A Computational Study of a Prebiotic Synthesis of D-Riboflavin
(Vitamin B2)
NIGEL AYLWARD
BMS Education Services Company,
Sea Meadow House,
Road Town, Tortola,
BRITISH VIRGIN ISLANDS
Abstract: - Ab initio applied computing is used to determine the viability of a plausible mechanism for the
formation of riboflavin from planetary and interstellar gases that contain the necessary essential elements. The
immutable laws of chemical thermodynamics and kinetics enable the intermediates in the synthesis to be
characterized and the activation energies to be established. The gases propyne, cyanogen, carbon monoxide,
and hydrogen are invoked in a synthesis of the isoalloxazine precursor of the vitamin riboflavin (Vitamin B2),
whilst the additional presence of hydrogen cyanide enables the surface-catalyzed, photochemically activated
synthesis of a D-ribitylamine requiring the magnesium metalloporphyrin catalyst. These two molecules then
bond in a Sn2 reaction to form the final vitamin structure.
The reactions have been shown to be feasible from the overall enthalpy changes in the ZKE approximation at
the HF and MP2 /6-31G* level and with acceptable activation energies.
Key-Words: - Prebiotic photochemical synthesis, isoalloxazine, D-ribitylamine, riboflavin, (vitamin B2),
Mg.porphin
Received: July 29, 2022. Revised: October 4, 2023. Accepted: October 17, 2023. Published: November 1, 2023.
1 Introduction
Riboflavin (Vitamin B2) consists of the sugar D-
ribitol bonded to a substituted isoalloxazine ring,
Figure 1 and Figure 6. The vitamin occurs as a
constituent of the two flavin coenzymes flavin
mononucleotide (FMN) and flavin adenine
dinucleotide (FAD) where the sugar is D-ribitol
rather than D-ribose, [1]. The structure has been
confirmed by chemical synthesis, [2], [3]. These
enzymes belong to the group of flavoproteins which
catalyze oxidation-reduction reactions where the
prosthetic coenzymes FMN and FAD are firmly
associated with the protein component, [1].
Reversible reduction of the isoalloxazine ring yields
FMNH2 and FADH2 in the mononucleotide and
dinucleotide, respectively, where the reduction of
the flavin coenzyme may involve a semiquinone,
[1]. The metalloflavoproteins contain one or more
metals as additional cofactors, [4]. Riboflavin
(vitamin B2), is a water-soluble vitamin, an
essential nutrient in higher organisms as it is not
endogenously synthesized, [5]. It is essential for
redox reactions necessary for energy production,
antioxidant protection, and metabolism of other B
vitamins, such as niacin, pyridoxine, and folate, [6].
Flavins have been recognized as being capable of
both one- and two-electron transfer processes, and
as playing a pivotal role in coupling the two-
electron oxidation of most organic substrates to the
one-electron transfers of the respiratory chain, [7],
[8]. Research is attempting to incorporate gases into
the synthesis of riboflavin, [9].
From a prebiotic perspective, [10], it is desirable
if the reactant molecules formed spontaneously from
a supposed prebiotic atmosphere to be inevitably
present. It has often been held that the atmosphere
of the Earth was originally mildly reducing, [4],
[11], implying the presence of concentrations of
carbon monoxide, ammonia, water, and hydrogen.
It is also supposed that the isoalloxazine was formed
from the gases propyne, cyanogen, carbon
monoxide, and hydrogen, whilst the D-ribitol entity
was formed from carbon monoxide, hydrogen
cyanide, and hydrogen.
This paper proposes a model for the initial
formation of the isoalloxazine present as an anion.
The D-ribose is described as being formed on a
Mg.porphin catalyst from the most abundant gases
carbon monoxide and hydrogen. which determines
the stereochemistry. It is present as a ribityl
ammonium compound.
These two molecules then combine in a Sn2
substitution reaction.to form the riboflavin vitamin.
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These reactions are assumed to occur mainly in the
liquid phase, [12].
The reactions described have been deduced as
kinetically and thermodynamically viable, but
photochemical excitation is required.
