QUANTUM MECHANICAL EVOLUTION OF FATTY ACIDS WORLD LIFE
Arvydas Tamulis and Mantas Grigalavicius
Vilnius University Institute of Theoretical Physics and Astronomy,
A. Gostauto street 12, Vilnius, Lithuania
Arvydas.Tamulis@tfai.vu.lt(Received October 5, 2009; Accepted May 28, 2010)(Abstract)
Quantum mechanical density functional theory
nonlocal gradient electron correlation interactions
methods are used for investigations of various
self-assembled photoactive fatty acid micelles. The
micelle systems studied are based on a photoactivesquarine sensitizer, an 8-oxo-guanine electron
donor, cytosine, a fatty acid and its precursor(pFA) molecules. The systems include a water
environment and consist of some 400 atoms andare up to about 4.5 nm in diameter. The quantum
mechanical based electron correlation interactions
are the source of the weak hydrogen and Van der
Waals chemical bonds that are critical to the
behavior of these systems. Polar solvent molecules
such as water increase the strength of these bonds
and thus play a central role in the self assembly andfunctioning of the systems studied. The distances
between the separated sensitizer, precursor of fatty
acid, and water molecules are comparable to Van
der Waals and hydrogen bonding radii. As a result,these nonlinear quantum interactions compress theoverall molecular system resulting in a smaller gap
between the HOMO and LUMO electron energy
levels allowing enhanced tunneling of photoexcitedelectrons from the sensitizer to pFA.
The most intense excited states of thephotoactive fatty acid micelles are partiallycomposed of LUMO+n states located on the fatty
acid
precursorswhenthebis(4-diphenylamine-2-phenyl)-squarine molecule
is covalently attached to the 8-oxo-guanine. This
coupling also promotes electron hopping(tunneling) to the pFA molecules during the mostintense absorption excited state. The photoexcitedelectron tunnels to the waste end of the pFA
molecules where it causes these molecules to split
due to intense rotation and vibration of the weakchemical bond that joins the waste piece to thefatty acid section of the pFA molecule.
The most intense absorption lines of thesquarine-8-oxo-guanine supermolecule were foundto be shifted to the red when these molecules wereassociated with fatty acid micelles. In addition, the8-oxo-guanine::cytosine-squarine supramolecule
was observed to have an absorption region thatcovered more of the visible spectrum than asquarine-8-oxo-guanine
supermolecule.
The
redward shift of the intense absorption lines would
allow a self reproducing micelle to absorb thelight in the longer wavelength region, which may
have been important in the environment that life
might have developed, in addition to extending thephotoactive period into the earlier morning andlater evening hours. That allowed better compete
Viva Origino 38 (2010) 4 - 17
© 2010 by SSOEL Japanfor such a kind of evolved photoactive micelles ofFatty Acids World life in getting the foodmolecules. Furthermore, one notes that thenucleotide caused wavelength shift and broadeningof the absorption pattern potentially gives thenucleotides an additional valuable role, other thanjust a purely genetic one in the early stages of thedevelopment of life.
The main quantum mechanical research resultof this paper is that life in the Earth or elsewhere in
the Space could have emerged in the form of
self-reproducing photoactive fatty acid micelles,
which step by step evolved to nucleotide
containing micelles due to an enhanced ability toabsorb visible light. The nucleotide molecules andtheir sequences, which in the first period of
evolution of fatty acid molecules were useful justfor better absorbance of the light in the longer
wavelength region, later in the peptide nucleic acid
(PNA) or RNA World living organisms took on therole of genetic information storage.
From the information theory point of view, thenucleotide molecules sequences in the Fatty Acids
World micelles carry positional information how to
directly provide better relaxation electron transport
along the nucleotide-sensitizer chain and in
addition providing complimentary copies of that
information to the next generation.
The result of self-assembly of molecules
depends on the electromagnetic forces between
electrons and in general is predicted by existenceof the universal constants. Molecules are built fromatoms therefore for the thermonuclear reactions
and atom synthesis in the stars are important also
the rest three fundamental forces: strong and weak
nuclear interactions and gravitation (for the
self-formation of stars). Universal constants ofphysical interactions did not changed in the
Universe during last 13.73 billion years therefore
the emergence of life was predicted before the timeof expansion of the Universe.
(Keywords)
self-reproducing fatty acid micelles; Fatty Acids
World life; life was predicted in the Universe;
photoexcitedelectrontunneling;
quantummechanical emergence of genetic material
molecules in protocells.
1. Introduction
The main idea of this article is that the life in the
Earth or elsewhere in the Space could haveemerged in the form of self-reproducing
photoactive fatty acid micelles due to quantum
mechanical interactions of molecules. As a-4-

Viva Origino 38 (2010) 4 - 17consequence of this quantum mechanical origin oflife we state that the emergence of life waspredicted in the Universe before the time of the
expansion of the Universe because the quantum
mechanical universal constants of physicalinteractions did not changed in the Universe during
last 13.73 billion years. The logical decision can bemade that God fine-tuned these universal physicalconstants for the purpose of the emergence of life.
Now is the right time to give new interpretation of
Old Testament basing on the newest quantum
biology scientific results.
The solution of basic questions of emergence andevolution of first living cells or protocells is tightly
connected now with rapidly developing artificial
living technologies in several laboratories roundthe world. The possibilities to synthesize artificial
self-reproducing minimal cells show also on thepossible ways of emergence of living protocells in
the Earth or elsewhere in the Space. Due to rapid
development of computers and quantum
mechanical methods and program packages also
exist possibilities to simulate the main processes ofquantum molecular dynamics self-assembly andphotosynthesis of minimal artificial cells consisting
up to 2000 atoms. The main artificial cells
developers are the USA scientists: Steen
Rasmussen, James Bailey, Hans Ziock (Los
Alamos National Laboratory - (LANL) [1-3];
Liaohai Chen (Argonne National Laboratory), andEuropean researchers in the Center for
Fundamental Living Technology at the Universityof Southern Denmark (Steen Rasmussen), in Italy(Pier Luigi Luisi’s group at RomaTre University),
Guenter von Kiedrowski at Ruhr-Universitaet
Bochum, John S. McCaskill, Uwe Tangen and
Patrick Wagler in Biomolecular Information
Processing research group at the same university,and in the European Center for Living Technology,
Venice. New synthesized programmable artificial
cells or nanobiorobots are planned to be used fornanomedicine, nanoecology, and for future
emerging new information technologies. Despite
the really useful benefits of these artificial living
technologies, one can foresee also some possible
dangerous events in the case these newly createdartificial living cells might self-mutate and escapeto the natural biospheres. Our research group create
molecular electronics logic gates regulating thephotosynthesis, growth and division of artificial
living cells and nanobiorobots in order to preventthe negative effects of these newly emerging
artificial living bioinformation technologies.
Molecular electronics and spintronics logicaldeviceswhich
regulate
photosynthesis,
self-assembling to the mobile computing structures,
selectively capturing and transporting nuclear,chemical and microbial pollutants already havebeen quantum mechanically designed [4–8]. It havebeen designed variety of the molecular spintronics
devices. They will regulate the photosynthesis andgrowth of artificial minimal living cells underconditions of external magnetic fields, while also

