Differences In Molecular Conformation Research Articles

Polymorphism Dependent Cytotoxicity, Cellular Uptake, and Live Cell Imaging Studies on Napthalimide-Vinyl-Phenothiazine Conjugate.

Polymorphism-dependent cytotoxicity and cellular uptake of drug molecules have been studied for the past two decades. However, the visualization of polymorph-dependent cellular uptake and cytotoxicity using microscopy imaging techniques has not yet been reported. The luminescent polymorph is an ideal candidate to validate the above hypothesis. Herein, we report the polymorph-dependent cellular uptake, cytotoxicity, and bio-imaging functions of polymorphs 1Y and 1R of a naphthalimide-phenothiazine dyad. These polymorphs show different luminescence colors in the solid state and exhibit aggregation-induced enhanced emission (AIEE) in the DMSO-Water mixture. Bioimaging, cytotoxicity assay, and fluorescence-activated cell sorting (FACS) studies revealed that these polymorphs show different levels of cytotoxicity, cellular uptake, localization, and imaging potential. Detailed photophysical, morphological, and biological studies revealed that the difference in molecular conformation in these polymorphs enables them to form aggregates of different sizes and morphology, which leads to the differential uptake of these into the cells and consequently shows different cytotoxicity and imaging potentials.

Organic Phase-Change Memory Transistor Based on an Organic Semiconductor with Reversible Molecular Conformation Transition.

Phase-change semiconductor is one of the best candidates for designing nonvolatile memory, but it has never been realized in organic semiconductors until now. Here, a phase-changeable and high-mobility organic semiconductor (3,6-DATT) is first synthesized. Benefiting from the introduction of electrostatic hydrogen bond (S···H), the molecular conformation of 3,6-DATT crystals can be reversibly modulated by the electric field and ultraviolet irradiation. Through experimental and theoretical verification, the tiny difference in molecular conformation leads to crystalline polymorphisms and dramatically distinct charge transport properties, based on which a high-performance organic phase-change memory transistor (OPCMT) is constructed. The OPCMT exhibits a quick programming/erasing rate (about 3 s), long retention time (more than 2h), and large memory window (i.e., large threshold voltage shift over 30V). This work presents a new molecule design concept for organic semiconductors with reversible molecular conformation transition and opens a novel avenue for memory devices and other functional applications.

Simple Approach to Macrocyclic Carbonates with Fast Polymerization Rates and Their Polymer-to-Monomer Regeneration

Designing polymeric materials for closed-loop material streams is the key to achieving a circular society. Here, a library of macrocyclic carbonates (MCs) was designed by a facile and direct one-pot, two-step synthesis approach without the use of a solvent at a 10 g scale. We demonstrate that anionic polymerization with tert-butoxide enables the ultrafast ring-opening polymerization (ROP) of MCs with high conversion (>97%) within seconds (3–10 s) at ambient temperature. The polymerization rate depends on the odd or even number of methylene groups between the carbonate linkages in the MCs, and not the overall ring size, yielding an “odd–even” effect. This polymerization rate is related to the difference in molecular conformation of the MCs, as determined by X-ray crystallography. The polymers (polypenta-, hexa-, heptamethylene carbonate) were subsequently regenerated back to their original MCs at a high selectivity (95–99 mol %) and good yields (70–85%), hence taking a step toward closing the loop on these long alkyl chain polycarbonates.

Experimental study on the flow and heat transfer behavior of polymer solutions in the closed liquid ring vacuum pump system

