Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations

We present a CHARMM Carbohydrate Solution Force Field (CSFF) suitable for nanosecond molecular dynamics computer simulations. The force field was derived from a recently published sugar parameter set.1 Dihedral angle parameters for the primary alcohol as well as the secondary hydroxyl groups were adjusted. Free energy profiles of the hydroxymethyl group for two monosaccharides (beta-D-glucose and beta-D-galactose) were calculated using the new parameter set and compared with similar force fields. Equilibrium rotamer populations obtained from the CSFF are in excellent agreement with NMR data (glucose gg:gt:tg approximately 66:33:1 and galactose gg:gt:tg approximately 4:75:21). In addition, the primary alcohol rotational frequency is on the nanosecond time scale, which conforms to experimental observations. Equilibrium population distributions of the primary alcohol conformers for glucose and galactose are reached within 10 nanoseconds of molecular dynamics simulations. In addition, gas phase vibrational frequencies computed for beta-D-glucose using this force field compare well with experimental frequencies. Carbohydrate parameter sets that produce both conformational energies and rotational frequencies for the pyranose primary alcohol group that are consistent with experimental observations should allow for increased accuracy in modeling the flexibility of biologically important (1-6)-linked saccharides in solution.     

Hydroxymethyl rotamer populations in disaccharides

Sixteen methyl glucopyranosyl glucopyranoside disaccharides (methyl beta-d-Glcp(p-Br-Bz)-(1-->x)-beta/alpha-d-Glcp) containing beta-glycosidic linkages (1-->2, 1-->3, 1-->4, and 1-->6) were synthesized and analyzed by means of CD and NMR spectroscopy in three different solvents. For each of these four types of disaccharides, a correlation was observed between the hydroxymethyl rotational populations around the C5-C6 bond of the glucopyranosyl residue II with the substituents and the anomeric configuration of the methoxyl group in residue I, as well as with the solvent. Nonbonded interactions, the stereoelectronic exo-anomeric effect, and hydrogen bonding were found to be responsible for the observed rotameric differences. Whereas the rotational populations of the (1-->6)-linked disaccharides are mainly dependent on the exo-anomeric effect, the (1-->2)-bonded disaccharides are strongly dependent on the anomeric configuration at C1, and the (1-->3)- and (1-->4)-linked disaccharides are mainly dependent on the substituents and the solvent. The population of the gt rotamer decreases as nonbonded interactions increase but increases as the exo-anomeric effect becomes greater, as well as in the presence of intramolecular hydrogen bonding to the endocyclic oxygen O5'. Comparison of the hydroxymethyl rotational preferences between our model disaccharides revealed a dependence on the glycosidic linkage type. Thus the population of the gg and gt rotamers decreases/increases from (1-->2)- (beta series), to (1-->6)-, to (1-->2)- (alpha series), to (1-->4)-, and to (1-->3)-bonded disaccharides respectively, while the tg rotamer population remains almost constant (around 20%), except for the (1-->3)- and (1-->4)-linked disaccharides with the intramolecular hydrogen bonding to O5', where this population decreases to 10%.     

Neutron diffraction and simulation studies of the exocyclic hydroxymethyl conformation of glucose

The techniques of neutron diffraction with isotopic substitution (NDIS) and molecular dynamics (MD) simulations have been used to examine the rotational conformation of the exocyclic hydroxymethyl group of D-glucopyranose. First order H/D NDIS experiments were performed on the H6 position in 3m aqueous glucose solutions where the average coherent scattering length of the exchangeable hydrogen atoms was zero (i.e., all correlations between exchangeable hydrogen atoms and other atoms cancel and thus are not present in the scattering data). This H6 experimental result suggests that no single conformation for the C4-C5-C6-O6 dihedral reproduces the observed scattering data well, but that a mixture of the gg and gt conformations, which has been suggested by NMR experiments, gives a reasonable agreement between the MD and experimental data.     

2-Deoxy-beta-D-erythro-pentofuranose: hydroxymethyl group conformation and substituent effects on molecular structure, ring geometry, and NMR spin-spin coupling constants from quantum chemical calculations.

