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Fullerenes: applications and generalizations Michel Deza Ecole Normale Superieure, Paris, and JAIST, Ishikawa Mathieu

Fullerenes: applications and generalizations

Michel Deza

Ecole Normale Superieure, Paris, and JAIST, Ishikawa

Mathieu Dutour Sikiric

Rudjer Boskovic Institute, Zagreb, and ISM, Tokyo

Paris, and JAIST, Ishikawa Mathieu Dutour Sikiric Rudjer Boskovic Institute, Zagreb, and ISM, Tokyo – p.
I. General setting – p. 2/151

I. General setting

I. General setting – p. 2/151

Polytopes and their faces

Polytopes and their faces A d -polytope : the convex hull of a finite subset of

A d-polytope: the convex hull of a finite subset of R d .

A face of P is the set {x P : f ( x ) = 0} where f is

linear non-negative function on P .

A face of dimension i is called i-face; for i= 0, 1, 2, d 2, d 1 it is called, respectively, vertex, edge, face, ridge and facet.

1 , 2 , d − 2 , d − 1 it is called, respectively, vertex
1 , 2 , d − 2 , d − 1 it is called, respectively, vertex
1 , 2 , d − 2 , d − 1 it is called, respectively, vertex

Skeleton of polytope

The skeleton of polytope P is the graph G ( P ) formed by vertices,

The skeleton of polytope P is the graph G ( P ) formed by vertices, with skeleton of polytope P is the graph G ( P ) formed by vertices, with two vertices adjacent if they form an edge. d-polytopes P and P are of the same combinatorial

with two vertices adjacent if they form an edge. d -polytopes P and P ′ are

type if G ( P ) G ( P ) .

The dual skeleton is the graph G ∗ ( P ) formed by facets with two dual skeleton is the graph G ( P ) formed by facets with two facets adjacent if their intersection is a ridge. (Poincaré) dual polytopes P and P on sphere S d 1 :

G ( P ) = G ( P ) .

Steinitz’s theorem: a graph is the skeleton of a 3 -polytope if and only if it : a graph is the skeleton of a 3-polytope if and only if it is planar and 3-connected, i.e., removing any two edges keep it connected.

of a 3 -polytope if and only if it is planar and 3 -connected , i.e.,
of a 3 -polytope if and only if it is planar and 3 -connected , i.e.,

4-cube

Regular d -polytopes:   self-dual d -simplex G ( α d ) = K d
Regular d -polytopes:   self-dual d -simplex G ( α d ) = K d
Regular d -polytopes:   self-dual d -simplex G ( α d ) = K d
Regular d -polytopes:   self-dual d -simplex G ( α d ) = K d

Regular d-polytopes:

 

self-dual d-simplex G ( α d ) = K d +1 ,

d-cube G ( γ d ) = H d = ( K 2 ) d and

its dual d-cross-polytope G ( β d ) = K 2 d dK 2 .

its dual d -cross-polytope G ( β d ) = K 2 d − dK 2
its dual d -cross-polytope G ( β d ) = K 2 d − dK 2

Euler formula

f -vector of d -polytope: ( f 0 , -vector of d-polytope: ( f 0 ,

, f d 1 , f d = 1) where f j is the

number of i-faces. Euler characteristic equation for a map on oriented ( d 1) -surface of genus g :

χ =

d

j

1

=0

( 1) j f j = 2(1 g ) .

For a polyhedron (3-polytope on S 2 ), it is f 0 f 1 + f 2 = 2.

p -vector: ( p 3 , v -vector: ( v 3 ,

) where p i is number of i-gonal faces. ) where v i is number of i-valent vertices.

So, f 0 = i 3 v i , f 2 = i 3 p i and 2f 1 = i 3 iv i = i 3 ip i .

i

3

(6 i) p i + (3 i) v i = 12.

i

3

A fullerene polyhedron has v i = 0 only for i = 3

and p i p i

=

0 only for i = 5, 6. So, (6 5) p 5 = p 5 = 12 .

= 0 only for i = 3 and p i = 0 only for i =

Definition of fullerene

Definition of fullerene A fullerene F n is a simple (i.e., 3 -valent) polyhedron (putative carbon

A fullerene F n is a simple (i.e., 3-valent) polyhedron (putative carbon molecule) whose n vertices (carbon atoms) are arranged in 12 pentagons and ( n 10) hexagons. The 3 n edges correspond to carbon-carbon bonds.

2

2

F n exist for all even n ≥ 20 except n = 22 . n exist for all even n 20 except n = 22.

1, 1 , 1 , 2 , 5 , 1, 1, 2, 5

, 1812,

20, 24, 26, 28, 30

, 60,

214127713,

, 200,

isomers F n , for n =

Thurston,1998, implies: no. of F n grows as n 9 . F n grows as n 9 .

C 6 0 ( I h ) , C 8 0 ( I h ) 60 ( I h ) , C 80 ( I h )

are only icosahedral (i.e., with highest

symmetry I h or I ) fullerenes with n 80 vertices.

I h or I ) fullerenes with n ≤ 80 vertices. preferable fullerenes, C n ,

preferable fullerenes, C n , satisfy isolated pentagon rule, but Beavers et al, August 2006, produced fullerenes, C n , satisfy isolated pentagon rule, but Beavers et al, August 2006, produced buckyegg:

C 84 (and T b 3 N inside) with 2 adjacent pentagons.

et al, August 2006, produced buckyegg : C 8 4 (and T b 3 N inside)

Examples

      buckminsterfullerene C 6 0 ( I h ) truncated icosahedron, soccer ball
      buckminsterfullerene C 6 0 ( I h ) truncated icosahedron, soccer ball
      buckminsterfullerene C 6 0 ( I h ) truncated icosahedron, soccer ball
   
   
 

buckminsterfullerene C 60 ( I h ) truncated icosahedron, soccer ball

F

36 ( D 6 h )

elongated hexagonal barrel

F

24 ( D 6 d )

icosahedron, soccer ball F 3 6 ( D 6 h ) elongated hexagonal barrel F 2
icosahedron, soccer ball F 3 6 ( D 6 h ) elongated hexagonal barrel F 2

The range of fullerenes

The range of fullerenes Dodecahedron F 2 0 ( I h ) : t h e

Dodecahedron F 20 ( I h ) :

the smallest fullerene

h e s m a l l e s t f u l l e r

Graphite lattice (6 3 ) as F :

the “largest fullerene"

t f u l l e r e n e Graphite lattice (6 3 ) as

Finite isometry groups

All finite groups of isometries of 3 -space are classified. In Schoenflies notations:

All finite groups of isometries of 3-space are classified. In Schoenflies notations:

All finite groups of isometries of 3 -space are classified. In Schoenflies notations:
 

C 1 is the trivial group 1 is the trivial group

C s is the group generated by a plane reflexion s is the group generated by a plane reflexion

C i = { I 3 , − I 3 } is the inversion group i = {I 3 , I 3 } is the inversion group

C m is the group generated by a rotation of order m of axis ∆ m is the group generated by a rotation of order m of axis

C m v ( ≃ dihedral group) is the group formed by C m and m mv (dihedral group) is the group formed by C m and m reflexion containing

C m h = C m × C s is the group generated by C m mh = C m × C s is the group generated by C m and the symmetry by the plane orthogonal to

S N is the group of order N generated by an antirotation

S N is the group of order N generated by an antirotation N is the group of order N generated by an antirotation

S N is the group of order N generated by an antirotation

Finite isometry groups

D m (≃ dihedral group) is the group formed of C m and m rotations
D m (≃ dihedral group) is the group formed of C m and m
rotations of order 2 with axis orthogonal to ∆
D mh is the group generated by D m and a plane
symmetry orthogonal to ∆
D md is the group generated by D m and m symmetry
planes containing ∆ and which does not contain axis of
order 2
D 2 h
D 2 d