The closed liquid ring vacuum pump system, which mainly includes the liquid ring vacuum pump and the heat exchanger, is widely used for gas pumping in various industries. In this paper, the energy saving effect in the liquid ring vacuum pump and the flow and heat transfer behavior in the shell-and-tube heat exchanger are investigated for aqueous solutions of rigid xanthan gum (XG) and flexible Polyacrylamide (PAM), and the effects of the concentration, Reynolds number, polymer conformation and flow geometry on the flow behavior of polymer solutions are studied. Results show that, despite the significant differences in molecular conformation and rheological properties between XG and PAM, the similar energy saving rate, about 1.5 ∼ 17.5%, is obtained in the liquid ring vacuum pump. However, in the shell-and-tube heat exchanger, XG solutions exhibit the more obvious pressure drop enhancement and heat transfer reduction than that of PAM solutions for the same concentration. Furthermore, due to the polymer shear degradation, the shaft power in the liquid ring vacuum pump decreases first and then stabilizes, conversely, the flow resistance decreases and the flow rate increases in the heat exchanger. The great difference in the flow condition between the intense rotating gas–liquid two-phase flow field and the gentle liquid pipe flow causes the different flow behavior for XG and PAM solutions.

Reply to the ‘Comment on “Polymorphism of levofloxacin: structure, properties and phase transformation”’ by Tejender S. Thakur, CrystEngComm, 2020, 22, DOI: 10.1039/C9CE01400D

Minor structural differences in molecular conformation were found where the levofloxacin molecule takes a less stable conformer in energy rather than the stable conformer as previously expected.

Charge density view on bicalutamide molecular interactions in the monoclinic polymorph and androgen receptor binding pocket

High-resolution single-crystal X-ray measurements of the monoclinic polymorph of bicalutamide and the aspherical atom databank approach have served as a basis for a reconstruction of the charge density distribution of the drug and its androgen receptor (AR) and albumin complexes. The contributions of various types of intermolecular interactions to the total crystal energy or ligand:AR energy were estimated. The cyan and amide groups secured the ligand placement in the albumin (Lys-137) and the AR binding pocket (Leu-704, Asn-705, Arg-752), and also determined the packing of the small-molecule crystals. The total electrostatic interaction energy on average was -230 kJ mol-1, comparable with the electrostatic lattice energy of the monoclinic bicalutamide polymorph. This is the result of similar distributions of electropositive and electronegative regions on the experimental and theoretical molecular electrostatic potential maps despite differences in molecular conformations. In general, bicalutamide interacted with the studied proteins with similar electrostatic interaction energies and adjusted its conformation and electrostatic potential to fit the binding pocket in such a way as to enhance the interactions, e.g. hydrogen bonds and π⋯π stacking.

Thermodynamic properties of the 1-butyl-3-methylimidazolium mesilate ionic liquid [C4mim][OMs] in condensed phase, using molecular simulations

This work presents a molecular dynamics simulation study of the vapor-liquid equilibrium curve for the 1-butyl-3-methylimidazolium mesilate ionic liquid [C4mim][OMs] along with other thermodynamic properties in condensed phase, such as: densities, surface tension, heats of vaporization, constant pressure heat capacities, and the dielectric constant. The latter were obtained using molecular simulation calculations employing a new non-polarizable classical force field developed in this work, for this ionic liquid experimental thermodynamic properties as well as calculated properties by molecular simulations are very scarce in the literature.The development of the force field for the [C4mim][OMs] ionic liquid involved first the parameterization of all-atom non-polarizable force fields for two well-studied imidazolium ionic liquids [C4mim][BF4], in order to validate first against existing experimental and calculated thermodynamic properties using molecular simulations. Even though many transferable force fields for ionic liquids have been developed in the past years, some of these force fields predict extremely well structural properties such as densities and radial distribution functions etc., while other force fields fail to predict accurately heats of vaporization, condensed phases properties such as dielectric constant and transport properties such as viscosity, diffusivity, and vice versa.The force fields developed in this work are centered on the OPLS functional, and were parameterized using a simple and robust methodology focused mainly in electrostatic charges determination and in the refinement of the most representative dihedral angles. The calculation of the electrostatic charges follows the methodology proposed by Salas et al. (J. Chem. Theory Compute. 2015, 11, 683–693) involving the inclusion of polarization effects in quantum mechanical calculations in order to represent implicitly the solvent by employing the experimental or calculated dielectric constant in conjunction with a restrain electrostatic potential fitted to an ionic liquid dimer, to account for the inclusion of solvation coordination effects.The dihedral angles were parameterized simultaneously from the energetic differences in molecular conformations between ab-initio calculations and the energies obtained with the classic force field. The force field validation for the ionic liquids 1-butyl-3-methylimidazolium tetrafluoroborate, [C4mim][BF4], and 1-butyl-3-metilimidazolium hexafluorophosphate [C4mim][PF6], gave good agreement for the properties calculated compared with experimental and literature results.Our motivation for this work focused mostly in force field development for specific individual ionic liquids capable of reproducing thermodynamic properties in condensed phase, such as density, heats of vaporization, surface tension, and static dielectric constants for applications oriented as absorption and reaction media for QM/MM and free energy calculations.