2 Problem Formulation
This proposed computational study of a plausible
synthesis of the vitamin riboflavin involves the
calculation of the enthalpy changes for reaction
intermediates in the ZKE approximation and the
calculation of activation energies at the HF level.
These activation energies may all be accessible as
the catalyst may absorb appreciable photochemical
activation (0.21 h). The computations tabulated in
this paper used the GAUSSIAN09, [13].
The standard calculations at the HF and MP2
levels including zero-point energy corrections at the
Hartree Fock level, [14], together with scaling, [15],
using the same basis set, 6-31G*, are as previously
published, [10]. Gibbs free energy calculations at
298.15 K and 1 atmosphere use the HF model, basis
set 6-31G*, and the zero point energy is not scaled.
The charge transfer complexes are less stable when
calculated at the Hartree Fock level, [14], and
activation energies calculated at the HF level
without scaling are less accurate.
If the combined energy of the products is less
than the combined energy of the reactants it may
show that the reaction is also likely to be
spontaneous at higher temperatures. This paper uses
the atomic unit of energy, the hartree, [13].
1h = 627.5095 kcal.mol-1. 1h = 4.3597482 x 10-18 J
Mullikan charges are in units of the electronic
charge.
3 Problem Solution
3.1 Total Energies (hartrees)
The initial reactants in this proposed prebiotic
synthesis of riboflavin are simple gases, propyne,
cyanogen, hydrogen cyanide, carbon monoxide, and
hydrogen. The intermediates by which these could
form riboflavin are listed in Table 1. The catalyst for
the formation of D-ribose is Mg.porphin.
These complexes are integral reactants in the
proposed synthesis. The energies of the stable
complexes to form the isoalloxazine and D-
ribitylamine are shown in Table 1.
Table 1. MP2 /6-31G* total energies and zero point
energies (hartrees) for the respective equilibrium
geometries
Molecule MP2 ZPE (HF)
hartree hartree
_____________________________________
propyne (1) -116.24181 0.06010
cyanogen (2) -185.17464 0.01550
4-imido but-2-yn cyanide (3)
-301.40714 0.08417
4,5-di-imido octan-2,6-diyne (4)
-417.67097 0.14999
4- (2-cyano 1-methanimido)-imido-5-imido
octan-2,6-diyne (5) -602.86341 0.17215
2,3-di-imido 5.6-dipropynyl 1,4-pyrazine (6)
-602.85931 0.17456
2,3-di-aziridon-2yl 5.6-dipropynyl 1,4-pyrazine
(7) -828.84266 0.19630
2,4-dioxo 6,7-di-propynyl -1,2,3,4-
tetrahydropteridine (8)
-829.03869 0.19824
1-dehydro 2,4-dioxo 6,7-di-propynyl -1,2,3,4-
tetrahydropteridine- (9)
-828.49238 0.18371
2,4-dioxo 6,7-di-propynyl 8-ethyl 1,2,3,4-
tetrahydropteridine (10)
-907.34615 0.25883
6,7-di-methyl 1-hydro 5,8,9-tri-dehydro
isoalloxazine (11) -829.02990 0.22830
9-dehydro 6,7-di-methyl 1-hydro isoalloxazine
(12) -830.35155 0.22671
1,9-didehydro 6,7-di-methyl isoalloxazine-
(13) -829.80088 0.21217
Mg.porphin (14) -1185.12250 0.29262
Mg.porphin.4CO (15)
-1636.80888 0.31847
Mg.porphin.(CO-)4 (16)
-1636.96846 0.32040
Mg.porphin.(CO-)3.C(-OH).CN (17)
-1730.20912 0.35688
Mg.porphin.H.C(-OH)4.CH2NH2. (18)
-1734.81264 0.45400
D-ribitylamine.(19) -552.30769 0.22547
D-ribitylamine+ (20) -552.67396 0.23064
D-riboflavin (21) -1326.27656 0.40325
6,7-di-methyl 9-ethyl isoalloxazine (22)
-908.66060 0.28772
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1,10 dihydro 6,7-di-methyl 9-ethyl
isoalloxazine (23) -909.82437 0.31290
CH3CH2NH3+ -135.04152 0.11511
CO -113.02122 0.00566
OH. -75.52257 0.00911
OH- -75.51314 0.00816
H2O -76.19685 0.02045
NH3 -56.35421 0.03700
H2 -1.14414 0.01056
3.2 The Overall Stoichiometry for the
Formation of the Riboflavin
The overall stoichiometry to form the riboflavin is
as follows,
2 CH3-C ≡ C-H + 2 N ≡ C – C ≡ N + 6 CO +
7H2 + HCN → C17H20 N4O6 + NH3
(1)
Riboflavin, Figure 1.
