NMR characterization of 1,1′‐binaphthyl‐2,2′‐diyl hydrogen phosphate binding to chiral molecular micelles

NMR spectroscopy was used to characterize the binding of the chiral compound 1,1′‐binaphthyl‐2,2′‐diyl hydrogen phosphate (BNP) to five molecular micelles with chiral dipeptide headgroups. Molecular micelles have covalent linkages between the surfactant monomers and are used as chiral mobile phase modifiers in electrokinetic chromatography. Nuclear overhauser enhancement spectroscopy (NOESY) analyses of (S)‐BNP:molecular micelle mixtures showed that in each solution the (S)‐BNP interacted predominately with the N‐terminal amino acid of the molecular micelle's dipeptide headgroup. NOESY spectra were also used to generate group binding maps for (S)‐BNP:molecular micelle mixtures. In these maps, percentages are assigned to the (S)‐BNP protons to represent the relative strengths of their interactions with a specified molecular micelle proton. All maps showed that (S)‐BNP inserted into a previously reported chiral groove formed between the molecular micelle's dipeptide headgroup and hydrocarbon chain. In the resulting intermolecular complexes, the (S)‐BNP protons nearest to the analyte phosphate group were found to point toward the N‐terminal Hα proton of the molecular micelle headgroup. Finally, pulsed field gradient NMR diffusion experiments were used to measure association constants for (R) and (S)‐BNP binding to each molecular micelle. These K values were then used to calculate the differences in the enantiomers' free energies of binding, Δ(ΔG). The NMR‐derived Δ(ΔG) values were found to scale linearly with electrokinetic chromatography (EKC) chiral selectivities from the literature. Copyright © 2010 John Wiley & Sons, Ltd.     

Concentrated solutions of polydisperse rodlike polymers in the isotropic and lyotropic liquid-crystalline phases. I. The effects of molecular length distribution on phase behavior

The earlier calculations of Moscicki and Williams of the phase behavior of rodlike macromolecules in solution incorporating a Gaussian distribution of rod lengths have been extended to include, in addition to a “basic” Gaussian distribution, a small amount of high-molecular-weight species which are characterized by a δ-function or “box-function” distribution. It is shown that C^*_p, the concentration of polymer at which the biphasic material (isotropic plus anisotropic phase) first appears may be substantially lowered in comparison with that for the system comprising only the basic distribution. The volume fraction Φ_A of anisotropic phase, the compositions of the two phases, and the distribution of species between the phases are calculated for a range of polymer concentration which spans the isotropic, biphasic, and anisotropic phase and, among several features obtained, it is shown that the high-molecular-weight species are essentially responsible for the initial formation of anisotropic phase in the biphasic system. The results of the calculations have important implications for the interpretation of published dielectric relaxation data for polyalkylisocyanates in solution at high concentration and for published shear-flow viscosity data for polyalkylisocyanates and poly(p-benzamide) in solution at high concentration and these are discussed in some detail.     

Role of electrostatic interactions for the domain shapes of Langmuir monolayers of monoglycerol amphiphiles

The role of electrostatic interaction in the domain morphology of amide, ether, ester, and amine monoglycerol monolayers (abbreviated as ADD, ETD, ESD, and AMD, respectively) with systematic variation in the molecular structure of the headgroup region is investigated. Experimental studies using Brewster angle microscopy (BAM) and grazing incidence X-ray diffraction (GIXD) show that the characteristic features of the condensed monolayer phase, such as domain morphology, crystallinity, and lattice parameters, are very different for these monoglycerols. Therefore, the intermolecular interactions of the four amphiphilic monoglycerols are investigated in detail. First, the dipole moments of four monoglycerols of similar structure but with different functional groups are calculated by a semiempirical quantum mechanical technique. The dipole moments for monoglycerols follow the sequence AMD < ETD < ESD < ADD for the population of conformers of compounds investigated. The dipolar repulsion energies for the amphiphilic monoglycerols are also calculated for different possible mutual orientations between the dipoles. The calculated dipolar energies also follow the same trend for different possible headgroup orientations. These results can explain the domain shape of the monoglycerols observed experimentally. Second, ab initio calculations on the basis of the HF/6-31G** method are performed for representative monoglycerol headgroup segments. The results show that the intermolecular interaction energy related to dimer formation follows the order ETD < ESD < AMD < ADD segments, similar to that observed in experiment except in the case of the AMD segment. The relative importance of intra- and intermolecular hydrogen bonding in dimers is analyzed. The enhanced role of the intermolecular interaction relative to intramolecular interaction in the case of AMD contributes to the relatively high intermolecular interaction energy for the particular conformation of the dimer of AMD segment as observed from ab initio calculation. The present work shows that the variations in headgroup molecular structure alter drastically the domain shape, and the theoretical calculations conclusively reveal the important role of the electrostatic interactions for the mesoscopic domain architecture.     