The effect of hydroxymethyl conformation (gg, gt, and tg rotamers about the C4-C5 bond) on the conformational energies and structural parameters (bond lengths, bond angles, bond torsions) of the 10 envelope forms of the biologically relevant aldopentofuranose, 2-deoxy-beta-D-erythro-pentofuranose (2-deoxy-D-ribofuranose) 2, has been investigated by ab initio molecular orbital calculations at the HF/6-31G level of theory. C4-C5 bond rotation induces significant changes in the conformational energy profile of 2 (2gt and 2tg exhibit one global energy minimum, whereas 2gg exhibits two nearly equivalent energy minima), and structural changes, especially those in bond lengths, are consistent with predictions based on previously reported vicinal, 1,3- and 1,4-oxygen lone pair effects. HF/6-31G-optimized envelope geometries of 2gg were re-optimized using density functional theory (DFT, B3LYP/6-31G), and the resulting structures were used in DFT calculations of NMR spin-spin coupling constants involving 13C (i.e., J(CH) and J(CC) over one, two, and three bonds) in 2gg according to methods described previously. The computed J-couplings were compared to those reported previously in 2gt to assess the effect of C4-C5 bond rotation on scalar couplings within the furanose ring and hydroxymethyl side chain. The results confirm prior predictions of correlations between 2J(CH), 3J(CH), 2J(CC) and 3J(CC), and ring conformation, and verify the usefulness of a concerted application of these couplings (both their magnitudes and signs) in assigning preferred ring and C4-C5 bond conformations in aldopentofuranosyl rings. The new calculated J-couplings in 2gg have particular relevance to related J-couplings in DNA (and RNA indirectly), where the gg rotamer, rather than the gt rotamer, is observed in most native structures. The effects of two additional structural perturbations on 2 were also studied, namely, deoxygenation at C5 (yielding 2,5-dideoxy-beta-D-erythro-pentofuranose 4) and methyl glycosidation at O1 (yielding methyl 2-deoxy-beta-D-erythro-pentofuranoside 5) at the HF/6-31G level. The conformational energy profile of 4 resembles that found for 2gt, not 2gg, indicating that 4 is an inappropriate structural mimic of the furanose ring in DNA. Glycosidation failed to induce differential stabilization of ring conformations containing an axial C1-O1 bond (anomeric effect), contrary to experimental data. The latter discrepancy indicates that either the magnitude of this differential stabilization depends on ring configuration or that solvent effects, which are neglected in these calculations, play a role in promoting this stabilization.     

Conformational analysis of beta-glycosidic linkages in 13C-labeled glucobiosides using inter-residue scalar coupling constants

Four beta-linked glucobioses selectively (13)C labeled at C1' or C2' have been prepared. The inter-residue coupling constants, J(CH), and J(CC), have been determined and related to the solution conformations of the disaccharides using Karplus-type relationships. Relying only on the experimental coupling constants, glycosidic linkage conformation in methyl alpha-sophoroside (methyl 2-O-beta-D-glucopyranosyl-alpha-D-glucopyranoside), methyl alpha-laminarabioside (methyl 3-O-beta-D-glucopyranosyl-alpha-D-glucopyranoside), and methyl alpha-cellobioside (methyl 4-O-beta-D-glucopyranosyl-alpha-D-glucopyranoside) were found to be close to those observed in the solid state (39 degrees < phi(H) < 41 degrees , -24 degrees < psi(H) < -36 degrees ). The laminarabioside and cellobioside were found to have conformations that accommodate an intramolecular hydrogen bond to O5' that is observed in the solid state. In all compounds, the exocyclic hydroxymethyl groups retain a conformation close to that observed in unsubstituted glucose (gt/gg 1:1). Methyl alpha-gentiobioside (methyl 6-O-beta-D-glucopyranosyl-alpha-D-glucopyranoside) shows greater flexibility at the psi-torsion than the other disaccharides, but the population distribution around the C5-C6 bond is essentially unaffected by substitution. None of the O2' hydroxyl groups of the beta-D-glucopyranosyl residues in any of the disaccharides appear to be involved in inter-residue hydrogen bonding since (1)JCH, (1)JCC, and (2)JCH values sensitive to C2'-O2' rotamer distribution remain close to those observed in methyl beta-D-glucopyranoside.     

