynamical properties of the Cr(III) ion in aqueous solution have been investigated using a combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation. The hydration structure of Cr(III) was determined in terms of radial distribution functions, coordination numbers, and angular distributions. The QM/MM simulation gives coordination numbers of 6 and 15.4 for the first and second hydration shell, respectively. The first hydration shell is kinetically very inert but by no means rigid and variations of the first hydration shell geometry lead to distinct splitting in the vibrational spectra of Cr(H(2)O)(6) (3+). A mean residence time of 22 ps was obtained for water ligands residing in the second hydration shell, which is remarkably shorter than the experimentally estimated value. The hydration energy of -1108 +/- 7 kcal/mol, obtained from the QM/MM simulation, corresponds well to the experimental hydration enthalpy value.     

Ab initio QM/MM dynamics of H3O+ in water

A molecular dynamics (MD) simulation based on a combined ab initio quantum mechanics/molecular mechanics (QM/MM) method has been performed to investigate the solvation structure and dynamics of H3O+ in water. The QM region is a sphere around the central H3O+ ion, and contains about 6-8 water molecules. It is treated at the Hartree-Fock (HF) level, while the rest of the system is described by means of classical pair potentials. The Eigen complex (H9O4+) is found to be the most prevalent species in the aqueous solution, partly due to the selection scheme of the center of the QM region. The QM/MM results show that the Eigen complex frequently converts back and forth into the Zundel (H5O2+) structure. Besides the three nearest-neighbor water molecules directly hydrogen-bonded to H3O+, other neighbor waters, such as a fourth water molecule which interacts preferentially with the oxygen atom of the hydronium ion, are found occasionally near the ion. Analyses of the water exchange processes and the mean residence times of water molecules in the ion's hydration shell indicate that such next-nearest neighbor water molecules participate in the rearrangement of the hydrogen bond network during fluctuative formation of the Zundel ion and, thus, contribute to the Grotthuss transport of the proton.     

The Jahn-Teller effect of the Cr(2+) ion in aqueous solution: Ab initio QM/MM molecular dynamics simulations

The hydration structure of Cr(2+) has been studied using molecular dynamics (MD) simulations including three-body corrections and combined ab initio quantum mechanical/molecular mechanical (QM/MM) MD simulations at the Hartree-Fock level. The structural properties are determined in terms of radial distribution functions, coordination numbers, and several angle distributions. The mean residence time was evaluated for describing ligand exchange processes in the second hydration shell. The Jahn-Teller distorted octahedral [Cr(H(2)O)(6)](2+) complex was pronounced in the QM/MM MD simulation. The first-shell distances of Cr(2+) are in the range of 1.9-2.8 A, which are slightly larger than those observed in the cases of Cu(2+) and Ti(3+). No first-shell water exchange occurred during the simulation time of 35 ps. Several water-exchange processes were observed in the second hydration shell with a mean residence time of 7.3 ps.     

Ab initio molecular dynamics study of glycine intramolecular proton transfer in water

We use ab initio molecular-dynamics simulations to quantify structural and thermodynamic properties of a model proton transfer reaction that converts a neutral glycine molecule, stable in the gas phase, to the zwitterion that predominates in aqueous solution. We compute the potential of mean force associated with the direct intramolecular proton transfer event in glycine. Structural analyses show that the average hydration number (N(w)) of glycine is not constant along the reaction coordinate, but rather progresses from N(w) = 5 in the neutral molecule to N(w) = 8 for the zwitterion. We report the free-energy difference between the neutral and charged glycine molecules, and the free-energy barrier to proton transfer. Finally, we identify the approximations inherent in our method and estimate the corresponding corrections to our reported thermodynamic predictions.     

Ab initio and QM/MM study of electron addition on the disulfide bond in thioredoxin

Thioredoxin controls the intracellular redox potential through a disulfide/dithiol couple. Under conditions of oxidative stress, this protein functions via one-electron exchange, in which formation of the disulfide radical anion occurs. Combined quantum mechanical (QM) and molecular mechanical (MM) calculations using two- and three-level ONIOM schemes were performed on the thioredoxin (Trx) protein of Chlamydomonas reinhardtii in its oxidized-disulfide and one-electron-reduced forms. In both cases, the active site disulfide moiety was described at the MP2(fc)/6-31+G(d) level, and larger regions of varying sizes around the active site were described at the B3LYP/6-31+G(d) level. The remainder of the 112 residues and 33 water molecules of the crystal structure (PDB entry 1EP7) were described by the AMBER force field. Adiabatic electron affinities were calculated for the disulfide bond in all systems. Separate QM or QM/QM calculations were performed on the QM regions to establish the role of the remainder of the protein on the active site properties. The radical anion species becomes more stable as the number of amide groups in the vicinity increases. One-electron reduction potentials were calculated for the small molecule models, and approximated for the protein for which the values are similar to the experimental one (approximately 0 V). This high reduction potential is due to interaction with the charged end of Lys40, as indicated by mutation in silico to norleucine. The inclusion of the protonated Asp30 side chain and a water molecule in the QM region leads to an increase in the electron affinity. Proton transfer from the Asp30 side chain to the Cys39 sulfur in the radical anion species is strongly disfavored. The radical anion is more stable than the protonated form, which is consistent with experimental results.     