X-Ray Diffraction Study of 2-Aminopropenenitrile at 97 K

2-Aminopropenenitrile crystallizes in the space group P2₁2₁2₁ with two molecules in the asymmetric unit. Both molecules show appreciable pyramidalization at the amino group. The crystal structure is built from approximately centrosymmetric dimers stabilized by hydrogen bonding between the amino group of each molecule and the nitrile group of its partner. The dimers are linked into chains by further hydrogen bonds in which the amino group of one molecule acts as donor, the amino group of the other as acceptor. The two types of molecule thus play different roles in the crystal structure. Electron density difference maps for the two independent molecules show characteristic bonding density features. The molecular structure as obtained by the low-temperature X-ray analysis is closely similar to that derived from ab initio molecular orbital calculations and leads to rotational constants close to those obtained from a microwave spectroscopic study.     

Regioselective protection of xylose for efficient synthesis of arabino-α-1,3-xylosides

We reported here an efficient regioselective protection strategy for xylose with two-step successive protections on 4- and 2-OH. This method enables the expeditious preparation of various xylose building blocks (3a–c, 5, 6). The rapid selective 2,4-protection especially facilitates the synthesis of 3-substituted xyloside structures. By this approach, typical arabino-α-1,3-xyloside disaccharide and trisaccharide, as fragment structure units from arabinoxylans, have been successfully synthesized.     

Production of ethanol from cellulosic biomass hydrolysates using genetically engineered saccharomyces yeast capable of cofermenting glucose and xylose

Recent studies have proven ethanol to be the idael liquid fuel for transportation, and renewable ligno cellulosic materials to be the attractive feed stocks for ethanol fuel production by fermentation. The major fermentable sugars from hydrolysis of most cellulosic biomass are D-glucose and D-xylose. The naturally occurring Saccharomyces yeasts that are used by industry to produce ethanol from starches and cane sugar cannot metabolize xylose. Our group at Purdue University succeded in developing genetically engineered Saccharomyces yeasts capable of effectively cofermenting glucose and xylose to ethanol, which was accomplished by cloning three xylose-metabolizing genes into the yeast. In this study, we demonstrated that our stable recombinant Sacharomyces yeast, 424A (LNH-ST), which contains the cloned xylose-metabolizing genes stably integrated into the yeast chromosome in high copy numbers, can efficiently ferment glucose and xylose present in hydrolysates from different cellulosic biomass to ethanol.     

The twist-bend nematic phase: molecular insights from a generalised Maier–Saupe theory

ABSTRACT

Bent-shaped liquid crystal dimers exhibit a non-conventional nematic phase, which in the last few years has been actively investigated. A structural model of this phase has been proposed, which is characterised by a helical modulation with a periodicity of the order of few molecular lengths. Such a model, which is generally denoted as twist-bend nematic (N_TB), is consistent with various experimental evidences and is supported by theories and simulations. Here, we will examine in more detail the features and the implications of a generalised Maier–Saupe theory, which was recently proposed to explain the origin and structure of the N_TB phase. In particular we will analyse the relevant molecular order parameters, with special attention to the polar and biaxial ones, and we will discuss the concept of ‘tilted director’, which may give rise to some ambiguity. The phase behaviour will be described as a function of the bend angle between the mesogenic moieties of a dimer, which in the generalised Maier–Saupe theory is the key molecular feature. Extension of the theory to include fluctuations of the bend angle will allow us to examine the effect of the molecular flexibility on the phase diagram.     