Finite isometry groups

I h = H 3 ≃ Alt 5 × C 2 is the group of
I h = H 3 ≃ Alt 5 × C 2 is the group of

I h = H 3 Alt 5 × C 2 is the group of isometries of the regular Dodecahedron

I h = H 3 ≃ Alt 5 × C 2 is the group of isometries
≃ Alt 5 is the group of rotations of the regular Dodecahedron I

Alt 5 is the group of rotations of the regular Dodecahedron

I

O h = B 3 is the group of isometries of the regular Cube

O

h = B 3 is the group of isometries of the regular Cube

O ≃ Sym (4) is the group of rotations of the regular Cube

O

Sym (4) is the group of rotations of the regular Cube

T d = A 3 ≃ Sym (4) is the group of isometries of the

T d = A 3 Sym (4) is the group of isometries of the regular Tetrahedron

 
T ≃ Alt (4) is the group of rotations of the regular

T

Alt(4) is the group of rotations of the regular

 

Tetrahedron

 
 
  T h = T ∪ − T

T h = T ∪ − T

T ≃ Alt (4) is the group of rotations of the regular   Tetrahedron    
T ≃ Alt (4) is the group of rotations of the regular   Tetrahedron    

Point groups

(point group) Isom ( P ) ⊂ Aut ( G ( P )) (combinatorial group)

(point group) Isom ( P ) Aut( G ( P )) (combinatorial group) Theorem (Mani, 1971) Given a 3-connected planar graph G , there exist a 3-polytope P , whose group of isometries is isomorphic to

1971) Given a 3 -connected planar graph G , there exist a 3 -polytope P ,

Aut( G ) and G ( P ) = G .

All groups for fullerenes (Fowler et al) are:

1. C 1 , C s , C i

2. C 2 , C 2 v , C 2 h , S 4 and C 3 , C 3 v , C 3 h , S 6

3. D 2 , D 2 h , D 2 d and D 3 , D 3 h , D 3 d

4. D 5 , D 5 h , D 5 d and D 6 , D 6 h , D 6 d

5. T , T d , T h and I , I h

, D 5 h , D 5 d and D 6 , D 6 h ,
, D 5 h , D 5 d and D 6 , D 6 h ,

Small fullerenes

24, D 6 d 26, D 3 h 28, D 2 28, T d 30,
24, D 6 d
26, D 3 h
28, D 2
28, T d
30, D 5 h
30, C 2 v
30, C 2 v
A C 540 – p. 15/151

A C 540

A C 540 – p. 15/151
A C 540 – p. 15/151

What nature wants?

Fullerenes or their duals appear in Architecture and nanoworld:

Fullerenes or their duals appear in Architecture and nanoworld:

Fullerenes or their duals appear in Architecture and nanoworld:

Biology: virus capsids and clathrine coated vesicles : virus capsids and clathrine coated vesicles

Organic (i.e., carbon) Chemistry Chemistry

also: (energy) minimizers in Thomson problem (for n unit charged particles on sphere) and Skyrme problem (for given baryonic Thomson problem (for n unit charged particles on sphere) and Skyrme problem (for given baryonic number of nucleons); maximizers, in Tammes problem, of minimum distance between n points on sphere

Which, among simple polyhedra with given number of faces, are the “best” approximation of sphere? Conjecture: FULLERENES

among simple polyhedra with given number of faces, are the “best” approximation of sphere? Conjecture: FULLERENES
among simple polyhedra with given number of faces, are the “best” approximation of sphere? Conjecture: FULLERENES

Graver’s superfullerenes

Almost all optimizers for Thomson and Tammes problems, in the range 25 ≤ n ≤

Almost all optimizers for Thomson and Tammes problems, in the range 25 ≤ n ≤ 125 are fullerenes. 25 n 125 are fullerenes.

Almost all optimizers for Thomson and Tammes problems, in the range 25 ≤ n ≤ 125

For n > 125 , appear 7 -gonal faces; for n > 300 : almost always. n > 125, appear 7-gonal faces; for n > 300: almost always.

However, J.Graver, 2005: in all large optimizers, the 5 - and 7 -gonal faces occurs in 12 distinct clusters, corresponding to a unique 5- and 7-gonal faces occurs in 12 distinct clusters, corresponding to a unique underlying fullerene.

optimizers, the 5 - and 7 -gonal faces occurs in 12 distinct clusters, corresponding to a
optimizers, the 5 - and 7 -gonal faces occurs in 12 distinct clusters, corresponding to a

Skyrmions and fullerenes

Conjecture (Battye-Sutcliffe, 1997):

Conjecture (Battye-Sutcliffe, 1997):

Conjecture (Battye-Sutcliffe, 1997):

any minimal energy Skyrmion (baryonic density isosurface for single soliton solution) with baryonic number (the number of nucleons) B 7 is a fullerene F 4 B 8 .

Conjecture (true for B < 107; open from ( b, a) = (1, 4) ):

there exist icosahedral fullerene as a minimal energy Skyrmion for any B = 5( a 2 + ab + b 2 ) + 2 with integers 0 b < a, gcd( a, b ) = 1 (not any icosahedral Skyrmion has minimal energy).

Skyrme model (1962) is a Lagrangian approximating QCD (a gauge theory based on SU (3) group). Skyrmions are special topological solitons used to model baryons.

QCD (a gauge theory based on SU (3) group). Skyrmions are special topological solitons used to
QCD (a gauge theory based on SU (3) group). Skyrmions are special topological solitons used to

Isoperimetric problem for polyhedra

Lhuilier 1782, Steiner 1842, Lindelöf 1869, Steinitz 1927, Goldberg 1933, Fejes Tóth 1948, Pólya 1954Isoperimetric problem for polyhedra Polyhedron of greatest volume V with a given number of faces and

Polyhedron of greatest volume V with a given number of faces and a given surface S ? V with a given number of faces and a given surface S ?

Polyhedron of least volume with a given number of faces circumscribed around the unit sphere?V with a given number of faces and a given surface S ? Maximize Isoperimetric Quotient

Maximize Isoperimetric Quotient for solids. Isoperimetric Quotient for solids.

Schwarz,1890:

IQ = 36π V 2

S

3

1 (with equality only for sphere)

In Biology: the ratio V (= 3 r for spherical animal of radius r ) affects heat gain/loss, nutritient/gas V (= 3 r for spherical animal of radius r ) affects heat gain/loss, nutritient/gas transport into
body cells and organism support on its legs.In Biology: the ratio V (= 3 r for spherical animal of radius r ) affects

S

r ) affects heat gain/loss, nutritient/gas transport into body cells and organism support on its legs.

Isoperimetric problem for polyhedra

polyhedron upper bound π Tetrahedron IQ( P ) 6 √ π 3 ≃ 0.302 6
polyhedron
upper bound
π
Tetrahedron
IQ( P )
6 √ π 3 ≃ 0.302
6
√ 3
π
π
Cube
6
Octahedron
≃ 0.524
3 √ 3 ≃ 0.605
6
π
≃ 0.637
πτ 7/2
πτ 7/2
Dodecahedron
5/4 ≃ 0.755
3 .5
3 .5 5/4
4
πτ
Icosahedron
√ 3 ≃ 0.829
≃ 0.851
15

IQ of Platonic solids

(τ = 1+ 5

2

: golden mean)

Conjecture (Steiner 1842):

Each of the 5 Platonic solids has maximal IQ among all isomorphic to it (i.e., with same skeleton) polyhedra (still open for the Icosahedron)Each of the 5 Platonic solids has maximal IQ among all isomorphic

IQ among all isomorphic to it (i.e., with same skeleton) polyhedra (still open for the Icosahedron)

Classical isoperimetric inequality

Classical isoperimetric inequality If a domain D ⊂ E n has volume V and bounded by

If a domain D E n has volume V and bounded by hypersurface of ( n 1) -dimensional area A , then Lyusternik, 1935:

IQ( D ) =

n n ω n V n1

A n

1

with equality only for unit sphere S n ; its volume is

ω n =

only for unit sphere S n ; its volume is ω n = n 2 π

n

2

π

2

) , where Euler’s Gamma function is

nΓ( n

2

Γ( n ) =

2

( n

2

)! for even n

π ( n2)!!