Unsupervised vector-based classification of single-molecule charge transport data.

The stochastic nature of single-molecule charge transport measurements requires collection of large data sets to capture the full complexity of a molecular system. Data analysis is then guided by certain expectations, for example, a plateau feature in the tunnelling current distance trace, and the molecular conductance extracted from suitable histogram analysis. However, differences in molecular conformation or electrode contact geometry, the number of molecules in the junction or dynamic effects may lead to very different molecular signatures. Since their manifestation is a priori unknown, an unsupervised classification algorithm, making no prior assumptions regarding the data is clearly desirable. Here we present such an approach based on multivariate pattern analysis and apply it to simulated and experimental single-molecule charge transport data. We demonstrate how different event shapes are clearly separated using this algorithm and how statistics about different event classes can be extracted, when conventional methods of analysis fail.

Crystallographic and computational study of t-butyl N-[3-hydroxy-1-phenyl-4-(pyridin- 2-ylsulfanyl)butan-2-yl]carbamate and its pyrimidin-2-yl analogue

Abstract The crystal structure analysis of the biologically-relevant title compound (1) shows the carbonyl-O2 and amide-H atoms to be anti, and perpendicular relationships between the carbamate residue and the pyridyl ring [dihedral angle=84.60(10)°] and between the carbamate and aryl ring [74.84(11)°]; the rings are approximately co-planar [12.07(17)°]. An intramolecular hydroxyl-O–H···N(pyridyl) hydrogen bond that closes a S(7) loop is noted. Of interest is the observation that this hydrogen bond is not found in the structure of the pyrimidinyl analogue (2) which was characterised as a monohydrate, i.e. 2·H2O, in an earlier study. Density-functional theory calculations show the observed conformation in 1 is 2.0 kcal/mol more stable than the conformation where the intramolecular hydrogen bond is absent. This energy difference reduces to ca 0.5 kcal/mol in the case of 2. The differences in molecular conformations found for 1 and 2 are therefore ascribed to the dictates of overall molecular packing, in particular due to the influence of lattice water in 2·H2O.

Two N-(2-phenylethyl)nitroaniline derivatives as precursors for slow and sustained nitric oxide release agents.

Notwithstanding its simple structure, the chemistry of nitric oxide (NO) is complex. As a radical, NO is highly reactive. NO also has profound effects on the cardiovascular system. In order to regulate NO levels, direct therapeutic interventions include the development of numerous NO donors. Most of these donors release NO in a single high-concentration burst, which is deleterious. N-Nitrosated secondary amines release NO in a slow, sustained, and rate-tunable manner. Two new precursors to sustained NO-releasing materials have been characterized. N-[2-(3,4-Dimethoxyphenyl)ethyl]-2,4-dinitroaniline, C16H17N3O6, (I), crystallizes with one independent molecule in the asymmetric unit. The adjacent amine and nitro groups form an intramolecular N-H...O hydrogen bond. The anti conformation about the phenylethyl-to-aniline C-N bond leads to the planes of the arene and aniline rings being approximately perpendicular. Molecules are linked into dimers by weak intermolecular N-H...O hydrogen bonds such that each amine H atom participates in a three-center interaction with two nitro O atoms. The dimers pack so that the arene rings of adjacent molecules are not parallel and π-π interactions do not appear to be favored. N-(4-Methylsulfonyl-2-nitrophenyl)-L-phenylalanine, C16H16N2O6S, (II), with an optically active center, also crystallizes with one unique molecule in the asymmetric unit. The L enantiomer was established via the configuration of the starting material and was confirmed by refinement of the Flack parameter. As in (I), there is an intramolecular N-H...O hydrogen bond between adjacent amine and nitro groups. The conformation of the molecule is such that the arene rings display a dihedral angle of ca 60°. Unlike (I), molecules are not linked via intermolecular N-H...O hydrogen bonds. Rather, the carboxylic acid H atom forms a classic, approximately linear, O-H...O hydrogen bond with a sulfone O atom. Pairs of molecules related by twofold rotation axes are linked into dimers by two such interactions. The packing pattern features a zigzag arrangement of the arene rings without apparent π-π interactions. These structures are compared with reported analogues, revealing significant differences in molecular conformation, intermolecular interactions, and packing that result from modest changes in functional groups. The structures are discussed in terms of potential NO-release capability.

