D4 definition optimized at the hybrid density functional PBE0 7 level of theory employing an Ahlrich’s

quadruple-zeta basis set 8 (def2-QZVP). Polarizabilities at imaginary frequencies are derived

Charge dependence
on these geometries with the def2-QZVP basis set for all main group elements augmented
Besides the geometrical D3 dispersion model, 1 there are semi-classical density dependent ap- with diffuse (2s2p1d)-functions except for hydrogen whose basis set is augmented by (2s2p)-
proaches like the Tkatchenko-Scheffler (TS) model 2 or the exchange dipole moment (XDM) functions. For transition metals, an additional set of diffuse (2s2p1d1f)-functions is provided.
model of Becke and Johnson. 3–5 In the newly presented approach, which is based on D3, This basis set will be abbreviated as aug-def2-QZVP in the following. Time-dependent den-
electronic structure information is included via atomic partial charges as continuous de- sity functional theory calculations are performed to compute the electric dipole polarizabil-
scriptors. Just like D3, the new scheme relies on reference systems for which the dynamic ities α(iω) with a variant of the PBE0 hybrid functional containing 37.5 % Fock exchange
polarizabilities are computed from first-principles time-dependent density functional theory (ax = 3/8, termed PBE38) employing the aug-def2-QZVP basis sets. Differently coordinated
(TD-DFT). In order to describe differently charged environments, which are not described hydrides (Am Hn and Bk Hl ) are used as model systems for atoms A and B having specific
sufficiently by using D3, charge dependencies need to be included in the reference molecules. fractional coordination numbers CNA/B , which are directly connected to the molecular envi-
Due to the fact that TD-DFT calculations employing a fractional electron occupation are ronment of the described atom A and B. This is exactly the same as in D3. The parameter
not possible with our available codes, the nuclear charges of the atoms A and B of the ref- a is adjusted for each element using cross-check systems where the calculated Mulliken par-
erence systems are varied to effectively describe different charge situations. In equation 2 tial charge is different from those of the reference systems (z A 6= z A,ref , to parametrize a).
the element specific scaling-function ζ of the reference polarizabilities (cf., equation 2 in the Additionally, we have calculated the cationic static polarizability for atoms with Z = 2 − 86
manuscript) are expressed as functions of the charges q A of the atoms. The effective nuclear and adjusted a manually to fit those data. All reference Mulliken partial charges q A,ref are
charge of atom A within the corresponding molecule can be defined as stored as constant values in the code. The stored reference dipole polarizabilities are then
scaled by the partial charge dependent function ζ to simulate effects from a higher or lower
zA = Z A + qA. (1)
electron density around the corresponding atom. The charge function is therefore a correc-
tion scheme for dipole polarizabilities to produce, after numerical integration, more accurate
Here, ZA equals the nuclear charge of atom A whereas q A is the specific calculated Mulliken 6
molecular dispersion coefficients.
partial charge for atom A within the molecule.

GFN-xTB derived charges

ζ(z A , z A,ref ) = ba1.47 exp(z ) log10 (zA,ref /zA )
A /z A,ref
(2)
Recently, a tight-binding (TB) Hamiltonian 9 was developed, which yields accurate Mulliken

Equation 2 introduces the element-specific parameter b which is obtained for each coordi- partial charges in a reasonable time frame even for systems with thousands of atoms. A

nation number by matching hybrid TD-DFT molecular dispersion coefficients of the refer- related self-consistent charge model (GFN-xTB 10 ) is used to calculate these charges which

ence systems (z A = z A,ref , to parametrize b). The structures of the reference systems are then serve as input for the presented charge dependent dispersion model. We have tested the