2 n 2

2

for odd n

is n Γ( n 2 Γ( n ) = 2 ( n 2 )! for even

Five Platonic solids

Five Platonic solids – p. 22/151
Five Platonic solids – p. 22/151
Five Platonic solids – p. 22/151
Five Platonic solids – p. 22/151
Five Platonic solids – p. 22/151
Five Platonic solids – p. 22/151
Five Platonic solids – p. 22/151

Goldberg Conjecture

Goldberg Conjecture 20 faces: IQ ( Icosahedron ) < IQ ( F 3 6 ) ≃

20 faces: IQ( Icosahedron ) < IQ( F 36 ) 0.848

Conjecture (Goldberg 1933):

The polyhedron with m 12 facets with maximal IQ is a fullerene (called “medial polyhedron” by Goldberg)

polyhedron IQ( P ) upper bound πτ 7/2 πτ 7/2 Dodecahedron F 20 ( I
polyhedron
IQ( P )
upper bound
πτ 7/2
πτ 7/2
Dodecahedron F 20 ( I h )
Truncated icosahedron C 60 ( I h )
Chamfered dodecahed. C 80 ( I h )
Sphere
3
.5
5/4 ≃ 0.755
≃ 0.9058
≃ 0.928
3
.5 5/4
≃ 0.9065
≃ 0.929
1
1
– p. 23/151
II. Icosahedral fullerenes – p. 24/151

II. Icosahedral fullerenes

II. Icosahedral fullerenes – p. 24/151

Icosahedral fullerenes

Call icosahedral any fullerene with symmetry I h or I

icosahedral any fullerene with symmetry I h or I All icosahedral fullerenes are preferable, except F

All icosahedral fullerenes are preferable, except F 2 0 ( I h ) F 20 ( I h )

n = 20 T , where T = a 2 + ab + b 2 ( = 20T , where T = a 2 + ab + b 2 (triangulation number) with 0 b a.

I h for a = b h for a = b

= 0 or b = 0 (extended icosahedral group);

I for 0< b < a (proper icos. group); T =7,13,21,31,43,57

b < a (proper icos. group); T =7,13,21,31,43,57 C 6 0 ( I h ) =
b < a (proper icos. group); T =7,13,21,31,43,57 C 6 0 ( I h ) =
b < a (proper icos. group); T =7,13,21,31,43,57 C 6 0 ( I h ) =
b < a (proper icos. group); T =7,13,21,31,43,57 C 6 0 ( I h ) =

C 60 ( I h ) = (1, 1) -dodecahedron C 80 ( I h ) = (2, 0) -dodecahedron

truncated icosahedron

chamfered dodecahedron

C 8 0 ( I h ) = (2 , 0) -dodecahedron truncated icosahedron chamfered dodecahedron
C 60 ( I h ) : (1, 1) - C 80 ( I h
C 60 ( I h ) : (1, 1) -
C 80 ( I h ) : (2, 0) -
C 140 ( I ) : (2, 1) -
dodecahedron
dodecahedron
dodecahedron
From 1998, C 80 ( I h ) appeared in Organic Chemistry in some
endohedral derivatives as La 2 @C 80 , etc.

Icosadeltahedra

Call icosadeltahedron the dual of an icosahedral fullerene icosadeltahedron the dual of an icosahedral fullerene

C 20 T ( I h ) or C 20 T ( I )

Geodesic domes: B.Fuller, patent 19542 0 T ( I h ) or C 20 T ( I ) ∗ ∗

Capsids of viruses: Caspar and Klug, Nobel prize 1982T ( I ) ∗ ∗ Geodesic domes: B.Fuller, patent 1954 O 45 4590 1450 3459

O 45 4590 1450 3459 1237 1267 2378 34 15 3489 1560 12 23 1256
O
45
4590
1450
3459 1237
1267
2378
34
15
3489
1560
12 23
1256
2348
O
34
15
1560
45
3489
1256
2348
1450
3459
4590
1267
2378
12
1237
23
3489 1256 2348 1450 3459 4590 1267 2378 12 1237 23 Dual C 6 0 ∗

Dual C

60 ( I h ) , ( a, b ) = (1, 1)

pentakis-dodecahedron

( I h ) , ( a, b ) = (1 , 1) pentakis-dodecahedron GRAVIATION (Esher

GRAVIATION (Esher 1952) omnicapped dodecahedron

( I h ) , ( a, b ) = (1 , 1) pentakis-dodecahedron GRAVIATION (Esher

Icosadeltahedra in Architecture

( a, b ) Geodesic dome ∗ (1, 0) ∗ (1, 1) Fullerene F 20
( a, b )
Geodesic dome
(1,
0)
(1,
1)
Fullerene
F 20 ( I h )
C 60 ( I h )
One of Salvador Dali houses
Artic Institute, Baffin Island
(3,
0)
Bachelor officers quarters, US
Air Force, Korea
(2,
2)
(4, 0)
(5,
0)
(6,
0)
C 180 ( I h )
C 240 ( I h )
C 320 ( I h )
C 500 ( I h )
C 720 ( I h )
U.S.S. Leyte
Geodesic Sphere, Mt Washington, New Hampshire
(8,
8)
US pavilion, Kabul Afghanistan
Radome, Artic dEW
Lawrence, Long Island
C 3840 ( I h )
(16, 0)
US pavilion, Expo 67, Montreal
C 5120 ( I h )
(18, 0)
Géode du Musée des Sciences, La Villete, Paris
C 6480 ( I h )
(18, 0)
Union Tank Car, Baton Rouge, Louisiana
C 6480 ( I h )

b = 0 Alternate, b = a Triacon and a + b Frequency (distance of two 5-valent neighbors) are Buckminster Fullers’s terms b = 0 Alternate , b = a Triacon and a + b Frequency (distance of

Triacon and a + b Frequency (distance of two 5 -valent neighbors) are Buckminster Fullers’s terms

Geodesic Domes

US pavilion, World Expo 1967, Montreal Spaceship Earth, Disney World’s Epcot, Florida
US pavilion, World Expo 1967, Montreal Spaceship Earth, Disney World’s Epcot, Florida
US pavilion, World Expo 1967, Montreal Spaceship Earth, Disney World’s Epcot, Florida
US pavilion, World Expo 1967, Montreal Spaceship Earth, Disney World’s Epcot, Florida

US pavilion, World Expo 1967, Montreal

Spaceship Earth, Disney World’s Epcot, Florida

US pavilion, World Expo 1967, Montreal Spaceship Earth, Disney World’s Epcot, Florida
US pavilion, World Expo 1967, Montreal Spaceship Earth, Disney World’s Epcot, Florida

Icosadeltahedra C n with a = 2

Icosadeltahedra C n with a = 2 ∗ C 8 0 ( I h ) ,

C 80 ( I h ) , ( a, b ) = (2, 0)

∗ C 8 0 ( I h ) , ( a, b ) = (2 ,

C 140 ( I ) , ( a, b ) = (2, 1)

Icosadeltahedra C

20 × 4 t ( I h ) (i.e., ( a, b ) = (2 t , 0) ) with t 4 are

used as schemes for directional sampling in Diffusion MRI (Magnetic Resonance Imaging) for scanning brain space more uniformly along many directions (so, avoiding sampling direction biases).used as schemes for directional sampling in Diffusion MRI ( Magnetic Resonance Imaging

) for scanning brain space more uniformly along many directions (so, avoiding sampling direction biases). –

C 60 (I h ) in leather

C 6 0 ( I h ) in leather Telstar ball, official match ball for 1970

Telstar ball, official match ball for 1970 and 1974 FIFA World Cup

C 60 ( I h ) is also the state molecule of Texas.

match ball for 1970 and 1974 FIFA World Cup C 6 0 ( I h )

The leapfrog of C 60 (I h )

The leapfrog of C 6 0 ( I h ) C 1 8 0 ( I
The leapfrog of C 6 0 ( I h ) C 1 8 0 ( I