providing a perspective for success in the synthesisof new forms of artificial living organisms [9-17].
The artificial minimal living cells that aresynthesized in LANL [1-3] are only a few (4-6)
nanometers in size. In their simplest form, thesecells consist of a micelle which acts as thecontainer, a light driven metabolism, and a genetic
system, whose functions are all very tightly
coupled. The container consists of amphiphilic
fatty acid (FA) molecules that self-assemble into a
micelle. The hydrophobic interior of the micelleprovidesanalternative
thermodynamic
environment from the aqueous or methanol exterior
and acts as a sticking point for the photosensitizer,
fatty acid precursors (pFA) (food), and the genetic
material. Peptide nucleic acid (PNA) is chosen as
the genetic material as it is far less polar than RNA
or DNA and therefore should stick to the micelle,
especially if hydrophobic chains are added to the
PNA backbone. The geometric and electronic
structure (without the presence of water and FA
molecules) was obtained by the quantum
mechanicalsemiempirical
PM3
methodimplemented
in
GAMESS-US[18]
or
TURBOMOLE [19] packages installed in Linuxservers cluster of our Theoretical MolecularElectronics and Spintronics research group.
The metabolism involves the photoexcitation ofan electron in various photosensitizers which arestabilized by the donation of an electron from
non-canonical PNA bases (for example,
8-oxo-guanine). The excited electron is in turnused to cleave a fatty acid precursor to yield
another fatty acid molecule, thereby allowing thecontainer to grow until it reaches an unstable sizeand divides. The artificial minimal cell could be
fed PNA monomers or use an essentially identicalmetabolism to convert a PNA precursor monomer
into a true monomer, thereby also providing thematerial to allow the double-stranded PNA “gene”
to replicate when it undergoes a random
dehybridization to yield two complementary
single-stranded templates [1-3]. Finally, as thedifferent nucleobases have different electron donor
and electron relay capabilities, there is also amechanism for natural selection, with some bases
and base orderings being superior to others in theirability to facilitate the metabolism. We can define
these self-replicating minimal artificial cells as
PNA World life referring on the similar definitionsof RNA or DNA World life.
The artificial minimal living cell contains on theorder of 103 atoms. Due to its small size, all its
processes, including its self-assembly fromcomponent molecules, its absorption of light, andits metabolism should in principle be investigatedusing quantum mechanical (wave) theory [9-17].
The main goal of this article is to demonstrate,by quantum mechanical methods which include
electron correlation effects, the mechanism of theemergence of the simplest forms of minimal livingorganisms which might occur in the hot andUV-rich environment of the Earth 3.9–3.6 billion-5-Viva Origino 38 (2010) 4 - 17

years ago or on other planets of the Universe.

exactly. In order to find acceptable approximate
eigenstates, we will need to make approximations
least at two different levels [20].

2. Procedure / Methodology
Biological molecules, supermolecules orsupramolecules (micelles) are the quantum systems
composed of quantum particles: nuclei (with Z
charges) and surrounding electrons possessing
elementarychargee=-1.602176487(40)x10-19
Coulomb. Elementary charge of electron is theuniversal constant. The electromagnetic interactionof two particles consequences on the interaction of
all other quantum particles therefore we are dealing
with the complex quantum many-body system. The
exact many-particle hamiltonian [20] for thissystem is:Level 1: The Born-Oppenheimer approximation(1.1)

The masses of the nuclei
at the distances
and the electrons possess the elementary mass
which are at the distances . The reduced Planck
constant is the universal constant:

The nuclei are much heavier and therefore move
much slower than the electrons. We can henceʻfreezeʼ them at fixed positions and assume theelectrons to be in instantaneous equilibrium withthem. In other words: only the electrons are kept as
players in our quantum many body problem. The
nuclei are deprived from this status, and reduced toa given source of positive charge, they becomeʻexternalʼ to the electron cloud. The nuclei do not
move any more, their kinetic energy is zero and thefirst term on the hamiltonian 1.1 disappears. The
last term reduces to a constant. We are left with the
kinetic energy of the electron gas, the potential
energy due to electron-electron interactions and thepotential energy of the electrons in the (nowexternal) potential of the nuclei. We write thisformally as:(1.2)
The kinetic and electron-electron terms of 1.2
depend only on the fact that we are dealing with aquantum many-electron system [20]. This part isuniversal. The system-specific information (which
nuclei, and on which positions) is given entirely
by

The first term of the equation 1.1 is the kinetic
energy operator for the nuclei, and the second forthe electrons.
The last three terms in the equation 1.1 describe
the Coulomb interaction between electrons andnuclei, between electrons and other electrons, andbetween nuclei and other nuclei. The force between
two separated electric charges is given by
Coulomb's law:

