Study on the molecular conformations of a- and β-D-2 -amino-2-deoxyglucopyranoses using ab initio method

Nguyen Dinh Thanh ^*), Dang Nhu Tai

Faculty of Chemistry, Hanoi University of Science, VIETNAM NATIONAL UNIVERSITY, HANOI

^*) [email protected]

             Introduction

Amino-sugars are extensively distributed in nature and play an important role in many biochemical processes. Aside from their critical role in energy metabolism pathways, amino-sugars are also important in recognition processes as components of glycopeptides and glycolipids. a-D-Glucosamine (i.e. a-D-2-amino-2-deoxygluco-pyranose) and b-D-glucosamine (i.e. b-D-2-amino-2-deoxyglucopyranose) are usually found in nature. Its polymer-chitin-forms the exoskeleton of almost all crustaceans, besides, a-D-glucosamine also takes part in component of keratin, group blood substances,…An important requirement of such force field based methods is that the computed energies of various conformers accurately reproduce the true conformational energy surface of molecules of interest. Accurate description of the complete conformational surface for even the simplest of monosaccharides, including the quintessential monosaccharide glucopyranose (glucose), is a formidable task given the size of the system and the large number of conformational degrees of freedom. Quantitative characterization for the conformational surface of simple monosaccharides like glucopyranose is a necessary first step to quantitatively model complex biological systems containing carbohydrates [1].

A particularly critical region of the glucopyranose conformational surface relates to rotation of the exocyclic hydroxymethyl group. This region of the conformational hypersurface has been studied both experimentally and theoretically for related model systems [2] and for glucopyranose [2, 3]. Polavarapu and Ewig [5] reported the first ab initio study of the various minimum energy exocyclic hydroxymethyl conformers for isolated molecules of D-glucopyranose. Cramer and Truhlar [3] later performed a through study of D-glucopyranose conformers using semiempirical methods with solvation and found that the energetic for the minimum conformations of the hydroxymethyl rotational surface are not significantly perturbed by solvation. Salzner and Schleyer [6] reported the conformation of the exocyclic hydroxymethyl group had no effect on the relative energies of the a- and b-anomers at the HF/6-31G(d)level of theory, in agreement with the earlier work by Polavarapu and Ewig [5] at the HF/4-31G level. Glennon et al [7] performed the extensive computational study of mono- and disaccharides to date, focusing on conformers of a-D-glucopyranose. Three minimum conformations were found along the exocyclic hydroxymethyl rotational surface designated GG (gauche gauche), GT (gauche trans), and TG (trans gauche), each separated by approximately 120^o dihedral rotation. The relative energy differences between conformers was found be small (<4 kJ/mol) and somewhat basic set dependent [7].

Even if the minima of the exocyclic hydroxymethyl rotational surface have been studied extensively, no previous theoretical work has addressed any aspect of the rotational transitional states connecting these minima. The energetics of rotation in simple amino-sugars are not only an interesting physical chemical problem but also has implications for understanding the conformational equilibrium and solvation of carbohydrates, as well as for force field parameterization. Aside from issues related specifically to carbohydrates, these systems also represent an interesting example of molecules with strong intramolecular interactions. The magnitude of intramolecular effects and the way in which they perturb rotational energy hypersurfaces is important when considering the structure and energetics of such molecules. Continuing the researches in this field [8], in this article we report ab initio quantum chemical results on various rotation conformers of a- and b-D-2-amino-2-deoxyglucopyranose (Figure l) to characterize quantitatively, for the first lime, the complete intrinsic gas-phase exocyclic hydroxymethyl rotational surface.

Computational Model

Structure, relative energies, and vibrational frequencies of the particular stationary points, including stable minima and the transition states connecting them, associated with rotation about the exocyclic C5-C6 bond have been determined at the restricted Hartree-Fock (RHF) at the correlated levels using basic sets ranging in quality from 6-31G(d) and 6-31G(2d,1p).

