Dynamics in the hydration shell of Hg2+ ion: classical and ab initio QM/MM molecular dynamics simulations

Kritayakornupong, Chinapong; Plankensteiner, Kristof; Rode, Bernd M.

doi:10.1016/s0009-2614(03)00301-4

Cited by 40 publications

(45 citation statements)

References 31 publications

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“…All frequencies of the Q 1 , Q 2 , and Q 3 modes of water molecules in the bulk are almost the same as the frequencies obtained from other simulations 36,[41][42][43] using the BJH-CF2 model of water, and are blue-shifted from the experimental frequencies for the pure liquid. 45 The red-shifts of the symmetric Q 1 and asymmetric Q 3 stretching modes of the water molecules in the first hydration shell for this ion are very similar to those observed for Co(III) 43 and Ti(III) 46 ions, and in contrast to the blue-shifted frequencies of divalent transition metal hydrates.…”

Section: Vibrational Ligand Motionssupporting

confidence: 79%

“…However, the motions leading to a change in dipole orientation are restricted and hence, the frequencies of R x and R y , are strongly blue-shifted, R x more than R y , as also found for Ni(II). 36 Similar blue-shifts of R x and R y have further been observed for Hg(II), 41 Fe(II)/Fe(III), 42 and Co(III). 43 The reorientational times of first ( 1 ) and second ( 2 ) order in the dipole moment direction of a water molecule are listed in Table 3.…”

Section: Structure Of the Cr(iii) Ion In Aqueous Solutionsupporting

confidence: 78%

“…45 The red-shifts of the symmetric Q 1 and asymmetric Q 3 stretching modes of the water molecules in the first hydration shell for this ion are very similar to those observed for Co(III) 43 and Ti(III) 46 ions, and in contrast to the blue-shifted frequencies of divalent transition metal hydrates. 36,41,42 Apparently, trivalent ions withdraw electron density from neighboring water ligands and thus weaken the O-H bonds, resulting in lower stretching vibration frequencies. Divalent ions seem to exert mainly polarization effects on the O-H bonds thereby strengthening these bonds.…”

Section: Vibrational Ligand Motionsmentioning

confidence: 99%

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Structure and dynamics of the Cr(III) ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation

2004

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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.

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Section: Vibrational Ligand Motionssupporting

confidence: 79%

Section: Structure Of the Cr(iii) Ion In Aqueous Solutionsupporting

confidence: 78%

Section: Vibrational Ligand Motionsmentioning

confidence: 99%

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Structure and dynamics of the Cr(III) ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation

2004

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“…27 and attempted exponential fit for Hg(II) in aqueous solution according to ab initio QM/MM-MD simulations. 12 Accurate experimental measurements and methodically further improved ab initio simulations will prove whether the absolute values obtained by us need to be corrected, but at least we can be quite confident that the relative scale of ligand exchange rates obtained from our QM/MM MD trajectories give a quite realistic picture of the stability/reactivity of the investigated ions. This relative scale lists the second-shell MRTs of the ions in the following order from lowest to highest values:…”

Section: Mrt Valuesmentioning

confidence: 79%

Characterization of dynamics and reactivities of solvated ions byab initiosimulations

et al. 2003

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Based on a systematic investigation of trajectories of ab initio quantum mechanical/molecular mechanical simulations of numerous cations in water a standardized procedure for the evaluation of mean ligand residence times is proposed. For the characterization of reactivity and structure-breaking/structure-forming properties of the ions a measure is derived from the mean residence times calculated with different time limits. It is shown that ab initio simulations can provide much insight into ultrafast dynamics that are presently not easily accessible by experiment.

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“…187 This method has also been extended for ab initio QM/MM and employed for simulations of cations in solution. 522 …”

Section: Electrostatics In Multiscale Modelingmentioning

confidence: 99%

Classical Electrostatics for Biomolecular Simulations

et al. 2013

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CONTENTS 1. Introduction 779 1.1. Electrostatic Problem 780 2. Methods for Computing the Long-Range Electrostatic Interactions 781 2.1. Ewald Summations 782 2.2. Particle−Mesh Methods That Use Fourier Transforms 784 2.3. Particle−Mesh Methods in Real Space 784 2.4. Fast Multipole Methods 786 2.5. Local Methods 786 2.6. Truncation Methods 787 2.6.1. Reaction Field Methods 789 2.7. Charge-Group Methods 789 2.8. Treatments and Artifacts of Boundary Conditions 790 3. Accurate Representation of the Electronic Charge 791 3.1. Charge Assignment Schemes 791 3.2. Point Multipoles 792 3.3. Continuous Representations of Molecular Charge Density 793 3.4. Polarization 795 3.5. Charge Transfer 797 3.6. Polarizable Force fields 798 4. Electrostatics in Multiscale Modeling 800 4.1. Long-Range Electrostatics in QM/MM 800 4.2. Continuous Functions in QM/MM 801 4.3. Electrostatics in Coarse-Grained Models 802 5. Other Developments 804 6. Summary and Perspective 805 Author Information 806 Corresponding Author 806 Notes 806 Biographies 806 Acknowledgments 806 References 806

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Dynamics in the hydration shell of Hg2+ ion: classical and ab initio QM/MM molecular dynamics simulations

Cited by 40 publications

References 31 publications

Structure and dynamics of the Cr(III) ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation

Structure and dynamics of the Cr(III) ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation

Characterization of dynamics and reactivities of solvated ions byab initiosimulations

Classical Electrostatics for Biomolecular Simulations

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