Pengfei Li1, Lin Frank Song, Kenneth M Merz. 1. Department of Chemistry, Department of Biochemistry and Molecular Biology, Michigan State University , 578 S. Shaw Lane, East Lansing, Michigan 48824-1322, United States.
Abstract
Highly charged metal ions act as catalytic centers and structural elements in a broad range of chemical complexes. The nonbonded model for metal ions is extensively used in molecular simulations due to its simple form, computational speed, and transferability. We have proposed and parametrized a 12-6-4 LJ (Lennard-Jones)-type nonbonded model for divalent metal ions in previous work, which showed a marked improvement over the 12-6 LJ nonbonded model. In the present study, by treating the experimental hydration free energies and ion-oxygen distances of the first solvation shell as targets for our parametrization, we evaluated 12-6 LJ parameters for 18 M(III) and 6 M(IV) metal ions for three widely used water models (TIP3P, SPC/E, and TIP4PEW). As expected, the interaction energy underestimation of the 12-6 LJ nonbonded model increases dramatically for the highly charged metal ions. We then parametrized the 12-6-4 LJ-type nonbonded model for these metal ions with the three water models. The final parameters reproduced the target values with good accuracy, which is consistent with our previous experience using this potential. Finally, tests were performed on a protein system, and the obtained results validate the transferability of these nonbonded model parameters.
Highly charged metal ions act as catalytic centers and structural elements in a broad range of chemical complexes. The nonbonded model for metal ions is extensively used in molecular simulations due to its simple form, computational speed, and transferability. We have proposed and parametrized a 12-6-4 LJ (Lennard-Jones)-type nonbonded model for divalent metal ions in previous work, which showed a marked improvement over the 12-6 LJ nonbonded model. In the present study, by treating the experimental hydration free energies and ion-oxygen distances of the first solvation shell as targets for our parametrization, we evaluated 12-6 LJ parameters for 18 M(III) and 6 M(IV) metal ions for three widely used water models (TIP3P, SPC/E, and TIP4PEW). As expected, the interaction energy underestimation of the 12-6 LJ nonbonded model increases dramatically for the highly charged metal ions. We then parametrized the 12-6-4 LJ-type nonbonded model for these metal ions with the three water models. The final parameters reproduced the target values with good accuracy, which is consistent with our previous experience using this potential. Finally, tests were performed on a protein system, and the obtained results validate the transferability of these nonbonded model parameters.
Highly
charged (trivalent and tetravalent) metal ions are of great
interest in both supramolecular,[1] biomolecular,[2] and rare-earth chemistry.[3] Some of these serve as the coordination center that performs structural,
catalytic, or electron-transfer functions, while others are well-known
biotoxins.[4−6] For example, iron–sulfur clusters have biochemical
functions involving the respiration and photosynthesis processes.[7] Iron in hemoglobin is involved in the transport
and transfers oxygen within organisms.[8] Lanthanide series elements have attracted significant attention
due to their specific electromagnetic and optical characteristics.[9] Their complexes serve as luminescent probes because
of their large Stokes shifts and emission lifetimes.[2] The actinide series elements, such as Th, U, and Pu, are
well known for their radioactivity.[10] All
of these can form highly charged metal ions, which pose a major challenge
to computational modeling. Indeed, effective and accurate modeling
of these ions will give insight into separation and recycling process
aimed at reducing their harmfulness to the environment.There
are several theoretical methods to model metal ions: quantum
mechanics (QM),[11,12] molecular mechanics (MM),[13−28] and the hybrid QM/MM method.[29,30] Classical force fields,
which use an analytical function to represent the relationship between
the energy and configuration of a system, have a significant speed
advantage over the quantum-based methods. It is the state-of-the-art
tool to study systems at the molecular level when combined with molecular
dynamics[31,32] or Monte Carlo methods.[33,34] For metal ions, there are several widely used models including the
bonded model,[19−24] nonbonded model,[13−18] and cationic dummy model.[25−27] The bonded model represents the
interaction between the ion and its surrounding residues via the bond,
angle, torsion, coulombic, and van der Waals (VDW) terms. Because
of the harmonic approximation used in the bonded model, it does not
simulate the processes involving chemical bond formation and dissociation.[19] The nonbonded model usually places an integer
charge on the metal ion and only uses the coulombic and VDW terms
to represent the intermolecular interactions between the metal ion
and surrounding particles. This simplification can result in a notable
underestimation for modeling systems with strong covalent bonds.[14] The dummy cationic model places the charge between
the metal ions and the ligating atoms to mimic the covalent bond.[25] Besides the models previously discussed, there
are also some polarizable force fields that have been developed for
metal ions in recent years.[35−41]Even though more accurate models exist, the 12-6 Lennard-Jones
nonbonded model is widely used due to its simple form, computational
efficiency, and excellent transferability characteristics.[13,15,16,42] However, in previous research, we found that the 12-6 Lennard-Jones
(LJ) nonbonded model could not reproduce several experimental properties
across a series of divalent metal ions due to the neglect of the ion-induced
dipole interaction.[18] For the divalent
metal ions, on average, there is a 50 kcal/mol underestimation for
the hydration free energy (HFE) if we want to reproduce the experimental
ion–oxygen distance (IOD) values, while there is ∼0.27
Å reduction for the IOD values if we reproduce the experimental
HFE values. In light of this, we proposed a 12-6-4 LJ-type nonbonded
model to account for the charge-induced dipole interaction.[18] After picking suitable parameters, it was demonstrated
that it was possible to reproduce the experimental HFE, IOD, and coordination
number (CN) values simultaneously for a series of divalent metal ions.
Furthermore, it was shown the new nonbonded model was readily transferable
to mixed systems such as salt solutions and nucleic acid systems.In the present work, we have estimated the 12-6 LJ parameters for
24 highly charged metal ions (18 M(III) ions and 6 M(IV) ions) for
three widely used water models (TIP3P,[43] SPC/E,[44] and TIP4PEW[45]), respectively. This illustrated that the 12-6
LJ nonbonded model has a much larger underestimation of the ion–water
interactions for the highly charged ions than for the mono and dications.
We next parametrized the 12-6-4 LJ-type nonbonded model for the 24
highly charged metal ions for the same three water models. In general,
these parameters simultaneously reproduce both the experimental HFE,
IOD, and CN values with good accuracy. Moreover, they are consistent
with previous research.[30,46−48] This work opens up new opportunities to simulate M(III) and M(IV)
ions in aqueous solution using classical models. Furthermore, we carried
out test simulations on a Fe(III)-containing protein system. Stable
trajectories were obtained with the metal binding site being well-conserved,
further supporting the excellent transferability of these parameters.