C 180 ( I h ) , ( a, b ) = (3, 0)

) C 1 8 0 ( I h ) , ( a, b ) = (3

C

180 ( I h ) as omnicapped

buckminsterfullerene C 60

) , ( a, b ) = (3 , 0) ∗ C 1 8 0 ∗

Triangulations, spherical wavelets

Triangulations, spherical wavelets Dual 4 -chamfered cube ( a, b ) = (2 4 = 16
Triangulations, spherical wavelets Dual 4 -chamfered cube ( a, b ) = (2 4 = 16

Dual 4-chamfered cube

( a, b ) = (2 4 = 16, 0) , O h

4 -chamfered cube ( a, b ) = (2 4 = 16 , 0) , O

Dual 4-cham. dodecahedron

C 5120 , ( a, b ) = (2 4 = 16, 0) , I h

Used in Computer Graphics and Topography of Earth

2 0 , ( a, b ) = (2 4 = 16 , 0) , I
III. Fullerenes in Chemistry and Biology – p. 34/151

III. Fullerenes in Chemistry and Biology

III. Fullerenes in Chemistry and Biology – p. 34/151

Fullerenes in Chemistry

Carbon C and, possibly, silicium Si are only 4 -valent elements producing homoatomic long stable

Carbon C and, possibly, silicium Si are only 4-valent elements producing homoatomic long stable chains or nets

Carbon C and, possibly, silicium Si are only 4 -valent elements producing homoatomic long stable chains
 

Graphite sheet: bi-lattice (6 3 ) , Voronoi partition of the hexagonal lattice ( A 2 : bi-lattice (6 3 ) , Voronoi partition of the hexagonal lattice (A 2 ), “infinite fullerene”

Diamond packing: bi-lattice D -complex, α 3 -centering of the lattice f.c.c.= A 3 : bi-lattice D -complex, α 3 -centering of the lattice f.c.c.= A 3

Fullerenes : 1985 (Kroto, Curl, Smalley): Cayley A 5 , C 6 0 ( I

Fullerenes: 1985 (Kroto, Curl, Smalley): Cayley A 5 , C 6 0 ( I h : 1985 (Kroto, Curl, Smalley): Cayley A 5 , C 60 ( I h ) , tr. icosahedon, football; Nobel prize 1996 but Ozawa (in japanese): 1984. “Cheap” C 60 : 1990. 1991 (Iijima): nanotubes (coaxial cylinders). Also isolated chemically by now: C 70 , C 76 , C 78 , C 82 , C 84 . If > 100 carbon atoms, they go in concentric layers; if < 20, cage opens for high temperature. Full. alloys, stereo org. chemistry, carbon: semi-metal.

layers; if < 20 , cage opens for high temperature. Full. alloys, stereo org. chemistry, carbon:

Allotropes of carbon

Diamond: cryst.tetrahedral, electro-isolating, hard, transparent. Rarely > 50 carats, unique > 800 ct : : cryst.tetrahedral, electro-isolating, hard, transparent. Rarely > 50 carats, unique > 800ct:

Diamond : cryst.tetrahedral, electro-isolating, hard, transparent. Rarely > 50 carats, unique > 800 ct :
Diamond : cryst.tetrahedral, electro-isolating, hard, transparent. Rarely > 50 carats, unique > 800 ct :

Cullinan 3106ct = 621g . Kuchner: diamond planets?

Hexagonal diamond (lonsdaleite): cryst.hex., very rare; 1967, in shock-fused graphite from several meteorites

Hexagonal diamond (lonsdaleite): cryst.hex., very rare; 1967, in shock-fused graphite from several meteorites

ANDR (aggregated diamond nanorods): 2005, hardest

ANDR (aggregated diamond nanorods): 2005, hardest

Graphite : cryst.hexagonal, soft, opaque, el. conducting Graphene : 2004, 2 D -carbon 1-atom thick,

Graphite: cryst.hexagonal, soft, opaque, el. conducting Graphene: 2004, 2D -carbon 1-atom thick, very conduc. and strained into semiconducting is better than silicon

Amorphous carbon (no long-range pattern): synthetic; coal and soot are almost such

Amorphous carbon (no long-range pattern): synthetic; coal and soot are almost such

Fullerenes : 1985, spherical; only soluble carbon form

Fullerenes: 1985, spherical; only soluble carbon form

Nanotubes: 1991, cylindric, few nm wide, upto few mm; nanobudes : 2007, nanotubes combined with : 1991, cylindric, few nm wide, upto few mm; nanobudes: 2007, nanotubes combined with fullerenes

Nanotubes : 1991, cylindric, few nm wide, upto few mm; nanobudes : 2007, nanotubes combined with
Nanotubes : 1991, cylindric, few nm wide, upto few mm; nanobudes : 2007, nanotubes combined with

Allotropes of carbon: pictures

a) g) Diamond b) Graphite c) Lonsdaleite d) C 60 (e) C 540 f) C
a)
g)
Diamond b) Graphite c) Lonsdaleite d) C 60 (e) C 540 f) C 70
Amorphous carbon h) single-walled carbon nanotube
– p. 37/151

Type of nanotubes: pictures

The (n,m) nanotube is defined by the vector C h = na 1 + ma
The (n,m) nanotube is defined by the vector C h = na 1 + ma 2
in infinite graphene sheet {6 3 } describing how to roll it up;
T is the tube axis and a 1 , a 2 are unit vectors of {6 3 } in 6-gon.
It is called zigzag, chiral, armchair if m = 0, 0< m < n , m = n resp.
– p. 38/151

Other allotropes of carbon

Carbon nanofoam: 1997, clusters of about 4000 atoms linked in graphite-like sheets with some 7 -gons : 1997, clusters of about 4000 atoms linked in graphite-like sheets with some 7-gons (negatively curved), ferromagnetic

1997, clusters of about 4000 atoms linked in graphite-like sheets with some 7 -gons (negatively curved),
1997, clusters of about 4000 atoms linked in graphite-like sheets with some 7 -gons (negatively curved),
Glassy carbon : 1967; carbyne : linear Acetilic Carbon  

Glassy carbon: 1967; carbyne: linear Acetilic Carbon

 
White graphite (chaoite): cryst.hexagonal; 1968, in shock-fused graphite from Ries crater, Bavaria ?

White graphite (chaoite): cryst.hexagonal; 1968, in shock-fused graphite from Ries crater, Bavaria

?

? Carbon(VI) ; ? metallic carbon ; ?  

? Carbon(VI); ? metallic carbon; ?

 

? Prismane C 8 , bicapped P rism 3

graphite:  diamond:  

 

diamond:

 
graphite:   diamond:  

Carbon and Anthropic Principle

Nucleus of lightest elements H, He, Li, Be (and Boron?) were produced in seconds after Big Bang, in part, by scenario: Deuterium H 2 , H 3 , He 3 , He 4 , H , Li H 2 , H 3 , He 3 , He 4 , H , Li 7 . If week nuclear force was slightly stonger, 100% hydrogen Univers; if weaker, 100% helium Univers.

, H , Li 7 . If week nuclear force was slightly stonger, 100% hydrogen Univers;
, H , Li 7 . If week nuclear force was slightly stonger, 100% hydrogen Univers;
Billion years later, by atom fusion under high t 0 in stars

Billion years later, by atom fusion under high t 0 in stars

3He 4 C 12

(12 nucleons, i.e., protons/neutrons), then Ni, O, Fe etc.

"Happy coincidence": energy level of C ≃ the energies of 3 He; so, reaction was

"Happy coincidence": energy level of C the energies of 3 He; so, reaction was possible/probable.

Without carbon, no other heavy elements and life could not appear. C : 18 . 5% of human ( 0 . 03% Universe) weight. C : 18.5% of human (0.03% Universe) weight.