4J(COCCH) and 4J(CCCCH) as probes of exocyclic hydroxymethyl group conformation in saccharides

[structure: see text] 1H NMR spectra of aldohexopyranosyl rings containing 13C-enrichment at either C1 or C3 reveal the presence of long-range 4J(C1,H6R/S) and 4J(C3,H6R/S) whose magnitudes depend mainly on the O5-C5-C6-O6 torsion angle. Using theoretical calculations (density functional theory, DFT; B3LYP/6-31G*) and conformationally constrained experimental model compounds, the magnitudes and signs of 4J(C1,H6R/S) and 4J(C3,H6R/S) have been established, and their dependencies on the geometry of the C1-O5-C5-C6-H6R/S and C3-C4-C5-C6-H6R/S coupling pathways, respectively, were determined. The latter dependencies mimic that observed previously for 4J(HH) in aliphatic compounds such as propane. DFT calculations also showed that inclusion of non-Fermi contact terms is important for accurate predictions of 4J(CH) values. Application to methyl alpha- and beta-D-glucopyranosides reveals different rotameric distributions about their hydroxymethyl groups, with the beta-anomer enriched in the gt rotamer, in agreement with recent multi-J redundant coupling analyses. 4J(C1,H6R/S) and 4J(C3,H6R/S) are expected to complement other recently developed J-couplings for the assignment of hydroxymethyl group conformation in oligosaccharides containing 1,6-glycosidic linkages.     

Intramolecular hydrogen bonding in disubstituted ethanes. A comparison of NH...O- and OH...O- Hydrogen bonding through conformational analysis of 4-amino-4-oxobutanoate (succinamate) and monohydrogen 1,4-butanoate (monohydrogen succinate) anions

Relative strengths of amide NH...O- and carboxyl OH...O- hydrogen bonds were investigated via conformational analysis of succinamate and monohydrogen succinate anions with the aid of vicinal proton-proton NMR couplings and B3LYP DFT quantum mechanical calculations for a variety of solvents. New experimental results for succinamate are compared with those obtained from previous studies of monohydrogen succinate. While some computational results for monohydrogen succinate were published previously, the results contained herein are the product of a more powerful methodology than that used earlier. The experimental results clearly show that intramolecular hydrogen-bond formation is more favored in aprotic solvents than in protic solvents for both molecules. Furthermore, the preference of the succinate monoanion for the gauche conformation is much stronger in aprotic solvents than that of succinamate, indicating that the OH...O- hydrogen bond is substantially stronger than its NH...O- counterpart, despite the approximately 5 kcal cost for formation of the E configuration of the carboxyl group needed to make an intramolecular hydrogen bond. The actual energy differences between formation of internal hydrogen bonds for monohydrogen succinate and succinamate anion were estimated by comparison of the relative values of K1 of the respective acids in water and DMSO by a procedure first developed by Westheimer. Recent theoretical work with succinamate highlights the necessity of considering substituent orientational degrees of freedom to understand the conformational equilibria of the central CH2-CH2 torsions in disubstituted ethanes. Similar methodology is applied here to succinic acid monoanion, by mapping potential-energy surfaces with respect to the CH2-CH2 torsional, carboxyl-substituent rotational, and carboxyl-proton E/Z isomeric degrees of freedom. Boltzmann populations were compared with gauche populations estimated from the experimentally determined coupling constants. The quantum mechanical results for succinamate show a much weaker tendency toward hydrogen bonding than for the succinic acid monoanion. However, the theoretical methods employed appear to substantially overestimate contributions from intramolecularly hydrogen-bonded structures for the succinic acid monoanion when compared with experimental results. Natural bond orbital analysis, applied to the quantum mechanical wave functions of fully optimized gauche and trans structures, showed a strong correlation between the population of amide sigma*(N-H) and carboxyl sigma*(O-H) antibonding orbitals and apparent hydrogen-bonding behavior.     