Study on four polymorphs of bifendate based on X-ray crystallography

Bifendate, a synthetic anti-hepatitis drug, exhibits polycrystalline mode phenomena with 2 polymorphs reported (forms A and B). Single crystals of the known crystalline form B and 3 new crystallosolvates involving bifendate solvated with tetrahydrofuran (C), dioxane (D), and pyridine (E) in a stoichiometric ratio of 1:1 were obtained and characterized by X-ray crystallography, thermal analysis, and Fourier transform infrared (FT-IR) spectroscopy. The differences in molecular conformation, intermolecular interaction and crystal packing arrangement for the four polymorphs were determined and the basis for the polymorphisms was investigated. The rotation of single bonds resulted in different orientations for the biphenyl, methyl ester and methoxyl groups. All guest solvent molecules interacted with the host molecule via an interesting intercalative mode along the [1 0 0] direction in the channel formed by the host molecules through weak aromatic stacking interactions or non-classical hydrogen bonds, of which the volume and planarity played an important role in the intercalation of the host with the guest. The incorporation of solvent-augmented rotation of the C–C bond of the biphenyl group had a striking effect on the host molecular conformation and contributed to the formation of bifendate polymorphs. Moreover, the simulated powder X-ray diffraction (PXRD) patterns for each form were calculated on the basis of the single-crystal data and proved to be unique. The single-crystal structures of the four crystalline forms are reported in this paper.

A new monoclinic polymorph of 1,1'-bis-(di-phenyl-thio-phosphor-yl)ferrocene.

The title compound, [Fe(C17H14PS)2], is a second monoclinic polymorph (P21/c, with Z' = 1) of the previously reported monoclinic (C2/c, with Z' = 1/2) form [Fang et al. (1995 ▸). Polyhedron, 14, 2403-2409]. In the new form, the S atoms lie to the same side of the mol-ecule with the pseudo S-P⋯P-S torsion angle being -53.09 (3)°. By contrast to this almost syn disposition, in the C2/c polymorph, the Fe atom lies on a centre of inversion so that the S atoms are strictly anti, with a pseudo-S-P⋯P-S torsion angle of 180°. The significant difference in mol-ecular conformation between the two forms does not result in major perturbations in the P=S bond lengths nor in the distorted tetra-hedral geometries about the P atoms. The crystal packing of the new monoclinic polymorph features weak Cp-C-H⋯π(phen-yl) inter-actions consolidating linear supra-molecular chains along the a axis. These pack with no directional inter-actions between them.

Synthesis and structures of N-alkyl-1,13-dimethoxychromeno- [2,3,4-kl]acridinium salts: the missing azaoxa[4]helicenium.

