Supporting Information

The interaction of diamond with biological matter is influenced by the diamond’s crystal

orientation

Viraj Damle1‡, Kaiqi Wu1‡, Oreste De Luca2, Natalia Ortí-Casañ3, Neda Norouzi1, Aryan

Morita1,4, Joop de Vries1, Hans Kaper1, Inge Zuhorn1, Ulrich Eisel3, Danny E.P Vanpoucke5,6,

Petra Rudolf 2, and Romana Schirhagl1

1. University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1,

9713AV, Groningen, The Netherlands

2. Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The

Netherlands

3. Department of Molecular Neurobiology, Groningen Institute for Evolutionary Life Sciences,

Faculty of Science and Engineering, University of Groningen, Nijenborgh 7, 9747 AG

Groningen, The Netherlands

4. Department of Dental Biomedical Sciences, Faculty of Dentistry, Universitas Gadjah Mada,

Jalan Denta 1 Yogyakarta 55281, Indonesia

5. Institute for Materials Research (IMO), Hasselt University, 3590 Diepenbeek, Belgium

6. IMOMEC, IMEC vzw, 3590 Diepenbeek, Belgium

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*Corresponding Author: Prof. Dr. Romana Schirhagl, University Medical Center Groningen,

Department of Biomedical Engineering, A. Deusinglaan 1, 9713 AV, Groningen, The

Netherlands

E-mail: romana.schirhagl@gmail.com

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Theoretical calculations

Materials methods

First principles spin-polarized calculations were performed within the projector augmented

waves (PAW) framework, implemented in VASP [1]. The electron exchange-correlation

interactions were described using the generalised gradient approximation (GGA) as devised by

Perdew, Burke and Ernzerhof (PBE) [2]. The various surfaces were simulated by periodic slabs,

with a 2x1 surface unit. The slab thickness was determined to obtain well-converged total

energies. The first Brillouin zone was sampled using a Monkhorst-Pack (MP) or Gamma ()

centered grid with a density sufficient to have the total energy of the systems converging within

1 meV. In Table S1 the slab thickness (in # of C layers) and k-point set for the different surface

orientations is presented.

Table S1. Slab thickness (number of relaxed layers on each side between brackets) and k-point

sets used for the different surface orientations.

# layers k-point set

<100> 16 (7) MP 8x16x1

<110> 19 (8) MP 15x10x1

<111> 20 (9) G 7x13x1

The structures were optimized using a conjugate gradient method with an energy convergence

criterion of 1.0E-7. Atomic charges were calculated using the Iterative Hirshfeld (Hirshfeld-I)

partitioning scheme as implemented in the HIVE code [3,4], using atom-centred Lebedev-Laikov

grids of 1202 grid points per radial shell [5,6]. Convergence of the iterative scheme was set to

1.0E-5 electron for each atom.

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Results and discussion

For the <100>, <110> and <111> orientations, we considered 2x1, 2x1, 1x1 surface

reconstructions, respectively as a starting geometry. For the clean and H-terminated <111>

surface, the 2x1 (or Pandey) reconstruction was also considered. However, we did not consider it

for the -F, -O and -OH termination as the 2x1 reconstruction is less stable than the 1x1

reconstruction upon termination in the case of the <111> surface. In each model, a full

monolayer surface termination (i.e., 1 functional group per surface C) was used. The formation

energy of the optimized surface models was calculated as:

E f=E surf−NC μC−N X μX ,

where E surf is the total energy of the optimized surface model, NC and N X the number of C and

surface groups (X=H, F, O, and OH), respectively, μC the chemical potential of C, which we set

to the value of a bulk diamond C atom, and μX the chemical potential of the surface group. For

H, F and O, μX was set to half the total energy of an X2 molecule, while for the OH group the

total energy of the neutral OH molecule was used. Based on the formation energy obtained at the

Perdew, Burke and Ernzehof (PBE) and HSE06 level (Table S2), the surface termination was

found to stabilize the diamond surface as the formation energy of a terminated surface is lower

than that of the clean surface. However, the order of preference for the termination is

independent of the surface orientation. From least to most preferred, we found clean < O (single-

bond) < H < O (double bond) < F < OH for PBE level calculations. Using the HSE06 hybrid

functional, nearly the same trend is found, with the exception of the order of the hydroxylated

and fluorinated <100> and <110> surfaces.