Level 2: Density Functional Theory:
Quantum mechanical electron correlationinteraction density functional theory (DFT)
methods i. e. high precision quantum mechanicalsimulations were used to investigate various
self-assembled photoactive bioorganic systems ofartificial minimal living cells [9–17]. The cellsystems studied in these articles are based on
peptide nucleic acid (PNA) and consist of up to2000 atoms (not including the associated water
solvent shells) and are about 8.0 nm in diameter.
The quantum simulations of single bioorganic
molecules possessing closed electronic shells startfrom a trial geometry (Cartesian coordinates of thenuclei). Using quantum mechanical semiempirical(e.g. PM3, PM6), Hartree–Fock (HF) and DFT
approaches
inthe
GAMESS-US[18],
TURBOMOLE [19] or ORCA [21, 22] program
packages, we obtain the lowest molecular energy
which parametrically depends on these coordinates.
The subsequent standard geometry optimization
procedure [23] minimizes the energy with respect
to the nuclear positions. Special care is required toverify that the obtained optimal molecular structure
is a global minimum in the phase space of thenuclear (3n-6, n being the number of atoms)
degrees of freedom.
In order to obtain accurate results ininvestigating supermolecules, two factors need to

Where
and
are the charges, andis theappears in
distance between them. Likewise,
Maxwell's equations, which describe the properties
of electric and magnetic fields and electromagnetic
radiation, and relate them to their sources.
is defined by the formula:
The value of

where
is the speed of light in vacuum andisthe magnetic constant or vacuum permeability.
All above mentioned constants: elementary, reduced Planck constant,andchargeare universal and according to most of scientists
did not changed from the beginning of the
Universe.
Unfortunately quantum mechanics Schrödinger
equation mathematically is not available to solve-6-Viva Origino 38 (2010) 4 - 17

be accounted for: i) the quality of the density
functional and ii) the quality of the molecularorbitals (extent of the phase space of thesingle-electron states). For simple covalently
bonded molecules we chose Becke's 3 parameterexchange functional [24] with non-local
Lee–Yang–Parr electron correlations [25] (DFTB3LYP). Currently, B3LYP is considered to be themost appropriate method for taking into accountelectron correlations in large closed-shellsupermolecules in which atoms are linked bycovalent bonds i. e. there are no Van der Waals orhydrogen bonds between atoms in a single
molecule. For simulations of the self-assembly of
bioorganic supramolecules in which the separate
molecules are associated by hydrogen bonds or
Van der Waals forces, the B3PW91, PBELYP [18,26] and PBE [19, 20, 26] methods were used. In
these two methods, exchange functionals include
some electron correlation effects at larger distancesthat provide relatively good descriptions of the Van
der Waals forces and hydrogen bonds. To obtainaccurate optimal molecular geometries for single
molecules, we use the 6-311G** basis set which
includes (5d, 7f) polarized atomic orbitals. For
self-assembly of pairs of bioorganic molecules we
add diffusion orbitals of the 6-31++G** basis set(the standard tables [27] give an appropriate basis
setdescription).
The
above-mentioned
6-311++G** basis set convention was adopted byJohn Pople and coworkers.

bis(4-diphenylamine-2-phenyl)-squarine} to pFA
molecule and splits it to the new released fatty acidand the head section (waste end, waste piece) ofprecursor of fatty acid.
The new released fatty acid joins the existing
micelle, growing it and the waste end is removing
out from micelle after photosynthesis. Afterreaching some critical size, the micelle divides into
two separate smaller micelles. We can define theseself-reproducing photoactive fatty acid micelles as
Fatty Acid World life referring on the similar
definitions of RNA or DNA World life.

Figure 1. A movie based visualization of the last 1762
steps of the geometry optimization of a self-reproducing
FA
based
micellesystemcontainingabis(4-dimehylamino-2-phenyl)-squarine molecule (in thecenter) that was done using semiempirical quantum
mechanical method PM3. This micelle contains also two
precursors of a FA, 2 waste ends of pFA, 6 FA and 37
water molecules (in total 427 atoms). Carbon atoms andtheir associated covalent bonds are shown as grey
spheres and sticks, hydrogens - light grey, oxygens - red,
nitrogens – blue.

3. Quantum mechanical self-assembly ofphotoactive fatty acid micelles
We used quantum mechanical density functional
theory methods that included nonlocal gradientelectron correlation interactions to investigate
various self-assembled photoactive fatty acidmicelles. The micelle systems studied are based ona photoactive squarine sensitizer, a fatty acid andits precursor (pFA). The systems include a water
environment and consist of some 400 atoms andare up to about 4.5 nm in diameter. The quantum
mechanical based electron correlation interactions
are the source of the weak hydrogen and Van der
Waals chemical bonds that are critical to the
behavior of these systems. Polar solvent molecules
such as water increase the strength of these bonds
and thus play a central role in the self assembly andfunctioning of the systems studied. The distances
between the separated sensitizer, precursor of fatty
acid, and water molecules are comparable to Van
der Waals and hydrogen bonding radii.
As a result, these nonlinear quantum
interactions compress the overall molecular system
resulting in a smaller gap between the HOMO andLUMO electron energy levels allowing enhanced
tunneling of photoexcited electrons from thesensitizer{eitherabis(4-dimethylamine-2-phenyl)-squarine (see in the
Figure 1 a movie based visualization of the last1762 steps of the geometry optimization) or a

The water molecules, which surround the entire
photosynthetic complex shown in moving 1762
images were found to stabilize the system. Thereby
reducing all the interatomic distances. The watermolecules
organized
intonano
ice-like
substructures. It is only because of the hydrogen
and Van der Waals bonds among thebis(4-dimethylamine-2-phenyl)-squarine and fatty
acid, and pFA molecules, and water molecules that
this system with 4.0 nm larger diameter exists. The
distances among the separated sensitizer and fatty
acid, and pFA molecules, and water molecules arecomparable to Van der Waals and hydrogenbonding radii, and therefore we may regard theminimal cell as single electron conjugatedsupramolecule that we can deal with using anelectroncorrelated
model.
Sincebis(4-dimethylamine-2-phenyl)-squarine moleculeinteracts with fatty acid, and pFA molecules andwith water molecules through their correlated-7-