Ab initio QM/MM simulation of Ag+ in 18.6% aqueous ammonia solution: structure and dynamics investigations

Structure and dynamics investigations of Ag(+) in 18.6% aqueous ammonia solution have been carried out by means of the ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulation method. The most important region, the first solvation shell, was treated by ab initio quantum mechanics at the Restricted Hartree-Fock (RHF) level using double-zeta plus polarization basis sets for ammonia and plus ECP for Ag(+). For the remaining region in the system, newly constructed three-body corrected potential functions were used. The average composition of the first solvation shell was found to be [Ag(NH(3))(2)(H(2)O)(2.8)](+). No ammonia exchange process was observed for the first solvation shell, whereas ligand exchange processes occurred with a very short mean residence time of 1.1 ps for the water ligands. No distinct second solvation shell was observed in this simulation.     

Ab initio molecular dynamics of excited-state intramolecular proton transfer around a three-state conical intersection in malonaldehyde

Excited-state potential energy surface (PES) characterization is carried out at the CASSCF and MRSDCI levels, followed by ab initio dynamics simulation of excited-state intramolecular proton transfer (ESIPT) on the S2(pipi*) state in malonaldehyde. The proton-transfer transition state lies close to an S2/S1 conical intersection, leading to substantial coupling of proton transfer with electronic relaxation. Proton exchange proceeds freely on S2, but its duration is limited by competition with twisting out of the molecular plane. This rotamerization pathway leads to an intersection of the three lowest singlet states, providing the first detailed report of ab initio dynamics around a three-state intersection (3SI). There is a significant energy barrier to ESIPT on S1, and further pyramidalization of the twisted structure leads to the minimal energy S1/S0 intersection and energetic terminal point of excited-state dynamics. Kinetics and additional mechanistic details of these pathways are discussed. Significant depletion of the spectroscopic state and recovery of the ground state is seen within the first 250 fs after photoexcitation.     

The Jahn-Teller effect of the TiIII ion in aqueous solution: extended ab initio QM/MM molecular dynamics simulations.

Combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, including only the first and the first and second hydration shells in the QM region, were performed for TiIII in aqueous solution. The hydration structure of TiIII is discussed in terms of radial distribution functions, coordination-number distributions and several angle distributions. Dynamical properties, such as librational and vibrational motions and TiIII-O vibrations, were evaluated. A fast dynamical Jahn-Teller effect of TiIII(aq) was observed in the QM/MM simulations, in particular when the second hydration shell was included into the QM region. The results justify the computational effort required for the inclusion of the second hydration shell into the QM region and show the importance of this effort for obtaining accurate hydration-shell geometries, dynamical properties, and details of the Jahn-Teller effect.     

Gold(I) in liquid ammonia: ab initio QM/MM molecular dynamics simulation

Structure and dynamics investigations of Au(I) ion in liquid ammonia have been performed by means of a molecular dynamics simulation based on ab initio quantum mechanical/molecular mechanical forces, where the first solvation shell was treated by quantum mechanics at Hartree-Fock level. The outer region of the system was described using a newly constructed classical three-body corrected potential. A rigid structure of the first solvation shell was observed with an average Au-N distance of 2.15 A and a coordination number of 2.0.     

An ab initio study of electronic spectra and excited-state properties of 7-azaindole in vapour phase and aqueous solution

The geometries of 7-azaindole (7AI), its tautomer (7AT), and 7AI–H₂O and 7AT–H₂O complexes were optimised in the ground state and some low-lying singlet excited states using the 3-21G basis set. Differences of total energies of the optimised ground and excited states and the vertical excitation energies of these systems were used to explain the observed electronic spectra. Effect of solvation of these systems in bulk water was studied using the polarized continuum model (PCM). The mode of binding of a water molecule in the S₂(n–π^*) excited state of 7AI was found to be quite different from those in its ground and π–π^* excited states. It is shown that crossing of the lowest two singlet excited-state potential surfaces S₁(π–π^*) and S₂(n–π^*) of 7AI occurs in the vapour phase under geometry relaxation while on interaction with water, the S₂(n–π^*) excited state is raised up appreciably going even above the S₃(π–π^*) excited state. Ground- and excited-state molecular electrostatic potential mapping was carried out, which led to valuable information regarding the nature of excited states of the above-mentioned systems.     