ΔH = -0.35518 h
The enthalpy change is negative indicating that this
may be the energetically favorable route to the
initial formation of the riboflavin. The intermediates
by which these stoichiometric reactions may have
occurred are as follows:
The first sequence involves the formation of the
isoalloxazine anion as,
2 CH3-C ≡ C-H + 2 N ≡ C – C ≡ N + 2 CO +
H2 → C12H9N4 O2- + H+
isoalloxazine- (2)
ΔH = 0.25355 h
The second sequence involves the formation of D-
ribitylamine+, where the Mg.porphin catalyst is
required to give the D-ribose configuration, [16].
4 CO + HCN + 6 H2 + H+ → C5H14N O4+
D-riboseamine
(3)
ΔH = -0.45052 h
This is followed by the bonding of the isoalloxazine
anion and D-ribitylamine cation in a Sn2
substitution reaction to give a neutral D-riboflavin
molecule as,
isoalloxazine- + D-ribitylamine+ → D-riboflavin +
NH3. (4)
ΔH = -0.15821 h
Molecules are numbered consecutively.
Subsections depict alternatives in the sequence of
the reaction mechanism.
A standard numbering of the atoms in riboflavin is
shown in Figure 1, [3], [17].
Fig. 1: Riboflavin
3.3 The Formation of 4-imido but-2-yn
cyanide
The polarization in the gases propyne and cyanogen
suggests a gas phase condensation reaction may
occur as,
CH3-C ≡ C- H + N ≡ C-C ≡ N →
(1) (2) (5)
4-imido but-2-yn cyanide (3)
ΔH = 0.01693 h
ΔG = 0.00115 h
The reaction appears marginally feasible.
The potential energy surface for the transfer reaction
between propyne and cyanogen is given in Figure 2.
CH3
C C C NH
N
C
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Fig. 2: The potential energy diagram for the
formation of 4-imido but-2-yn cyanide where the x-
axis is C(C≡ ) –C(CN) and the y-axis is the H(N)-
C(C≡ ) bond extension. The reactants are at
(2.5,1.8), the 4-imido but-2-yn cyanide at (1.4,1.2),
and the saddle point at (1.7,1.5). The energy = -
300.0 + X h.
The activation energy for the forward reaction
was calculated as 0.120 h and 0.102 for the reverse
reaction.
3.4 The Formation of 4,5-di-imido octan-2,6-
diyne
Another molecule of propyne may also be added in
a further equilibrium reaction as shown,
CH3-C ≡ C- H + CH3-C≡ C-C(=NH)-C≡N →
(1) (3) (6)
4,5-di-imido octan-2,6-diyne. (4)
ΔH = -0.01691 h
The activation energy for the second addition
was 0.100 h and 0.101 for the reverse reaction. The
combined energy for the addition of two molecules
of propyne to cyanogen is then,
ΔH = 0.00002 h
3.5 The Formation of 4- (2-cyano 1-
methanimido)-imido-5-imido octan-2,6-diyne
A further condensation may involve the reaction of
the cyanogen with 4,5-di-imido octan-2,6-diyne as,
4,5-di-imido octan-2,6-diyne + cyanogen →
(7)
4- (2-cyano 1-methanimido)-imido-5-imido octan-
2,6-diyne (5)
ΔH = -0.01189 h
ΔG = 0.002856 h
The addition reaction is favorable and treated as
a transfer reaction followed by ring closure. A 1:4
addition reaction would also suffice. The potential
energy surface for the first addition is given in
Figure 3.