Method
Potential
Form
In present work, we employed the nonbonded
model in the AMBER force field[49]In eq 1, the U(r) is the nonbonded interaction
potential between
atoms i and j at distance r. It consists of electrostatic
and VDW terms. Herein e represents the charge of
the proton, while Q and Q are the partial charge of
atoms i and j. The partial charge
of metal ions is always treated as an integer number in the nonbonded
model. The VDW interaction part uses a 12-6 Lennard-Jones (LJ) potential,
in which there are two parameters (ε and Rmin,)
that need to be determined. Using the geometric combining rule, the
well depth of the LJ potential isFor the Rmin parameters,
there are two widely used combining rulesandEquation 3 is employed in the AMBER[50] and CHARMM[51] force
fields, while eq 4 is used in the OPLS force
field.[52] In the present work, we employed
the Lorentz–Berthelot combining rules, which is the union of
eqs 2 (Lorentz combining rule) and 3 (Berthelot combining rule).For the 12-6-4 LJ-type
potential, we employed the following expressionAn r–4 term was added to describe
the ion-induced dipole interaction, which cannot be overlooked for
highly charged systems. The parametrization work concentrated on the
determination of the Rmin,, ε for the different metal
ions, and the C4 term between the metal ion and oxygen atoms of the different
water models. In the present work, we have determined the parameters
for three widely used water models (TIP3P,[43] SPC/E,[44] and TIP4PEW[45]) independently. Previous work demonstrated that
it is necessary to design different parameters for these water models
due to their different geometries, charge distributions, and VDW parameters.[14,18,53]
HFE Calculation
The thermodynamic integration (TI)
method[54−57] was used to simulate the HFE values. TI calculates the free-energy
change between two different states of a system. An initial-state/final-state
mixing potential was used during the simulation, in which V0 and V1 represent
the potential of the initial and final state, respectively, while
λ governs the mixing between the two states. k determines whether the mixing is linear or of higher order (k = 1 is linear).The ion solvation process
is modeled
as transfer of an isolated metal ion from the gas to liquid phase.
In the present work, we employed the thermodynamic cycle depicted
in Figure 1. To avoid the “end-point
catastrophe”, we employed the linear scaling soft-core TI method[58] to obtain the ΔGVDW term.
Figure 1
Thermodynamic cycle describing the determination
of the hydration
free energy of ions.
In eq 7, r is the
distance between the dummy atom and the surrounding
particles, while σ is the distance at which the two particles’
VDW interaction is equal to zero. Here the ε is the well depth
and α is a constant set to 0.5. The “end-point catastrophe”
problem is largely avoided because there is limited energy penalty
induced between the dummy atom and proximal particles when the VDW
potential of the dummy atom is turned on.As seen from eq 8, the free-energy of each
process is obtained via the integration of the derivative of the potential
with respect to λ. Herein we employed Gaussian quadrature[59] (eq 9) to evaluate the
integral in an efficient way.Thermodynamic cycle describing the determination
of the hydration
free energy of ions.As illustrated in Figure 1, we obtained
the HFE values based on the free-energy changes associated with four
processes: ΔGVDW, ΔGEle+Pol, −ΔGEle+Pol, and −ΔGVDW. Herein the HFE value is computed using HFE = 1/2 × (ΔGVDW + ΔGEle+Pol – (−ΔGEle+Pol –
ΔGVDW)). The ΔGEle+Pol and −ΔGEle+Pol are ΔGEle and −ΔGEle respectively, when the 12-6 nonbonded model
is employed. At first, a dummy atom was placed in the center of a
cubic water box (with size ∼32 Å × 32 Å ×
32 Å) with the closest water molecule ∼1.5 Å away
from it. There are in total 722 water molecules in the TIP3P or SPC/E
water boxes, while there are 732 water molecules in the TIP4PEW water box. Afterward 1000 steps of steepest descent minimization
were performed, followed by 1000 steps conjugate gradient minimization.
Then, a 500 ps heating procedure was performed to heat the system
from 0 to 300 K in the NVT ensemble. Next, we equilibrated the system
for 500 ps at 300 K and 1 atm using the NPT ensemble. The final snapshot
from the equilibration simulation was used as the initial structure
for the calculation of ΔGVDW. To
balance accuracy and speed, we used the four-window linear soft-core
scaling process to obtain the ΔGVDW value with λ values of 0.1127, 0.5, 0.88729, and 0.98, respectively.
The simulation of last window was used to further equilibrate the
system but was not used in the free-energy evaluation. The final snapshot
was used to initiate the determination of ΔGEle+Pol. For the ΔGEle+Pol calculation process, a nine-window linear scaling scheme was utilized
with λ values of 0, 0.2544, 0.12923, 0.29707, 0.5, 0.70292,
0.87076, 0.97455, and 1, respectively. Afterward, the −ΔGEle+Pol calculation process was carried out
in a similar manner. In these simulations, the first and last windows
(λ equal to 0 and 1) are not used in the final free-energy calculation
but to further equilibrate the system. Finally, the −ΔGVDW simulation procedure was carried out using
a three-window linear soft-core scaling process in which λ was
set at 0.1127, 0.5, and 0.88729, respectively. For the determination
of ΔGVDW and −ΔGVDW, each window was simulated for 300 ps, with
the last 200 ps used for data collection. The ΔGEle+Pol and −ΔGEle+Pol simulations covered 200 ps, with the last 150 ps used for data collection
in each window. All TI simulations were performed in the NPT ensemble.We have employed two different methods to evaluate the uncertainty
of the simulated HFE values in the present work. These results are
gathered in the Supporting Information (SI).
The first method (Set 1) divided each sampling segment (ΔGVDW, ΔGEle+Pol, −ΔGEle+Pol, and −ΔGVDW) into two even portions and estimated the
uncertainties for the VDW and electrostatic plus polarization free-energy
determinations. For example, we have 200 ps of sampling for each window
for the determination of ΔGVDW and
−ΔGVDW. We used the first
100 ps of sampling to calculate the ΔGVDW-part 1 and −ΔGVDW-part 1 values, while we used the later
100 ps of sampling to obtain the ΔGVDW-part 2 and −ΔGVDW-part 2. Then, we assessed the uncertainty of the VDW free-energy determination
by calculating the standard deviation based on these four values.
The uncertainty of the electrostatic plus polarization free-energy
determination was obtained in a similar manner with each fragment
using 75 ps of sampling. Subsequently, we obtain the total uncertainty
in the HFE value by adding the uncertainties of the VDW and electrostatic
plus polarization free-energy determinations.The second method
(Set 2) uses eq 10, in
which the τ is the autocorrelation
time of observable A while (⟨A2⟩)1/2 is
the standard deviation of A. T is
the sampling time of the simulation and δA is
the final uncertainty of the observable A. The final
HFE values given in the spreadsheets given in the SI are depicted as ⟨A⟩ ±
σ. Again, the uncertainty of the VDW and electrostatic plus
polarization free-energy determinations were evaluated separately,
and the final uncertainty was treated as their sum. Herein we used
a τ value equal to 500 fs for the
VDW free-energy determinations, while we used 250 fs for the electrostatic
plus polarization scaling part. We obtained these values based on
test simulations, and they are consistent with previous work.[60]The Set 1 approach yields uncertainties in the range of 0.1–7.5
kcal/mol with an average of ∼1.2 kcal/mol, while Set 2 gives
uncertainties in the range of 1.1 to 2.0 kcal/mol with an average
of ∼1.4 kcal/mol. On the basis of these analyses, we estimate
that the HFE uncertainty is in the ±2.0 kcal/mol range, which
is quite small given the magnitude of HFEs we are computing.