Stereoelectronic effects in ring-chain tautomerism of 1,3-diarylnaphth[1,2-e][1,3]oxazines and 3-alkyl-1-arylnaphth[1,2-e][1,3]oxazines

The disubstitution effects of X and Y in 1-(Y-phenyl)-3-(X-phenyl)-2,3-dihydro-1H-naphth[1,2-e][1,3]oxazines on the ring-chain tautomerism, the delocalization of the nitrogen lone pair (anomeric effect), and the (13)C NMR chemical shifts were analyzed by using multiple linear regression analysis. Study of the three-component equilibrium B<==>A<==>C revealed that the chain<==>trans (A<==>B) equilibrium constants are significantly influenced by the inductive effect (sigma(F)) of substituent Y on the 1-phenyl ring. In contrast, no significant substituent dependence on Y was observed for the chain<==>cis (A<==>C) equilibrium. There was an analogous dependence for the epimerization (C<==>B) constants of 1-(Y-phenyl)-3-alkyl-2,3-dihydro-1H-naphth[1,2-e][1,3]oxazines. With these model compounds, significant overlapping energies of the nitrogen lone pair was observed by NBO analysis in the trans forms B (to sigma*(C1-C1'), sigma*(C1-C10b), and sigma*(C3-O4)) and in the cis forms C (to sigma*(C1-H), sigma*(C1-C10b), and sigma*(C3-O4)). The effects of disubstitution revealed some characteristic differences between the cis and trans isomers. However, the results do not suggest that the anomeric effect predominates in the preponderance of the trans over the cis isomer. When the (13)C chemical shift changes induced by substituents X and Y (SCS) were subjected to multiple linear regression analysis, negative rho(F)(Y) and rho(F)(X) values were observed at C-1 and C-3 for both the cis and trans isomers. In contrast, the positive rho(R)(Y) values at C-1 and the negative rho(R)(X) values at C-3 observed indicated the contribution of resonance structures f (rho(R) > 0) and g (rho(R) < 0), respectively. The classical double bond-no-bond resonance structures proved useful in explaining the substituent sensitivities of the donation energies and the behavior of the SCS values.     

Manifestation of stereoelectronic effects on the calculated carbon-hydrogen bond lengths and one bond (1)J(C-H) NMR coupling constants in cyclohexane,six-membered heterocycles,and cyclohexanone derivatives

Cyclohexane (1), oxygen-, sulfur-, and/or nitrogen-containing six-membered heterocycles 2-5, cyclohexanone (6), and cyclohexanone derivatives 7-16 were studied theoretically [B3LYP/6-31G(d,p) and PP/IGLO-III//B3LYP/6-31G(d,p) methods] to determine the structural (in particular C-H bond distances) and spectroscopic (specifically, one bond (1)J(C-H) NMR coupling constants) consequences of stereoelectronic hyperconjugative effects. The results confirm the importance of n(X) --> sigma*(C-H)(app) (where X = O, N), sigma(C-H)(ax) --> pi*(C=O), sigma(S-C) --> sigma*(C-H)(app), sigma(C-S)-->sigma*(C-H)(app), beta-n(O) --> sigma*(C-H), and sigma(C-H) --> sigma*(C-H)(app) hyperconjugation, as advanced in previous theoretical models. Calculated r(C-H) bond lengths and (1)J(C-H) coupling constants for C-H bonds participating in more than one hyperconjugative interaction show additivity of the effects.     

Hydroxymethyl group conformation in saccharides: structural dependencies of (2)J(HH), (3)J(HH), and (1)J(CH) spin-spin coupling constants

Experimental and theoretical methods have been used to correlate (2)J(HH) and (3)J(HH) values within the exocyclic hydroxymethyl groups (CH(2)OH) of saccharides with specific molecular parameters, and new equations are proposed to assist in the structural interpretation of these couplings. (3)J(HH) depends mainly on the C-C torsion angle (omega) as expected, and new Karplus equations derived from J-couplings computed from density functional theory (DFT) in a model aldopyranosyl ring are in excellent agreement with experimental values and with couplings predicted from a previously reported general Karplus equation. These results confirm the reliability of DFT-calculated (1)H-(1)H couplings in saccharides. (2)J(HH) values depend on both the C-C (omega) and C-O (theta) torsions. Knowledge of the former, which may be derived from other parameters (e.g., (3)J(HH)), allows theta to be evaluated indirectly from (2)J(HH). This latter approach complements more direct determinations of theta from (3)J(HCOH) and potentially extends these more conventional analyses to O-substituted systems lacking the hydroxyl proton. (1)J(CH) values within hydroxymethyl fragments were also examined and found to depend on r(CH), which is modulated by specific bond orientation and stereoelectronic factors. These latter factors could be largely, but not completely, accounted for by C-C and C-O torsional variables, leading to only semiquantitative treatments of these couplings (details discussed in the Supporting Information). New equations pertaining to (2)J(HH) and (3)J(HH) have been applied to the analysis of hydroxymethyl group J-couplings in several mono- and oligosaccharides, yielding information on C5-C6 and/or C6-O6 rotamer populations.     

