A unified formulation of the constant temperature molecular dynamics methods
Summary (3 min read)
A. Basis sets and electronic structure methods
- A systematic study by stepwise hydration of CdCl2 was carried out at the DFT level, i.e., water molecules were added to previously optimized CdCl2-(H2O)n structures for n = 1– 24.
- Incremental water binding free energies and optimized structures have been computed.
- As previously done for HgCl2 and Hg(OH)2, the oxygen and hydrogen atoms have been described with the 6- 31G** basis sets.
- Full geometry optimizations were carried out at B3PW91 level without any symmetry restrictions.
- All the calculations were carried out with the Gaussian03 program.
B. DFT molecular dynamics
- The thermal stability of the largest cluster studied here, CdCl2-(H2O)24, has been tested using Born-Oppenheimer molecular dynamics (BO-MD) simulations at the B3PW91 level.
- The simulations were carried out with the Geraldyn2.1 code based on the method developed by Raynaud et al.,27 which uses the velocity-Verlet integration scheme.
- The electronic structure DFT calculations (done with Gaussian09) involve 669 molecular orbitals and the 10 ps BO-MD simulation took 26 CPU days on 32 processors@2.8 GHz running the Linux versions of Geraldyn2.1Gaussian09.
A. The isolated CdCl2 molecule and calibration of the Cd,Cl valence basis sets
- For bare CdCl2, at the MP2/RECP(Cd)+cc-pVTZ(Cl) level, the Cd-Cl bond distance is 2.254 Å, to be compared with the experimental value of 2.266 Å.31, 32 We emphasize that the corresponding B3PW91 optimized distance (2.273 Å) is in excellent agreement with these values.the authors.the authors.
- Here the authors note that while the Cl-Hg-Cl angle is 178.6◦ for bare HgCl2, 33 for CdCl2 the Cl-Cd-Cl angle is perfectly linear.
- The authors shall later make this comparison in the context of the water binding energies.
- The authors proceed now to address the water-microsolvated species.
B. Geometries of the CdCl2-(H2O)n optimized complexes
- The interaction of CdCl2 with water was studied via stepwise solvation by adding a number (n) of water molecules to the system, with n = 1–24.
- Special care was taken in order to insure that all the Cl-Cd-Cl–Ow (Ow stands for water oxygens) and Cd-Cl-Ow-Ow dihedral angles were properly sampled with each additional water molecule.
- Note that the Cl-Cd-Cl angle goes back to being almost linear at 176◦.
- Therefore, the authors report here only the lowest energy structure without the assurance that it is the absolute minimum at 0 K in each case.
C. Continous solvent models
- In order to address the possible effects of the polar aqueous medium on the geometry of the optimized structures including explicit water molecules, for selected values of n the authors performed calculations using the Polarizable Continuum Model (PCM) of Tomasi et al.34 and the implicit solvation (SMD) method of Marenich et al.35 as implemented in Gaussian09.
- The authors find that for these cases the PCM scheme leads to similar optimized geometries as those obtained in vacuo, with Cd-Cl and Cd-Ow distances slightly longer (∼0.1 Å) than those obtained in vacuo.
- Note that changes to the Cl-H distances are smaller, except for n = 12.
- In the case with large n (n = 21), the “internal” water molecules directly interacting with CdCl2 already show hydrogen bonding with “external” second solvation shell waters; therefore the different solvation schemes of these external water molecules do not appreciably affect their bonding pattern with the solute and, thus, the optimized structures are very similar with both methods.
D. Water binding energies
- At this stage it is interesting to compare these water binding energies with those previously reported for the HgCl2 case.
- Second, note the presence of three regimes for both solutes; each curve has, grosso modo, two growth regions (where the slope of the second region is smaller than the slope of the first region) separated by a plateau.
- This has been achieved by performing a single-point calculation for the solute with the geometry it attains in each microsolvated system.
- Table III shows the evolution of the total and incremental deformation energies at the B3PW91/6-31G** level as functions of n.
E. Solute-water bonding analysis
- The bonding situation in the CdCl2-(H2O)n hydrated complexes was studied by means of the Natural Bond Orbital scheme.
- Apart from the polarized covalent bond between Cd and the two Cl, it has been possible to identify four donor-acceptor interactions, i.e., bonds, between four water molecules and the cadmium center, all of them in equatorial positions with respect to the axial Cl atoms.
- This is further highlighted by scrutinizing the WIberg Bond Indexes (WBI).
- Indeed, for the latter only two bonds were found between the water molecules and HgCl2 in the pentahydrated complex; even with six solvating water molecules, the water hydrogen bond network expands but no other Hg–Ow interaction was found.
- Thus, the magnitude of the microsolvation energy is clearly associated with the strength of the bonding interaction between the metal center and the closest water molecules, Cd being more covalent than Hg.
F. DFT Born-Oppenheimer molecular dynamics
- To address the role of thermal effects on the largest solvated structure, several of Born–Oppenheimer MD simulations (B3PW91/6-31G**) at 700 K were carried out.
- At this point the authors recall that the Gibbs free energy of the hexacoordinated-Cd structure is only 5 kcal/mol lower than that of the pentacoordinated-Cd species, so that these simulations reveal the greater dynamic stability of the latter structures at higher temperatures.
- Note also that, during the hexacoordination, no water-exchange was observed as it is the same water molecule that gets into the first coordination sphere and that is expulsed after a few hundredths of femtoseconds.
- The shape of the radial distribution function is in line with very little exchange between the two solvation spheres, at least during the 10 ps of the longest simulation the authors performed, in line with the analysis of the Cd-Ow bond distance evolution.
IV. CONCLUSIONS AND PERSPECTIVES
- Aqueous solvation of CdCl2 is crucial in the context of the transmembrane passage of this species into the cellular environment.
- The hybrid DFT method was calibrated against MP2 energetic and structural results for small n.
- The first solvation shell is shown to consist of 12 water molecules (eight of them not coordinated to Cd), in sharp contrast with the much bulkier HgCl2 case, where ∼24 molecules are needed to fully form the first solvation sphere.
- Several BO molecular dynamics simulations at high temperature of the largest cluster, CdCl2–(H2O)24, were done.
- The authors best estimate of the free energy difference between the pentacoordinatedCd and the statically more stable hexacoordinated-Cd is 5.6 kcal/mol, corresponding to the largest cluster CdCl2(H2O)24.
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Q2. What future works have the authors mentioned in the paper "Aqueous microsolvation of cdcl 2 : density functional theory and born-oppenheimer molecular dynamics studies" ?
However, the authors stress that the conclusions ( especially those concerning the penta vs. hexacoordination around Cd ) extracted from these simulations pertain only to gas-phase hydration since the dynamic many-body effects arising from the third and subsequent shells of solvation are missing, therefore, further studies must be done to accurately address the solvation in the liquid medium. 21 In particular when the authors consider the full liquid solvation they wish to answer if, as they found for HgCl2, there exists an CdCl2– ( H2O ) k effective solute, what is the number k and what are its symmetry properties, i. e., the local coordination environment of the Cd atom in the liquid phase. Their final goal will be to study the structural and energetic properties of CdCl2 in the condensed liquid phase through classical MC simulations and applying the quasi-chemical theory of Pratt et al. using refined ab initio derived interaction potentials. The understanding of the solvation of CdCl2 in the condensed aqueous phase requires the use of sophisticated classical Cd ( II ) -water, Cl-water and CdCl2water-water non-additive interaction potentials in conjunction with Monte Carlo or molecular dynamics simulations for the solution.