The most stable overall rotational conformation of the a-D-2-amino-2-deoxygluco-pyranose and b-D-2-amino-2-deoxyglucopyranose, in which the hydroxyl groups at C1 through C4 are in a counterclockwise arrangement, was chosen as the reference state (Figure 1), consistent with Polavarapu and Ewig [5] and Glennon et al [2]. Although various secondary hydroxyl substates, which will certainly be populated in solution and quite possibly could be populated in the gas phase, may perturb the relative energies of the primary alcohol conformations, only the lowest energy arrangement (determined by Polavarapu and Ewig [5]) of the C1 through C4 hydroxyls was chosen for analysis of the hydroxymethyl rotational surface. The various stationary points associated with exocyclic hydroxymethyl rotation were located by displacement of the O5-C5-C6-O6 dihedral angle in 60^o increments, followed by reoptimization. Each stationary point was verified as a minimum or a transition state via analytic second derivative calculations. To ensure that each stationary point located along the C5-C6 rotational surface represents the most stable structure within the counterclockwise arrangement, the exocyclic hydroxyl rotational surface was also explored by rotation about the C6-O6 bond. Completely optimized structures were obtained for each stationary point at the RHF level using the 6-31G(d) and 6-31G(2d,1p) basic sets. All calculations were performed using GAMESS 6.2 electronic structure package [8] on PC Pentium 1.7GHz in Linux RedHat 8.0 OS version

Result and Discussion

The conformational energy surfaces of hexoses, in general, and of glucopyranose, in particular, are extremely complex.  Given the rotational freedom of the hydroxyl groups, there are thousands of possible conformers. However, the complexity can be greatly reduced when intramolecular hydrogen bonding is considered in preliminary conformation search, i.e., the low lying conformation should maximize intramolecular hydrogen bonding. For the isolated molecule, the hydroxyls prefer to orient in such a way as to yield a cooperative hydrogen bonding that is as efficient as possible. For glucopyranose, the OH groups may take clockwise (Figure 1a and 1c) or counterclockwise (Figure 1b and 1d) orientations. It was found previously that the counterclockwise orientation is preferred, and that preference was confirmed in this work.

Figure 1. TG conformation of a- and β-D-2-amino-2-deoxyglucopyranoses with appropriate atom labels: (a, c) counterclockwise and (b, d) clockwise (respectively). Bond distances are those obtained at the RHF 6-31G(d) and 6-311G(2d,1p) levels of theory (see Table 1).

Figure 1 and Table 1 shows a three-dimensional representation of the most stable conformer of a- and β-D-2-amino-2-deoxyglucopyranoses in the counterclockwise arrangement, designated TG (trans gauche) along with important bond distances obtained at the RHF 6-31G(d) and 6-31G(2d,1p) levels. Basis set expansion through 6-31G(2p,1d) was found to only moderately affect these structural parameters.

- In case of a-D-2-amino-2-deoxygluco-pyranose: For the C-C, C-O, C-N, O-H and N-H bonds, basis set expansion causes a contraction (ca. 0.0002-0.0068 Å) while the C-H bonds are elongated (ca. 0.0006-0.0012 Å).

- In case of β-D-2-amino-2-deoxygluco-pyranose: For the C-C, C-O, O-H and N-H bonds, basis set expansion causes a contraction (ca. 0.0000-0.0027 Å) while the C-H bonds are elongated (ca. 0.0007-0.0014 Å); especially, the C-N bond is not changed.

The reason for this is not clear; it could be a result of the limited flexibility of the 6-31G(d) basis set.

Table 1. The bond distances of TG conformation of a-D-2-amino-2-deoxy-glucopyranose at the RHF 6-31G (d) and 6-31G (2d, 1p) levels of theory.