IOD and
CN Calculation
A metal ion (with an integer
+3 or +4 partial charge) was solvated in the center of a cubic water
box (with the same size as described in the HFE simulation part).
Then, 1000 steps of steepest descent and 1000 steps of conjugated
gradient minimization were carried out to relax the initial structure.
Afterward, a 500 ps “heating” simulation was performed
in the NVT ensemble that took the system from 0 to 300 K. Next, 500
ps of equilibration, followed by 2 ns of sampling were performed at
300 K and 1 atm. Snapshots were stored every 0.5 ps (every 500 steps
for 4000 snapshots in total) for the subsequent IOD and CN analysis.
The radial distribution function (RDF) of the ion and wateroxygen
atom was then calculated based on the average volume of the entire
trajectory in the range of 0−5.0 Å with a grid resolution
of 0.01 Å. The IOD value was evaluated based on two quadratic
fits of the RDF. The first quadratic fit was performed using the points
within ±0.1 Å of the first peak of RDF. In this way, the
apex value was obtained with an accuracy of 0.01 Å. The second
quadratic fitting was done based on the points within ±0.1 Å
of the apex obtained from the first fitting. In total, 21 points were
used for each fit. The maximum given by the second fitting was treated
as the final IOD value to two decimal places. The CN value was obtained
by integrating from the origin to the first minimum of the RDF.The AMBER 12 suite of programs[49] was used
to perform the simulations, while the Amber Tools suite of programs[49] was utilized to carry out the data analysis.
The particle mesh Ewald (PME)[61−63] method and periodic boundary
condition (PBC) were employed throughout. The time-step was 1 fs,
while the cutoff was set to 10 Å. For the temperature control,
the Langevin algorithm was utilized with a collision frequency equal
to 5.0 ps–1. The isotropic pressure algorithm was
used to control the pressure. The pressure relaxation time was set
to 10 and 1 ps in the TI and standard MD simulations, respectively.
The SHAKE[64,65] algorithm was employed to restrain the bond
lengths involving hydrogen atoms. Herein the “three-point”
algorithm was used for the water molecules.[65]
Results and Discussion
Experimental Values
The HFE values
for all M(III) and
M(IV) ions investigated were taken from Marcus.[66] They were determined based on using ΔhydG0[H+] = −1056 kJ/mol.[66] It is one of the most complete databases regarding the
thermodynamic properties of ions. The IOD and CN values for M(III)
ions were taken from Marcus’ review,[67] while the IOD and CN values for the M(IV) ions were taken from a
number of sources.[68−71] The experimental effective ionic radii were obtained from Shannon.[72] On the basis of the IOD values and effective
ionic radii, we estimated the effective radii of the coordinated water
and display the data in Table 1. Some highly
charged ions that readily hydrolyze water such as As3+,
Sn4+, and Pb4+ ions[30] were not considered in the present work.
Table 1
Experimental
HFE and IOD Values of
M(III) and M(IV) Metal Ions
metal ion
electron
configuration
HFE (kcal/mol)a
IOD (Å)b
CNb
effective
ion radii (Å)
first shell
water radii (Å)
Al3+
[Ne]
–1081.5
1.88
6
0.54
1.34
Fe3+
[Ar]3d5
–1019.4
2.03
6
0.65
1.38
Cr3+
[Ar]3d3
–958.4
1.96
6
0.62
1.34
In3+
[Kr]4d10
–951.2
2.15
6
0.80
1.35
Tl3+
[Xe]4f145d10
–948.9
2.23
4–6
0.89
1.34
Y3+
[Kr]
–824.6
2.36
8
0.90
1.46
La3+
[Xe]
–751.7
2.52
8.0–9.1
1.03
1.49
Ce3+
[Xe]4f1
–764.8
2.55
7.5
1.01
1.54
Pr3+
[Xe]4f2
–775.6
2.54
9.2
0.99
1.55
Nd3+
[Xe]4f3
–783.9
2.47
8.0–8.9
0.98
1.49
Sm3+
[Xe]4f5
–794.7
2.44
8.0–9.9
0.96
1.48
Eu3+
[Xe]4f6
–803.1
2.45
8.3
0.95
1.50
Gd3+
[Xe]4f7
–806.6
2.39
8.0–9.9
0.94
1.45
Tb3+
[Xe]4f8
–812.6
2.40
8.0–8.2
0.92
1.48
Dy3+
[Xe]4f9
–818.6
2.37
7.4–7.9
0.91
1.46
Er3+
[Xe]4f11
–835.3
2.36
6.3–8.2
0.89
1.47
Tm3+
[Xe]4f12
–840.1
2.36
8.1
0.88
1.48
Lu3+
[Xe]4f14
–840.1
2.34
8
0.86
1.48
Hf4+
[Xe]4f14
–1664.7
2.16c
8c
0.85
1.31
Zr4+
[Kr]
–1622.8
2.19c
8c
0.86
1.33
Ce4+
[Xe]
–1462.7
2.42d
9d
0.87
1.55
U4+
[Rn]6d15f1
–1567.9
2.42e
9–11e
0.89
1.53
Pu4+
[Rn]5f4
–1520.1
2.39f
8f
0.86
1.53
Th4+
[Rn]
–1389.8
2.45e
9–11e
0.94
1.51
Referenced from Marcus.[66]
Referenced or calculated from
Marcus.[67]
From Hagfeldt et al.[71]
From Sham.[68]
From Moll et al.[70]
From
Ankudinov et al.[69]
Referenced from Marcus.[66]Referenced or calculated from
Marcus.[67]From Hagfeldt et al.[71]From Sham.[68]From Moll et al.[70]From
Ankudinov et al.[69]
Scanning Parameter Space
To balance time and accuracy,
we performed parameter scanning using two parallel curves. One is
for Rmin/2 from 0.9 to 2.3 Å with
0.1 Å intervals without the C4 term
(namely using the 12-6 LJ nonbonded model), while the other is for
the same Rmin/2 value sets with a constant C4 term equal to 500 kcal/mol·Å4. The ε values are obtained for each Rmin/2 value based on the noble gas curve (NGC), which
was previously developed.[14] The HFE, IOD,
and CN values for each parameter point are collected in Tables SI.1
and SI.2 in the Supporting Information (SI).
These data points might be useful to those who want to parametrize
the 12-6 LJ or 12-6-4 LJ-type nonbonded model with different target
values from the present work.