Fig. 3: Potential energy surface for the addition of
cyanogen to 4,5-di-imido octan-2,6-diyne. The x-
axis is the N-C bond formation, the y-axis is the H-
N bond formation. The reactants are at (2.2,1.6), the
product at (1.4,1.2), and the saddle point at (1.8,1.2).
The energy is -600.0 +X h.
The activation energy for the reaction was
calculated as 0.120 h for the condensation and 0.120
h for the reverse reaction.
CH3
C C C NH
NH
CCC
CH3
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3.6 The Formation of 5.6-dipropynyl 1,4-
pyrazine
The 4- (2-cyano 1-methanimido)-imido-5-imido
octan-2,6-diyne may cyclicise to form a pyrazine
derivative as,
4- (2-cyano 1-methanimido)-imido-5-imido octan-
2,6-diyne → (8)
2,3-di-imido 5.6-dipropynyl 1,4-pyrazine (6)
ΔH = 0.00625 h
The cyclization is favorable with an activation
energy of 0.006 h. The combined enthalpy change
for the addition of the cyanogen molecule is then,
ΔH = -0.00564 h
3.7 The Formation of 2,3-di-aziridon-2yl 5.6-
dipropynyl 1,4-pyrazine
The di-imido groups of the pyrazine derivative are
prone to reaction with two molecules of carbon
monoxide to form aziridone ring substituents as,
2,3-di-imido 5.6-dipropynyl 1,4-pyrazine + 2 CO
→ (9)
2,3-di-aziridon-2yl 5.6-dipropynyl 1,4-pyrazine. (7)
ΔH = 0.06614 h
The enthalpy change for the first addition was
calculated as,
ΔH = 0.027 h
where the activation energy was the same as the
enthalpy change, [18].
The enthalpy change for the second addition was
calculated as,
ΔH = 0.031 h
where the activation energy was the same as the
enthalpy change.
3.8 The formation 2,4-dioxo 6,7-di-propynyl -
1,2,3,4-tetrahydropteridine
The 2,3-di-aziridon-2yl 5.6-dipropynyl 1,4-pyrazine
may rearrange bonding to give a pteridine
derivative, [3], as,
2,3-di-aziridon-2yl 5.6-dipropynyl 1,4-pyrazine →
(10)
2,4-dioxo 6,7-di-propynyl -1,2,3,4-
tetrahydropteridine (8)
ΔH = -0.19190 h
The activation energy for the rearrangement was
0.238 h and for the reverse 0.316 h.
The molecule may experience keto–enol
isomerization, [3].
3.8.1 The formation of 1-dehydro 2,4-dioxo 6,7-
di-propynyl -1,2,3,4-tetrahydropteridine-
At this stage in the mechanism the molecule may
ionize in the presence of hydroxyl anion as,
2,4-dioxo 6,7-di-propynyl -1,2,3,4-
tetrahydropteridine + OH- → H2O +
(11)
1-dehydro 2,4-dioxo 6,7-di-propynyl -1,2,3,4-
tetrahydropteridine - (9)
ΔH = -0.13776 h
A further reaction could occur at this point with D-
ribitylamine.
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3.8.2 The formation of 2,4-dioxo 6,7-di-propynyl
8-ethyl 1,2,3,4-tetrahydropteridine
At this point in the reaction sequence the pteridine
anion may react with an alkyl ammonium
compound in a classical Sn2, [19], substitution
reaction. To reduce computing time this is first
computed here using ethylamine cation as,
1-dehydro 2,4-dioxo 6,7-di-propynyl -1,2,3,4-
tetrahydropteridine - + CH3CH2NH3+ → NH3 +
(12)
2,4-dioxo 6,7-di-propynyl 8-ethyl 1,2,3,4-
tetrahydropteridine (10)
ΔH = -0.17380 h
The activation energy was calculated as -0.086 h,
and for the reverse reaction 0.081 h.
3.9 The formation of 6,7-di-methyl 1-hydro
5,8,9-tri-dehydro isoalloxazine
The 2,4-dioxo 6,7-di-propynyl -1,2,3,4-
tetrahydropteridine may cyclize as,
2,4-dioxo 6,7-di-propynyl -1,2,3,4-
tetrahydropteridine → (13)
6,7-di-methyl 1-hydro 5,8,9-tri-dehydro
isoalloxazine (11)
ΔH = 0.03554 h
The activation energy for the ring closure was 0.130
h and .0.129 h for the reverse.
