European Commission PROJECT NMP3-CT-2003-504937 “Multifunctional percolated nanostructured ceramics fabricated from hydroxylapatyte” Computational Molecular

European CommissionPROJECT NMP3-CT-2003-504937“Multifunctional percolated nanostructured ceramics fabricated from hydroxylapatyte”

PERCERAMICS PERCERAMICS

Computational Molecular Nanostructures and Mechanical Properties of

Bystrov V., Paramonova E., Bystrova N., Sapronova A., Filippov S.

Institute of Mathematical Problems of Biology RAS, Pushchino,

142290, Moscow region, Russia

e-mail: [email protected] , [email protected]

Hydroxyapatite

mailto:[email protected]










European CommissionPROJECT NMP3-CT-2003-504937

“Multifunctional percolated nanostructured ceramics fabricated from hydroxylapatyte”

PERCERAMICS PERCERAMICS

Computational Molecular Nanostructures and Mechanical

Properties of Hydroxyapatite

Bystrov V., Paramonova E., Bystrova N., Sapronova A., Filippov S.

Institute of Mathematical Problems of Biology RAS, Pushchino, 142290, Moscow region, Russia

e-mail: [email protected] [email protected]









PERCERAMICS

Project NMP3-CT-2003-504937 of FP6 ( EC ) on 2004-2006 years.

Multifunctional percolated nanostructured ceramics fabricated from hydroxylapatite

The project will develop a percolated nanostructured electrically polarized ceramics (CER) fabricated from hydroxylapatite (HAP) to improve quality of bone eligible bioimplants, work out new material for immobilization of microorganisms for their further use to product of various biologically active compounds (BAC) and purify the environment. A surface of CER will provide a relevant biological – non-biological interface to adhere cells/microorganisms.

A surface morphology of CER will be supplied at a nano scale eligible for a cell receptor “tail” size and will be “packed” from HAP nanoparticles. The CER surface will be charged and supplied with a web of the canals. Engineering support employing knowledge acquired from computational physics research on charging and adhesion/cohesion by HAP nanoparticles will be provided.

To meet CER applications the project is focused to: investigation of yeast cell physiology in biofilms immobilised in novel matrices; immobilization of bacterial cells and yeasts for the purification of the environment, bioremediation and industrial biotechnological processes; working out of active dry preparations of immobilized microorganisms; fabrication of bone eligible implants.

The results are planned to implement in industry, medicine, environment and biotechnologies. New benefits in safety of environment, health and biotechnologies will be challenged.

Professionals from computational and material physics, chemistry, engineering of materials and their characterization, microbiology, biotechnology, wastewater treatment, orthopaedics and industries will be involved on a multidisciplinary approach and a critical mass of the project. A sustainable development at relevant industries and research will spurt. The project partners’ cooperation will become stronger and reach European networking scale to strengthen and integrate the European Research Area.х



PERCERAMICS PERCERAMICS Computational Molecular

Nanostructures and Mechanical Properties

of Hydroxyapatite

Hydroxyapatite [Ca5(PO4)3OH; (HAP)]

corresponds to structure of mineral bone’s component

leads to the new bone formation generated by osteoblasts on its surface

if charged and polarized

•has specific surface characteristics

•improves adhesion properties

•provide additional stimulation of the interaction with living cells

Processes of a charge transfer in the HAP structure cause the arising of the polarization and have electrets-like character

Mechanism of polarization and surface electrical / mechanical (adhesion) properties changes are not clear





of Hydroxyapatite

Purpose:

Investigation of the HAP structural changes

and

analyse mechanisms of charge transfer

using the computer simulation of HAP crystal nanostructures

Software:

Voxel; HyperChem; Crystals; Babel; Gaussian-98





of Hydroxyapatite

Used experimental data on HAP structure from ftp://ftp.geo.arizona.edu/pub/xtal/data/AMCfiles/01209.amc

atom x y z Biso B(1,1) B(2,2) B(3,3) B(1,2) B(1,3)Ca1 0,66667 0,33333 0,00144 0,00408 0,00408 0,0033 0,00204 0Ca2 -0,00657 0,24706 0,25 0,00308 0,00353 0,00417 0,00156 0P 0,36860 0,39866 0,25 0,00223 0,0025 0,0034 0,00127 0

O1 0,48500 0,32890 0,25 0,0036 0,0044 0,0059 0,0027 0O2 0,46490 0,58710 0,25 0,0035 0,0031 0,0105 0,0016 0O3 0,25800 0,34350 0,0703 0,005 0,0096 0,007 0,00505 -0,0025

O(H) 0 0 0,1979 0,003 0,003 0,012 0,0015 0H 0 0 0,04 3,3

In the program Crystals http://www.xtl.ox.ac.uk/crystals.html are received the *.pdb file with coordinates of all atoms (for one and several channels) and qualitative images of HAP structure.

ftp://ftp.geo.arizona.edu/pub/xtal/data/AMCfiles/01209.amc










http://www.xtl.ox.ac.uk/crystals.html





Parameters of the elementary crystal cell unit: a = b = 9,4166 Angstrem = 0,94166 nm, c = 6,8745 Angstrem = 0,68745 nm.