Hybrid QM/MM simulation of the hydration phenomena of dipalmitoylphosphatidylcholine headgroup

The polar headgroup of dipalmitoylphosphatidylcholine (DPPC) molecule both in gas phase and aqueous solution is investigated by the hybrid quantum mechanical/molecular mechanical (QM/MM) method, in which the polar head of DPPC molecule and the bound water molecules are treated with density functional theory (DFT), while the apolar hydrocarbon chain of DPPC molecule is treated with MM method. It is demonstrated that the hybrid QM/MM method is both accurate and efficient to describe the conformations of DPPC headgroup. Folded structures of headgroup are found in gas phase calculations. In this work, both monohydration and polyhydration phenomena are investigated. In monohydration, different water association sites are studied. Both the hydration energy and the quantum properties of DPPC and water molecules are calculated at the DFT level of theory after geometry optimization. The binding force of monohydration is estimated by using the scan method. In polyhydration, more extended conformations are found and hydration energies in different polyhydration styles are estimated.     

Thermotropic and lyotropic phase properties of glycolipid diastereomers: role of headgroup and interfacial interactions in determining phase behaviour

Recent advances in the area of glycobiology have been paralleled by progress in our understanding of the physical properties of glycoglycerolipids (GGLs). These advances have been accelerated by interest in the new found roles of these simple glycolipids in nature, by advances in synthetic procedures, and by an interest in the technological application of a group of amphiphiles with unique physical and chemical properties. Here, we consider the phase properties of some GGL/water systems containing either a single hexopyranoside or pentopyranoside headgroup. Recent calorimetric and X-ray diffraction measurements of some GGL diastereomers suggest that both headgroup and interfacial hydration play a major role in determining both lyotropism and mesomorphic phase properties as the chemical structure of the lipid headgroup, interface and hydrocarbon chains are systematically altered. For GGLs of a given chain length, interactions between the headgroup/interface and water determine whether or not a highly ordered, lamellar crystalline phase is formed, the number of such phases and their rate of formation and, in some cases, the nature of the molecular packing of those phases. In the liquid crystalline phases, the hydrocarbon chains determine the area per molecule in the lamellar liquid crystalline phase, but it is the cross-sectional area of the hydrated headgroup and the penetration of water into the interface which determines the nature of the non-lamellar phases, probably through small changes in interfacial geometry as the lateral stresses in the headgroup region increase.     

A molecular mechanics-NMR pseudoenergy approach to the solution conformation of glycolipids

We present here a protocol for the determination of oligosaccharide solution conformation from a combination of molecular mechanics calculations and NMR distance constraints treated as pseudoenergies. As an illustration of our methodology we have chosen the determination of the solution conformation of the tetrasaccharide headgroup of the glycolipid globoside. In order to test the ability of our methodology to avoid becoming trapped in local minima, we have chosen three starting structures, well displaced from one another in conformational space. The structures obtained upon convergence of the calculations with distance constraint pseudoenergies were quite similar to one another. For two of the three glycosidic linkages in globoside, the results from the calculations were virtually identical for each of the three starting structures. We also apply our protocol to a model which allows for the existence of multiple conformers in an effort to explore the possibility of conformational flexibility in the oligosaccharide headgroup of globoside.     

Application of Dichlorovinyl Xyloside for the Novel Synthesis of 2,3,4‐Tri‐O‐methyl‐D‐xylono‐1,5‐lactone

A novel synthesis of 2,3,4‐tri‐O‐methyl‐D‐xylopyranose, 4, and its oxidation product 2,3,4‐tri‐O‐methyl‐D‐xylono‐1,5‐lactone, 5, are reported. The new synthesis applies a regioselective Wittig‐like reaction of tetra-O-acetyl-D-xylopyranase, 1, with triphenylphosphine and carbon tetrachloride to yield an O‐dichlorovinyl xyloside protected at C‐1, 2. The protecting group facilitates the permethylation of xylose and is removed under the methylation conditions, to yield tetra-O-acetyl-D-xylopyranase, 3. The anomeric methyl group was removed under mildly acidic conditions to give 2,3,4‐tri‐O‐methyl‐D‐xylopyranose, 4, in good yield. Compound 4 was oxidized using pyridinium chlorochromate to give the title compound, 5, in 95% yield.     