3.10 The formation of 9-dehydro 6,7-di-
methyl 1-hydro isoalloxazine
The 6,7-di-methyl 1-hydro 5,8,9-tri-dehydro
isoalloxazine may react with hydrogen radicals or
molecular hydrogen as,
6,7-di-methyl 1-hydro 5,8,9-tri-dehydro
isoalloxazine + H2 → (14)
9-dehydro 6,7-di-methyl 1-hydro isoalloxazine (12)
ΔH = -0.18835 h
3.11 The formation of 6,7-di-methyl 1,9-
didehydro isoalloxazine
The ionization of 9-dehydro 6,7-di-methyl 1-hydro
isoalloxazine may be represented as,
9-dehydro 6,7-di-methyl 1-hydro isoalloxazine +
OH- → H2O + (15)
1,9-didehydro 6,7-di-methyl isoalloxazine- (13)
ΔH = -0.13340 h
The charges on nitrogen atoms 1,3,9 and 10 were -
0.74, -0.92, -0.66, and -0.53, respectively.
Before this 6,7-di-methyl 1,9-didehydro
isoalloxazine nucleophile may act as a nucleophilic
reagent and react with D-ribitylamine + the D-
ribitylamine needs to be synthesized.
3.12 The formation of D-ribitylamine
To form the steric D-ribose sugar requires a catalyst
Mg.porphin or Fe.porphin, [20], [21], where the
magnetic vector of radiation, or the presence of a
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magnetic field within the catalyst can induce a
directed charge polarization, [16].
3.13 The formation of Mg.porphin.4CO
The carbon monoxide may react with the catalyst
Mg.porphin to produce a magnesium bound or
nitogen bound adduct where the latter is of higher
energy induced by radiation, [16]. The products may
be represented as,
Mg.pprphin + CO → Mg.CO.porphin
and
Mg.pprphin + CO → Mg.porphin.CO
To form the required sugar requires the formation of
four carbon monoxide adducts to be added in
separate additions to give a tetra-dentate complex,
represented as,
Mg.porphin + 4CO →
(14) (16)
Mg.porphin.4CO (15)
ΔH = 0.40170 h
This complex may then be excited to weakly bond
as a free radical complex as,
Mg.porphin.4CO → (17)
Mg.porphin.(CO-)4 (16)
ΔH = -0.15786 h
The net charge on the adducts for Fe.porphin. (CO-
)4 is 0.217, whilst that of the Fe.porphin ring atoms
is -0.217
Alternate bonding during excitation is expected
to yield some D-erythrose and D-threose isomers.
The bonded structure used for the calculation of the
surface potential energy for the formation of the
analogous D-ribose is given in Figure 4.
.
Fig. 4: The Fe.porphin.(CO-)5.structure used for the
analogous potential energy surface
An isovalue through the potential energy
surface for the potential energy surface for
Fe.porphin.(CO-)5 is shown in Figure 5 displaying
charge asymmetry induced by the magnetic field in
the molecule.
Fig. 5: An isosurface for the analogous potential
energy surface of Fe.porphin.(CO-)5. Adduct -
positive, porphin ring –negative
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The potential energy surfaces depict an
asymmetric charge distribution when the molecule
mounts a diamagnetic response to the presence of a
magnetic vector in the molecule arising from
photochemical excitation where the electric vector is
in plane and the magnetic vector perpendicular to
the porphin plane, [16], or from the presence of the
a coordinated ferrous atom in the porphin molecule.
This charge surge causes the bonded carbon
monoxide adducts to bond in an anticlockwise
direction when viewed from above, to pick up a
proton, or react further to give higher sugars.
3.14 The formation of Mg.porphin.(CO-)4.H-CN
The asymmetric charge directs the reaction with a
hydrogen cyanide molecule to be as shown.