Helical structures are interesting due to their inherent chirality. Helicenium ions are triarylmethylium structures twisted into configurationally stable helicenes through the introduction of two heteroatom bridges between the three aryl substituents. Of the configurationally stable [4]helicenium ions, derivatives with sulfur, oxygen and nitrogen bridges have already been synthesised. However, one [4]helicenium ion has proven elusive, until now. We present herein the first synthesis of the 1,13-dimethoxychromeno[2,3,4-kl]acridinium (DMCA(+)) [4]helicenium ion. A series of six differently N-substituted DMCA(+) ions as their hexafluorophosphate salts are reported. Their cation stability was evaluated and it was found that DMCA(+) is ideally suited as a phase-transfer catalyst with a pKR+ of 13.0. The selectivity of nucleophilic addition to the central carbon atom of DMCA(+) has been demonstrated with diastereotopic ratios of up to 1:10. The single-crystal structures of several of the DMCA(+) salts were determined, and structural differences between N-aryl- and N-alkyl-substituted cations were observed. The results of a comparative study of the photophysics of the [4]helicenium ions are presented. DMCA(+) is found to be a potent red-emitting dye with a fluorescence quantum yield of 20 % in apolar solvents and a fluorescence lifetime of 12 ns. [4]Helicenium ions, including DMCA(+), all suffer from solvent-induced quenching, which reduces the fluorescence quantum yields significantly (ϕfl < 5 %) in polar solvents. A difference in photophysical properties is observed between N-aryl- and N-alkyl-substituted DMCA(+), which has tentatively been attributed to a difference in molecular conformation.

A series of N-(2-phenylethyl)nitroaniline derivatives as precursors for slow and sustained nitric oxide release agents.

2,4-Dinitro-N-(2-phenylethyl)aniline, C14H13N3O4, (I), crystallizes with one independent molecule in the asymmetric unit. The adjacent amine and nitro groups form an intramolecular N-H...O hydrogen bond. The anti conformation about the ethyl C-C bond leads to the phenyl and aniline rings being essentially parallel. Molecules are linked into dimers by intermolecular N-H...O hydrogen bonds, such that each amine H atom participates in a three-centre interaction with two nitro O atoms. Though the dimers pack so that the arene rings of adjacent molecules are parallel, the rings are staggered and π-π interactions do not appear to be favoured. 4,6-Dinitro-N,N'-bis(2-phenylethyl)benzene-1,3-diamine, C22H22N4O4, (II), differs from (I) in the presence of a second 2-phenylethylamine group on the substituted ring. Compound (II) also crystallizes with one unique molecule in the asymmetric unit. Both amine groups are involved in intramolecular N-H...O hydrogen bonds with adjacent nitro groups. Although one ethyl group adopts an anti conformation as in (I), the other is gauche, with the result that the pendant phenyl rings are not parallel. The amine group that is part of the gauche conformation participates in a three-centre N-H...O hydrogen bond with the nitro group of a neighbouring molecule, leading to dimers as in (I). The other amine H atom does not form any intermolecular hydrogen bonds. The packing leads to separations of ca 3.4 Å of the parallel anti phenyl and aminobenzene rings. 2-Cyano-4-nitro-N-(2-phenylethyl)aniline, C15H13N3O2, (III), differs from (I) only in having a cyano group in place of the 2-nitro group. The absence of the adjacent nitro group eliminates the intramolecular N-H...O hydrogen bond. Molecules of (III) adopt the same anti conformation about the ethyl group as in (I), but crystallize in the higher-symmetry monoclinic space group P21/n. The molecules are linked into dimers via N-H...N amine-cyano hydrogen bonds, while the nitro groups are not involved in any N-H...O interactions. Owing to the different symmetry, the molecules pack in a herringbone pattern with fewer face-to-face interactions between the rings. The closest such interactions are about 3.5 Å between rings that are largely slipped past one another. 4-Methylsulfonyl-2-nitro-N-(2-phenylethyl)aniline, C15H16N2O4S, (IV), differs from (I) in having a methylsulfonyl group in place of the 4-nitro group. The intramolecular N-H...O hydrogen bond is present as in (I). However, unlike (I), the conformation about the ethyl group is gauche, so the two arene rings are nearly perpendicular rather than parallel. The packing is significantly different from the other three structures in that there are no intermolecular hydrogen bonds involving the N-H groups. The molecules are arranged in tetragonal columns running along the c axis, with the aniline rings mostly parallel and separated by ca 3.7 Å. Taken together, these structures demonstrate that modest changes in functional groups cause significant differences in molecular conformation, intermolecular interactions and packing.