Table 1. (continuing)

- In case of a-D-2-amino-2-deoxygluco-pyranose: For a TG glucopyranose, the counterclockwise conformation was found to be 6.39 kJ/mol more stable than the corresponding clockwise conformation at the RHF 6-31G(d) level (Absolute energies of the TG counterclockwise and clockwise conformations are -663.506325 and -663.503889 hartrees, respectively).

- In case of β-D-2-amino-2-deoxygluco-pyranose: For a TG glucopyranose, the counterclockwise conformation was found to be 1.23 kJ/mol more stable than the corresponding clockwise conformation at the RHF 6-31G(d) level (Absolute energies of the TG counterclockwise and clockwise conformations are -663.499892 and -663.500346 hartrees/atom, respectively).

Figure 2 shows a graphical representation of the hydroxymethyl rotational energy surface at both the RHF 6-31G (d) and 6-31G (2d, 1p) levels. The rotational surface consists of three stable minima. Starting from the most stable rotational conformer at the RHF 6-31G (d) level we have the following results:

- In case of a-D-2-amino-2-deoxygluco-pyranose: TG, in which the hydroxymethyl group is approximately parallel to the ring with a O5-C5-C6-O6 dihedral angle (g) of 166.37^o, rotation about g leads initially to transition structure TS1 (g=-130.11^o), and then to a second minimum structure GG (g=-57.09^o), in which the hydroxymethyl group is roughly perpendicular to the glucopyranose ring. Continued rotation about g leads to a second transition state, TS2 (g=-0.64^o), followed by a third minimum, GT (g=58.97^o). Further rotation about g leads back to the initial structure TG through a third transition state, TS3 (g=108.74^o).

- In case of β-D-2-amino-2-deoxygluco-pyranose: TG, in which the hydroxymethyl group is approximately parallel to the ring with a O5-C5-C6-O6 dihedral angle (g) of 166.97^o, rotation about g leads initially to transition structure TS1 (g=-131.23^o), and then to a second minimum structure GG (g=-57.37^o), in which the hydroxymethyl group is roughly perpendicular to the glucopyranose ring. Continued rotation about g leads to a second transition state, TS2 (g=-1.62^o), followed by a third minimum, GT (g=59.04^o). Further rotation about g leads back to the initial structure TG through a third transition state, TS3 (g=108.71^o).

Aside from slight variation in the C5-C6 bond distance between each minimum and their associated rotational transition states due to electron-electron repulsion, the overall structures of the various rotational conformers are very similar, with the orientation of the primary hydroxyl group as only exception.

Tables 2 and 3 represent the relative energetic data for each stationary point on the rotational surface at various ab initio computational levels. The relative energetic data for each stationary point are only modestly influenced by basis set augmentation over the range 6-31G(d),  6-31G(2d,1p), with shifts of less 2.5 kJ/mol (for a-D-2-amino-2-deoxygluco-pyranose) and 3 kJ/mol (for β-D-2-amino-2-deoxygluco-pyranose) overall  (see Table 2). Three minimum conformations (TG, GG and GT) are found to be different in energy:

-In case of a-D-2-amino-2-deoxygluco-pyranose: The TG conformation is most stable, and the relative energy differences between two remain minimum conformers (GG and GT) are 3.59 and 2.69 kJ/mol at the RHF 6-31G(d) and RHF 6-31G(2d,1p), respectively. Thus, the TG conformer is, maybe, the more stable one in the gas phase. The relative final ordering, obtained at the RHF 6-31G(d) for free energies, is GG (-0.04)>TG (0.0)>GT (0.04).

-In case of β-D-2-amino-2-deoxygluco-pyranose: The three minimum conformations (TG, GG, GT) are found to be very closed in energy. The relative energy difference between three minimum conformers (TG, GG and GT) is less than 1 kJ/mol at the RHF 6-31G(d) and RHF 6-31G(2d,1p), with the GG conformation being more stable at all. Thus, the GG conformer is, maybe, the more stable one in the gas phase. The relative final ordering, obtained at the RHF  6-31G(d) for free energies, is GT (-0.11) > TG (0.0) > GG (0.01).