12-6 LJ Parameters Estimation
On the basis of the quadratic
fitting of the data points from the parameter scans without the C4 term (see the SI), we estimated the HFE and IOD parameter sets. The two parameter
sets are shown in Tables 2 and 3, while the estimated absolute and percent errors are shown
in Table SI.3. Similar to our parametrization
of divalent metal ions using the 12-6 LJ nonbonded model,[14] the Rmin/2 parameters
in the HFE parameter set are in excellent agreement with the VDW radii
calculated using the quantum-mechanical scaling principle (QMSP) method.[73] For the Al3+, Y3+, and
La3+ ions, the estimated Rmin/2 values in the estimated HFE parameter set for the TIP3P water
model are 0.981, 1.454, and 1.628 Å respectively. The calculated
VDW radii are 1.046, 1.481, and 1.642 Å, respectively, based
on the QMSP method. There is only a 6.2, 1.8, and 0.9% difference
between these two sets of values. This further validates the physical
meaningful of our parametrization work. Moreover, the estimated Rmin/2 values used in the 12-6 LJ parameter sets
could be used as the VDW radii for RESP charge-fitting procedures.
For example, in the work of Kuznetsov et al.,[74] they used 1.4 Å as the VDW radius for the RESP charge fitting
for both the Fe2+ and Fe3+ ions, while for the
IOD parameter set the Fe2+ radius was determined to be
1.409 Å in our previous research.[18] Herein, the IOD parameter sets for the Fe3+ ion estimated
the radius as 1.386, 1.386, and 1.375 for the TIP3P, SPC/E, and TIP4PEW water models, respectively.
Table 2
Estimated HFE Parameter
Set for M(III)
and M(IV) Metal Ions Using the 12-6 LJ Nonbonded Potential
TIP3P
SPC/E
TIP4PEW
Rmin/2 (Å)
ε (kcal/mol)
Rmin/2 (Å)
ε (kcal/mol)
Rmin/2 (Å)
ε (kcal/mol)
Al3+
0.981
0.00000832
0.991
0.00001107
0.876
0.00000026
Fe3+
1.082
0.00011017
1.091
0.00013462
0.984
0.00000907
Cr3+
1.188
0.00089969
1.196
0.00103208
1.096
0.00015019
In3+
1.202
0.00114198
1.209
0.00128267
1.110
0.00020260
Tl3+
1.206
0.00122067
1.213
0.00136949
1.114
0.00022027
Y3+
1.454
0.02639002
1.459
0.02759452
1.375
0.01205473
La3+
1.628
0.09399072
1.629
0.09454081
1.553
0.05807581
Ce3+
1.595
0.07688443
1.597
0.07786298
1.519
0.04525501
Pr3+
1.568
0.06441235
1.571
0.06573030
1.492
0.03655251
Nd3+
1.548
0.05605698
1.551
0.05726270
1.471
0.03064622
Sm3+
1.522
0.04630154
1.526
0.04772212
1.445
0.02431873
Eu3+
1.503
0.03994409
1.507
0.04122946
1.425
0.02014513
Gd3+
1.495
0.03745682
1.499
0.03868661
1.417
0.01863432
Tb3+
1.481
0.03336723
1.485
0.03450196
1.403
0.01619682
Dy3+
1.468
0.02986171
1.472
0.03091095
1.389
0.01400886
Er3+
1.431
0.02133669
1.436
0.02236885
1.350
0.00909668
Tm3+
1.421
0.01937874
1.426
0.02034021
1.340
0.00808758
Lu3+
1.421
0.01937874
1.426
0.02034021
1.340
0.00808758
Hf4+
1.087
0.00012321
1.098
0.00015685
0.977
0.00000741
Zr4+
1.139
0.00036479
1.149
0.00044254
1.031
0.00003240
Ce4+
1.353
0.00941798
1.360
0.01020237
1.257
0.00270120
U4+
1.209
0.00128267
1.218
0.00148497
1.105
0.00018227
Pu4+
1.273
0.00339720
1.281
0.00379705
1.172
0.00067804
Th4+
1.463
0.02858630
1.468
0.02986171
1.370
0.01141046
Table 3
Estimated IOD Parameter Set for M(III)
and M(IV) Metal Ions Using the 12-6 LJ Nonbonded Potential
TIP3P
SPC/E
TIP4PEW
Rmin/2 (Å)
ε (kcal/mol)
Rmin/2 (Å)
ε (kcal/mol)
Rmin/2 (Å)
ε (kcal/mol)
Al3+
1.297
0.00471279
1.296
0.00465074
1.285
0.00401101
Fe3+
1.386
0.01357097
1.386
0.01357097
1.375
0.01205473
Cr3+
1.344
0.00848000
1.343
0.00838052
1.333
0.00743559
In3+
1.461
0.02808726
1.461
0.02808726
1.450
0.02545423
Tl3+
1.513
0.04321029
1.513
0.04321029
1.502
0.03962711
Y3+
1.602
0.08034231
1.602
0.08034231
1.590
0.07447106
La3+
1.718
0.15060822
1.718
0.15060822
1.707
0.14295367
Ce3+
1.741
0.16721338
1.741
0.16721338
1.729
0.15845086
Pr3+
1.733
0.16134811
1.734
0.16207614
1.722
0.15343866
Nd3+
1.681
0.12564307
1.681
0.12564307
1.669
0.11803919
Sm3+
1.659
0.11189491
1.659
0.11189491
1.647
0.10475707
Eu3+
1.666
0.11617738
1.666
0.11617738
1.655
0.10948690
Gd3+
1.623
0.09126804
1.623
0.09126804
1.612
0.08544204
Tb3+
1.630
0.09509276
1.630
0.09509276
1.619
0.08912336
Dy3+
1.609
0.08389240
1.609
0.08389240
1.597
0.07786298
Er3+
1.602
0.08034231
1.602
0.08034231
1.590
0.07447106
Tm3+
1.602
0.08034231
1.602
0.08034231
1.590
0.07447106
Lu3+
1.588
0.07351892
1.588
0.07351892
1.577
0.06841702
Hf4+
1.499
0.03868661
1.501
0.03931188
1.483
0.03393126
Zr4+
1.519
0.04525501
1.521
0.04595090
1.503
0.03994409
Ce4+
1.684
0.12758274
1.689
0.13084945
1.667
0.11679623
U4+
1.684
0.12758274
1.689
0.13084945
1.667
0.11679623
Pu4+
1.662
0.11371963
1.666
0.11617738
1.645
0.10359269
Th4+
1.708
0.14364160
1.713
0.14710519
1.690
0.13150785
Combining the data with
previous work on M(II) metal ions, we summarized the absolute and
percent errors for the 12-6 LJ nonbonded model for M(II), M(III),
and M(IV) ions in Tables 4 and 5. These results, taken as a whole, show that the underestimation
of the 12-6 LJ nonbonded model increases dramatically as the charge
on the metal ion increases. For example, for the TIP3P water model,
the average absolute error goes from ∼50 kcal/mol for M(II)
ions to ∼80 kcal/mol for M(III) and ∼240 kcal/mol for
M(IV) ions for the IOD parameter set, while the average absolute error
of the IOD values for the HFE parameter set increases from −0.27
Å for M(II) ions to −0.29 Å for M(III) ions and −0.58 Å
for M(IV) ions. For some of the monovalent ions, it is possible to
reproduce both the experimental HFE and IOD values at the same time;[53] this underestimation of the 12-6 LJ nonbonded
model is pretty small and can almost be neglected. Because there are
significant errors associated with the 12-6 LJ nonbonded model for
highly charged ions, we did not carry out further refinement work
on the estimated 12-6 LJ parameters because the resultant parameters
would be of limited usefulness.