Conformational behavior of poly(L-lactide) studied by infrared spectroscopy

This paper reports the analysis of the C=O stretching region of poly(L-lactide). This spectral band splits into up to four components, a phenomenon that a priori can be explained in terms of carbonyl-carbonyl coupling or specific interactions (such as C-H...O hydrogen bonding or dipole-dipole). Hydrogen bonding can be discarded from the analysis of the C-H stretching spectral region. In addition, low molecular weight dicarbonyl compounds of chemical structure similar to that of PLLA, such as diacyl peroxides, show a remarkable splitting of the carbonyl band attributed to intramolecular carbonyl-carbonyl coupling. Several mechanisms can be responsible for this behavior, such as mechanical coupling, electronic effects, or through-space intramolecular TDC (transition dipole coupling) interactions. Intermolecular dipole-dipole interactions (possible in the form of interchain TDC interactions) are proven to be of minor relevance taking into account the spatial structure of the PLLA conformers. The Simply Coupled Oscilator (SCO) model, which only accounts for mechanical coupling, has been found to predict adequately the relative intensity of the symmetric and asymmetric bands of dicarbonyl compounds. The dispersion curves predicted for PLLA by the SCO model also match those given by more general treatments, such as Miyazawa's first-order perturbation theory. Hence, the SCO model is adopted here as an adequate yet simple tool for the interpretation of band splitting caused by intramolecular coupling of polylactide. The four components observed in the C=O stretching band of semicrystalline PLLA are attributed to the four possible conformers: gt, gg, tt, and tg. The narrow bands observed for the interlamellar material are attributed to highly ordered chains, indicating the absence of a truly amorphous phase in the crystalline polymer. The interphase seems to extend over the whole interlamellar region, showing the features of a semiordered metastable phase. In amorphous PLLA, bands corresponding to gt, gg, and tt conformers also can be resolved by second derivative techniques, and curve-fitting results provide information about the conformational population at different temperatures.     

Thermal response in crystalline Ibeta cellulose: a molecular dynamics study

The influence of temperature on structure and properties of the cellulose Ibeta crystal was studied by molecular dynamics simulations with the GROMOS 45a4 force-field. At 300 K, the modeled crystal agreed reasonably with several sets of experimental data, including crystal density, corresponding packing and crystal unit cell dimensions, chain conformation parameters, hydrogen bonds, Young's modulus, and thermal expansion coefficient at room temperature. At high-temperature (500 K), the cellulose chains remained in sheets, despite differences in the fine details compared to the room-temperature structure. The density decreased while the a and b cell parameters expanded by 7.4% and 6%, respectively, and the c parameter (chain axis) slightly contracted by 0.5%. Cell angles alpha and beta divided into two populations. The hydroxymethyl groups mainly adopted the gt orientation, and the hydrogen-bonding pattern thereby changed. One intrachain hydrogen bond, O2'H2'...O6, disappeared and consequently the Young's modulus decreased by 25%. A transition pathway between the low- and high-temperature structures has been proposed, with an initial step being an increased intersheet separation, which allowed every second cellulose chain to rotate around its helix axis by about 30 degrees . Second, all hydroxymethyl groups changed their orientations, from tg to gg (rotated chains) and from tg to gt (non-rotated chains). When temperature was further increased, the rotated chains returned to their original orientation and their hydroxymethyl groups again changed their conformation, from gg to gt. A transition temperature of about 450 K was suggested; however, the transition seems to be more gradual than sudden. The simulated data on temperature-induced changes in crystal unit cell dimensions and the hydrogen-bonding pattern also compared well with experimental results.     