All the stationary points identified on the hydroxymethyl rotational surface consist of conformations that are influenced by intramolecular interactions between the C6 hydroxyl and nearby oxygens (A hydrogen bond is defined by an O-H distance of less 2.6 Å and an O-H-O angle of greater than 120^o, consistent with the definition of Glennon et al [7]):

 -In case of a-D-2-amino-2-deoxygluco-pyranose: In the TG conformer the C6 hydroxyl forms an intramolecular hydrogen bond with O4 (O6H-O4 distance 2.1116 Å, O6-O6H-O4 angle 132.77^o), and in the TS1 transition state, this hydrogen bond is not maintained (O6H-O4 distance 3.0006 Å, O6-O6H-O4 angle 75.28^o). In the GG conformer, O6H does not form a hydrogen bond with O4 (O6H-O4 distance 4.1639 Å, O6-O6H-O4 angle 50.21^o), a instead of orienting toward O4, O6H orients toward O5 in this conformer and form a hydrogen bond with O5 formed (O6H-O5 distance 2.3447 Å, O6-O6H-O5 angle 104.67^o), but it is not a true hydrogen bond. In the TS2 transition state O6H does form a hydrogen bond with O5 (O6H-O5 distance 1.9530 Å, O6-O6H-O5 angle 119.99^o). But the GT conformer, O6H although still oriented toward O5, form a hydrogen bond with O5 but it is also not true hydrogen bond (O6H-O5 distance 2.3616 Å, O6-O6H-O5 angle 104.16^o). The one of two hydrogen atom of the amino-group also forms the intramolecular hydrogen bond with the oxygen atom of hydroxyl at C1. The values of N2H-O1 distances and N2-N2H-O1 angles for the conformation are following:  GG conformer 2.4213 Å, 103.26^o; GT conformer 2.4180 Å, 103.29^o;  TG conformer 2.4159 Å,  103.35^o; TS1 conformer 2.4222 Å, 103.39; TS2 conformer 2.4233 Å, 103.13^o; TS3 conformer 2.4174 Å, 103.45^o.

-In case of β-D-2-amino-2-deoxygluco-pyranose: In the TG conformer the C6 hydroxyl forms an intramolecular hydrogen bond with O4 (O6H-O4 distance 2.1174 Å, O6-O6H-O4 angle 132.38^o), and in the TS1 transition state, this hydrogen bond is not maintained (O6H-O4 distance 3.0552 Å, O6-O6H-O4 angle 72.76^o). Instead of orienting toward O4, O6H orients toward O5 in the GG conformer, but O6H does not form a true hydrogen bond with O5 (O6H-O5 distance 2.3450 Å, O6-O6H-O5 angle 104.86^o). In the TS2 transition state O6H does form a hydrogen bond with O5 (O6H-O5 distance 1.9604 Å, O6-O6H-O5 angle 119.19^o). But the GT conformer, O6H does not form a hydrogen bond with O5 although still oriented toward O5 (O6H-O5 distance 2.36670 Å, O6-O6H-O5 angle 104.22^o. Similarly in case of a-D-2-amino-2-deoxygluco-pyranose, the one of two hydrogen atom of the amino-group also forms the intramolecular hydrogen bond with the oxygen atom of hydroxyl at C1. The values of N2H-O1 distances and N2-N2H-O1 angles for the conformation are following:  TG conformer  2.4494 Å, 102.63^o; GG conformer  2.4516 Å, 102.11^o;  GT conformer 2.4490 Å, 102.34^o; TS1 conformer 2.4492 Å, 102.62^o; TS2 conformer 2.4533 Å, 102.06^o; TS3 conformer 2.4411 Å, 103.05^o.