Table 4
Estimated Average Absolute and Percent
IOD Errors (in Brackets) for the 12-6 HFE Parameter Set against Experimental
Values for Divalent, Trivalent, and Tetravalent Metal Ionsa
M(II)
M(III)
M(IV)
TIP3P
avg. IOD error
–0.27 (−12.4%)
–0.29 (−12.8%)
–0.58 (−25.0%)
IOD error SD
0.14 (7.8%)
0.14 (7.4%)
0.15 (7.0%)
SPC/E
avg. IOD error
–0.26 (−12.3%)
–0.28 (−12.4%)
–0.57 (−24.5%)
IOD error SD
0.14 (7.6%)
0.13 (7.2%)
0.14 (6.6%)
TIP4PEW
avg. IOD error
–0.36 (−16.8%)
–0.41 (−18.1%)
–0.74 (−32.0%)
IOD error SD
0.17 (10.2%)
0.16 (9.2%)
0.17 (8.2%)
Absolute IOD errors are in angstroms.
Table 5
Estimated Average
Absolute and Percent
HFE Errors (in brackets) for the 12-6 IOD Parameter Set against Experimental
Values for Divalent, Trivalent, and Tetravalent Metal Ionsa
M(II)
M(III)
M(IV)
TIP3P
avg HFE error
51.1 (−11.5%)
82.7 (−9.3%)
244.3 (−15.7%)
HFE error SD
25.2 (4.5%)
42.7 (3.6%)
62.7 (3.3%)
SPC/E
avg HFE error
51.9 (−11.7%)
81.8 (−9.2%)
244.9 (−15.8%)
HFE error SD
24.3 (4.3%)
41.6 (3.5%)
61.8 (3.2%)
TIP4PEW
avg HFE error
67.2 (−15.2%)
108.0 (−12.3%)
283.0 (−18.2%)
HFE error SD
27.5 (4.5%)
46.4 (3.7%)
65.1 (3.3%)
Absolute HFE errors are in kilocalories
per mole.
Absolute IOD errors are in angstroms.Absolute HFE errors are in kilocalories
per mole.
12-6-4 Parameter Determination
After initial parameter
selection and subsequent fine-tuning, the final 12-6-4 parameters
were determined. The final optimized 12-6-4 parameters are given in
Table 6 while the simulated HFE, IOD, and CN
values are shown in Table SI.4. These parameters
reproduce the experimental HFE values by ±1 kcal/mol and the
IOD values by ±0.01 Å for the M(III) ions, while they reproduce
the HFE values by ±2 kcal/mol and the IOD values by ±0.01
Å for the M(IV) ions. Just as in the 12-6-4 parameter sets for
divalent metal ions, the Rmin/2 terms
are similar between the three water models, while the C4 term for TIP4PEW water is generally larger
than for the other two water models for the same metal ion. This may
due to the smaller dipole of the TIP4PEW water model (2.32
D) relative to the TIP3P (2.35 D) and SPC/E (2.35 D) water models.
Figure 2 shows the accuracy comparison between
the 12-6-4 parameter set and the 12-6 parameter sets for divalent,
trivalent, and tetravalent metal ions. We can see that there is significant
improvement in the accuracy using the 12-6-4 parameter set, which
is able to reproduce the experimental HFE and IOD values simultaneously.
While for the 12-6 LJ nonbonded model, if you want to reproduce the
experimental HFE values, the error in the simulated IOD values would
increase along with the formal charge of the metal ions. Vice versa,
if you simulate the IOD values using the 12-6 LJ nonbonded model,
the error of the calculated HFE would increase markedly with an increase
in the oxidation state of the metal ion in question.
Table 6
Final Parameters for the 12-6-4 LJ-Type
Nonbonded Model for Metal Ions in Three Water Models
TIP3P
SPC/E
TIP4PEW
Rmin/2 (Å)
ε (kcal/mol)
C4 (kcal/mol·Å4)
Rmin/2 (Å)
ε (kcal/mol)
C4 (kcal/mol·Å4)
Rmin/2 (Å)
ε (kcal/mol)
C4 (kcal/mol·Å4)
Al3+
1.369
0.01128487
399
1.375
0.01205473
406
1.377
0.01232018
488
Fe3+
1.443
0.02387506
428
1.450
0.02545423
442
1.448
0.02499549
519
Cr3+
1.415
0.01827024
258
1.414
0.01809021
254
1.408
0.01703790
322
In3+
1.491
0.03625449
347
1.487
0.03507938
349
1.486
0.03478983
425
Tl3+
1.571
0.06573030
456
1.569
0.06484979
455
1.564
0.06268139
535
Y3+
1.630
0.09509276
216
1.624
0.09180886
209
1.624
0.09180886
294
La3+
1.758
0.17997960
152
1.763
0.18380968
165
1.755
0.17769767
243
Ce3+
1.782
0.19865859
230
1.786
0.20184160
242
1.776
0.19392043
315
Pr3+
1.780
0.19707431
264
1.782
0.19865859
272
1.774
0.19235093
348
Nd3+
1.724
0.15486311
213
1.735
0.16280564
235
1.720
0.15202035
297
Sm3+
1.711
0.14571499
230
1.703
0.14021803
224
1.706
0.14226734
314
Eu3+
1.716
0.14920231
259
1.721
0.15272873
273
1.711
0.14571499
345
Gd3+
1.658
0.11129023
198
1.646
0.10417397
186
1.652
0.10769970
280
Tb3+
1.671
0.11928915
235
1.666
0.11617738
227
1.665
0.11556030
313
Dy3+
1.637
0.09900804
207
1.637
0.09900804
206
1.639
0.10014323
298
Er3+
1.635
0.09788018
251
1.629
0.09454081
247
1.628
0.09399072
328
Tm3+
1.647
0.10475707
282
1.633
0.09675968
262
1.638
0.09957472
356
Lu3+
1.625
0.09235154
249
1.620
0.08965674
247
1.617
0.08806221
331
Hf4+
1.600
0.07934493
827
1.592
0.07543075
810
1.599
0.07884906
956
Zr4+
1.609
0.08389240
761
1.609
0.08389240
760
1.610
0.08440707
895
Ce4+
1.766
0.18612361
706
1.761
0.18227365
694
1.761
0.18227365
835
U4+
1.792
0.20665151
1034
1.791
0.20584696
1043
1.791
0.20584696
1183
Pu4+
1.752
0.17542802
828
1.750
0.17392181
828
1.753
0.17618319
972
Th4+
1.770
0.18922704
512
1.773
0.19156806
513
1.758
0.17997960
625
Figure 2
(a) HFE errors for the
12-6 IOD and 12-6-4 parameter sets for M(II),
M(III), and M(IV) metal ions. (b) IOD errors for the 12-6 HFE and
12-6-4 parameter sets for the M(II), M(III), and M(IV) metal ions.