Viva Origino 38 (2010) 4 - 17hydrogen atom bonded to another electronegative
atom and this hydrogen atom exist in two quantum
states. The hydrogen bonds and Van der Waals
weak chemical bonds (dispersion forces) play a
critical role in the quantum mechanical electron
correlations interaction based self-assembly of thephotosynthetic center and functioning of thephotosynthetic processes of the artificial minimalcells.
The best available method to simulate in minimalcells these Van der Waals dispersion forces andhydrogen bonds is to perform quantum mechanicalnon-local density functional potential calculations[8-15]. Other approaches, such as lowest level ofcorrection (MP2) [20], multiconfiguration selfconsistent field (MCSCF) [20] or complete active
space SCF (CASSCF) [20], in principle moresuited to model dispersion forces, would not beapplicable for micelles and artificial cells due tothe huge computational cost.
As one can see in Figure 1 after geometry
optimization these molecules self-organized to theregular structure due to accounting the quantum
electron correlations interactions, i. e. due to thebalance of weak electrostatic, hydrogen bonding
and weak dispersion Van der Waals forces:
1) the bis(4-dimethylamine-2-phenyl)-squarinesensitizer molecule is in the center;2) fatty acid molecules are oriented by theirhydrophobic
ends
to
the
bis(4-dimethylamine-2-phenyl)-squarine sensitizer
molecule;
3) precursor of fatty acid molecule is oriented bytheirhydrophilic
end
to
the
bis(4-dimethylamine-2-phenyl)-squarine sensitizer
molecule;4) most of the water molecules self-organize into
clusters of nano ice-like substructures. Furthermore,
all the interatomic distances between the sensitizer{either a bis(4-dimethylamine-2-phenyl)-squarine
or a bis(4-diphenylamine-2-phenyl)-squarine} andthe pFA molecule become reduced, i. e. thephotosynthetic system become more compressed
due to the presence of the water molecules.
To sum it up, all fatty acid micelles and artificial
minimal cells, including macromolecular naturalliving systems, are self-assembling and achieve thisbased on interactions involving weak electrostaticforces (due to a small internal shift of the whole
conjugated valence electron cloud from theelectron-donor tail to the electron-acceptor head)and other quantum (dispersion, H-bonding) fineeffects. The emergence of artificial or natural life apriori relies on the existence of these weak
quantummechanicalelectroncorrelationinteractions.
The result of self-assembly of molecules depends
on the electromagnetic forces between electrons
and in general is predicted by existence of theuniversal constants: permittivity of free space,
speed of light in vacuum, vacuum permeability,
Planck constant, etc. (see section 2 of this article).
Molecules are built from atoms therefore for the

Figure 2. Van der Waals radii spheres of all atoms infatty acid HO-CO-(CH2)10-CH3. The Van der Waals
spheres of carbon atoms and their associated covalentbonds are shown as green spheres, hydrogens are inlight grey, oxygens – red.

electrons, intermolecular distances and surface area
calculations are critical in understanding the timedependent electron tunneling processes associatedwith the various excited states of this micelle.
To achieve a better understanding of thequantum mechanical self-assembling process of thephotoactive fatty acid micelles, it was calculatedtheelectronic
structure
of
fatty
acid
HO-CO-(CH2)10-CH3 by the B3LYP method usingrather a wide basis set 6-311++G** (see Figure 2).
The sum of Lowdin charges on the hydrophilic
head of fatty acid and on the fragment (HO-CO-)
was equal to -0.14 of electron charge. Since thismolecule is neutral (the total sum of Lowdin
charges = 0.00), on the rest part of the hydrophobic
tail of this fatty acid the charge will be equal to+0.14 of electron charge due to a small quantum
mechanical internal shift of the whole conjugatedvalence electron cloud from the electron-donor tailto the electron-acceptor head. An additional factor
for the repulsion of fatty acid tails is that the tails
are covered by positively charged hydrogen atoms.
The summary of the detailed investigations ofquantum mechanical self-assembly of various fatty
acid micelles and artificial minimal cells models isthat fatty acids in the vacuum are not able toperform self-assembly due to the quantum
dispersion forces and due to the alternating chargeof the different groups -CH2- in the tails because
really these two kinds of attraction forces are small.
Dispersion forces are weak Van der Waals
intermolecular forces that arise from the attractive
force between quantum multipoles. The morecompetitive electrostatic repulsion forces which
destroy micelles and artificial cells in the vacuum
due to the negative charges on the heads of FA andsmall positive charges on the FA tails, andadditionally because the tails of fatty acids arecovered by positively charged hydrogen atoms.
The electron correlations interactions amongpolar solvent (e.g. water, methanol) molecules,
fatty acid, precursor of fatty acid, and waste ends
of precursor of fatty acid molecules leads toappearing the additional attraction dispersion
forces and hydrogen bonds. A hydrogen bond is a
special type of quantum attractive interaction thatexists among an electronegative atom and a-8-Viva Origino 38 (2010) 4 - 17

thermonuclear reactions and atom synthesis in thestars are important also the rest three fundamental
forces: strong interaction, weak interaction (alsoknown as "strong" and "weak nuclear force") andgravitation (for the self-formation of stars). Most ofphysicists agree that universal constants of physicalinteractions did not changed in the Universe during
last 13.73 ± 0.12 billion years therefore theemergence of life was predicted before the time of
expansion of the Universe, i. e. before the time
when it was the early quark matter – gluon plasma.
Some physicists have explored the notion that if
the fundamental physical constants had sufficiently
different values, our Universe would be soradically different that intelligent life would
probably not have emerged, and that our Universe
therefore seems to be fine-tuned for intelligent life
[28].