S2 S3
amount of computer time for a large system having 3601 atoms (green fluorescence protein, is very similar for covalent and ionic connections (cf. Li2 and LiH in Table A1) while the co-
PDB code: 1GFL, 11 charge: -6). The computation time of the self-consistent Mulliken valent coordination number enables the distinction between such cases. Consequently, more
partial charges takes about 30 minutes on a desktop computer. Compared to standard reference systems can be considered in the Gaussian average, which cover both situations for
Kohn-Sham DFT calculations such a computation can be regarded as negligible. A self- each element. Reference systems can therefore be supplemented with homoatomic molecules
consistent TB model (i.e., GFN-xTB) is preferred due to the principally simpler computation like alkali or halogen dimers.
of gradients which will be developed in future work.
Polarizability definitions
The covalent coordination number
For clarity, all possible polarizability notations are given below to dispose any occuring confu-
In order to distinguish covalent and ionic bonding situations between atom pairs the D3 sion. We start with the molecular polarizabilities at imaginary frequencies of the symmetric
functional form for the CN is modified. The new scheme is termed the covalent coordination hydride reference molecules Am Hn which is denoted as αAm Hn (iω) (having m chemically
number (CNA
cov ), which is given by equal atoms A and n equally charged hydrogen atoms). Because of the fact that we are
interested in atomic polarizabilities at imaginary frequencies of atom A within the refer-
NX
exp −k1 |ENA − ENB + k2 |2
atoms



CNA
cov = h  A,cov B,cov i . (3) ence system Am Hn , αAm Hn (iω) is reduced by its scaled hydrogen contribution as shown in
B6=A 1 + exp −16 4(R 3R+R
AB
)
−1
equation 4,
1 h Am Hn n i
Equation 3 is mostly identical to the D3 case and differs only in the numerator, which always αA,ref (iω) = α (iω) − αH2 (iω)ζ(z HA,ref , z H2 ) . (4)
m 2
equals one in D3. The exponential function in the numerator is adjusted to approximately
The charge dependent atomic polarizability of atom A is introduced by the product of
match Wiberg bond orders for single bonds (computed with GFN-xTB). The variables k1
αA,ref (iω) and the reference specific charge function, ζ(z A , z A,ref ) (cf., equation 2), as follows
and k2 have the values 0.016 and 19.089. In Table A1 the geometrical coordination number
from D3 (CNA ) and the covalent coordination number of the new D4 model (CNA
cov ) are
αA,ref (iω, z A ) = αA,ref (iω)ζ(z A , z A,ref ). (5)
given for various diatomic molecules. It is noted that the geometrical coordination number

Table A1: Geometrical (D3) and covalent (D4) fractional coordination numbers. Considered Equation 5 is solved on-the-fly for all element specific reference systems. After this, a Gaus-
atoms are highlighted in bold font.
sian weighting function WAA,ref is used to obtain charge dependent and hybridization weighted
D3 D4 polarizabilities at imaginary frequencies for atom A (see section below for details):
molecule CNA CNA
cov

Li-H 0.986 0.801 A,ref

NX
Li-Li 0.941 0.923 αA (iω) ≡ αA,ref (iω, z A , CNcov
A
)= αA,ref (iω, z A ) WAA,ref (6)
C-H 0.987 0.918 A,ref =1
C-F 1.000 0.785
F-H 0.998 0.740
F-F 0.979 0.961

S4 S5
Here, we introduce a short-hand notation for the final polarizability at imaginary frequencies valent coordination number in the denominator (see equation 8). In case both coordination
A,ref −8
for atom A, αA (iω), and declare N A,ref as the number of reference systems for the chemical numbers match (CNA
cov = CNcov ), ΩA becomes very large (ε = 10 ). This way, we ensure

element corresponding to atom A. that the contribution of the exactly matched reference system is dominant in the Gaussian
average. The factor of 3.5 inside the square root of the denominator and the value of 2.0
The modified Gaussian interpolation scheme
inside the square root of the nominator were adjusted manually to smooth the weighting

The introduction of charge dependent scaling functions ζ and covalent CNs leads to a modi- function between different reference systems. Equation 8 depends on the average reference

fied charge dependent Casimir-Polder formula which is given in equation 10. First, we need covalent coordination number CNA,av
cov (see equation 9), which is necessary to counteract the

to introduce the contribution of the polarizability in reference system (with given CNA,ref
cov ) divergence behavior of the polarizabilities in case of high covalent CNs. Figure 1 shows the
NPA,ref
A,ref
to the polarizability of atom A (with WA = 1), which is given by performance of both weighting functions (D3 and D4) regarding to their ability of connecting
A,ref =1
the calculated homoatomic C6AA dispersion coefficients for the given reference coordination
exp −ΩA (CNA A,ref 2
 
cov − CNcov ) number. The new Gaussian weighting function (red curve) yields plateaus around the ref-
WAA,ref = A,ref (7)
NP
exp −ΩA (CNA A,ref 2
 
cov − CNcov ) 50
A,ref =1 D3
D4
with 45

40
q
A,ref
NX 2CNA,av
cov
ΩA = q  (8)