New Polymorph of 1,3,5-Triazine-2,4,6-triaminehexaacetic Acid

Single crystal of a new polymorph of 1,3,5-triazine-2,4,6-triaminehexaacetic acid has been growth and characterized. The structure of the title polymorph crystallized in the monoclinic space group C2/c with the unit cell parameters a = 20.443(4) A, b = 10.5104(14) A, c = 9.8022(11) A, β = 118.212(6)°, V = 1855.9(5) A3, Z = 4, R = 0.112, Rw = 0.273 and S = 1.038. The principal feature of the new polymorph is characterized by a bundle of molecular columns each of which is built up of molecular units stacked along c in the offset face-to-face manner. Significance of hydrogen bonding interactions in regulating the assembly of molecules in the structure is then demonstrated. Detailed differences in molecular conformation, type and pattern of hydrogen bonding interactions are discussed and distinguished from the previous polymorph. The vibrational and electronic spectroscopic studies are included. Microwave-assisted crystal growth and structure of 1,3,5-triazine-2,4,6-triaminehexaacetic acid new polymorph.

Conformational bias imposed by source microseeds results in structural ambiguity.

The p38 MAP kinase pathway is an essential component of numerous cellular signalling networks which are usually activated in response to extracellular environmental stress conditions. In addition to the canonical activation, several alternative activation pathways have been identified for p38; one of these, in which p38 is initially phosphorylated on Tyr323 and consequently autoactivated, is exclusive to T cells and is induced by TCR activation. Intrinsically active and inactive mutants at position 323 have been developed in order to evaluate the structural changes that occur upon TCR-induced activation. In order to promote crystal growth, cross streak-seeding techniques were utilized. This technique has gained popularity in promoting crystal growth when spontaneous nucleation induces critical defects or is being entirely hindered. The crystal characteristics of some mutants were highly similar to those of the wild-type source seeds (form A). In contrast, other mutants crystallized spontaneously with a different space group and molecular packing (form B). One of the active mutants (Y323T) crystallized in both crystal forms, displaying different packing characteristics and significant differences in molecular conformation that were clearly dictated by the source seeds. This implies that the source seeds used in cross streak-seeding could, in some cases, impose bias on the structural outcome of the studied molecule. Such incidents could occur when the conformational freedom permits crystal packing while not reflecting the authentic structure.

Structures of four bis(pyridine-2-yl) ketone arylhydrazone derivatives: differences in molecular conformations and intermolecula interactions

Crystal structures of bis(pyridine-2-yl) ketone arylhydrazone derivatives, [ 6 , (py) 2 C=NNHC 6 H 4 X ( X = H, 2-O 2 N, 4-O 2 N and 4-I] have been determined from data collected at 120 K. A third polymorph of ( 6 : X = 4-O 2 N) has been characterized. Compounds, ( 6 : X = 2-O 2 N) and two of the three now known polymorphs of ( 6 : X = 4-O 2 N), β - [Bakir and Brown, J. Mol. Struct. 641 (2002) 183–191] and γ [this study], have similar conformations, which are quite distinct from that of α -( 6 : X = 4-O 2 N) [Bakir et al, Acta Crystallogra. C 61 (2005) o607–o609] and ( 6 : X = 4-I) [this study]. The molecular conformation of ( 6 : X = H) is intermediate between the two extremes. For compound ( 6 : X = H), the supramolecular arrangement is made from C—H···N hydrogen bond, π···π stacking and C—H-(arene) interactions, while that for ( 6 : X = 4-I) is composed of N—H···N, C—H···N and C—H-π interactions. C—HO and π···π stacking interactions are present in γ -( 6 : X = 4-O 2 N). In contrast, ( 6 : X = 2-O 2 N) exists as discrete molecules with no intermolecular contacts within the appropriate sum of van der Waals radii.