Time‐dependent Density Functional Theory Study on the Hydrogen‐bonded Dimers Formed by Gauche‐1PA and Trans‐1PA

Three hydrogen bonding complexes of the gauche‐1PA dimer (GG), trans‐1PA dimer (TT) and mixed dimer (GT) have been calculated for the geometry conformations and excited‐state energies. The electron distribution at the site of C‐O of H‐donor moiety in HOMO transfers to the direction of O‐H of H‐acceptor moiety in LUMO. The hydrogen bond between two 1PAs is the bridge of the intermolecular charge transfer. By the Zhao and Han's excited‐state hydrogen bonding dynamics rule, the first excited‐state hydrogen bonding change has been discussed without optimizing the excited‐state geometry conformations. According to the distinct difference between GT and GG (TT), we concluded that two gauche‐1PA monomers of one dimer are transformed at the same time to two trans‐1PA monomers.     

On the unusual 2J(C2-H(f)) coupling dependence on syn/anti CHO conformation in 5-X-furan-2-carboxaldehydes

A remarkable difference for (2)J(C(2)-H(f)) coupling constant in syn and anti conformers of 5-X-furan-2-carboxaldehydes (X = CH(3), Ph, NO(2), Br) and a rationalization of this difference are reported. On the basis of the current knowledge of the Fermi-contact term transmission, a rather unusual dual-coupling pathway in the syn conformer is presented. The additional coupling pathway resembles somewhat that of the J(H-H) in homoallylic couplings, which are transmitted by hyperconjugative interactions involving the pi(C=C) electronic system. The homoallylic coupling pathway can be labeled as sigma*(C-H) <-- pi(C=C) --> sigma*(C-H). In the present case, this additional coupling pathway, using an analogous notation, can be labeled as sigma*(C(2)-C(C)) <-- LP(1)(O(1))...LP(2)(O(C)) --> sigma*(C(C)-H(f)) (sigma*(C(2)-C(C))) where O(1) and O(C) stand for the ring and carbonyl O atoms, respectively. This additional coupling pathway is not activated in the anti conformers since both oxygen lone pairs do not overlap.     

Conformational analysis and vibrational assignments of 2,2,3,3-tetrafluoro-1-propanol CHF2CF2CH2OH as three-rotors system

The conformational stability of 2,2,3,3-tetrafluoro-1-propanol was investigated by DFT-B3LYP/6-311+G** and ab initio MP2/6-311+G** calculations. The calculated potential energy curves of the molecule at DFT-B3LYP level were consistent with five distinct minima that correspond to gauche(-)-gauche-gauche (G1gg), trans-trans-gauche (Ttg), trans-gauche-gauche (Tgg), trans-gauche-gauche(-) (Tgg1) and gauche(-)-gauche-trans (G1gt) conformers in the order of decreasing relative stability. The equilibrium constants for the conformational interconversion of 2,2,3,3-tetrafluoro-1-propanol were calculated and found to correspond to an equilibrium mixture of about 38% G1gg, 28% Ttg, 13% Tgg, 11% Tggt and 10% G1gt conformations at 298.15K. The vibrational frequencies of 2,2,3,3,-tetrafluoro-1-propanol in its five stable forms were computed at B3LYP level and complete vibrational assignments were made based on normal coordinate calculations and comparison with experimental data of the molecule.     

Determination of the structure of cellulose II.

The structure of regenerated cellulose is shown by x-ray diffraction to be comprised of an array of antiparallel chain molecules. The determination was based on the intensity data from rayon fibers and utilized rigid-body least-squares refinement techniques. The unit cell is monoclinic with space group P2(1) and dimensions a = 8.01 A, b = 9.04 A, c = 10.36 A (fiber axis), and gamma = 117.1 degrees. Models containing chains with the same sense (parallel) or alternating sense (antiparallel) were refined against the intensity data. The only acceptable model contains antiparallel chains. The -CH2OH groups of the corner chain are oriented near to the gt position while those of the center chain are near to the tg position. Both chains possess an O3-H-O5' intramolecular hydrogen bond, and the center chain also has an O2'-H-O6 intramolecular bond. Intermolecular hydrogen bonding occurs along the 020 planes (o6-h-o2 bonds for the corner chains and O6-H-O3 bonds for the center chains) and also along the 110 planes with a hydrogen bond between the O2-H of the corner chain and the O2' of the center chain. This center-corner chain hydrogen bonding is a major difference between the native and regenerated structures and may account for the stability of the latter form.     