Multiscale QM/MM molecular dynamics study on the first steps of guanine damage by free hydroxyl radicals in solution

Understanding the damage of DNA bases from hydrogen abstraction by free OH radicals is of particular importance to understanding the indirect effect of ionizing radiation. Previous studies address the problem with truncated DNA bases as ab initio quantum simulations required to study such electronic-spin-dependent processes are computationally expensive. Here, for the first time, we employ a multiscale and hybrid quantum mechanical-molecular mechanical simulation to study the interaction of OH radicals with a guanine-deoxyribose-phosphate DNA molecular unit in the presence of water, where all of the water molecules and the deoxyribose-phosphate fragment are treated with the simplistic classical molecular mechanical scheme. Our result illustrates that the presence of water strongly alters the hydrogen-abstraction reaction as the hydrogen bonding of OH radicals with water restricts the relative orientation of the OH radicals with respect to the DNA base (here, guanine). This results in an angular anisotropy in the chemical pathway and a lower efficiency in the hydrogen-abstraction mechanisms than previously anticipated for identical systems in vacuum. The method can easily be extended to single- and double-stranded DNA without any appreciable computational cost as these molecular units can be treated in the classical subsystem, as has been demonstrated here.     

Ab initio molecular dynamics study of the keto-enol tautomerism of acetone in solution.

We have studied the keto-enol interconversion of acetone to understand the mechanism of tautomerism relevant to numerous organic and biochemical processes. Applying the ab initio metadynamics method, we simulated the keto-enol isomerism both in the gas phase and in the presence of water. For the gas-phase intramolecular mechanism we show that no other hydrogen-transfer reactions can compete with the simple keto-enol tautomerism. We obtain an intermolecular mechanism and remarkable participation of water when acetone is solvated by neutral water. The simulations reveal that C deprotonation is the kinetic bottleneck of the keto-enol transformation, in agreement with experimental observations. The most interesting finding is the formation of short H-bonded chains of water molecules that provide the route for proton transfer from the carbon to the oxygen atom of acetone. The mechanistic picture that emerged from the present study involves proton migration and emphasizes the importance of active solvent participation in tautomeric interconversion.     

Theoretical modeling of open-shell molecules in solution: a QM/MM molecular dynamics approach

In this work, the GLOB model, an effective and reliable computational approach well suited for ab initio and QM/MM molecular dynamics simulations of complex molecular systems in solution, has been applied to study two representative open-shell systems, the cobalt(II) ion and the glycine radical in aqueous solution, with special reference to their structural and magnetic properties. The main structural features of the solvent cage around the cobalt ion and the hydrogen bonding patterns around the neutral and zwitterionic forms of the glycine radical have been investigated in some detail. The general good agreement with experiments supports the use of the present model to investigate more challenging and biological/technological relevant open-shell systems.     

Ab initio excited-state dynamics of the photoactive yellow protein chromophore

The photoisomerization mechanism of the neutral form of the photoactive yellow protein (PYP) chromophore is investigated using ab initio quantum chemistry and first-principles nonadiabatic molecular dynamics (ab initio multiple spawning or AIMS). We identify the nature of the two lowest-lying excited states, characterize the short-time behavior of molecules excited directly to S2, and explain the origin of the experimentally observed wavelength-dependent photoisomerization quantum yield.     

Ab initio molecular dynamics study of liquid methanol

We present a density-functional theory based molecular-dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare well with recent neutron diffraction data, except for an underestimate of the oxygen–oxygen correlation. We observe that, in line with infrared spectroscopic data, the hydroxyl stretching mode is significantly red-shifted in the liquid. A substantial enhancement of the dipole moment is accompanied by significant fluctuations due to thermal motion. Our results provide valuable data for improvement of empirical potentials.     

Structure and dynamics of Au+ ion in aqueous solution: ab initio QM/MM MD simulations

Structure and dynamics of hydrated Au(+) have been investigated by means of molecular dynamics simulations based on ab initio quantum mechanical molecular mechanical forces at Hartree-Fock level for the treatment of the first hydration shell. The outer region of the system was described using a newly constructed classical three-body corrected potential. The structure was evaluated in terms of radial and angular distribution functions and coordination number distributions. Water exchange processes between coordination shells and bulk indicate a very labile structure of the first hydration shell whose average coordination number of 4.7 is a mixture of 3-, 4-, 5-, 6-, and 7-coordinated species. Fast water exchange reactions between first and second hydration shell occur, and the second hydration shell is exceptionally large. Therefore, the mean residence time of water molecules in the first hydration shell (5.6 ps/7.5 ps for t*= 0.5 ps/2.0 ps) is shorter than that in the second shell (9.4 ps/21.2 ps for t*= 0.5 ps/2.0 ps), leading to a quite specific picture of a "structure-breaking" effect.