of Hydroxyapatite

x y z

нм

Ca1 0,6278 0,3139 0,0010

Ca2 -0,0062 0,2326 0,1719

P 0,3471 0,3754 0,1719

O1 0,4567 0,3097 0,1719

O2 0,4378 0,5528 0,1719

O3 0,2429 0,3235 0,0483

O(H) 0 0 0,1360

H 0 0 0,0275

a b c

9,4166 9,4166 6,8745

x y z Å

atom

Ca1 6,2777 3,1389 0,0099

Ca2 -0,0619 2,3265 1,7186

P 3,4710 3,7540 1,7186

O1 4,5671 3,0971 1,7186

O2 4,3778 5,5285 1,7186

O3 2,4295 3,2346 0,4833

O(H) 0 0 1,3605

H 0 0 0,2750

Parameters of cell unit:





of Hydroxyapatite

HAP structure

channels (parallel with c axes )





of Hydroxyapatite

H+ ion rotation model H+ ion transportation

polarization / depolarization are attributed to rotation of a proton around OH- in the colon-like channels

proton turns around O22- ion, then moves to the next vacancy O-

proton transfer on the large distances in the channels





of Hydroxyapatite

Proton transfer as possible mechanism of HAP polarization

Mathematical description of the system 1. Model of a discrete medium

2

220 1

1 1,

2 2n

n n nn

uH m m u u V u

t

m - proton mass, un - proton displacement

(1)

Varying (1) yields the Euler–Lagrange equations of motion

2

21 0 1 12

2n nn n n

d u dum m m u u udt dt

0.n

n

dV uF

du (2)

1 - damping in the system, F = qE - external field (q – charge, E - electric field),

Quantum-chemical calculations of proton transport between two methylamine molecules with and without external electric field, carried out with the GAUSSIAN-98 code http://www.gaussian.com (as example)





of Hydroxyapatite

–191.28

–191.27

–191.29

–191.300 0.5 1.0 1.5 2.0 r, Å

U, arb. un. |2|1.0

0.5

0

a

–191.28

–191.27

–191.29

–191.300 0.5 1.0 1.5 2.0 2.5 r, Å

b

–191.28

–191.29

–191.30

0 0.5 1.0 1.5 2.0 r, Å

U, arb. un. |2|1.0

0.5

0

a

–191.28

–191.27

–191.29

–191.300 0.5 1.0 1.5 2.0 2.5 r, Å

b

0.5

0

1.0

Change of spacing Change of electric field

http://www.gaussian.com/







of Hydroxyapatite

2.Continuous medium model

(N and l0 = c0/0 0

N and l0 = c0/0 0

2 2

21 0

1 1, .

2 2

u uH dx m mc V u x t

t x

(3)

2 41 10, 0 .

2 4V u Au Bu A B

2 220 2 2

0

1 0,dV ud u du

mc m Fc ds ds du

vv

Potential energy

(4)

(5)

equation of motion





of Hydroxyapatite

*

0 tanh2

a su u

2 *0sech a s

1/ 2**

0

1,

Aa

c m

proton subsystem

ion subsystem





of Hydroxyapatite

Sofware for computational visualization and animation of Hydroxyapatite structure

1.The CRYSTALS software package for single crystal X-ray structure refinement and analysis consists of CRYSTALS, Cameron and specially recompiled versions of SIR92 and SHELXS. 2. The CINEMA 4D XL Bundle includes advanced tools for professional users, including character animation utilities and advanced rendering and particle features.

To visualize molecular structures we have used a plug-in for Cinema 4D developed in the

Institute of Mathematical Problems of Biology RAS.





of Hydroxyapatite

Cinema 4D equipped with the plug-in can build molecular models

from PDB-files and has enabled us to employ in the visualization

the following technologies of professional computer 3D-graphics:

1.. Use of character animation (forward and inverse kinematics) for modeling conformational changes.

2.. Use of expressions for modeling the behavior of molecular groups.

3.. Use of particle systems for special effects to

visualize objects without clearly defined shape.



PERCERAMICS PERCERAMICS Computation of Molecular

Nanostructure and Mechanical Properties

of Hydroxyapatite

P 6/m

Explored initial HAP structure (group of symmetry are: P6/m and P63/m.)





of Hydroxyapatite

P 63/m

Са

OH

P

O





of Hydroxyapatite

P 63/m

Са onlyOH

Ca

P

O

Fig.4.(a, b). Tree-dimensional HAP structures (one channel), P 6/m symmetry

P 6/m

P 6/m





of Hydroxyapatite





of Hydroxyapatite





of Hydroxyapatite





of Hydroxyapatite

As results were obtained detailed computational structural models (quantum-chemical, soliton and continual) and calculated parameters of HAP nanoparticles for different symmetry groups. These results were obtained by using and adaptation of HyperChem, Crystals, Gaussian-98 and several special elaborated software of Dr. Bystrov group from IMPB. The calculated structural HAP properties and peculiarities allow us to understand (to clarify) the mechanism of charge (proton) transport (transfer) and surface charging of HAP nanoparticles. The estimated values of surface charge is ~ 0.1 C/m2 which is corresponded to known experimental data.

CONCLUSION

Documents

European Commission PROJECT NMP3-CT-2003-504937 “Multifunctional percolated nanostructured ceramics fabricated from hydroxylapatyte” Computational Molecular