Mg.porphin.(CO-)4 + H-CN →
(18)
Mg.porphin.(CO-)3.C(-OH).CN (17)
ΔH = -0.06343 h
3.15 The formation of Mg.porphin.H.C(-
OH)4. CH2NH2.
Further hydrogenation, [22], forms the D-ribose
hydroxyl groups as,
Mg.porphin.(CO-)3.C(OH)-CN + 4H2 →
(19)
Mg.porphin.H.C(-OH)4.CH2NH2. (18)
ΔH = 0.02178 h
3.16 The formation of D-ribitylamine
The Mg.porphin.H.C(-OH)4.CH2NH2 may be fully
reduced with hydrogen molecules or free radicals to
release the catalyst as,
Mg.porphin.H.C(-OH)4.CH2NH2 + 2H2 →
→ Mg.porphin + (20)
. D-ribitylamine.(19)
ΔH = -0.29106 h
The molecule may be further protonated as,
D-ribitylamine. + H+ → D-ribitylamine+.
(20) (21)
ΔH = - 0.36167 h
3.17 The formation of D-riboflavin
The isoalloxazine anion and the D-ribityl cation
may react as, isoalloxazine- + D-ribitylamine+ →
D-riboflavin + NH3 (22)
D-riboflavin (21)
-
CO
OC
C
OO
C
N
Mg
N
NN
CH2NH 2
H
H
H
H
H
CH3
C
CCN
N
C
C
C
CH3
CNH
N
CCO
C
O
H
H
CH2
OH
H
OH
H
OH
H
CH2OH
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ΔH = -0.15821 h
Fig. 6: D-riboflavin
3.17.1 The formation of 6,7-di-methyl 9-ethyl
1,10 dihydro isoalloxazine
The riboflavin molecule may carry hydrogen for
hydrogenation reactions at the N1 and N10 positions
as illustrated here with a reduced 9-substituent to
reduce computing time as,
6,7-di-methyl 9-ethyl isoalloxazine + H2 →
(22) (23)
1,10-dihydro 6,7-di-methyl 9-ethyl isoalloxazine
(23)
ΔH = -0.00642 h
4 Conclusion
The gaseous reactants used in this proposed
synthesis have all been found or inferred as being
present in interstellar space, [23], [24], and many
are found on individual moons and planets of our
solar system, [25]. The catalyst Mg.porphin has also
been cited as from the time of photosynthesis, [26].
The photochemically catalyzed addition reactions of
the simple gases propyne, cyanogen, and hydrogen
may plausibly form the isoalloxazine molecular
structure prone to keto-enol isomerization, whilst
the photochemically activated surface catalysed
oligomerization of carbon monoxide followed by
hydrogenation may form the steric selected D-ribityl
sugar. The anion and cation may then participate in
a Sn2 substitution reaction to form the vitamin., The
reactions do appear to be thermodynamically viable
with acceptable activation energies. If the
concentrations of the gases were very low, the time
for reactions, which could be astronomical, should
have allowed some product from the synthesis to
cover the planet at the same time as peptides and
proteins were being formed, [27], as implied and
inevitable according to the immutable laws of
chemistry. The existence of this molecule as an
enzyme prosthetic group does suggest it is of
extreme antiquity.
Further work at a higher accuracy may alter the
values given here.
Acknowledgement:
Appreciation is expressed to Gaussian Inc.
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[2] A.M.Michelson, The chemistry of nucleosides
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p.162.
[3] E.H.Rodd Ed., The chemistry of carbon
compounds, Elsevier Publ. Vol.1V, 1960,
p.1741.
[4] A.L.Lehninger, Biochemistry,Worth, New
York, 1975, pp. 339.
[5] J.Balasubramaniam, J. Christodoulou, and S.
Rahman. Disorders of riboflavin metabolism.
Journal of inherited metabolic disease,
42(4),2019, pp.608-619.
[6] A.M. Aljaadi, A.M. Devlin and T.J Green,
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DOI: 10.37394/23208.2023.20.30
Nigel Aylward
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303
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WSEAS TRANSACTIONS on BIOLOGY and BIOMEDICINE
DOI: 10.37394/23208.2023.20.30
Nigel Aylward
E-ISSN: 2224-2902
304
Volume 20, 2023