(a) HFE errors for the
12-6 IOD and 12-6-4 parameter sets for M(II),
M(III), and M(IV) metal ions. (b) IOD errors for the 12-6 HFE and
12-6-4 parameter sets for the M(II), M(III), and M(IV) metal ions.
Trivalent
Metal Ions
Main Group and Transition-Metal Ions
These metal ions
have much stronger ion–water interactions than the Ln3+ ions. Some of them are extremely inert ions. They form a stable
octahedral structure with water molecules in the first solvation shell.
Data in Table 1 indicate that the average effective
radius of the first solvation shell water is ∼1.35 Å for
the first several metal ions, which is consistent with strong interactions
between the coordinated water molecules and these metal ions. These
values are close to previously proposed coordinated water radius (∼1.34
Å).[75] The corresponding average values
are ∼1.49 Å and ∼1.46 Å for the Ln3+ and the M(IV) metal ions, respectively, which implies a smaller
electronic cloud overlap between the metal ion center and each of
the coordinated water molecules.Al3+, In3+, and Tl3+ are group IV ions. For the C4 parameters derived herein, we obtained a sequence of
Tl3+ > Al3+ > In3+. The Al3+ ion is the smallest M(III) ion, resulting in a relatively
larger C4 term due to its strong covalent
interaction
with coordinated water molecules. Tl has two oxidation states, +1
and +3, and the HFE values of the Tl+ and K+ are almost the same in Marcus’ HFE set.[66] Tl3+ could have very strong covalent interactions
with the surrounding residues. The reduced electric potential of M(III)
+ 3e– = M is −1.67, −0.3382, and +0.72
eV for Al3+, In3+, and Tl3+, respectively.[76] The positive reduction potential of Tl3+ makes it a very reactive species. It readily obtains electrons from
its surroundings, which may be the reason for a strong charge-transfer
effect between the Tl3+ ion and the surrounding water molecules.
The 12-6-4 parameters of In3+ and Tl3+ ions
gave an excellent prediction for the HFE and IOD values but overestimated
the CN value (8 instead of 6), and this is mainly due to the lack
of a correction for the water–water interactions in the first
solvation shell during the simulations. The water–water interactions
were parametrized to reproduce the pure liquid water properties in
the original parameter design. However, the first solvation shell
water molecules of the highly charged metal ions should more strongly
repel one another due to their bigger charge separations. This effect
is smaller for M(I) and M(II) metal ions, but it dramatically increases
for the highly charged ions. Meanwhile, this kind of effect may decrease
in protein systems due to the preorganization of the metal ion binding
sites.Fe3+ has a larger C4 term
than Al3+, the smallest M(III) ion, which suggests that
Fe3+ has a stronger interaction with its surrounding water
molecules. This is consistent with quantum-mechanical charge-field
molecular dynamics (QMCF-MD) simulations, which shows that the force
constant between the ion and the oxygen of first solvation shell water
molecules (kion-O) is 198 N/m for
Fe3+ compared with 185 N/m for Al3+.[30] This is a consequence of both electrostatic
and covalent interactions. The Fe3+ ion has an average
1.85e[47] charge (from a Mulliken analysis)
in the QMCF simulation, while Al3+ ion has a corresponding
value of 2.5 e,[77] which implies that there
is a stronger charge-transfer effect for the Fe3+ ion and
its surrounding water molecules than for the Al3+ ion.
There is a slight overestimation of the CN for Fe3+ ions.
Also, as previously discussed, this may be due to the underestimation
of the interactions between the first solvation water molecules. While
this effect is operative in aqueous solution, it will likely be less
of an issue in protein systems (see discussion below).
Y3+ and Ln3+ Ions
The +3 oxidation
state is the typical oxidation state of the Ln elements, with the
exception that Eu2+ and Ce4+ could also be observed.
This is because Eu2+ has a half-filled 4f orbital while
Ce4+ has the same electronic configuration as Xe. The interaction
of the Ln3+ ions with surrounding water molecules would
be expected to have more ionic character than the M(III) ions previously
discussed. For example, the C4 terms between
the Ln3+ ions and water molecules are between 152 and 282
kcal/mol·Å4, which is smaller than the 258–456
kcal/mol·Å4 range seen for the other +3 metal
ions previously discussed. Previous simulations found that the kion-O values are much smaller for the
Ln3+ ions; for example, La3+, Ce3+, Lu3+, and Er3+ have kion-O values ∼110 N/m, while the values for the
Al3+ and Fe3+ ions are 185 and 203 N/m, respectively.[46] The Ln3+ ions have effective ionic
radii in the range of 0.86 to 1.03 Å and IOD values in the range
of 2.34 to 2.55 Å. These values are similar to that of the Ca2+ ion (whose effective ionic radius and IOD value is 1.00[72] and 2.46 Å,[78] respectively). Therefore, they have been used as probes to investigate
the role of Ca2+ ions in biological systems.[79]From Table 6, we
observe that the La3+ and Gd3+ ions have the
smallest C4 terms among the Ln3+ ions. This may be because they have either totally empty or half-filled
4f orbitals, making them more likely to form isolated ions, which
reduces the covalent character of their bonds with coordinated water
molecules. It is easy to see the “lanthanide contraction”
effect from Table 1. The effective ion radius
decreases monotonically with an increase in the metal ions’
atomic number due to the poor shielding of the 4f electrons toward
5s and 5p orbitals.[80] A similar tendency
can also be seen for the HFE and IOD values along the series. Our
final Rmin/2 parameters are consistent
with this pattern as well. Meanwhile, the CN also decreases along
the Ln3+ ion series. Previous work reached the conclusion
that the lighter Ln3+ ions (La3+ to Nd3+) prefer a CN of ∼9 and the heavier ions (Gd3+ to
Tb3+) prefer a CN of ∼8, while the middle ions such
as Sm3+ and Eu3+ have CN between these two values.[81−86] It was proposed that the former Ln3+ ions have a tricapped
trigonal prism structure, which then shifts to a distorted bicapped
trigonal prism structure for the heavier elements as one of the two
capping water molecules leaves the first solvation shell.[87] Generally speaking, there is a good agreement
between the 12-6-4 parameters for the HFE, IOD, and CN values with
experiment, with the exception that some of the CN values were slightly
overestimated. The final parameters gave a CN in the range of 9 to
10 for Ln3+ ions rather than the range of 8 to 9 reported
in the literature. As previously discussed, this may be due to the
fact that there is no water–water interaction correction term
in the present parametrization process. Moreover, the CN values given
by Marcus (as shown in Table 1) likely also
vary under different experimental conditions (counterions used solute
concentration, etc.). Among all ions, Al3+, Y3+, and La3+ have the same electron configurations as the
noble gas atoms Ne, Kr, and Xe, respectively. Using the TIP3P water
model as an example, we can see their C4 values decrease from 399 to 216 and 152 kcal/mol·Å4, respectively.
