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a r t i c l e i n f o a b s t r a c t
Article history: This study constructed the relationship between L-amino acids and four-carbon D-sugar using quantum
Received 4 July 2016 theory. Theoretically, an L-amino acid could react with the ketone to afford the corresponding Schiff base
Accepted 15 July 2016 which may take place an Aldol reaction with a molecule of formaldehyde. An assumption is proposed
Available online xxx
that the Aldol addition products with (R) or (S) configuration could have different quantity due to the
effect from stereogenic center of L-amino acid. By hydrolysis of the Aldol addition, different D- or L-sugar
Keywords:
would form. Thus, B3LYP, WP1MPW91 and wB97XD theories were used for the energy difference
D-Sugar
computations at the 6-311þþG(2d,p) level in the gas phase, or in water using PCM and SMD model,
L-Amino acids
Conformational study
respectively. The predicted ee value sequence agrees well to the experimental result in the asymmetric
Energy difference synthesis of 3-carbon sugar using five L-amino acids. Further theoretical study exhibited that 4-carbon D
DFT sugar should form if the corresponding L-amino acid is used. The ee values of the 4-carbon sugar are
bigger than those of 3-carbon D-sugars catalyzed by the same L-amino acids. This looks like the chiral
amplification in the procedure.
Ó 2016 Elsevier Ltd. All rights reserved.
Scheme 1. (left in dash frame) Formation of three-carbon sugar (8) from CHO; (right)
* Corresponding author. E-mail address: zhuhuajie@hotmail.com (H.-J. Zhu). L-amino acids used in the chiral catalytic formation of 8.
http://dx.doi.org/10.1016/j.tet.2016.07.047
0040-4020/Ó 2016 Elsevier Ltd. All rights reserved.
Please cite this article in press as: Zhao, D.; et al., Tetrahedron (2016), http://dx.doi.org/10.1016/j.tet.2016.07.047
2 D. Zhao et al. / Tetrahedron xxx (2016) 1e5
values of 2.9e4.2. L-Glutamic acid (5) led to 21.4% ee formation of 8 the Aldol addition, this intermediate 13 could decompose into the
or 34.8% under the same acidic conditions. Under the prebiotic corresponding D- or L-sugar 8 and the L-amino acid in water, re-
conditions, the atmosphere contained huge CO2, which could dis- spectively. Thus, the de values of 13 should be the same as ee values
solve in water and lead to water having about pH value of 5.6. This of the sugar 8. In this report, activation energy barriers are not
datum is smaller than 4.2 but larger than 6.5. Thus, this weak acidic considered since the reaction could take place at room tempera-
condition could be a good benefit to synthesize D-sugar in prebiotic ture. For a clear statement, (R)-13 and (S)-13 are used, respectively,
environment. to representative (2R,20 S)-13 and (2S,20 S)-13, and the de values of
This discovery is extremely important and valid. A logical the intermediate 13 should be regarded as the ee values of the
question then rises: should the other D-sugars such as 4-carbon corresponding D-sugar.