There is no apparent relation between those interaction that are within the specific hydrogen-bonding threshold and the stability of the conformers, suggesting that the somewhat arbitrary definition of hydrogen bonding loses its meaning when referring to intramolecular interactions in carbohydrates. Interestingly, the intramolecular hydrogen bond between the hydrogen atom of the amino-group and the oxygen atom of hydroxyl at C1in all conformers has same stability, and it is sometime not a true hydrogen bond due to the longer N2H-O1 bonds and the smaller N2-N2H-O1 angles.

Figure 2. Relative energy diagram (kJ/mol) at the RHF 6-31G(d) (solid line) and 6-31G(2d,1p) (dashed line) levels of theory for the stationary points along the exocyclic hydroxymethyl rotational surface of a-D-2-amino-2-deoxyglucopyranose (A) and of β-D-2-amino-2-deoxyglucopyranose (B). The internal coordinate g is defined as the O6-C6-C5-O5 dihedral angle.

Table 2.  Relative Energy, DE, for Conformations of a-D-2-Amino-2-deoxygluco-pyranose (kJ/mol)

^a Values in parentheses are the O5-C5-C6-O6 dihedral angles of  the RHF                              6-31G(2d,1p) optimized geometries. ^b Absolute energies for the TG conformation, in hartrees, are -663.506325 and -663.572522 (in case of α-D-2-amino-2-deoxygluco-pyranose) and -663.499892 and -663.566929 (in case of β-D-2-amino-2-deoxygluco-pyranose) for RHF 6-31G(d) and RHF 6-31G(2d,1p) calculations, respectively. The TG conformer was defined as zero by convention.

The intrinsic exocyclic hydroxymethyl rotational barriers in glucopyranose are substantial, ranging from ~40 kJ/mol for TS1 to ~19 kJ/mol for TS3 and to ~28 kJ/mol for TS2 (in case of a-D-2-amino-2-deoxygluco-pyranose) and from ~40 kJ/mol for TS1 to ~27 kJ/mol for TS2 and to ~ 19 kJ/mol for TS3 (in case of β-D-2-amino-2-deoxygluco-pyranose), depending on the level of theory. Similar to the minima, the basis set augmentation has affected on the structures or the relative energies of the rotational transition states. Moreover, based on the final ab initio results, the relative transition state energies are in order TS2>TS1~TS3 (in case of a-D-2-amino-2-deoxygluco-pyranose) and TS3<TS2<TS1 (in case of β-D-2-amino-2-deoxygluco-pyranose), indicating that the most facile interconversion in the gas phase is between TG and GT (in both above cases). From the above results, it can be shown that in the gase phase, the tautomeric equilibrium of aminoglucopyranose shift toward α-form (see Figure 3), because the α-form of D-2-amino-2-deoxygluco-pyranose is more stable than β-form with energy difference about -16.8899 kJ/mol [at 6-31G(d) level] and          -14.6844 kJ/mol [at 6-31G(2d,1p) level]. This one also agrees with the experimental data about properties of aminoglucopyranose in water solutions. It is possible its α-form is more stable due to the formation of hydrogen intramolecular bond between NH₂ group and  α-OH group.

Figure 3. The tautomeric transformation of aminoglucose.

Table 3. Corrected Energies for Conformations of a-D-2-Amino-2-deoxygluco-pyranose (kJ/mol)

            ^a Zero-point vibrational energy (ZPVE) corrections were calculated from harmonic vibrational frequencies determined at the RHF 6-31G(d) level and scaled by a factor of 1.00 in accord with known overestimates at this level.  ^b =D(E + ZPVE) + C_pT and  =+T. are the relative gas-phase enthalpy and free energy, respectively.

Conclusions

We have described the rotational energy surface for the exocyclic hydroxymethyl group of a-D-2-amino-2-deoxyglucopyranose and of b-D-2-amino-2-deoxygluco-pyranose using high-level ab initio methods. These data definitively establish the potential energy surface along this coordinate in the gas phase.

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