experimental results by only 0.3 or 0.2 nm, which
is within the value of experiment errors [2]. Thisagreement implies that the quantum mechanicallymodeled self-assembled structures of minimal cells
very closely approximate the real ones.
Part of water and waste end molecules were
removed from the self-assembled fatty acid micelleshown in the Figure 1. The final self-assembled
and reduced micelle is shown in the Figure 5. The
spectrum calculations of this reduced micelle were
performed using the time dependent (TD) DFT
PBE method with the 6-31G basis set together withCOSMO water solvent model installed in ORCA
quantum chemical package on our research group
Linux cluster. The calculated most intense
spectrum line (black bar) is shown in the Figure 16.
Quantum mechanical electron correlation based
simulations of the above described fatty acidmicelle drawn in Figure 5 show it to be complex
system, as only the entire ensemble of sensitizer,
pFA, FA, and water molecules yields stablesystems with a functioning photosynthetic process.
Our studies show the importance of modeling as
much of the full system as possible in order toobtain realistic results. Already just removing small
parts of the FA, or water molecules leads tostructural changes, as well as a shift in the
spectroscopic values associated with thephotoexcited electron tunneling from thephotosensitizer{eitherabis(4-dimethylamine-2-phenyl)-squarineorbis(4-diphenylamine-2-phenyl)-squarine} to thepFA molecules. Removing larger parts, e.g. more
FA or water molecules leads to degradation of thefatty acid micelle. Furthermore our results showthat inclusion of an ever greater fraction of the trueamount of water present, as well as a greater

4.
Quantummechanicalevolutionofphotoactive fatty acid micelles
We have performed a QM semiempirical PM3and DFT PBE/6-31G methods for geometry
optimization of photoactive fatty acid micelles
using two types of squarine molecules Sq(I) andSq(II) (see Figures 3 and 4) and precursor of fatty
acid
molecule:pFA–
Fragment
C6H5-CO-(CH2)-O-CO-(CH2)6-CH3.
C6H5-CO-(CH2)- represents the head section (wasteend, waste piece) of the pFA which is eliminatingfrom micelle after the photosynthesis.
The electron tunneling and associated lightabsorption of the most intense transitions ofself-assembled artificial minimal cells as calculatedby the TD DFT method differs from spectroscopic

Figure 3. Image of bis(4-dimethylamine-2-phenyl)squarine – Sq(I) molecule

Figure 4. Image of bis(4-diphenylamine-2-phenyl)squarine - Sq(II) molecule

Figure 5. The last image of reduced self-assembled fatty
acid micelle contains Sq(I) molecule (in the center), pFA
molecule (in the bottom-left), six fatty acid molecules and
14 water molecules.

-9-Viva Origino 38 (2010) 4 - 17

Table 1. Excitation transitions energies of a photoactive fatty acid micelle containing Sq(I) molecule, pFA molecule, six
fatty acid molecules and 14 water molecules were calculated using TD DFT PBE method with the 6-31G basis set
together with COSMO water solvent method in the ORCA program package. The weight of the individual excitations are
given if larger than 0.01. Arrow → indicates the direction of individual electron transition from ground state HOMO-m tocertain excited state LUMO+n.

Excitedstate #

Individual transitions
HOMO-m → LUMO+n

Weight ofindividualtransition

Energy(eV)Wavelength(nm)

Oscillator strength(arbitrary units)

10

HOMO → LUMO

0.913

2.7

453.8

2.7235

11

HOMO → LUMO+1

0.999

2.8

450.6

0.0001

17

HOMO-1 → LUMO+1

0.99

3.0

417.7

0.0001

difference of electron charge density (certain
excited-state - ground-state) for the photosynthetic
center of the photoactive fatty acid artificial
micelle and performed the visualized the electron
charge tunneling associated with certain excitedstate transitions (see Figures 6-8).
Spectrum of micelle given in the Figure 5 isplaced in the Table 1 and in the Figure 6 (black
bar: SQ(I)+pFA). The electron charge transfer
trajectories in different excited states are shown in
the Figures 7-9.
The most intense electron tunneling transitionsof the 10th excited state should not induce
metabolic photo dissociation of pFA molecule
because the transferred electron cloud is located on
the Sq(I) molecule (see Figure 7).
Figure 6. The intense absorption lines of the investigatedsquarine based derivatives: 1) minimal cell based on
Sq(I) and pFA (Fig. 5) (black bar), 2) minimal cell basedon Sq(II) sensitizer and pFA molecules, six fatty acidmolecules and 40 water molecules (blue bar), 3) micellebased on Sq(II)-8-oxo-guanine+pFA+40 H2O (Fig. 10)(green bars), 4) red bars represents the absorption
spectrumlines
ofSq(II)-8-oxo-guanine::cytosine+pFA+50 H2O minimal
cell (Fig. 13). Spectra calculated using TD DFT revPBE
methodwith
the
6-31G*
basis
set.
The
8-oxo-guanine::cytosine-squarine supramolecule wasobserved to have an absorption region that covered moreof the visible spectrum than a squarine-oxo-guanine
supermolecule.

number of fatty acid, pFA, and nucleobase
molecules to begin to approach a complete fatty
acid micelle or artificial minimal cell, results in ashift of the absorption spectrum to the red for the
protocell photosynthetic center, leading to an evercloser approach to the real experimental value [15].
These results indicate that the fatty acid micelle isacting as a single quantum mechanical based
system. Trials with different simulation methods
also show that only the QM electron correlation
TD DFT simulations give results exactlycomparable with spectroscopic results and all othermore simplified QM methods such as local
gradient DFT or ab initio Hartree-Fock give
structures and spectra that are far from theexperimentally measured ones.
It was taken from TD DFT calculations the

Figure 7. Visualization of the electron charge tunnelingassociated with the tenth excited state. The transition isfrom the Sq(I) to the same squarine molecule otheratoms. The electron cloud hole is indicated by the dark
blue color while the transferred electron cloud location
is designated by the grey color. Carbon atoms and theirassociated covalent bonds are shown as green sticks,
hydrogens are in light grey, oxygens – red, nitrogens –blue.