6 (a.u.)
A,ref=1 3.5(CNA
cov − CN A,ref 2
cov ) + ε 35

CAA
30
and
A,ref
NX
1
CNA,av
cov = CNA,ref
cov . (9) 25
N A,ref A,ref=1

20
The stored reference polarizabilities at imaginary frequencies are scaled by ζ(z A , z A,ref ) and
used in a Gaussian average (over CNA A A A
cov ) to obtain the α (iω,z ,CNcov ) from which disper- 15
0 0.5 1 1.5 2 2.5 3 3.5 4 4.5
sion coefficients are numerically integrated on-the-fly. The Gaussian weighting function is CNA

designed in such a way that it matches the reference polarizabilities in case that the calculated Figure 1: Comparison between the D3 and the D4 Gaussian weighting function and their
abilities of connecting pre-calculated homoatomic CAA 6 dispersion coefficients (atoms are
covalent CN is equal to the reference one. Compared to the D3 Gaussian weighting function, highlighted in green) obtained from carbon reference systems as a function of the coordination
number CNA (D3: CNA ; D4: CNA cov ). All reference points are highlighted via vertical
the scaling factor of 4.0 in the exponential function is replaced with a sum over all reference lines. The blue dotted curve represents the D3 weighting function while the new scheme is
systems for atom A, which includes the difference between the present and the reference co- represented by the red curve. It should be noted that polarizabilities are weighted in D4,
while D3 weights over CAB6 dispersion coefficients.

S6 S7
erence CNs, which demonstrates the “knock-out” criterion employed in the new function derived from third-order perturbation theory, via
around the reference coordination (via ΩA ). This is different in D3, in which the interpola-
C9ABC ≡ CABC
9 (CNA A B B C C
cov , z , CNcov , z , CNcov , z )
tion is smoother (blue dashed curve), however, not necessarily yielding the reference value Z ∞ (11)
3
of CAA at CNA A,ref =− dω αA (iω)αB (iω)αC (iω).
6 cov = CNcov . In equation 10, the final atom pairwise dispersion coefficient in π 0
D4 is given. The polarizability of an atom A/B with effective nuclear charge z A /z B and co-
In equation 11 we use again the short-hand notation of αA/B/C (iω). The D4 model is capable
valent coordination number CNA B
cov /CNcov is obtained by weighting over all ζ scaled reference
of calculating equation 11 from the correct C9ABC expression whereas D3 approximates these
systems of atom A/B. The contribution of hydrogen is scaled by ζ(z HA , z H2 )/ζ(z HB , z H2 )
coefficients. The accuracy of this approximation for C9ABC coefficients will be discussed
(where the reference effective charge of hydrogen in dihydrogen is z H2 = 1.0) and subtracted
elsewhere.
to obtain the correct polarizability of atom A/B (at CNA,ref B,ref
cov /CNcov ) from the molecular
In the following we summarize the procedure of D4 in a step by step scheme:
polarizability αAm Hn (iω) or αBk Hl (iω).
1) Scaling of stored reference molecule TD-DFT polarizabilities by ζ to include a charge
A B
C6AB ≡ CAB A B
6 (CNcov , z , CNcov , z ) dependence into the model.
3
Z ∞ (10)
= dω αA (iω) αB (iω)
π 0 2) Calculation of system specific polarizabilities at imaginary frequencies as Gaussian

Equation 10 uses the short-hand notation of αA/B (iω) (see equation 5) and additionally intro- averages (via CNA
cov ) over reference polarizabilities.