sugar could form via the similar procedure? However, there is no
any experimental or theoretical investigation to show asymmetric
formation of four-carbon sugar (C4H8O4, 9) or others catalyzed by L- 3. Computational section and discussion
amino acids. In this study, we investigate the asymmetric formation
of four-carbon sugar catalyzed by different L-amino acids. The The calculations were performed using density functional the-
prediction clearly exhibits that high ee values of four-carbon sugar, ory (DFT),11 because energies,12 analytic gradients, and true analytic
theoretically, could be obtained using the corresponding L-amino frequencies,13 are available for all DFT models. We used the B3LYP,14
acids, such as phenylalanine. WP1MPW91,15 and wB97XD16 theories at the bases sets of 6-
311þþG(2d,p) in calculations.17 Frequency calculations were also
performed.18 Solvent effects were modeled through the use of the
2. Theoretical section polarizable continuum model (PCM)19 and solvation model density
(SMD),20 respectively. In our recent study, the methods mentioned
Theoretically, an L-amino acid could react with hydroxyl acet- above exhibited valid data to explain the experimental data by
aldehyde (7) to form the corresponding Schiff base 12 (Scheme 2). conformational study.21
The second CHO molecule would react with the intermediate 12 to The conformations of (R)-13 and (S)-13 were searched using
afford 13 with either (R) or (S) configuration at C-2 in different ratio, different conformational search packages, such as ComputeVOA,
which would depend on the both of (1) their relative energy dif- Barista, respectively, via MMFF94S force field. All conformations
ferences and the (2) Aldol reaction activation energy barrier. Base that were found were used in optimizations at the B3LYP/6-31G(d)
on the reports from Breslow,4,10 the Aldol reaction could take place level in the gas phase first. These geometries with relative energy
at room temperature to afford 13, that means the activation ener- from 0 to 2.5 Kcal/mol were used for further optimizations using
gies (DG1 and DG2 in Fig. 1) are not high. Therefore, this Aldol re- five different quantum methods. The first one is to optimize the
action is reversible at room temperature. The distributions of B3LYP/6-31G(d)-conformations at the B3LYP/6-311þþG(2d,p) level
products (2R,20 S)-13 and (2S,20 S)-13 should majorly depend on in the gas phase (method 1). The second one is to use the B3LYP/6-
their energy differences (DE in Fig. 1). The bigger the relative energy 311þþG(2d,p)-optimized geometries in optimizations at the same
difference is, the bigger the quantity difference of (2R,20 S)-13 and level in water using PCM model (method 2). The third method is to
(2S,20 S)-13 should be. Namely, the higher the de value will be. After optimize the B3LYP/6-31G(d)-geometries at the WP1PW91/6-
311þþG(2d,p) level in the gas phase (method 3), and then these
WP1PW91/6-311þþG(2d,p)-optimized conformers were re-
computed at the same level in water using PCM model (method
4). Finally, the geometries were then optimized at the wB97XD/6-
311þþG(2d,p) level in water using SMD model (method 5). The
smallest energy differences between (R)-13 and (S)-13 were then
computed using the lowest energy of (R)-13 and (S)-13. Every
method can afford its corresponding smallest energy difference.
Then, the differences were used for quantity computations of (R)-13
and (S)-13, respectively, using Arrhenius Eq. 1.
Q ¼ keDE=RT (1)
where Q is the quantity of intermediate (R)-13 or (S)-13, k is
Scheme 2. Formation of three-carbon sugar (8) catalyzed by L-amino acids. a constant, R is the gas constant (8.314 J mol1 k1), T is the ab-
solute temperature, 298 K is used in the calculations. DE is the
Fig. 1. Coordinates for plausible reaction paths from mixture of 12 and CH2O to 13. Herein, (R)-13 and (S)-13 are used, respectively, to representative (2R,20 S)-13 and (2S,20 S)-13. Two
cases exist in the procedure. Case 1: the reaction barrier (DG2) to (S)-13 is higher than that to (R)-13 (DG1); case 2: the reaction barrier (DG2) to (S)-13 is smaller than that to (R)-13
(DG1). Since the sugar obtained has D-type of AC, the product (S)-13 should have lower relative energetics than (R)-13.
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D. Zhao et al. / Tetrahedron xxx (2016) 1e5 3
energy difference. Then, the ratio of (S)-13 to (R)-13 should be values were 12.1%, 22.1% and 6.2% using the total electronic energy,
computed using Eq. 2: zero point energy and Gibbs free energy, respectively. The experi-
mental ee was 5.4%, or 19% under the acidic condition
QS eDES =RT (pH¼2.9e4.2). Method 4 predicted well for (R)-13 using L-valine (4)
¼ DE =RT ¼ eðDES DER Þ=RT (2)
QR e R using the three kind of energies, especially using Gibbs free energy
in ee predictions (6.2% predicted vs 5.4% in experiments). Another
On the other hand, the sum of fractions of (R) and (S)-isomers
good prediction way is method 1 by using Gibbs free energy, the
should be 1 (Eq. 3):
predicted ee value is 7.7% (entry 11), and the experimental ee was
QS þ QR ¼ 1 (3) 5.4%. Methods 1 and 3 cannot predict the accurate energy differ-
ences. Among all five computational methods, method 5 gave the
Combinational uses of Eqs. 2 and 3, we can compute the de poorest prediction, for example, only the predicted ee value
values for (R)-13 and (S)-13 for each method. The results are (smallest ee is 12.1%) for L-alanine (1) closed to the experimental ee
summarized in Table 1. % (1.6%), other predictions did not match the experimental results
(Table 1, entries 10, 15, 20 and 25).