- 10 -

Viva Origino 38 (2010) 4 - 17

The electron tunneling transitions of the 11th and17th excited states should induce metabolic photo
dissociation of pFA molecule because thetransferred electron cloud is located on the head(the waste piece) of pFA molecule (see Figures 8
and 9).
A similar self-assembled fatty acid micellewhich contains Sq(II) sensitizer and pFA
molecules, six fatty acid molecules and 40 watermolecules, was investigated quantum chemically.
The expectation was that the additional four
aromatic rings will initiate the electron transport
from Sq(II) to the pFA molecule in the mostintense excited state (see blue bar in the Figure 6).
Summarizing we can state that such a micelles

Figure 8. Visualization of the electron charge tunnelingassociated with the eleventh excited state. The transitionis from the Sq(I) (in the center) to the pFA (in thebottom-left) molecule.

which possess only Sq(I) or Sq(II) sensitizers
should not self-reproduce efficiently because thephotosynthetic electron transitions from Sq(I) or
Sq(II) to the pFA molecule are not intense and in
the narrow blue light absorbance region.
The geometry optimization of modified
self-assembled fatty acid micelle containing Sq(II)molecule with attached covalently 8-oxo-guanine,pFA molecule and 40 water molecules (see Figure10) were performed by using PBELYP/3-21 withGAMESS-US package and done calculations ofspectrum using TD DFT revPBE method with the
6-31G* basis set using ORCA package.
Moving figures of this article expose theself-assembly of fatty acid micelles. One can veryclearly watch how due to quantum electron
correlation forces and hydrogen bonding
interactions (dashed lines) the water molecules are
self-assembling to the nano crystals and attaching
to the squarine and fatty acid molecules, how theseforces compress all the complex quantum system –micelle. Only DFT nonlocal gradient methods(such as PBELYP) give the right hydrogen bonding
distances comparable with experimental vales (seedashed lines in the Figures 10 and 13). The
semiempirical PM3 method only partially gives thehydrogen bonding interactions therefore thesupramolecule visualization program does notshows the dashed lines (see Figure 1) because thecalculated hydrogen bonding distances are toolarge in comparison with experimental distances.
The most intense excited states of thephotoactive fatty acid micelles are partiallycomposed of LUMO+n states located on the fatty
acid precursors when the Sq(II) molecule iscovalently attached to the 8-oxo-guanine. This
coupling also promotes electron hopping(tunneling) to the pFA molecules during the mostintense absorption excited state.

Figure 9. Visualization of the electron charge
tunneling associated with the seventeenth excitedstate. The transition is from the Sq(I) to the pFA
molecule.

Figure 10. A movie based visualization of the last stepsof the geometry optimization of a self-reproducing FA
based micelle system containing a Sq(II) moleculewith attached covalently 8-oxo-guanine (in thebottom-right), pFA molecule (in the bottom) and 40
water molecules. Dashed lines means the hydrogenbonds.

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Viva Origino 38 (2010) 4 - 17
Table 2. Excitation transitions energies of a fatty acid micelle containing Sq(II) molecule with attached covalently
8-oxo-guanine and pFA molecule, and 40 water molecules were calculated using TD DFT revPBE method with the
6-31G* basis set in the ORCA program package. The weight of the individual excitations are given if larger than 0.1.

Excitedstate #
8
10

Weight ofindividualtransition

Energy(eV)Wavelengt
h (nm)

Oscillator strength(arbitrary units)

HOMO-7 → LUMO

0.88

2.48

500.8

0.21

HOMO → LUMO

0.54

HOMO-12 → LUMO

0.13

2.54

488.0

1.92

Individual transitions
HOMO-m → LUMO+n

The absorption spectrum of the photoactive fatty
acid micelle given in the Figure 10 is detailed
placed in the Table 2 and in the Figure 6 (greenbars). The electron charge transfer trajectories indifferent excited states are shown in the Figures 11
and 12.
The electron tunneling transitions of the 8th and10th excited states of this micelle should induce
metabolic photo dissociation of pFA molecule
because the transferred electron cloud is located on
the head (the waste piece) of pFA molecule (seeFigures 11 and 12) where it causes this molecule tosplit due to intense rotation and vibration of the
weak chemical bond that joins the waste piece tothe fatty acid section of the pFA molecule.
The intense 8th excited state is composed mainly
from one individual transition HOMO-7 → LUMO
with weight equal to 0.88 (see Table 2) and otherindividual transitions contributions are at mostequal to 0.02 therefore it is possible to say thatelectron in this excited state most probably willtunneling from HOMO-7 to LUMO.
The most intense 10th excited state iscomposed mainly from two individual transitions
HOMO → LUMO with weight equal to 0.54 (seeTable 2), HOMO-12 → LUMO with weight equal
to 0.13 and other individual transitions
contributions are at most equal to 0.10 therefore it
is possible to say that electron in this excited state
most probably will tunneling from HOMO-m to
LUMO.
The intense absorption lines (see green bars in
the Figure 6) of the squarine-8-oxo-guanine
supermolecule were found to be shifted to the red
when these molecules were associated with simple
fatty acid micelle shown in the Figure 5 (black bar)and similar micelle with Sq(II) molecule (blue bar).
The geometry optimization of more complex
photoactive fatty acid micelle containing Sq(II)attached covalently to 8-oxo-guanine::cytosine
supramolecule, pFA and 50 water molecules (seeFigure 13) were performed by using PBELYP/3-21
with GAMESS-US package and done calculationsof spectrum using TD DFT revPBE method withthe 6-31G* basis set using ORCA package.
The part of absorption spectrum of thephotoactive fatty acid micelle given in the Figure
13 is placed in the Table 3 and in the Figure 6 (redbars). The electron charge transfer trajectories indifferent excited states are shown in the Figures 14

Figure 11. Visualization of the electron charge tunnelingassociated with the eighth excited state. The transition isfrom the Sq(II) (in the top) to the same Sq(II) moleculeand partially to the pFA molecule (in the bottom).

Figure 12. Visualization of the electron charge
tunneling associated with the tenth excited state. The
transition is from the Sq(II) (in the top) to the same
Sq(II) molecule and partially to the pFA molecule (inthe bottom).

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Viva Origino 38 (2010) 4 - 17
Table 3. Excitation transitions energies of a fatty acid micelle containing Sq(II) molecule with attached covalently
8-oxo-guanine::cytosine supramolecule and pFA molecule, and 50 water molecules were calculated using TD DFT
revPBE method with the 6-31G* basis set in the ORCA program package. The weight of the individual excitations are
given if larger than 0.09.