Without carbon, no other heavy elements and life could not appear. C : 18 . 5%
Without carbon, no other heavy elements and life could not appear. C : 18 . 5%
La C 8 2 first Endohedral Fullerene compound C 1 0 P h 9 OH
La C 8 2 first Endohedral Fullerene compound C 1 0 P h 9 OH

La C 82 first Endohedral Fullerene compound

C 10 P h 9 OH

Exohedral Fullerene compound (first with a single hydroxy group attached)

compound C 1 0 P h 9 OH Exohedral Fullerene compound (first with a single hydroxy

First non-preferable fullerene compound

First non-preferable fullerene compound T b 3 N @ C 8 4 with a molecule of

T b 3 N @C 84 with a molecule of

triterbium nitride inside Beavers et al, 2006: above "buckyegg". Unique pair of adjacent pentagons makes the pointy end. One Tb atom is nestled within the fold of this pair.triterbium nitride inside Beavers et al, 2006: above "buckyegg"

pair of adjacent pentagons makes the pointy end. One Tb atom is nestled within the fold

Terrones quasicrystalline cluster

In silico: from C 60 and F 40 ( T d ) ; cf. 2
In silico: from C 60 and F 40 ( T d ) ; cf. 2 atoms in quasicrystals

Onion-like metallic clusters

Onion-like metallic clusters Palladium icosahedral 5 -cluster P d 561 L 60 ( O 2 )
Onion-like metallic clusters Palladium icosahedral 5 -cluster P d 561 L 60 ( O 2 )

Palladium icosahedral 5-cluster

P d 561 L 60 ( O 2 ) 180 ( OAc ) 180

α Outer shell Total # of atoms # Metallic cluster ∗ 1 C 20 (
α
Outer shell
Total # of atoms
# Metallic cluster
1
C 20 ( I h )
13
[ Au 13 ( PMe 2 P h) 10 Cl 2 ] 3+
2
RhomDode 80 ( O h )
55
Au 55 ( P P h 3 ) 12 Cl 6
4
RhomDode 320 ( O h )
309
P t 309 ( P hen 36 O 30 ± 10 )
5
C 500 ( I h )
561
P d 561 L 60 ( O 2 ) 180 ( OAc ) 180
Icosahedral and cuboctahedral metallic clusters
5 C 500 ( I h ) 561 P d 561 L 60 ( O 2

Nanotubes and Nanotechnology

Helical graphite Deformed graphite tube Nested tubes (concentric cylinders) of rolled graphite; use(?): for composites
Helical graphite
Deformed graphite tube
Nested tubes (concentric cylinders) of rolled graphite;
use(?): for composites and “nanowires”

Applications of nanotubes/fullerenes

Fullerenes are heat-resistant and dissolve at room t 0 . There are thousands of patents

Fullerenes are heat-resistant and dissolve at room t 0 . There are thousands of patents for their commercial applications Main areas of applications (but still too expensive) are:

There are thousands of patents for their commercial applications Main areas of applications (but still too
 

El. conductivity of alcali-doped C 6 0 : insulator K 2 C 6 0 but superconductors K of alcali-doped C 60 : insulator K 2 C 60 but superconductors K 3 C 60 at 18K and Rb 3 C 60 at 30K (however, it is still too low transition T c )

Catalists for hydrocarbon upgrading (of heavy oils, methane into higher HC, termal stability of fuels etc.) (of heavy oils, methane into higher HC, termal stability of fuels etc.)

Pharmaceceuticals: protease inhibitor since derivatives of C 6 0 are highly hydrophobic and antioxydant (they : protease inhibitor since derivatives of C 60 are highly hydrophobic and antioxydant (they soak cell-damaging free radicals)

Superstrong materials, nanowires? ?

Now/soon : buckyfilms, sharper scanning microscope

Now/soon: buckyfilms, sharper scanning microscope : buckyfilms, sharper scanning microscope

Now/soon : buckyfilms, sharper scanning microscope

Nanotubes/fullerenes: hottest sci. topics

Ranking (by Hirsch-Banks h-b index) of most popular in 2006 scientific fields in Physics:Nanotubes/fullerenes: hottest sci. topics Carbon nanotubes 12.85, nanowires 8.75, quantum dots 7.84, fullerenes 7.78,

Carbon nanotubes 12.85, nanowires 8.75, quantum dots 7.84, fullerenes 7.78, giant magnetoresistance 6.82, M-theory 6.58, quantum computation 5.21,

Chem. compounds ranking: C 60 5.2, gallium nitride 2.1,

h-index of a topic, compound or a scholar is the highest number T of published articles on this topic, compound or by this scholar that have each received T citations. h-b index of a topic or compound is h-index divided by the number of years that papers on it have been published.on this topic, compound or by this scholar that have each received ≥ T citations. h-b

of a topic or compound is h -index divided by the number of years that papers

Chemical context

Crystals: from basic units by symm. operations, incl. translations, excl. order 5 rotations (“cryst. restriction”). : from basic units by symm. operations, incl. translations, excl. order 5 rotations (“cryst. restriction”). Units: from few (inorganic) to thousands (proteins).

translations, excl. order 5 rotations (“cryst. restriction”). Units: from few (inorganic) to thousands (proteins).
translations, excl. order 5 rotations (“cryst. restriction”). Units: from few (inorganic) to thousands (proteins).
Units: from few (inorganic) to thousands (proteins). Other very symmetric mineral structures: quasicrystals ,
Units: from few (inorganic) to thousands (proteins). Other very symmetric mineral structures: quasicrystals ,

Other very symmetric mineral structures: quasicrystals, fullerenes and like, icosahedral packings (no translations but rotations of order 5).

Fullerene-type polyhedral structures (polyhedra,

nanotubes, cones, saddles,

) were first observed

with carbon. But also inorganic ones were considered:

boron nitrides, tungsten, disulphide, allumosilicates

and, possibly, fluorides and chlorides. May 2006, Wang-Zeng-al.: first metal hollow cages

Au n = F n 4 (16 n 18). F Au n = F n − 4 ( 16 ≤ n ≤ 18 ).

2

28 is the smallest; the gold

clusters are flat if n < 16 and compact (solid) if n > 18.

∗ is the smallest; the gold clusters are flat if n < 16 and compact (solid)

Stability of fullerenes

Stability of a molecule : minimal total energy, i.e.,

Stability of a molecule: minimal total energy, i.e.,

Stability of a molecule : minimal total energy, i.e.,

I -energy and -energy and

the strain in the 6 -system. 6-system.

Hückel theory of I -electronic structure: every eigenvalue λ of the adjacency matrix of the graph corresponds to an orbital of energy α + λβ , where α is the Coulomb parameter (same for all sites) and β is the resonance parameter (same for all bonds). The best I -structure: same number of positive and negative eigenvalues.

the resonance parameter (same for all bonds). The best I -structure: same number of positive and
the resonance parameter (same for all bonds). The best I -structure: same number of positive and

Fullerene Kekule structure

Perfect matching (or 1-factor) of a graph is a set of disjoint edges covering all vertices. A (or 1-factor) of a graph is a set of disjoint edges covering all vertices. A Kekule structure of an organic compound is a perfect matching of its carbon skeleton, showing the locations of double bonds.

structure of an organic compound is a perfect matching of its carbon skeleton, showing the locations
A set H of disjoint 6 -gons of a fullerene F is a resonant

A

set H of disjoint 6-gons of a fullerene F is a resonant

pattern if, for a perfect matching M of F , any 6-gon in H

is

M -alternating (its edges are alternatively in and off M ).

Fries number of F is maximal number of M -alternating

Fries number of F is maximal number of M -alternating

hexagons over

all perfect matchings M ;

Clar number is maximal size of its resonant pattern.