Determining the Local Shear Viscosity of a Lipid Bilayer System by Reverse Non‐Equilibrium Molecular Dynamics Simulations

The parallel shear viscosity of a dipalmitoylphosphatidylcholine (DPPC) bilayer system is studied by reverse non‐equilibrium molecular dynamics simulations (RNEMD) with two different united‐atom force fields. The results are related to diffusion coefficients and structural distributions obtained by equilibrium molecular simulations. We investigate technical issues of the algorithm in the bilayer setup, namely, the dependence of the velocity profiles on the imposed flux and the influence of the thermostat on the calculated shear viscosity. We introduce the concept of local shear viscosity and investigate its dependence on the slip velocity of the monolayers and the particle density at the headgroup–water interface and the tail–tail interface. With this we demonstrate that the lipid bilayer is more viscous than the surrounding water phase, and that slip takes place near the headgroup region and in the centre of the bilayer where the alkyl tails meet. We also quantify the apparent increase in viscosity of the water molecules entangled at the water–headgroup interface.     

Spacer effect on triazole-linked sugar-based surfactants

A series of alkyl triazole glycoside surfactants, ATGs, differing in the length of the alkyl linker between the sugar and the triazole, was synthesized and investigated on their surfactant properties and phase behavior in water. The results indicate no significant impact of the linker on surface and interphase properties, whereas the phase behavior is affected. Higher affinity for the bicontinuous cubic phase potentially favors methylene-linked ATGs over higher homologs for drug-delivery applications. A comparison of glucose and xylose reveals a tendency for high Krafft points for propargyl xyloside based ATGs. This disfavors these surfactants with respect to both glucose analogs and higher homologs.     

VB2000: Pushing valence bond theory to new limits

Full valence bond (VB) calculations for a system of N electrons have always been hindered by the rapidly growing value of N!, which effectively imposes a limit N < 20. Often, however, not all electrons in a molecule are of interest; if we focus on a “group” G of N_G electrons (e.g., in an “active” region), then it is N_G! that sets the limit. In this work, group function (GF) theory is used to represent a molecule as a collection of interacting electron groups, each with a many‐electron wave function of any chosen form (e.g., VB, MO‐SCF, MCSCF), and each GF is optimized individually in a step‐by‐step process. An efficient VB algorithm allows for up to 14 electrons in any VB group and this combination of GF and VB methods greatly extends the range of feasibility of molecular calculations with VB‐type wave functions: Thus, (1) a large system can be divided into any number of smaller subsystems (groups); (2) each group may contain any chosen number of electrons; (3) the form of any group function (including its level of accuracy) may be chosen at will by the program user. A number of sample calculations are briefly presented. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Topological Model for Dipole–Quadrupole Polarizability and Its Application to Analysis of Discriminating Intermolecular Interactions

A simplified model for calculating the dipole and dipole–quadrupole polarizabilities A_i,jk is suggested. The model is based on the mean energy method and on the topological approximation to the bond order matrix. Pseudoinvariants of the A_i,jk tensor are calculated to evaluate the degree of molecular dissymmetry, which is responsible for the discriminating intermolecular forces. The method is illustrated by calculations for a number of chiral molecules and comparison of the calculated indices with the experimentally evaluated twisting ability of molecules during the nematic–cholesteric phase transition.     

Large Amplitude Motions in Fruit Flavors: The Case of Alkyl Butyrates

To accurately characterize the large amplitude motions and soft degrees of freedom of isolated molecules, sampling their conformational landscape by molecular mechanics and quantum chemical calculations may provide a valuable insight into the structure and dynamics. However, the resulting models need to be validated by a reliable experimental counterpart. For ethyl pentanoates, which belong to the family of fruit esters, benchmark calculations at different levels of theory showed that the C−C bond in proximity to the ester carbonyl group exhibits a large amplitude motion that is extremely sensitive to the choice of quantum chemical method and basis set. In such cases, insights from high-resolution molecular jet techniques are ideal to accurately identify and characterize soft degrees of freedom. Here, we report on the most abundant conformer of ethyl 2-ethyl butyrate using Fourier-transform microwave spectroscopy. We show that – unlike other structurally related pentanoates for which gas-phase and crystallographic data is available – ethyl 2-ethyl butyrate possesses a C_s symmetry plane under molecular jet conditions.     