Neutralization-Reionization of alkenylammonium cations: An experimental and ab initio study of intramolecular N-H … C=C interactions in cations and hypervalent ammonium radicals

A series of isomeric hexenylammonium and hexenyldimethylammonium cations were neutralized by collisional electron transfer in the gas phase in an attempt to generate hypervalent ammonium radicals. The radicals dissociated completely on the 4.8–5.4 µs time scale. Radicals in which the hexene double bond was in the 3-, 4-, and 5-positions dissociated by competitive N-H and N=C bond cleavages. Allylic 2-hexen-1-ylammonium and 2-hexen-1-yldimethylammonium radicals underwent predominant cleavages of allylic N-C bonds. Deuterium labeling experiments revealed no intramolecular hydrogen transfer from the hypervalent ammonium group to the hexene double bond. Ab initio and density functional theory calculations showed that alkenylammonium and alkenylmethyloxonium ions preferred hydrogen bonded structures in the gas phase. The stabilization through intramolecular H bonding in 3-buten-1-ylammonium and 3-buten-1-yl methyloxonium ions was calculated by B3LYP/6-311G(2d,p) at 26 and 18 kJ mol^?1, respectively. No intramolecular hydrogen bonding was found for the allylammonium ion. The hypervalent 3-buten-1-yl-methyloxonium radical was calculated to be unbound and predicted to dissociate exothermically by O-H bond cleavage. This dissociation may provide kinetic energy for the hydrogen atom to overcome a small energy barrier for exothermic addition to the double bond. The 3-butten-1-ylammonium and allylammonium radicals were found to be bound and preferred gauche conformations without intramolecular hydrogen bonding. Vertical neutralization of alkenylammonium ions was accompanied by small Franck-Condon effects. The failure to detect stable or metastable hypervalent alkenylammonium radicals was ascribed to the low activation barriers to exothermic dissociations by N-H and N-C bond cleavages.     

Nanomechanical control of glucopyranose rotamers

Single molecules of beta-1 --> 6-linked d-glucose polysaccharides, when stretched in an atomic force microscope, display a hookean-like elasticity unusual for polymers. High-level ab initio calculations and microsecond-scale molecular dynamics simulations reveal that this elasticity is governed by force-induced rotations of the exocyclic group on the glucopyranose rings from their short and less energetic gt and gg conformations to the extended and high-energy tg state. These observations indicate that a simple stretching of 1 --> 6-linked glucose polysaccharides provide a unique means to control glucopyranose rotamer populations.     

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. When the hydroxymethyl groups are for example, gg-gg-gg, and the hydroxyl groups are rotated from all clockwise, "c", to all counterclockwise, "r", the minimum energy positions of the bridging dihedral angles (phi(H) and psi(H)) move from the region of conformational space of (-, -), relative to (0 degrees , 0 degrees), to a new position defined by (+, +). Further, it was found previously that the relative energies of alpha-maltose gg-gg-c and "r" conformations were very close to one another; however, the DP-3's relative energies between hydroxyl "c" or "r" rotamers differ by more than one kcal/mol, in favor of the "c" form, even though the lowest energy DP-3 conformations have glycosidic dihedral angles similar to those found in the alpha-maltose study. Preliminary solvation studies using COSMO, a dielectric solvation method, point to important solvent contributions that reverse the energy profiles, showing an energy preference for the "r" forms. Only structures in which the rings are in the chair conformation are presented here.     

A study on the mechanism of dissolution of the cellulose/NH3/NH4SCN system. I

Ammonia/ammonium thiocyanate (NH₃/NH₄SCN) is an excellent swelling agent and solvent for cellulose, even at a high degree of polymerization. Because polymorphic conversion in cellulose has been a long-standing, perplexing, troublesome problem, we have undertaken to study that mechanism. Solid state CP/MAS ¹³C-NMR and X-ray analysis proved to be very useful analytical techniques for the task. It appears that during temperature cycling, specific cellulosic inter- and intramolecular hydrogen-bonds are broken as polymorphic conversion proceeds sequentially from the polymorph I to III, and finally at total solvation to amorphous. This proceeds correspondingly via transformation of the polymorph conformations of CH₂OH from trans-gauche, “tg,” to gauche-trans, “gt,” to gauche-gauche, “gg.” © 1994 John Wiley & Sons, Inc.