Table 1 It was found that L-type sugar might produce under weak basic
The relative energy of intermediate (R)-13 and (S)-13 and the predicted ee for condition (pH¼8e9) or neutron condition (pH¼6.5e7.5) with
D-sugar 8 and experimental ee values a small ee value.4 However, this reaction system could be of a weak
Entry Amino Method DE(SeR) of 13 (kcal/mol) Calcd ee (%) for 8e Exp. acidic environment since the formation of Schiff base (12) led to the
acid ee (%) relative strong conjugation formation of lone pair of electrons of N
DETa DE0 DG DET DE0 DG
atom to the sp2 C, which can reduce the base of N atom. Thus, the
1 1 1 0.396 0.448 0.158 32.3 36.2 13.3 1.6b
whole molecule should exhibit weak acidic. This is helpful forma-
2 2 0.132 0.126 0.165 11.1 10.7 13.9
3 3 0.098 0.282 0.424 8.3 23.4 34.4 tion of D-type sugar.
4 4 0.138 0.153 0.250 11.6 12.9 20.8 It is amazing that the predicted product should be L-sugar using
5 5 0.220 0.144 0.420 18.4 12.1 54.4 L-glutamic amino acid and L-serine (Table 1, entries 6e10 and
6 2 1 1.439d 1.119 1.027 83.9 73.8 70.0 0.6b 21e25). These are conflict to the experimental results. Why only
7 2 1.273 0.618 0.569 79.2 48.0 44.7
8 3 1.459 1.091 0.301 84.4 72.7 24.9
the two predictions disagree with the experimental results? The
9 4 1.515 0.825 0.390 85.7 60.3 31.8 possible reason may be the characteristics of the two amino acids.
10 5 1.168 0.916 0.649 75.6 64.9 50.0 For example, serine (5) has a terminal eOH and glutamic amino
11 3 1 0.618 0.504 0.091 48.0 40.2 7.7 5.4b acid (5) has a eCOOH. Both groups easily form H-bonds with other
12 2 0.548 0.520 0.725 43.3 41.3 54.6
terminal eOH in intermediate 13, affording a big head-tail con-
13 3 0.898 0.564 0.707 100.0 44.4 53.5
14 4 0.645 0.511 0.884 49.7 40.7 63.4 nection cyclic structure when conformational search is performed
15 5 0.705 0.343 0.393 53.4 282 32.1 (Fig. 2). Such a big cyclic structure is not easily formed under water
16 4 1 0.219 0.222 0.127 18.3 18.6 10.7 5.4b since the huge number of water molecules could break down the
17 2 0.178 0.143 0.395 15.0 12.1 32.2 19.0c head-tail connected circle. For example, it should be a 9-atom ring
18 3 0.269 0.139 0.450 22.4 11.7 36.3
19 4 0.144 0.265 0.074 12.1 22.1 6.2
structure in the intermediate 13 using L-serine and 11-atom ring
20 5 0.277 0.355 0.294 23.0 29.1 24.3 structure using L-glutamic amino acid, respectively (Fig. 2). The
21 5 1 1.993 2.048 1.757 93.3 93.9 90.2 21.4b formation of H-bonds may change the energy sequence of (R)-13
22 2 1.829 1.757 1.176 91.3 90.2 75.9 34.8c and (S)-13. Other amino acids, such as L-alanine (1) L-phenylalanine
23 3 1.680 2.037 1.785 89.0 93.8 90.7
(3) and L-valine (4) had no any terminal eOH or eCOOH, they could
24 4 2.767 1.920 1.392 98.2 92.5 82.6
25 5 2.726 2.730 2.875 98.0 98.0 98.5 not form such big head-tail connected structures in 13. The energy
sequences predicted using these L-amino acids agree to the ex-
a
DET: Total electronic energy difference. DE0: Zero-point energy difference. DG:
Gibbs free energy difference.