Tetravalent
Metal Ions
There are only
a few M(IV) ions that exist in aqueous solution, while the others
are readily hydrolyzed into polynuclear complexes in water.[68−71] Table 1 shows the M(IV) ions examined herein.
These ions exist in at least highly acidic solution. The CN values
of these metal ions are greater than 8, with some of them being ∼10
according to experiment.[68−71] Previous work found that Pu(IV), Th(IV), and U(IV)
could strongly bind to transferrin, an iron-transport protein.[88] Hence, the parameters developed herein might
facilitate theoretical research on the biotoxicity of these M(IV)
ions.The Zr4+ and Hf4+ are in the IVB
group. Even though Hf4+ has a larger atomic number than
Zr4+, due to the “lanthanide contraction”
effect, it has a smaller effective radius, smaller IOD, smaller HFE,
and a bigger C4 term than Zr4+. These observations reflect its stronger interaction with the surrounding
water molecules. In contrast, Ce4+ and Th4+ are
in the same group where the larger atomic number (Th4+)
has the bigger ionic radius, bigger HFE, and smaller C4 terms. This may be because they share the same electronic
structure as Xe and Rn, respectively. Besides these ions, Zr4+ is another M(IV) ion that has a noble gas atom’s electronic
structure (the same as Kr). There is also a single trend for the C4 terms of Zr4+, Ce4+,
and Th4+ ions for each specific water model. For instance,
the C4 terms for the TIP3P water model
are 761, 706, and 512 kcal/mol·Å4, respectively.Th, U, and Pu are in the An series and are the largest elements
investigated in the present work. Their tetravalent metal ions exist
only in highly acidic solutions. Canaval et al. investigated Th4+ in aqueous solutions using the QMCF-MD method. They found
a stable nine-coordinate complex, and even the third layer of water
molecules has a bigger mean residence time than that of pure water,
implying they are stabilized by the highly charged Th4+ ion.[48] U4+ fluoresces due
to the electron transition between the 6d15f1 and 5f2 electronic configurations.[200] The U4+ ion has the largest C4 term of all of the M(IV) metal ions investigated. Frick
et al. investigated the U4+ ion in aqueous solution using
the QMCF-MD method, and the CN value was characterized as 9, while
the average charge of U4+ was predicted to be +2.68 from
Mulliken population analyses.[300] Odoh et
al. simulated the Pu3+, Pu4+, PuO2+, and PuO22+ ions in water solution
using the Car–Parrinello molecular dynamics method.[89] They predicted that the pKa value for the first hydrolysis step for the Pu3+, Pu4+, PuO2+, and PuO22+ ions is 6.65, 0.17, 9.51, and 5.70, respectively, showing
a general tendency that the larger the charge of the metal center,
the lower the pKa value of the first hydrolysis
reaction. Hf4+, Zr4+, and Pu4+ have
relatively smaller IOD values among the tetravalent ions, where they
all have experimental CNs of ∼8.[71] Ce4+ was determined to have an experimental CN of ∼9,[68] while U4+ and Th4+ have
CNs between 9 and 11.[71] Soderholm et al.
proposed that counterions also play a key role in the first solvation
shell structure, while the 9-, 10-, or 11-coordinated Th4+ have very small energy differences and are in a dynamic equilibration.[90] The simulated HFE and IOD values of the 12-6-4
parameter set are in excellent agreement with the experiment. The
simulated CN values of most of the M(IV) ions are ∼10, with
Hf4+ having a CN ∼8 for the TIP4PEW and
SPC/E water models. Herein, the TIP3P model always predicted a larger
CN value than the other two water models, which may be because it
has a smaller C12 term (∼582.0 × 105 kcal·Å12/mol) than that of the SPC/E (∼629.4
× 105 kcal·Å12/mol) and TIP4PEW (∼656.1 × 105 kcal·Å12/mol) models.
Redox Ion Pairs
Later, we analyze several
redox pairs to explore the consistency of the C4 parameters we determined with respect to the behavior of
these pairs in aqueous solution. We also calculated the relative HFE
between each redox pair for the TIP3P water model (see below). The
divalent metal ions’ 12-6-4 parameters are from previous work.[18] A nine-windows TI simulation (50 ps of equilibration
and 150 ps of sampling for each window) was performed forward and
backward, respectively, to obtain the final results. The results further
validate the method employed in the present work. For example, the
simulated relative HFEs of Fe2+/Fe3+, Cr2+/Cr3+, and Ce3+/Ce4+ ion
pairs were 580.2, 516.9, and 698.2 kcal/mol, while the experimental
values are 579.6, 516.2, and 697.6 kcal/mol, respectively.[66]
Fe2+/Fe3+ Ion Pairs
The experimental
IOD values shrink ∼0.08 Å from 2.11 Å of Fe2+ to 2.03 Å of Fe3+ ion. Moin et al. investigated
ferrous and ferric ions in water using the QMCF-MD method. They obtained
a force constant kion-O of 193
N/m for Fe3+, which is almost twice as strong as that of
Fe2+ (93 N/m), while the effective charges (from a Mulliken
population analysis) for the Fe2+ ion are in the range
of 1.25 to 1.45 (with an average of 1.36), and for the Fe3+ ion it is in the range of 1.70 to 1.95 (with an average of 1.85).[47] Fe2+/Fe3+ redox pairs
exist broadly in biologically related system such as the Fe–S
proteins and heme structures.[7,91] Moreover, Fe2+/Fe3+ redox pairs play fundamental roles in many electron-transfer
processes. We have determined the 12-6-4 parameters for Fe2+ ion with three different water models in previous work.[18] For the TIP3P water model, the final optimized
parameters were Rmin/2 = 1.457 Å,
ε = 0.02710805 kcal/mol, and C4 =
163 kcal/mol·Å4.[18] From the 12-6-4 parameters determined for the Fe3+ ion
herein, we find that the Rmin/2 decreases
slightly as the outer shell electron number decreases, while the C4 term increases by ∼2.5 times relative
to Fe2+. This is consistent with a ratio between the C4 terms for a trivalent and divalent ion of
[3/2]2 = 2.25, which is derived from the original ion-induced
dipole equation (eq 11 in a prior publication[18]).
Cr2+/Cr3+ Ion Pairs
Cr3+ forms a stable Cr(H2O)63+ complex
in the aqueous phase. The Cr2+ and Cr3+ ions
have [Ar]3d4 and [Ar]3d5 electronic structures,
respectively, where the Cr(H2O)62+ complex has a strong Jahn–Teller effect while the Cr(H2O)63+ molecule has a standard octahedral
configuration. The IOD values decreases from 2.08 to 1.96 Å for
the Cr2+ and Cr3+ ions. Using the TIP3P water
model as a representative example, we observe that the Rmin/2 parameter decreases from 1.431 to1.405 Å, while
the C4 term increases from ∼137
to ∼258 kcal/mol·Å4 for the Cr2+ and Cr3+ ions (the Cr2+ parameters are reported
in reference (18)).
