Supporting materials
In this section, detailed properties for the zinc-complexes used in our parameterization
and test calculations are presented. These include the optimized structures (Figures S1-S6) and
binding energies (Table S1-S3). In most cases, results from SCC-DFTB and PM3 calculations
were compared to B3LYP values. For the zinc-ammonia interactions, where B3LYP was shown
to overestimate the total binding energies, MP2/6-311+G(d,p) single point calculations at the
B3LYP optimized structures were also included; B3LYP gives rather reliable incremental
binding energies (see the main text for detailed discussions).
Table S1. Comparison of energetics at different levels.a
Species B3LYP/MP2c SCC-DFTB PM3
Zn2+·(H2O) -103.6[63.1] -95.5[61.9] -67.3[47.8]
Zn2+·(H2O)2 -193.5(-89.9)[95.0] -185.7(-90.2)[94.9] -123.5(-56.2)[73.2]
Zn2+·(H2O)4 -296.0(-102.6)[141.9] -286.7(-101.0)[146.9] -195.4(-72.0)[109.6]
Zn2+·(H2O)6 -348.9(-52.8)[167.3] -328.0(-41.3)[168.7] -205.9(-10.4)[117.4]
Zn2+·(NH3) -137.8/-127.2 -107.6 -125.4
Zn2+·(NH3)2 -246.8(-109.0)/-234.3(-107.1) -211.4(-103.8) -227.1(-101.8)
Zn2+·(NH3)3 -307.6(-60.9)/-297.6(-63.3) -272.8(-61.3) -306.2(-79.1)
Zn2+·(NH3)4 -352.8(-45.2)/-345.8(-48.2) -321.6(-48.9) -373.3(-67.1)
Zn2+·(NH3)3(H2O)b -31.8 [156.3] -40.9 [158.2] -19.4 [132.5]
Zn2+·(NH3)3(OH-)b -271.6 -307.1 -290.1
a. The basis set used in the calculations (mostly B3LYP) is 6-311+G(d,p). The numbers without
parentheses or brackets are binding energies relative to infinitely separated Zn2+ and water
molecules. The numbers with parentheses are incremental binding energies as the number of
ligand (H2O or NH3) molecules increases. The numbers in the brackets are the proton affinities
of Zn2+ bound water.
b. The numbers are the binding energies of the ligand (H2O or OH-) to Zn2+(NH3)3. The numbers
with brackets are the deprotonation energy of the Zn ion bound water.
c. The values before slashes are B3LYP results. These after slashes are MP2/6-311+G(d,p) single
point results at B3LYP geometries.
Table S2. Energetics for model zinc-Cys species.a
Species B3LYP SCC-DFTB PM3
[Zn(SH)]+b -423.2 -413.6 -417.4
Zn(SH)2b -635.6(-212.4) -630.8(-217.2) -655.2(-237.8)
Zn(SH)2(H2O)2c -18.6 -26.3 -6.1
ZnF d -16.2 -14.8 -18.8
ZnF-ETOH d -14.7 -12.3 +1.6
ZnF-ETOM d -71.3 -59.2 -47.1
ZnF-H2O d -15.9 -10.9 +1.4
Zn(SMe)2e 113.3(204.3) 96.4(194.2) 105.8(195.8)
Zn(SMe)2(H2O)2e 143.1[152.5] 129.7[153.1] 129.1[128.1]
Zn(SMe)2(CH2NH)2e 154.2(240.2) 139.3(230.6) 144.9(230.3)
a. The structures are optimized at the B3LYP level with the following basis set: Lanl2dz for Zn;
Lanl2dz augmented with polarization function for S; and 6-31G(d) for the others. Single point
energies were calculated with the 6-311+G(d,p) basis. For Zn(SH)+, Zn(SH)2, Zn(SH)2(H2O)2,
Zn(SMe)2 and Zn(SMe)2(H2O)2, the structures are also optimized with the 6-311+G(d,p) basis
set.
b. The numbers without parentheses are binding energies relative to infinitely separated Zn2+ and
SH- molecules. The numbers with parentheses are binding energies of the second SH-.
c. The numbers are the binding energies of the two water molecules to Zn(SH)2.
d. The numbers are the binding energies of the fourth ligand (CH2=NH, C2H5OH, C2H5O- and
H2O, in order) to Zn(CH2=NH)(SH)2.
e. The numbers are the deprotonation energies (DPE). The numbers without the parentheses or
brackets are the first DPE from the Zn2+ bound HSMe, and the numbers with parentheses are the
DPE from the second Zn2+ bound HSMe. The numbers in brackets are the DPE from the Zn2+
bound water molecule.
