DFTr studies of five- and six-residue cyclic-β(1→4) cellulosic molecules.

Density functional (DFT) conformational in vacuo studies of cellobiose have shown that ϕ(H) -anti conformations are low in energy relative to the syn forms, while the ψ(H) -anti forms are higher in energy. Further, as the cellulosic fragments became larger than a disaccharide and new hydrogen bonding interactions between multiple residues become available, stable low energy ϕ(H) -anti, and ψ(H) -anti cellulosic structures became possible. To test the stability of cyclic anti-conformations, a number of β-linked five- and six-residue molecules were created and then energy optimized in solvent (water, n-heptane) using the implicit solvation method COSMO at the B3LYP level of theory.

DFT energy optimization of a large carbohydrate: cyclomaltohexaicosaose (CA-26).

CA-26 is the largest cyclodextrin (546 atoms) for which refined X-ray structural data is available. Because of its size, 26 D-glucose residues, it is beyond the scope of study of most ab initio or density functional methods and to date has only been computationally examined using empirical force fields. The crystal structure of CA-26 is folded like a figure "8" into two 10 D-glucoses long antiparallel left-handed V (Verkleisterung)-type helices with a "band-flip" and "kink" at the top and bottom of the helices.

Male-specific sesquiterpenes from Phyllotreta flea beetles.

Flea beetles in several genera are known to possess male-specific sesquiterpenes, at least some of which serve as aggregation pheromones that attract both sexes. In continuing research on the chemical ecology of Phyllotreta flea beetles, six new male-specific sesquiterpenes were identified, one from P. striolata (hydroxyketone 9) and five from P.

DFTMD studies of β-cellobiose: conformational preference using implicit solvent.

Previous DFT in vacuo studies on the conformational preferences for cellobiose showed that upon optimization the φ(H)-anti conformations were of lower energy than the syn forms. Upon optimization using an implicit solvation method, COSMO, the syn or observed form was still not predicted to be of lower energy than the φ(H)-anti form, even though optimization after addition of several explicit water molecules did show a relative energy difference favoring the syn form. In order to examine the predictive ability of COSMO on this carbohydrate, constant energy dynamics, DFTMD, simulations were carried out on low energy syn and φ(H)-anti conformations with and without COSMO included during the dynamics.

27 ps DFT molecular dynamics simulation of alpha-maltose: A reduced basis set study.

DFT molecular dynamics simulations are time intensive when carried out on carbohydrates such as alpha-maltose. In a recent publication (Momany et al., J.

DFTMD studies of glucose and epimers: anomeric ratios, rotamer populations, and hydration energies.

Results are presented from density functional molecular dynamics (DFTMD) simulations, based on constant energy dynamics, of glucose and its cyclic form of 6-carbon epimers. Both in vacuo and an implicit solvent method (COSMO) were examined, including simulations of low-energy conformations of each molecule. Analysis of the DFTMD results includes the following: energies averaged over the simulation time, calculated anomeric ratios, hydroxyl and hydroxymethyl rotamer populations, and hydration energies.

DFT conformation and energies of amylose fragments at atomic resolution. Part 2: 'Band-flip' and 'kink' forms of alpha-maltotetraose.

In Part 2 of this series of DFT optimization studies of alpha-maltotetraose, we present results at the B3LYP/6-311++G** level of theory for conformations denoted 'band-flips' and 'kinks'. Recent experimental X-ray studies have found examples of amylose fragments with conformations distorted from the usual syn forms, and it was of interest to examine these novel structural motifs by the same high-level DFT methods used in Part 1. As in Part 1, we have examined numerous hydroxymethyl rotamers (gg, gt, and tg) at different locations in the residue sequence, and include the two hydroxyl rotamers, the clockwise 'c' and counterclockwise 'r' forms.

DFT conformation and energies of amylose fragments at atomic resolution. Part 1: Syn forms of alpha-maltotetraose.

DFT optimization studies of 90 syn alpha-maltotetraose (DP-4) amylose fragments have been carried out at the B3LYP/6-311++G** level of theory. The DP-4 fragments studied include V-helix, tightly bent conformations, a boat, and a (1)C(4) conformer. The standard hydroxymethyl rotamers (gg, gt, tg) were examined at different locations in the residue sequence, and their influence on the bridge conformations phi/psi values and conformer energy is described.

DFT conformational studies of alpha-maltotriose.

Recent DFT optimization studies on alpha-maltose improved our understanding of the preferred conformations of alpha-maltose. The present study extends these studies to alpha-maltotriose with three alpha-D-glucopyranose residues linked by two alpha-[1-->4] bridges, denoted herein as DP-3's. Combinations of gg, gt, and tg hydroxymethyl groups are included for both "c" and "r" hydroxyl rotamers.