A fullerene is k -resonant if any i ≤ k disjoint hexagons

A

fullerene is k -resonant if any i k disjoint hexagons

form a resonant pattern. Any fullerene is 1-resonant; conjecture: any preferable fulerene is 2-resonant. Zhang et al, 2007is 1-resonant; conjecture : any preferable fulerene is 2-resonant. : all 3-resonant fullerenes: C 6 0 : all 3-resonant fullerenes: C 60 ( I h ) and a F 4 m

for m = 5, 6, 7, 8, 9, 9, 10, 12. All 9 are k -resonant for k 3.

a F 4 m for m = 5 , 6 , 7 , 8 , 9

Life fractions

Life fractions life : DNA and RNA (cells) 1 / 2 -life : DNA or RNA
Life fractions life : DNA and RNA (cells) 1 / 2 -life : DNA or RNA

life: DNA and RNA (cells) : DNA and RNA (cells)

1/ 2 -life : DNA or RNA (cell parasites: viruses ) /2-life: DNA or RNA (cell parasites: viruses)

“naked” RNA, no protein (satellite viruses, viroids)(cells) 1 / 2 -life : DNA or RNA (cell parasites: viruses ) DNA, no protein

DNA, no protein (plasmids, nanotech, “junk” DNA,) “naked” RNA, no protein (satellite viruses, viroids) no life : no DNA, nor RNA (only

no life: no DNA, nor RNA (only proteins, incl. prions) : no DNA, nor RNA (only proteins, incl. prions)

)

Atom DNA Prion size ≃ 0.25 ≃ 2 Cryo-EM ≃ 5 11 nm Virus capsides
Atom
DNA
Prion
size
≃ 0.25
≃ 2
Cryo-EM
≃ 5
11
nm
Virus capsides
20 − 50 − 100 − 400
SV40, HIV, Mimi

Viruses: 4 th domain (Acytota)? But crystals also self-assembly spontaneously. 4th domain (Acytota)? But crystals also self-assembly spontaneously.

Viral eukaryogenesis hypothesis (Bell, 2001). hypothesis (Bell, 2001).

Icosahedral viruses

Virus: virion , then (rarely) cell parasite.

Virus: virion , then (rarely) cell parasite. virion, then (rarely) cell parasite.

Virus: virion , then (rarely) cell parasite.

Watson and Crick, 1956:Virus: virion , then (rarely) cell parasite. "viruses are either spheres or rods". In fact, all,

"viruses are either spheres or rods". In fact, all, except most complex (as brick-like pox virus) and enveloped (as conic HIV) are helical or (1 2 of all) icosahedral.

Virion: protein shell (capsid ) enclosing genome capsid) enclosing genome

(RNA or DNA) with

3 911 protein-coding genes.

Shere-like capsid has 60 T protein subunits, but EM resolves only clusters ( capsomers ), incl. 12 pentamers 60T protein subunits, but EM resolves only clusters (capsomers), incl. 12 pentamers (5 bonds) and 6-mers; plus, sometimes, 2- and 3-mers.

 

Bonds are flexible: ≃ 5 0 deviation from mean direction. Self-assembly: slight but regular changes in bonding. 5 0 deviation from mean direction. Self-assembly: slight but regular changes in bonding.

Bonds are flexible: ≃ 5 0 deviation from mean direction. Self-assembly: slight but regular changes in
Bonds are flexible: ≃ 5 0 deviation from mean direction. Self-assembly: slight but regular changes in

Caspar- Klug (quasi-equivalence ) principle: virion minimizes by organizing capsomers in min. number T of locations with quasi-equivalence) principle: virion minimizes by organizing capsomers in min. number T of locations with non-eqv. bonding. Also, icosah. group generates max. enclosed volume for given subunit size. But origin, termodynamics and kinetics of this self-assembly is unclear. Modern computers cannot evaluate capsid free energy by all-atom simulations.)

cannot evaluate capsid free energy by all-atom simulations.) So, capsomers are 10 T + 2 vertices

So, capsomers are 10T + 2 vertices of icosadeltahedron

C

20 T , T = a 2 + ab + b 2 (triangulation number). It is

symmetry of capsid , not general shape (with spikes).

Lower pseudo-equivalence when 2-, 3-mers appear and/or different protein type in different locations.

Hippocrates: disease = icosahedra (water) body excess Lower pseudo-equivalence when 2 -, 3 -mers appear and/or different protein type in different locations. –

and/or different protein type in different locations. Hippocrates: disease = icosahedra (water) body excess – p.

Capsids of icosahedral viruses

( a, b ) T = a 2 + ab + b 2 Fullerene Examples
( a, b )
T = a 2 + ab + b 2
Fullerene
Examples of viruses
(1, 0)
1
F 20 ( I h )
B19 parvovirus, cowpea mosaic virus
(1, 1)
3
C
60 ( I h )
picornavirus, turnip yellow mosaic
virus
(2, 0)
4
C
80 ( I h )
human hepatitis B, Semliki Forest virus
(2, 1)
7l
C
HK97, rabbit papilloma virus, Λ-like viruses
140 ( I ) laevo
(1, 2)
7d
C
140
( I ) dextro
(3, 1)
13l
C
polyoma (human wart) virus, SV40
rotavirus
260 ( I ) laevo
(1, 3)
13d
C
infectious bursal disease virus
260
( I ) dextro
(4, 0)
16
C
herpes virus, varicella
320 ( I h )
(5, 0)
25
C
adenovirus, phage PRD1
500 ( I h )
(3, 3)
27
C
pseudomonas phage phiKZ
540 ( I ) h
(6, 0)
36
C
infectious canine hepatitis virus, HTLV1
720 ( I h )
(7, 7)
147
C
Chilo iridescent iridovirus (outer shell)
2940 ( I h )
(7, 8)
169d
C
3380 ( I ) dextro
(7, 10)
219d?
C
Algal chlorella virus PBCV1 (outer shell)
Algal virus PpV01
4380 ( I )

Examples

Examples Satellite , T = 1 , of TMV, helical Tobacco Mosaic virus 1st discovered (Ivanovski,

Satellite, T = 1, of TMV, helical Tobacco Mosaic virus 1st discovered (Ivanovski, 1892), 1st seen (1930, EM)

Tobacco Mosaic virus 1st discovered (Ivanovski, 1892), 1st seen (1930, EM) Foot-and-Mouth virus, T = 3

Foot-and-Mouth virus,

T = 3

Tobacco Mosaic virus 1st discovered (Ivanovski, 1892), 1st seen (1930, EM) Foot-and-Mouth virus, T = 3

Viruses with (pseudo) T = 3

Poliovirus Human Rhinovirus (polyomyelitis) (cold)
Poliovirus Human Rhinovirus (polyomyelitis) (cold)
Poliovirus Human Rhinovirus (polyomyelitis) (cold)
Poliovirus Human Rhinovirus (polyomyelitis) (cold)

Poliovirus

Human Rhinovirus

(polyomyelitis)

(cold)

Poliovirus Human Rhinovirus (polyomyelitis) (cold)
Poliovirus Human Rhinovirus (polyomyelitis) (cold)

Viruses with T = 4

Human hepatitis B Semliki Forest virus
Human hepatitis B Semliki Forest virus
Human hepatitis B Semliki Forest virus
Human hepatitis B Semliki Forest virus

Human hepatitis B

Semliki Forest virus

Human hepatitis B Semliki Forest virus
Human hepatitis B Semliki Forest virus

More T = a 2 viruses

Sindbis virus, Herpes virus, T = 4 T = 16
Sindbis virus, Herpes virus, T = 4 T = 16
Sindbis virus, Herpes virus, T = 4 T = 16
Sindbis virus, Herpes virus, T = 4 T = 16

Sindbis virus,

Herpes virus,

T = 4

T = 16

Sindbis virus, Herpes virus, T = 4 T = 16
Sindbis virus, Herpes virus, T = 4 T = 16

Human and simian papilloma viruses

Polyoma virus, Simian virus 40 , T = 7 d T = 7 d
Polyoma virus, Simian virus 40 , T = 7 d T = 7 d
Polyoma virus, Simian virus 40 , T = 7 d T = 7 d
Polyoma virus, Simian virus 40 , T = 7 d T = 7 d

Polyoma virus,

Simian virus 40,

T = 7d

T = 7d

Polyoma virus, Simian virus 40 , T = 7 d T = 7 d
Polyoma virus, Simian virus 40 , T = 7 d T = 7 d