It is important to note that in the case of the O termination of the <100> surface, the C-

surface-dimers broke during structure optimization, leading to a short C-O double bond (1.194

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Å), in contrast to the longer single bonds at the <011> (1.355 Å) and <111> (1.311 Å) surfaces.

The hydroxyl-groups on the other hand formed networks of hydrogen bridges on the <011> and

<111> surfaces, contributing to their stability. Within an aqueous environment, we may therefore

expect to observe a prevalently hydroxyl-terminated surface, or termination with groups

presenting similar reactivity.

Table S2 The formation energy of various diamond surface-terminations at the PBE level.

Formation energies at the HSE06 level are given between brackets. All energies are in eV per

surface C.

2x1 <100> 2x1 <110> 1x1 <111> 2x1 <111>

Clean 1.883 ( 2.079) 1.451 ( 1.648) 1.772 ( 1.861) 1.175 ( 1.408)

-H 0.017 (-0.012) -0.228 (-0.306) -0.335 (-0.403) 0.308 ( 0.338)

-F -1.560 (-1.655) -1.097 (-1.283) -1.767 (-1.907) -

-O -0.255 (-0.146) 0.818 ( 0.994) 0.353 ( 0.698) -

-OH -1.622 (-1.213) -1.255 (-0.929) -2.406 (-2.066) -

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Figure S1 Ball-and-stick representation of the differently terminated diamond surfaces,

investigated using first principles simulations. For each structure a top view (top) of a 2x2

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surface unit is shown. The side view (bottom) presents the atomic positions in the top most

layers of the simulated system.

HeLa cell cultures

Figure S2 Nearly confluent layer of HeLa cells on low index diamond crystals after 2 days of

incubation as imaged using an optical microscope.

XPS analysis

Figure S3 shows the detailed XPS spectra of the C1s core level region of the three acid-treated

low index diamond surfaces. The spectral intensity of the C1s, O1s and Na1s lines inform on the

elemental composition of the surfaces before and after BH3-THF reduction, as shown for the

<100> surface in table S3. The fit of the C1s spectra allowed us to determine the various surface

functional groups and determine their relative abundance on the surfaces before and after BH3-

THF reduction, as detailed in table S4 again for the case of the <100> surface.

The survey XPS spectra obtained from oxidized, EDC-NHS activated, pristine and aged low

index diamond surfaces are shown in Fig S4. Tiny amounts of gold visible in the spectrum stem

from the presence of the gold mesh placed 1 mm above the sample to avoid charging.

Figure S5 instead shows the detailed spectra of the C1s, N1s, O1s and Na1s core level regions

collected from the same oxidized, EDC-NHS activated, pristine and aged low index diamond

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surfaces. These spectra were used to calculate the relative abundances of functional groups

reported in the main text of the paper.

Figure S3 Detailed XPS spectra of the C1s core level region (dots) and corresponding fit

(continuous lines) to determine the presence of different functional groups.

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Table S3 Atomic composition of <100> surface before and after BH3-THF reduction.

XPS LineBinding Energy

(eV)

Atom %

Before reduction After reduction

C 1 s 284.8 71.35 79

O 1 s 531.7 23.29 18

Na 1 s 1070.5 2.66 2

Table S4. Surface functional groups of <100> surface before and after BH3-THF reduction.

XPS LineBinding Energy

(eV)

Group %

Before reduction After reduction

-COOH 288.2 1.13 --

-C=O 287.0 7.67 1

-C-O- 285.6 14.46 16.

-C-C- 284.8 60.96 79

Defects

C=C283.5 15.78 4

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Figure S4 XPS survey spectra collected from <100>, <110> and <111> diamond surfaces after different surfaces treatments.

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Figure S5. Detailed XPS spectra of the C1s, O1s, N1s, Na1s core level regions for the <100>, <110>, <111> diamond surfaces after different surface treatments.

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