Ce3+/Ce4+ Ion Pairs
Cerium has
both +3 and +4 oxidation states. Ce4+ is the most stable
state because it shares the same electronic configuration with Xe.
Just like the two oxidation pairs previously discussed we find that
the Rmin/2 value decreases while the C4 term increases significantly with increasing
charge. For example, for the parameters determined for the TIP3P water
model, the Rmin/2 decreased ∼0.03
Å, while the C4 term increased by
∼480 kcal/mol·Å4.
Validation
on a Protein System
PDB entry 4BV1 was used to obtain
the starting coordinates for this modeling exercise. It is a superoxide
reductase (SOD) found in Nanoarchaeum equitans. It is a protein tetramer with each monomer having a metal site
containing an Fe3+ ion. The structure has been determined
by using X-ray crystallography to a resolution of 1.90 Å. The
tetramer structure is shown in Figure 3, while
Chain C with its metal site is shown in Figure 4. The metal site contains four histidine groups, one cysteine group,
and one water molecule. By treating Chain C as the initial structure,
we performed three simulations with different parameter sets (the
HFE, IOD, and 12-6-4 parameter sets). For the 12-6-4 parameter set,
the C4 terms between the Fe3+ ion and atom types other than wateroxygen were evaluated using
eq 11. The TIP3P water model was employed during
the simulations. Details of the simulation procedures and the polarizability
of each atom type are given in the SI.
Figure 3
PDB entry 4BV1. Water molecules are not shown in the
Figure, the ferric ion is
shown as a sliver sphere. This picture was created by VMD.[92]
Figure 4
Chain C in PDB entry 4BV1 (left) and a close up of the metal site in Chain C
(right). The ferric ion is represented as a silver sphere, and it
is coordinated by one Cys, four His, and one water molecule. The figures
were made using VMD.[92]
A total of 10 ns of
sampling was performed during the simulation, and snapshots were stored
after each 500 fs. The HFE parameter set prefers a smaller CN (of
4), and the metal ion moves out from the binding pocket, while stable
metal complex structures were obtained for the simulations using the
IOD and 12-6-4 parameter sets. An RMSD analysis was performed over
the heavy atoms of the backbone and the metal site for the simulations
by treating the initial structure (experimental structure) as reference.
The results are depicted in Figure 5. The RMSD
of the heavy backbone atoms fluctuated around ∼1.2 Å,
while the RMSD of the metal site was ∼0.5 Å. These values
illustrate that the metal binding site is stable during the course
of the simulations.
Figure 5
RMSD of heavy atoms of backbone (left) and the metal site (right,
including the binding water molecule) for simulations with IOD and
12-6-4 parameter sets using the initial structure (experimental structure)
as reference.
We have also performed an RMSF analysis
of the backbone heavy atoms
for each residue together with the oxygen atom in the metal site binding
water. The results are shown in Figure 6. From
this Figure it can be seen that the metal site residues: residue His10
(residue number 11), His 35 (residue number 36), His 41 (residue number
42), Cys 97 (residue number 98), and His 100 (residue number 101),
all have relatively small RMSF values (∼0.5 Å). The metal
site binding water (residue number 115, is not shown in the Figure
since the protein ends at residue number 112) has a RMSF of ∼0.6
Å for both the simulations with the IOD and the 12-6-4 parameter
sets. These results further validated that the metal ion site is stable
over the course of the simulations.
Figure 6
RMSF of heavy atoms of
the protein residues in the simulations
using IOD and 12-6-4 parameter sets.
PDB entry 4BV1. Water molecules are not shown in the
Figure, the ferric ion is
shown as a sliver sphere. This picture was created by VMD.[92]Chain C in PDB entry 4BV1 (left) and a close up of the metal site in Chain C
(right). The ferric ion is represented as a silver sphere, and it
is coordinated by one Cys, four His, and one water molecule. The figures
were made using VMD.[92]RMSD of heavy atoms of backbone (left) and the metal site (right,
including the binding water molecule) for simulations with IOD and
12-6-4 parameter sets using the initial structure (experimental structure)
as reference.RMSF of heavy atoms of
the protein residues in the simulations
using IOD and 12-6-4 parameter sets.
Conclusions
In this work, we have estimated the 12-6
LJ parameters and determined
the 12-6-4 LJ-type parameters for 24 highly charged metal ions (18
M(III) ions and 6 M(IV) ions) with three water models (TIP3P, SPC/E
and TIP4PEW) based on a parameter scanning protocol. We
have shown that with the increasing charge of the metal ions there
is a notable decrease in the accuracy of the 12-6 LJ nonbonded model.
Using TIP3P as an example, the average underestimation of the HFE
values increases from ∼50 kcal/mol for M(II) ions to ∼80
kcal/mol for M(III) ions and to ∼240 kcal/mol for M(IV) ions
when trying to reproduce the experimental IOD values. The average
underestimation of the IOD values increases from −0.27 to −0.29
Å and −0.58 Å for the M(II), M(III), and M(IV) ions,
respectively, when trying to reproduce the experimental HFE values.The 12-6-4 LJ-type nonbonded model, which we previously described,
addresses this problem in a consistent manner. It improves the accuracy
of the 12-6 LJ nonbonded model remarkably with just a slight increase
in computational cost. This parameter set, derived in this work, reproduced
several experimental values (HFE, IOD, and CN) with good accuracy.
They reproduce the HFE within ±1 kcal/mol for the M(III) ions
and ±2 kcal/mol for M(IV) ions while reproducing the experimental
IOD values to within ±0.01 Å. Moreover, excellent quantitative
and qualitative agreement with previous experimental and computational
work supports the validity of the 12-6-4 LJ-type nonbonded model.
Testing in a protein system also revealed good transferability of
the parameters determined herein.
Authors: Jiří Šponer; Giovanni Bussi; Miroslav Krepl; Pavel Banáš; Sandro Bottaro; Richard A Cunha; Alejandro Gil-Ley; Giovanni Pinamonti; Simón Poblete; Petr Jurečka; Nils G Walter; Michal Otyepka Journal: Chem Rev Date: 2018-01-03 Impact factor: 60.622
Authors: Tamar Cranford-Smith; Mohammed Jamshad; Mark Jeeves; Rachael A Chandler; Jack Yule; Ashley Robinson; Farhana Alam; Karl A Dunne; Edwin H Aponte Angarita; Mashael Alanazi; Cailean Carter; Ian R Henderson; Janet E Lovett; Peter Winn; Timothy Knowles; Damon Huber Journal: J Biol Chem Date: 2020-04-02 Impact factor: 5.157