Viruses with T = 13

Rice dwarf virus Bluetongue virus
Rice dwarf virus Bluetongue virus
Rice dwarf virus Bluetongue virus
Rice dwarf virus Bluetongue virus

Rice dwarf virus

Bluetongue virus

Rice dwarf virus Bluetongue virus
Rice dwarf virus Bluetongue virus

Viruses with T = 25

PRD1 virus Adenovirus (with its spikes)
PRD1 virus Adenovirus (with its spikes)
PRD1 virus Adenovirus (with its spikes)
PRD1 virus Adenovirus (with its spikes)

PRD1 virus

Adenovirus (with its spikes)

PRD1 virus Adenovirus (with its spikes)
PRD1 virus Adenovirus (with its spikes)

More I h -viruses

Pseudomonas phage phiKZ, HTLV1 virus, T = 27 T = 36
Pseudomonas phage phiKZ, HTLV1 virus, T = 27 T = 36
Pseudomonas phage phiKZ, HTLV1 virus, T = 27 T = 36
Pseudomonas phage phiKZ, HTLV1 virus, T = 27 T = 36

Pseudomonas phage phiKZ,

HTLV1 virus,

T = 27

T = 36

Pseudomonas phage phiKZ, HTLV1 virus, T = 27 T = 36
Pseudomonas phage phiKZ, HTLV1 virus, T = 27 T = 36

Special viruses

Special viruses Archeal virus STIV, T = 31 Algal chlorella virus PBCV1 (4th: ≃ 331 .

Archeal virus STIV, T = 31

Special viruses Archeal virus STIV, T = 31 Algal chlorella virus PBCV1 (4th: ≃ 331 .

Algal chlorella virus PBCV1

(4th: 331.000 bp), T = 169

chlorella virus PBCV1 (4th: ≃ 331 . 000 bp), T = 169 Sericesthis iridescent virus, T

Sericesthis iridescent virus, T = 7 2 + 49 + 7 2 = 147 ? T = 7 2 + 49 + 7 2 = 147?

Tipula iridescent virus, T = 12 2 + 12 + 1 2 = 157 ? T = 12 2 + 12 + 1 2 = 157?

virus, T = 7 2 + 49 + 7 2 = 147 ? Tipula iridescent virus,

HIV conic fullerene

Capsid core Shape (spikes): T ≃ 71?
Capsid core
Shape (spikes): T ≃ 71?

Mimivirus and other giants

Mimivirus and other giants Largest (400nm), >150 (bacteria Micoplasma genitalium ), 1 3 0 of its
Mimivirus and other giants Largest (400nm), >150 (bacteria Micoplasma genitalium ), 1 3 0 of its

Largest (400nm), >150 (bacteria Micoplasma genitalium),

1

30 of its host Acanthamoeba Polyphaga (record:

1

10 ).

Largest genome: 1.181.404 bp; 911 protein-coding genes >182 (bacterium Carsonella ruddii). Icosahedral: T = 1179

Giant DNA viruses (giruses): if >300 genes, >250nm. Ex-"cells-parasiting cells" as smallest bacteria do now?Giant DNA viruses ( giruses

giruses ): if >300 genes, >250nm. Ex-"cells-parasiting cells" as smallest bacteria do now? – p. 65/151

Viruses: big picture

1mm 3 of seawater has ≃ 10 million viruses; all seagoing viruses ≃ 270 million mm 3 of seawater has 10 million viruses; all seagoing viruses 270 million tons (more 20 x weight of whales).

3 of seawater has ≃ 10 million viruses; all seagoing viruses ≃ 270 million tons (more
3 of seawater has ≃ 10 million viruses; all seagoing viruses ≃ 270 million tons (more
Main defense of multi-cellulars, sexual reproduction, is not effective (in cost, risk, speed) but arising

Main defense of multi-cellulars, sexual reproduction, is not effective (in cost, risk, speed) but arising mutations give chances against viruses. Wiped out: <10 viruses.

Origin : ancestors or vestiges of cells, or gene mutation. Or evolved in prebiotic “RNA

Origin: ancestors or vestiges of cells, or gene mutation. Or evolved in prebiotic “RNA world" together with cellular forms from self-replicating molecules?

Viral eukaryogenesis hypothesis (Bell, 2001):

Viral eukaryogenesis hypothesis (Bell, 2001):

nucleus of eukaryotic cell evolved from endosymbiosis event: a girus took control of a micoplasma (i.e. without wall) bacterial or archeal cell but, instead of replicating and destroying it, became its ”nucleus”.

5-8 % of human genome: endogeneous retroviruses; In November 2006, Phoenix , 5 Mya old, was % of human genome: endogeneous retroviruses; In November 2006, Phoenix, 5 Mya old, was resurrected.

5-8 % of human genome: endogeneous retroviruses; In November 2006, Phoenix , 5 Mya old, was
5-8 % of human genome: endogeneous retroviruses; In November 2006, Phoenix , 5 Mya old, was
IV. Some fullerene-like 3-valent maps – p. 67/151

IV. Some fullerene-like 3-valent maps

IV. Some fullerene-like 3-valent maps – p. 67/151

Useful fullerene-like 3-valent maps

Mathematical Chemistry use following fullerene-like maps:

Mathematical Chemistry use following fullerene-like maps:

Mathematical Chemistry use following fullerene-like maps:

Polyhedra ( p 5 , p 6 , p n ) for n = 4 , ( p 5 , p 6 , p n ) for n = 4, 7 or 8 (v min = 14, 30, 34)

 

Aulonia hexagona (E. Haeckel 1887): plankton skeleton

Azulenoids ( p 5 , p 7 ) on torus g = 1 ; so, p ( p 5 , p 7 ) on torus g = 1; so, p 5 = p 7

 
 

azulen

is an isomer C 1 0 H 8 of naftalen

is an isomer C 10 H 8 of naftalen

is an isomer C 1 0 H 8 of naftalen
 
   
   
( p 5 , p 6 , p 7 ) = (12 , 142 ,

( p 5 , p 6 , p 7 ) = (12, 142, 12) , v = 432, D 6 d

( p 5 , p 6 , p 7 ) = (12 , 142 , 12)

Schwarzits

Schwarzits ( p 6 , p 7 , p 8 ) on minimal surfaces of constant ( p 6 , p 7 , p 8 ) on minimal surfaces of constant negative curvature (g 3). We consider case g = 3:

negative curvature ( g ≥ 3 ). We consider case g = 3 : Schwarz P

Schwarz P -surface

g ≥ 3 ). We consider case g = 3 : Schwarz P -surface Schwarz D

Schwarz D -surface

Take a 3 -valent map of genus 3 and cut it along zigzags 3-valent map of genus 3 and cut it along zigzags

Take a 3 -valent map of genus 3 and cut it along zigzags and paste it
Take a 3 -valent map of genus 3 and cut it along zigzags and paste it

and paste it to form D - or P -surface.

One needs 3 non-intersecting zigzags. For example, Klein regular map 7 3 has 5 types of such 3 non-intersecting zigzags. For example, Klein regular map 7 3 has 5 types of such triples; D 56.

non-intersecting zigzags. For example, Klein regular map 7 3 has 5 types of such triples; D

(6 , 7)-surfaces

(6 , 7) -surfaces (1 , 1) D 168 : putative carbon, 1992, (Vanderbilt-Tersoff) (0 ,
(6 , 7) -surfaces (1 , 1) D 168 : putative carbon, 1992, (Vanderbilt-Tersoff) (0 ,

(1, 1)

D 168: putative carbon, 1992, (Vanderbilt-Tersoff)

, 1) D 168 : putative carbon, 1992, (Vanderbilt-Tersoff) (0 , 2) (1 , 2) (

(0, 2)

168 : putative carbon, 1992, (Vanderbilt-Tersoff) (0 , 2) (1 , 2) ( p 6 ,

(1, 2)

( p 6 , p 7 = 24) , v = 2p 6 + 56 = 56(p 2 + pq + q 2 )

Unit cell of (1, 0) has p 6 = 0, v = 56: Klein regular map (7 3 ) . D 56, D 168 and (6, 7) -surfaces are analogs of F 20 ( I h ) , F 60 ( I h ) map (7 3 ) . D 56 , D 168 and (6 , 7) -surfaces are and icosahedral fullerenes.