Phase Transition and Structural Investigations in 50.5, 50.6 and 50.7

Abstract

We report X-ray diffraction, density, ultrasonic velocity and refractive index studies in the N(p-n-pentyloxy benzylidene) p-n-alkylaniline compounds, viz. 50.5, 50.6 and 50.7. The nematic-smectic A (NA) transition is found to be weak first order in 50.6 while it is second order in 50.5 and 50.7. The salient features observed are cybotactic clusters in the nematic phase in all the compounds, molecular tilt which was inferred due to the end alkyl chains tilt causing orienta-tional disorder (smaller orientational order parameters ‘s’ than expected) in smectic A phase, smectic F phase and large tilt angle variation in smectic C phase in a small temperature range in 50.5. The observed results are discussed in the light of available data in other n0.m compounds.     

Synthesis and structural study of carbocyclic analogues of 1,2-disubstituted nucleosides

The compounds (±)-cis- and (±)-trans-9-[(2-hydroxymethyl) cyclopentyl]guanine (1 and 2 respectively) were efficiently synthesized by the construction of the purine base on the primary amino group of cis- and trans-2-aminocyclopentylmethanol. The 3D structures of these two 1,2-disubstituted carbanucleosides in DMSO were determined using molecular dynamics calculations with experimental NMR restraints on the basis of the information obtained from a ROESY spectrum. These structures were compared with those obtained in vacuo using molecular dynamics and AM1 semiempirical calculations. The global structures of the two compounds are very similar in the two environments studied, meaning that the structural determination in the gas phase can be extrapolated to molecular simulation studies in solution for compounds of this type.     

Pharmacophore modelling of structurally unusual diltiazem mimics at L-type calcium channels

The purpose of this theoretical study was to investigate the molecular features of some structurally unusual calcium antagonists with experimentally proved affinity to the diltiazem-binding site at L-type calcium channels. Therefore, sterical and electronic characteristics of cis-/trans-diclofurime, the verapamil-like derivatives McN-5691 and McN-6186 as well as the natural products papaverine, laudanosine, antioquine and tetrandrine were compared with the pharmacophoric requirements detected for classical diltiazem-like derivatives. This yielded a common pharmacophore model for all of these compounds. Based on this model, one single negative molecular electrostatic potential induced by the free electron pairs of the oxime oxygen of trans-diclofurime was detected that might be responsible for the stronger effects compared to the cis isomer. Furthermore, the dual diltiazem- and verapamil-like features of McN-5691 (and McN-6186) as well as the distinct pharmacophoric assignment of the laudanosine enantiomers may be interpreted on a molecular level. Finally, the crucial partial structure of the bis-benzylisoquinoline derivatives antioquine and tetrandrine being responsible for the calcium antagonistic effects could be revealed by superposition on the most active benzothiazepinone derivative 8-methoxydiltiazem. The results obtained for these unusual diltiazem mimics are discussed taking into consideration earlier findings for classical diltiazem-like derivatives.     

Partial ordering of tripivaloylmethane at 110 K

Tripivaloylmethane [systematic name: 4‐(2,2‐dimethylpropanoyl)‐2,2,6,6‐tetramethylheptane‐3,5‐dione], C₁₆H₂₈O₃, is known to crystallize at room temperature in the space group R3m with three molecules in the unit cell. The molecules are conformationally chiral and pack so that each molecular site is occupied with equal probability by the two enantiomers. Upon cooling to 110 K, the structure partially orders; two molecules in the unit cell order into two different conformations of opposite chirality, while the third remains disordered. The symmetry of the resulting crystal is P3, with each of the molecules lying about a different threefold rotation axis. This paper describes an unusual case of order–disorder phase transition in which the structure partially orders by changes of molecular conformation in the single crystals. Such behaviour is of interest in the study of phase transitions and molecular motion in the solid state.