Table S3. Energetics for model zinc-Glu species.a
Species B3LYP SCC-DFTB PM3
Zn2+(HCOO-)·OH- -244.7(-216.8) -261.4(-218.1) -244.2(-194.6)
Zn2+(HCOO-)·H2O -52.9(-357.9)[204.3] -50.2(-368.1)[211.9] -29.0(-334.7)[187.9]
Zn2+(HCOO-)(CH2NH)2·OH- -159.4 -180.9 -172.4
Zn2+(HCOO-)(CH2NH)2·H2O -18.7[254.5] -15.0[257.3] -7.4[238.2]
a. The structures are optimized at the B3LYP level with the following basis set: Lanl2dz for Zn;
Lanl2dz augmented with polarization function for S; and 6-31G(d) for the others. Single
point energies were calculated with the 6-311+G(d,p) basis. Then numbers without
parentheses are the binding energies of OH- or H2O; those with parentheses are the binding
energies of HCOO-; those with brackers are the deprotonation energy of Zn bound water. In
the calculation of binding energies, the fragments are fully optimized except for the di-Zn
complexes.
Figure Captions.
Figure S1. Optimized structures of complexes formed between Zn2+ and different number of
water molecules. Distances are given in Angstroms and angles are in degrees. The numbers after
the slashes are values for complexes with one water deprotonated (indicated with the shortest Zn-
O distance). The numbers without parentheses or brackets are obtained at the B3LYP/6-
311+G(d,p) level; those in the parentheses are PM3 values; those in the brackets are obtained
with the SCC-DFTB method.
Figure S2. Optimized structures of complexes formed between Zn2+ and different number of
ammonia molecules. Also included are compounds formed between Zn(NH3)32+ and water or
hydroxyl ion. Distances are given in Angstroms and angles are in degrees. The numbers without
parentheses or brackets are obtained at the B3LYP/6-311+G(d,p) level; those in the parentheses
are PM3 values; those in the brackets are obtained with the SCC-DFTB method.
Figure S3. Optimized structures of complexes formed between Zn2+ and SH-. Also included are
compounds formed between Zn(SH)2 and two water molecules. Distances are given in
Angstroms and angles are in degrees. The numbers without parentheses or brackets are obtained
at the B3LYP/6-311+G(d,p) level; those in the parentheses are PM3 values; those in the brackets
are obtained with the SCC-DFTB method.
Figure S4. Optimized structures of complexes formed between Zn(SH)2(CH2=NH) and a
number of small ligands (CH2=NH, C2H5OH, C2H5O- and water). Distances are given in
Angstroms and angles are in degrees. The numbers without parentheses or brackets are obtained
at the B3LYP level with double-zeta plus polarization quality basis set (see footnote of Table 2);
those in the parentheses are PM3 values; those in the brackets are obtained with the SCC-DFTB
method.
Figure S5. Optimized structures of complexes Zn(HSMe)2, Zn(HSMe)2(H2O)2 and
Zn(HSMe)2(CH2=NH)2 with different protonation state of HSMe and H2O. Distances are given
in Angstroms and angles are in degrees. The numbers without parentheses or brackets are
obtained at the B3LYP level with either the 6-311+G(d,p) basis (normal text) or double-zeta plus
polarization quality basis set (in italics; see footnote of Table 2); those in the parentheses are
PM3 values; those in the brackets are obtained with the SCC-DFTB method.
Figure S6. Optimized structures of Zn2+ complexes with carboxylic ligands. Distances are given
in Angstroms and angles are in degrees. The numbers without parentheses or brackets are
obtained at the B3LYP level with either the 6-311+G(d,p) basis (before the slashes) or double-
zeta plus polarization quality basis set (after the slashes; see footnote of Table 3); those in the
parentheses are PM3 values; those in the brackets are obtained with the SCC-DFTB method.