-surfaces are analogs of F 2 0 ( I h ) , F 6 0 (
(6 , 8) -surfaces (1 , 1) (0 , 2) P 192 , p 6

(6 , 8)-surfaces

(6 , 8) -surfaces (1 , 1) (0 , 2) P 192 , p 6 =
(6 , 8) -surfaces (1 , 1) (0 , 2) P 192 , p 6 =
(6 , 8) -surfaces (1 , 1) (0 , 2) P 192 , p 6 =

(1, 1)

(0, 2) P 192, p 6 = 80

( p 6 , p 8 = 12) , v = 2p 6 + 32 = 48(p 2 + pq + q 2 )

(1, 2)

Starting with (1, 0) : P 48 with p 6 = 8 while unit cell with p 6 = 0 is P 32 - Dyck regular map (8 3 )

P 48 with p 6 = 8 while unit cell with p 6 = 0 is

More (6 , 8)-surfaces

More (6 , 8) -surfaces (0 , 2) v = 120 , p 6 = 44
More (6 , 8) -surfaces (0 , 2) v = 120 , p 6 = 44

(0, 2) v = 120, p 6 = 44

(1, 2)

( p 6 , p 8 = 12) , v = 2p 6 + 32 = 30(p 2 + pq + q 2 )

Unit cell of p 6 = 0: P 32 - Dyck regular map (8 3 )

32 = 30( p 2 + pq + q 2 ) Unit cell of p 6

Polycycles

A finite ( p, q ) -polycycle is a plane 2 -connected finite graph, such that : ( p, q ) -polycycle is a plane 2-connected finite graph, such that :

all interior faces are (combinatorial) p -gons, p -gons,

all interior vertices are of degree q , q ,

all boundary vertices are of degree in [2 , q ] . [2, q ].

vertices are of degree q , all boundary vertices are of degree in [2 , q
vertices are of degree q , all boundary vertices are of degree in [2 , q

a (5, 3) -polycycle

vertices are of degree q , all boundary vertices are of degree in [2 , q

Examples of (p, 3)-polycycles

p = 3 : 3 3 , 3 3 − v, 3 3 − e
p = 3 : 3 3 , 3 3 − v, 3 3 − e

p

= 3 : 3 3 , 3 3 v, 3 3 e ;

p = 3 : 3 3 , 3 3 − v, 3 3 − e ;
p = 4 : 4 3 , 4 3 − v, 4 3 − e

p

= 4 : 4 3 , 4 3 v, 4 3 e , and

 

P 2 × A with A = P n 1 , P N , P Z

 
 
  Continuum for any p ≥ 5 . But 3 9 proper (5 , 3) -polycycles,

Continuum for any p 5. But 39 proper (5, 3) -polycycles, i.e., partial subgraphs of Dodecahedron

p = 6 : polyhexes=benzenoids

p

= 6: polyhexes=benzenoids

Theorem

(i) Planar graphs admit at most one realization as ( p, 3) -polycycle (ii) any unproper ( p, 3) -polycycle is a ( p, 3) -helicene (homomorphism into the plane tiling {p 3 } by regular p -gons)

( p, 3) -polycycle is a ( p, 3) -helicene (homomorphism into the plane tiling {
( p, 3) -polycycle is a ( p, 3) -helicene (homomorphism into the plane tiling {

Icosahedral fulleroids (with Delgado)

3-valent polyhedra with p = ( p 5 , p n > 6 ) and -valent polyhedra with p = ( p 5 , p n> 6 ) and icosahedral symmetry (I or I h ); so, v = 20 + 2p n ( n 5) vertices.

face orbit size number of orbits 60 30 20 12 any ≤ 1 ≤ 1
face orbit size
number of orbits
60
30
20
12
any ≤ 1 ≤ 1
1
face
degrees 5, n
any
3t
2t
5t

A n,k : ( p 5 , p n ) = (12 + 60k,

B n,k : ( p 5 , p n ) = (60k, 12 5 k 1 ) with k 1, n = 5t > 5.

60

k

6 ) with k 1, n > 6,

n

n6

Also: infinite series for n = 7 generalizing A 7 ,1 b and n = 8; obtained from (2k + 1, 0) -dodecahedron by decorations (partial operations T 1 and T 2 , respectively).

Jendrol-Trenkler (2001): for any integers n 8 and m 1, there exists an Jendrol-Trenkler (2001): for any integers n ≥ 8 and m ≥ 1 I (5 , n I (5, n ) -fulleroid with p n = 60m .

any integers n ≥ 8 and m ≥ 1 , there exists an I (5 ,

Decoration operations producing 5-gons

Triacon T 1 Triacon T 2 Triacon T 3 Pentacon P
Triacon T 1
Triacon T 2
Triacon T 3
Pentacon P

I -fulleroids

p 5 n; p n v # of Sym A 72 7, 60 260 2
p 5
n; p n
v
# of
Sym
A
72
7, 60
260
2
I
7,1
A
72
8, 30
200
1
8,1
I h
A
72
9, 20
180
1
9,1
I h
60
10, 12
140
1
B 10,1
I h
312
11, 60
740
?
A 11,5
132
12, 20
300
A 12,2
192
12, 30
440
1
A 12,3
I h
432
13, 60
980
?
A 13,7
252
14, 30
560
1
A 14,4
I h
120
15, 12
260
1
B 15,2
I h

Above (5 , n ) -spheres: unique for their p -vector ( p 5 , p (5, n ) -spheres: unique for their p -vector ( p 5 , p n ) , n > 7

B 15,2 I h Above (5 , n ) -spheres: unique for their p -vector (

1st smallest icosahedral (5 , 7)-spheres

1st smallest icosahedral (5 , 7) -spheres F 5 , 7 ( I ) a =

F 5 ,7 ( I ) a = P ( C 140 ( I )) ; v = 260

Dress-Brinkmann (1996) 1st Phantasmagorical Fulleroid

I ) a = P ( C 1 4 0 ( I )) ; v =

2nd smallest icosahedral (5 , 7)-spheres

2nd smallest icosahedral (5 , 7) -spheres F 5 , 7 ( I ) b =

F 5 ,7 ( I ) b = T 1 ( C 180 ( I h )) ; v = 260

Dress-Brinkmann (1996) 2nd Phantasmagorical Fulleroid

= T 1 ( C 1 8 0 ( I h )) ; v = 260

The smallest icosahedral (5 , 8)-sphere

The smallest icosahedral (5 , 8) -sphere F 5 , 8 ( I h ) =

F 5 ,8 ( I h ) = P ( C 80 ( I h )) ; v = 200

icosahedral (5 , 8) -sphere F 5 , 8 ( I h ) = P (

The smallest icosahedral (5 , 9)-sphere

The smallest icosahedral (5 , 9) -sphere F 5 , 9 ( I h ) =

F 5 ,9 ( I h ) = P ( C 60 ( I h )) ; v = 180

icosahedral (5 , 9) -sphere F 5 , 9 ( I h ) = P (

The smallest icosahedral (5 , 10)-sphere

The smallest icosahedral (5 , 10) -sphere F 5 , 1 0 ( I h )

F 5 ,10 ( I h ) = T 1 ( C 60 ( I h )) ; v = 140

(5 , 10) -sphere F 5 , 1 0 ( I h ) = T 1

The smallest icosahedral (5 , 12)-sphere

The smallest icosahedral (5 , 12) -sphere F 5 , 1 2 ( I h )

F 5 ,12 ( I h ) = T 3 ( C 80 ( I h )) ; v = 440

(5 , 12) -sphere F 5 , 1 2 ( I h ) = T 3

The smallest icosahedral (5 , 14)-sphere

The smallest icosahedral (5 , 14) -sphere F 5 , 1 4 ( I h )

F 5 ,14 ( I h ) = P ( F 5 ,