Differential EI fragmentation pathways for peracetylated C-glycoside ketones as a consequence of bicyclic ketal ring structures.

Several C-glycoside ketones and peracetylated C-glycoside ketones have been synthesized from 13 structurally-diverse aldoses sugars (including isotope labeled [1-(13)C]Glc, [U-(13)C]Glc, and [6, 6'-(2)H(2)]Glc) via an aqueous-based Knoevanagel condensation with aliphatic 1,3-diketones. Sodium adduct molecular ions observed by MALDI-TOF MS confirmed that the reactions are essentially quantitative, and that the acetylation products are the expected peracetylated C-glycoside ketones, rather than cyclized ketofurans. Analysis of the peracetylated C-glycoside ketones by gas chromatography-EI-MS show characteristic fragment ions that have been assigned to four distinct fragmentation pathways.

DFT studies of the disaccharide, alpha-maltose: relaxed isopotential maps.

The disaccharide, alpha-maltose, forms the molecular basis for the analysis of the structure of starch, and determining the conformational energy landscape as the molecule oscillates around the glycosidic bonds is of importance. Thus, it is of interest to determine, using density functionals and a medium size basis set, a relaxed isopotential contour map plotted as a function of the phi(H) and psi(H) dihedral angles. The technical aspects include the method of choosing the starting conformations, the choice of scanning step size, the method of constraining the specific dihedral angles, and the fitting of data to obtain well defined contour maps.

DFT study of alpha- and beta-D-allopyranose at the B3LYP/6-311++G ** level of theory.

One hundred and two conformations of alpha- and beta-D-allopyranose, the C-3 substituted epimer of glucopyranose, were geometry optimized using the density functional, B3LYP, and the basis set, 6-311++G **. Full geometry optimization was performed on different ring geometries and on the hydroxymethyl rotamers (gg/gt/tg). Analytically derived Hessians were used to calculate zero point energy, enthalpy, and entropy.

Determination of the preferred conformation of the bicyclic Galerucella pheromone using density functional theory optimization and calculations of chemical shifts.

A pheromone from the beetle, Galerucella calmariensis, was recently isolated and identified (Bartelt, R. J. et al.

Structural characterization of alpha-zein.

A variety of published physical measurements, computational algorithms, and structural modeling methods have been used to create a molecular model of 19 kDa alpha-zein (Z19). Zetaeins are water-insoluble storage proteins found in corn protein bodies. Analyses of the protein sequence using probability algorithms, structural studies by circular dichroism, infrared spectroscopy, small-angle X-ray scattering (SAXS), light scattering, proton exchange, NMR, and optical rotatory dispersion experiments suggest that Z19 has approximately 35-60% helical character, made up of nine helical segments of about 20 amino acids with glutamine-rich "turns" or "loops".

DFT study of alpha- and beta-D-galactopyranose at the B3LYP/6-311++G** level of theory.

Forty-one conformations of alpha- and beta-d-galactopyranose were geometry optimized using the B3LYP density functional and 6-311++G** basis set. Full geometry optimization was performed on different ring geometries and different hydroxymethyl rotamers (gg/gt/tg). Analytically derived Hessians were used to calculate zero point energy, enthalpy, and entropy.

B3LYP/6-311++G** geometry-optimization study of pentahydrates of alpha- and beta-D-glucopyranose.

Five water molecules were placed in 37 different configurations around alpha- and beta-D-glucopyranose in the gt, gg, and tg conformational states, and the glucose-water complexes were geometry optimized using density functionals at the B3LYP/6-311++G** level of theory. The five water molecules were organized in space and energy minimized using an empirical potential, AMB02C, and then further geometry optimized using DFT algorithms to minimum energy positions. Electronic energy, zero point vibrational energy, enthalpy, entropy, stress energy on glucose and the water cluster, hydrogen-bond energy, and relative free energy were obtained for each configuration using thermodynamic procedures and an analytical Hessian program.

Modeling bacterial UDP-HexNAc: polyprenol-P HexNAc-1-P transferases.

Protein N-glycosylation in eukaryotes and peptidoglycan biosynthesis in bacteria are both initiated by the transfer of a D-N-acetylhexosamine 1-phosphate to a membrane-bound polyprenol phosphate. These reactions are catalyzed by a family of transmembrane proteins known as the UDP-D-N-acetylhexosamine: polyprenol phosphate D-N-acetylhexosamine 1-phosphate transferases. The sole eukaryotic member of this family, the d-N-acetylglucosamine 1-phosphate transferase (GPT), is specific for UDP-GlcNAc as the donor substrate and uses dolichol phosphate as the membrane-bound acceptor.

DFT study of alpha- and beta-D-mannopyranose at the B3LYP/6-311++G** level.