perimental results. Therefore, the real head-tail connection struc-
b
See Ref. 10 for details, the pH values were not mentioned in this reference. ture may not exist in real case. To examine the assumption, the
c
pH values in reactions were from 2.9 to 4.3. See Ref. 4 for more details. lowest energy geometries of (R)-13 and (S)-13 using L-glutamic
d
The italic data means the results do not agree to the experiments. amino acid and L-serine were analyzed (Fig. 2). As the expected,
e
The ee values of D-sugar 8 equal to the de values of 13.
both (R)-13 and (S)-13 using L-glutamic amino acid formed the
headetail connected circle with two H-bonds. (R)-13 using L-serine
As mentioned above, the de values of 13 should be the same as formed head-tail connected structure with one H-bond while (S)-
the ee value of sugar 8 obtained in experiments. Therefore, the de 13 did not form H-bond using L-serine. Obviously, the ring sizes of
values of 13 should be used as the ee values of D-sugar in the fol- 9-atom could be easily broken in water environment.
lowing discussion. The best prediction is to use method 2 to predict If all of the head-tail connected structures using L-serine and L-
the ee values of sugar 8 catalyzed by L-valine. The predicted ee glutamic acid are removed from the energy computations and
Fig. 2. The cyclic head-tail connection structures of (R)-13 and (S)-13 catalyzed by L-glutamic amino acid and L-serine.
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4 D. Zhao et al. / Tetrahedron xxx (2016) 1e5
analysis, the energy difference sequence of (R)-13 and (S)-13 may 15, respectively, for each computational method. The results are
reversed. Therefore, all of the conformations without the head-tail summarized in Table 3.
connections were used in the computations using the four
methods. The calculation results are listed in Table 2. Fortunately, Table 3
the predicted sugar should be D-type using L-serine now, its ee Predicted relative energy of (R)-15 and (S)-15 and their ee values for D-sugar 10
value was 11% (entry 3, Table 2), the experimental value is only 0.6. catalyzed by the five L-amino acids
The D-sugar was also predicted with ee values of 34e95% catalyzed Entry Amino acid Method DE(SeR) of 15 (kcal/mol) Calcd ee (%) for 10b
Scheme 3. (left in dash frame) Formation of four-carbon sugar (10) from CHO; (right) L-amino acids used in chiral catalytic formation of 10.
that were recorded by MMFF94S force field were then used in values of 15 should be also equal to the ee values of the four-carbon
optimizations at the B3LYP/6-31G(d) level in the gas phase. Then, D-sugar 10. Thus, as mentioned above, the de values predicted for 15
the five methods mentioned above were used for optimizations of should equal to the ee of four-carbon D-sugar in the following
all conformers of 15 with relative energy from 0 to 2.5 Kcal/mol. discussions.
Again for clarity, (R)-15 and (S)-15 were, respectively, used to rep- It is found that the method 2 predicted all the sugar formed
resentative (3R,20 S)-15 and (3S,20 S)-15 in the following discussions. should be D-type catalyzed by the five L-amino acids except for L-4
The quantity differences were then calculated between the lowest as a catalyst when Gibbs free energy values were used (entry 17).
energy conformer of (S)-15 and the lowest energy conformer (R)- More importantly, the most predicted ee values for D type of
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D. Zhao et al. / Tetrahedron xxx (2016) 1e5 5
4-carbon sugar are bigger than those of 3-carbon sugar using the References and notes
same L amino acid. For a clear comparison, the energy differences
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L-1 and L-4, respectively, as the catalysts 7. Levine, M.; Kenesky, C.; Mazori, D.; Breslow, R. Org. Lett. 2008, 10, 2433e2436.
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DET DE0 DG DET DE0 DG mura, H.; Mathew, S.; Wells, D.; Pandya, U.; Armstrong, A.; Blackmond, D.
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16 4 0.144 0.265 d 12.1 22.1 d 1158e1159.
9. Breslow, R.; Cheng, Z. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 9144e9146.
DE(SeR) of 15 (kcal/mol) Calcd ee (%) for 10a
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2 1 2 1.9565 1.653 0.389 92.9 88.5 31.7
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Supplementary data
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