duces the short-hand notation of the weighted and charge dependent dispersion coefficients, 3) Calculation of the dispersion coefficients CAB by numerical Simpson integration from
6
C6AB , which is also used in the manuscript. In the D4 model, dispersion coefficients are di- the system specific polarizabilities obtained in step (2).
rectly calculated from weighted polarizabilities instead of weighting precalculated reference
The steps given above describe the working procedure of the actual program during the cal-
dispersion coefficients as it was done in D3. In comparison to the D3 model, an additional
culation of charge dependent pairwise CAB
6 dispersion coefficients for an arbitrary molecule.
loop over the 23 imaginary frequencies is required (Simpson integration), however, the ad-
The additivity of these pairwise dispersion coefficients can be exploited to derive a molecular
ditional computational costs are negligible in a QM context. The use of polarizabilities
dispersion coefficient according to
instead of precomputed pairwise dispersion coefficients also facilitates the computation of
higher-order, many-body coefficients. For example, the dispersion coefficient of the leading NA B
atoms Natoms
X X
Cmol
6 = Cpq
6 , (12)
nonadditive term describing the three-body long-range dispersion interaction is defined, as p q

where p and q refer to atoms of the particular molecules A and B, respectively. Here, the
molecular dispersion coefficient is expressed as a sum over atomic dispersion terms. 12

S8 S9
Parametrization of the ζ scaling function Table A2: Parameter a and b in the ζ scaling function for all elements adjusted to fit
molecular dispersion coefficients of the reference systems z A = z A,ref to parametrize b, and to
As given in the manuscript the charge function is defined as fit cationic static polarizabilities of each element z A 6= z A,ref to parametrize a. The parameter
a is an element specific parameter which is adjusted to fit cationic static polarizabilities of
Part C the bold-face labeled systems (with the exception of alkali metals, here we use different a
parameter for CN=0 and CN=1; for hydrogen the a parameter was adjusted by hand to fit
z }|
{
1.47 exp z A /z A,ref log z A,ref /z A


| {z } chemical intuition) while the b parameter were adjusted separately for each reference system
ζ(z A ) = |{z}
b a Part A . to match their calculated TD-DFT molecular C6 coefficient at the described level of theory.
Part B While using the implemented GBSA(H2 O) method, different Mulliken partial charges are
calculated. For this case all b parameter were re-adjusted to cancel artifacts.
• z A : Effective nuclear charge of atom A (see equation 1)
Element System Fitset a(element) bGas (CN) bGBSA(H2O) (CN)
• z A,ref : Reference effective nuclear charge of atom A in reference system Am Hn
1 0001 H 3.976 1.000 1.000
1001 H2 3.976 1.000 1.000
Part A The functional dependency in the exponent of the charge function is obtained from
2 0002 He 100.000 0.998 0.998
explicitly calculated polarizabilities at imaginary frequencies where the nuclear charges of
3 0003 Li 562.341 0.972 0.972
the m chemically equivalent atoms within each reference system Am Hn are varied to simulate
1003 LiH 10.000 0.622 0.658
a modified fractional electron occupation.
4 0004 Be 4.000 0.988 0.988

Part B In case that both effective nuclear charges match (z = z A A,ref

), the exponent of 1004 BeH 4.000 0.989 0.989

the charge function is equal to zero which enables the parametrization of the parameter b by 2004 BeH2 4.000 0.994 1.015

recreating the explicitly calculated molecular dispersion coefficient of the particular reference 5 0005 B 6.000 0.994 0.994

system. One has to note that this parameter is reference system dependent. 1005 BH 6.000 0.994 0.994
2005 BH2 6.000 0.994 0.994
Part C In case that both effective nuclear charges do not match (z A 6= z A,ref ), the exponent 3005 BH3 6.000 0.995 0.995
of the charge function is not equal to zero. For each element molecular dispersion coefficients 4005 B2 H6 6.000 0.959 0.957
of different cationic cross-check systems are used to parametrize a. Additionally, the cationic 6 0006 C 5.623 0.997 0.997
static polarizabilities α(0) for each element of the periodic system are used to check the 1006 CH 5.623 0.996 0.996


parametrization of the element specific a parameter. The factor exp z A /z A,ref within the 2006 C 2 H2 5.623 1.012 1.012
exponent of the charge function ensures the proper scaling behavior (stronger scaling for 3006 C 2 H4 5.623 1.016 1.015
cationic systems (z A > z A,ref ) , damped scaling for anionic systems (z A < z A,ref ). 4006 C 2 H6 5.623 1.022 1.021
5006 C 6 H6 5.623 1.002 1.002

S10 S11