Excitedstate #

14

32

Individual transitions
HOMO-m → LUMO+n

Weight ofindividualtransition

HOMO-9 → LUMO

0.23

HOMO-3 → LUMO

0.2

HOMO → LUMO

0.19

HOMO-11 → LUMO

0.17

HOMO → LUMO

0.36

HOMO-14 → LUMO

0.28

Figure 13. A movie based visualization of the last stepsof the geometry optimization of a self-reproducing FA
based micelle system containing a Sq(II) molecule with
attached
covalently
8-oxo-guanine::cytosine
supramolecule (the bottom-right), pFA molecule(extending to the bottom-left) and 50 water molecules.

Energy(eV)Wavelength(nm)

Oscillator strength(arbitrary units)

2.34

530.2

0.72

2.68

463.3

1.9

Figure 14. Visualization of the electron charge
tunneling associated with the 14th state. The transitionis from the Sq(II) (in the top) to the same Sq(II)molecule and partially to the pFA molecule (in thebottom).

and 15.
The electron tunneling transitions of the 14th and32nd excited states of this micelle should induce
metabolic photo dissociation of pFA molecule
because the transferred electron cloud is located on
the head (the waste piece) of pFA molecule (seeFigures 14 and 15) where it causes this molecule tosplit due to intense rotation and vibration of the
weak chemical bond that joins the waste piece tothe fatty acid section of the pFA molecule.
The intense 14th excited state is composed
mainly from four individual transitions HOMO-9→ LUMO with weight equal to 0.23 (see Table 3),
HOMO-3 → LUMO with weight equal to 0.2,
HOMO → LUMO with weight equal to 0.19,
HOMO-11 → LUMO with weight equal to 0.17
and other individual transitions contributions are at
most equal to 0.09 therefore it is possible to saythat electron in this excited state most probably
will tunneling from HOMO-m to LUMO.
The most intense 32nd excited state is composed
mainly from two individual transitions HOMO →LUMO with weight equal to 0.36 (see Table 2),
HOMO-14 → LUMO with weight equal to 0.28

Figure 15. Visualization of the electron charge
tunneling associated with the 32nd excited state. The
transition is from the Sq(II) (in the top) to the same
Sq(II) molecule and partially to the pFA molecule (inthe bottom).

and other individual transitions contributions are at
most equal to 0.09 therefore it is possible to saythat electron in this excited state most probably
will tunneling from HOMO-m to LUMO.
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Viva Origino 38 (2010) 4 - 17

Table 4. Atomic Lowdin charges with hydrogens
summed into carbon atoms of neutral and anion pFA
molecules calculated by B3LYP/6-311++G**
method.

Figure 16. Geometrical structure of pFA molecule.
There are numerated heavy C and O atoms from 1 to
9 in the head section (waste end, waste piece) of thismolecule and from 10 to 13 in the part of FA
fragment.

Summarizing it is possible to make statements
concerning three our investigated photosynthetic
centers of fatty acid micelles. The most intense
excited states of the photoactive fatty acid micelles
are partially composed of LUMO+n states locatedon the fatty acid precursor molecule when thebis(4-diphenylamine-2-phenyl)-squarine molecule
is covalently attached to the 8-oxo-guanine. This
coupling also promotes electron hopping(tunneling) to the pFA molecules during the mostintense absorption excited state. The photoexcitedelectron tunnels to the head section (the waste
piece) of the pFA molecules where it causes thesemolecules to split due to intense rotation andvibration of the weak chemical bond that joins thewaste piece to the fatty acid section of the pFA
molecule.
In order to understand process of photodissociationof pFA molecule but reduce expenses ofcomputations it was investigated the electronic
structure of single neutral pFA molecule (seeFigure 16) by using B3LYP/6-311++G** method.
After geometry reoptimization procedure it was
obtained the electronic structure of negative ion ofthismolecule
using
unrestricted
B3LYP/6-311++G** method.
Atomic Lowdin charges in Table 4 are withhydrogens summed into carbon atoms, i.e. theatomic charges of hydrogens are already added tothe atomic charge of neighboring carbon atom. The
sum of Lowdin charges of atoms from No 1 to 9 of

Number ofatom

Neutral pFA

Anion of pFA

1

C

0.035

-0.130

2

C

0.021

-0.047

3

C

0.091

0.002

4

C

-0.119-0.146

5

C

0.035

-0.063

6

C

0.017

-0.047

7

C

0.196

0.045

8

O

-0.308-0.490

9

C

0.307

0.257

10

O

-0.380-0.385

11

C

0.299

0.291

12

C

0.087

0.069

13

O

-0.342-0.370Sumofcharges on 0.274
1-9 atoms-0.620neutral pFA molecule are equal to 0.274 of electron
charge (e) while the sum on the same atoms inanion pFA molecule is equal to -0.620 e (see Table4). It means that almost entire (-0.894 e) additional
electron after self-consistent field procedure
localizes on the waste end of pFA molecule while
only -0.106 e charge of additional electron
localizes on FA fragment of this molecule.
Data of bond orders of selected chemical bonds ofneutral and anion pFA molecules are presented inTable 5.
Analysis of selected bond orders of neutral andanion pFA molecules shows that the mostweakness chemical bond order is between 9th and10th atoms in the neutral pFA molecule. The
additional electron which is placed on the waste
end of pFA molecule decrease the bond order from0.772 to 0.734 between 9th and 10th atoms.

Table 5. Bond orders of selected chemical bonds of neutral and anion pFA molecules calculated by
B3LYP/6-311++G** method.