Thirty-five conformations of alpha- and beta-d-mannopyranose, the C-2 substituted epimer of glucopyranose, were geometry optimized using the density functional (B3LYP), and basis set (6-311++G**). Full geometry optimization was performed on the hydroxymethyl rotamers (gg/gt/tg) and an analytical hessian program was used to calculate the harmonic vibrational frequencies, zero point energy, enthalpy, and entropy. The lowest energy conformation investigated is the beta-tg in the (4)C(1) chair conformation.

Alternansucrase acceptor reactions with D-tagatose and L-glucose.

Alternansucrase (EC 2.4.1.

Conformational analysis of chirally deuterated tunicamycin as an active site probe of UDP-N-acetylhexosamine:polyprenol-P N-acetylhexosamine-1-P translocases.

Tunicamycins are potent inhibitors of UDP-N-acetyl-D-hexosamine:polyprenol-phosphate N-acetylhexosamine-1-phosphate translocases (D-HexNAc-1-P translocases), a family of enzymes involved in bacterial cell wall synthesis and eukaryotic protein N-glycosylation. Structurally, tunicamycins consist of an 11-carbon dialdose core sugar called tunicamine that is N-linked at C-1' to uracil and O-linked at C-11' to N-acetylglucosamine (GlcNAc). The C-11' O-glycosidic linkage is highly unusual because it forms an alpha/beta anomeric-to-anomeric linkage to the 1-position of the GlcNAc residue.

B3LYP/6-311++G** study of monohydrates of alpha- and beta-D-glucopyranose: hydrogen bonding, stress energies, and effect of hydration on internal coordinates.

Twenty-six monohydrates of alpha- and beta-D-glucopyranose were studied using gradient methods at the B3LYP/6-311++G** level of theory. Geometry optimization was carried out with the water molecules at different configurations around the glucose molecule. A new nomenclature for hydrated carbohydrates was developed to describe the water configurations.

B3LYP/6-311++G** study of alpha- and beta-D-glucopyranose and 1,5-anhydro-D-glucitol: 4C1 and 1C4 chairs, (3,O)B and B(3,O) boats, and skew-boat conformations.

Geometry optimization, at the B3LYP/6-311++G** level of theory, was carried out on 4C1 and 1C4 chairs, (3,O)B and B(3,O) boats, and skew-boat conformations of alpha- and beta-D-glucopyranose. Similar calculations on 1,5-anhydro-D-glucitol allowed examination of the effect of removal of the 1-hydroxy group on the energy preference of the hydroxymethyl rotamers. Stable minimum energy boat conformers of glucose were found, as were stable skew boats, all having energies ranging from approximately 4-15 kcal/mol above the global energy 4C1 chair conformation.

Oxidation and metal-ion affinities of a novel cyclic tetrasaccharide.

The cyclic tetrasaccharide, cyclo-(-->6)-alpha-D-Glcp-(1-->3)-alpha-D-Glcp-(1-->6)-alpha-D-Glcp-(1-->3)-alpha-D-Glcp-(1-->), was oxidized in high yield to a dicarboxylic acid, cyclo-(-->6)-alpha-D-Glcp-(1-->3)-alpha-D-GlcpA-(1-->6)-alpha-D-Glcp-(1-->3)-alpha-D-GlcpA-(1-->). The parent and oxidized compound were then screened for the ability to form stable complexes with 20 metal cations. Ion-exchange thin-layer chromatography was utilized to survey binding in aqueous and 50% methanolic solutions.

A DFT/ab initio study of hydrogen bonding and conformational preference in model cellobiose analogs using B3LYP/6-311++G**.

A series of beta-cellobiose analogs were studied at the B3LYP/6-311++G** level of theory to isolate and understand how the various electronic components of the beta-(1-->4)-linked disaccharide, cellobiose, contribute to the energetic stability of the molecule in vacuo. Previous studies on beta-cellobiose (see accompanying paper) showed that the most energetically stable conformation was that in which the dihedral angle phi (phi(H)) was 'flipped' by approximately 180 degrees relative to the 'normal' form. From our examination of eight sets of structures in which different combinations of functional hydroxyl and hydroxymethyl groups were removed, it was determined that only beta-cellobiose and one other analog (analog 7, beta-xylobioside), an analog in which both hydroxymethyl groups were removed but the exocyclic hydroxyl groups retained, can form a 'cooperative' hydrogen-bonding network.

Ab initio computational study of beta-cellobiose conformers using B3LYP/6-311++G**.

The molecular structure of 27 conformers of beta-cellobiose were studied in vacuo through gradient geometry optimization using B3LYP density functionals and the 6-311++G** basis set. The conformationally dependent geometry changes and energies were explored as well as the hydrogen-bonding network. The lowest electronic energy structures found were not those suggested from available crystallographic and NMR solution data, where the glycosidic dihedral angles fall in the region (phi, psi) approximately (40 degrees, -20 degrees ).