Chemical bonds
9-10
C-O

Neutral pFA
0.772

Anion of pFA
0.734

7-8

1.980

2.143

1.295

1.332

10-11

C-O
O-C

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Viva Origino 38 (2010) 4 - 17

It is known in molecular physics that additional
electron which fall down on the molecularfragment initiate the vibrations and rotations of all
chemical bonds in this fragment and it is large
probability that the most weakness chemical bond
between 9th and 10th atoms will be broken. This
photodissociation process of pFA molecule wasobserved experimentally in LANL "Protocell
Assembly" project [1, 2].
The new fatty acid from dissociated pFA
molecule will join to minimal cell, therefore thisminimal cell will grow and later spontaneously
break in two new minimal cells and once again will
use pFA molecules during the photo excitation
processes for generation the new FA molecules, etc.
This photoinduced autocatalytic bioorganic system
was experimentally proved in the papers [1-3], andcalled in LANL "Protocell Assembly" project asminimal artificial living cell or protocell.
The most intense absorption lines of thesquarine-8-oxo-guanine supermolecule were foundto be shifted to the red when these molecules wereassociated with fatty acid micelles (see green bars
situated from left to right in the Figure 6). Red bars
represents the absorption spectrum lines ofSq(II)-8-oxo-guanine::cytosine+pFA(I)+50
H 2O
minimal cell calculated using TD DFT revPBE
method with the 6-31G basis set. In addition, the8-oxo-guanine::cytosine-squarine supramolecule

was observed to have an absorption region thatcovered more of the visible spectrum than asquarine-oxo-guanine supermolecule.
The redward shift of the intense absorption lines
would allow a self reproducing micelle to absorb
the light in the longer wavelength region, which
may have been important in the environment thatlife might have developed, in addition to extending
the photoactive period into the earlier morning andlater evening hours. That allowed better compete
for such a kind of evolved photoactive micelles ofFatty Acids World life in getting the foodmolecules. Furthermore, one notes that thenucleotide caused wavelength shift and broadeningof the absorption pattern potentially gives thenucleotides an additional valuable role, other thanjust a purely genetic one in the early stages of thedevelopment of life.
Most probably, that appearance of the simplest
self-reproducing photoactive fatty acid micelles
were in the period of 3.9-3.8 billion years before,
i.e. just after formation of stable core in the Earth.
Later these photoactive fatty acid micelles evolved
incorporating nucleotide molecules (most probably
in the period of 3.8-3.7 billion years before), see
Figure 17.
The nucleotide molecules and their sequences in
the first period of evolution of Fatty Acid World
were useful just for better absorbency of the light

PNA World [1-3, 15]

RNA World

DNA World

3.6-3.5 109 Years before

3.5-3.3 109

Y

F

A

A

T

T

Y

Fatty Acids Micelles [17]93.9-3.8 10 Y

C

I

D

S

8-oxo-Guanine Micelles [17]93.8-3.7 10 Y

W

O

R

L

D

8-oxo-Guanine:Cytosine
Micelles3.7-3.6 109 Y

Figure 17. Demo nstration of the main results of our present and recent papers. We state that Life in the Earth orelsewhere in the Space emerged in the form of self-reproducing photoactive fatty acid micelles which step by step
evolved to the nucleotide containing micelles due to better possibilities absorb the visible light.

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Viva Origino 38 (2010) 4 - 17

in the longer wavelength region. Later, in the PNA
or RNA Worlds, these nucleotides were used forthe genetic information storage (see Figure 17). If
to say strictly, from the information theory point ofview, the nucleotide molecules sequences in the
Fatty Acids World micelles carry positional
information how to directly provide betterrelaxationelectrontransport
along
thenucleotide-sensitizer chain but this is not theconvenient understanding of genetic information.
The addition possibility of guanine::cytosine
supramolecules containing fatty acid micelles toprovide complimentary copies of that positional
information to the next generation corresponds tothe convenient understanding of genetic
information.

light in the longer wavelength region, which may
have been important in the environment that life
might have developed, in addition to extending thephotoactive period into the earlier morning andlater evening hours. This would have allowed
better competition for such evolved photoactive
micelles (Fatty Acids World Model) in obtaining
food molecules. Furthermore, one notes that thenucleotide caused wavelength shift and broadeningof the absorption pattern potentially gives thenucleotides an additional valuable role, other thanjust a purely genetic one in the early stages of thedevelopment of life.
The nucleotide molecules and their sequences
which in the first period of evolution of fatty acidmolecules were useful just for better absorbency ofthe light in the longer wavelength region, later in
the PNA or RNA World, were used for genetic
information storage. From the information theory
point of view, nucleotide sequences in the Fatty
Acids World micelles carry positionallyinformation on how to directly provide better
electron transport along the nucleotide-sensitizer
chain and in addition providing complementary
copies of that information to the next generation.

5. Conclusions
In the proposed model, three quantum
mechanical processes led to the emergence ofphotoactive fatty acid micelles containing an
8-oxo-guanine::cytosine base pair at the earlystages of emergence of life on the Earth:1) All macromolecular living systems, including
photoactive fatty acid micelles, are self-assembling
and achieve this based on interactions involving
weak electrostatic forces (due to a small internal
shift of the whole conjugated valence electron
cloud from the electron-donor tail to theelectron-acceptor head) and other quantum(dispersion, H-bonding) fine effects. The result of
self-assembly of molecules depends on theelectromagnetic forces between electrons and ingeneral is predicted by existence of the universal
constants. Universal constants of physicalinteractions did not changed in the Universe during
last 13.73 billion years therefore the emergence oflife was predicted before the time of the expansionof the Universe.
2) The most intense excited states of thephotoactive fatty acid micelles are partiallycomposed of LUMO+n states located on the fatty
acid
precursorswhenthebis(4-diphenylamine-2-phenyl)-squarine molecule
is covalently attached to the 8-oxo-guanine. This
coupling also promotes electron hopping(tunneling) to the pFA molecules during the mostintense absorption excited state. The photoexcitedelectron tunnels to the waste end of the pFA
molecules where it causes these molecules to split
due to intense rotation and vibration of the weakchemical bond that joins the waste piece to thefatty acid section of the pFA molecule;3) The most intense absorption lines of thesquarine-8-oxo-guanine supermolecule were foundto be shifted to the red when these molecules wereassociated with fatty acid micelles. In addition, the8-oxo-guanine::cytosine-squarine supramolecule
was observed to have an absorption region thatcovered more of the visible spectrum than asquarine-8-oxo-guanine
supermolecule.
The
redward shift of the intense absorption lines would
allow a self reproducing micelle to absorb the

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