In situ STM study of the adsorption and electropolymerization of o-, m-, and p-ethylaniline molecules on Au(111) electrode

Cyclic voltammetry (CV) and in situ scanning tunneling microscopy (STM) were employed to study the adsorption and polymerization of the geometric isomers of ethylaniline (EA) on a Au(111) single-crystal electrode in 0.5 M H(2)SO(4). All three isomers, namely o-, m-, and p-EA, were adsorbed in highly ordered structures, identified as Au(111)-(4 x 2 square root(3))rect for m- and p-EA and (4 square root(3) x 4 square root(3))R30 degrees for o-EA, at the onset potentials (approximately 0.9 V [vs. reversible hydrogen electrode]) for electropolymerization. Raising the potential in excess of 0.9 V resulted in oxidation and polymerization of m- and o-EA, but decomposition of p-EA. Molecular-resolution STM imaging revealed that poly(m-EA) and poly(o-EA), denoted respectively as m- and o-PEA, exhibited distinctively different molecular shapes. More specifically, m-PEA molecules were predominantly linear and aligned preferentially in the 121 directions of the Au(111) surface; whereas o-PEA molecules were ill-defined in shape and in dimension. These differences in molecular conformation stemmed from unlike arrangements of adsorbed monomers at 0.9 V. Notably, m-EA were adsorbed in zigzags with two nearest neighbors separated by approximately 0.5 nm, which were spatially so similar to the backbones of m-PEA that m-EA molecules coupled readily when the potential was raised high enough to induce the oxidation of m-EA. In contrast, the arrangement of o-EA molecules was so different from the ideal configuration of its polymer that molecules coupled randomly to yield crooked polymer chains less than 20 nm in length. The effect of potential on the structure of m-PEA was examined also, revealing notable branching of linear m-PEA if the electrochemical potential was set at 1.1 V.

Understanding the differences in molecular conformation of carbohydrate and protein in endosperm tissues of grains with different biodegradation kinetics using advanced synchrotron technology

Conventional “wet” chemical analyses rely heavily on the use of harsh chemicals and derivatization, thereby altering native seed structures leaving them unable to detect any original inherent structures within an intact tissue sample. A synchrotron is a giant particle accelerator that turns electrons into light (million times brighter than sunlight) which can be used to study the structure of materials at the molecular level. Synchrotron radiation-based Fourier transform IR microspectroscopy (SR-FTIRM) has been developed as a rapid, direct, non-destructive and bioanalytical technique. This technique, taking advantage of the brightness of synchrotron light and a small effective source size, is capable of exploring the molecular chemistry within the microstructures of a biological tissue without the destruction of inherent structures at ultraspatial resolutions within cellular dimensions. This is in contrast to traditional ‘wet’ chemical methods, which, during processing for analysis, often result in the destruction of the intrinsic structures of feeds. To date there has been very little application of this technique to the study of plant seed tissue in relation to nutrient utilization. The objective of this study was to use novel synchrotron radiation-based technology (SR-FTIRM) to identify the differences in the molecular chemistry and conformation of carbohydrate and protein in various plant seed endosperms within intact tissues at cellular and subcellular level from grains with different biodegradation kinetics. Barley grain (cv. Harrington) with a high rate (31.3%/h) and extent (78%), corn grain (cv. Pioneer) with a low rate (9.6%/h) and extent of (57%), and wheat grain (cv. AC Barrie) with an intermediate rate (23%/h) and extent (72%) of ruminal DM degradation were selected for evaluation. SR-FTIRM evaluations were performed at the National Synchrotron Light Source at the Brookhaven National Laboratory (Brookhaven, NY). The molecular structure spectral analysis involved the fingerprint regions of ca. 1720–1485 cm −1 (attributed to protein amide I C O and C N stretching; amide II N H bending and C N stretching), ca. 1650–950 cm −1 (non-structural CHO starch in endosperms), and ca. 1185–800 cm −1 (attributed to total CHO C O stretching vibrations) together with agglomerative hierarchical cluster and principal component analyses. Analyses involving the protein amide I features consistently identified differences between all three grains. Other analyses involving carbohydrate features were able to differentiate between wheat and barley but failed however to differentiate between wheat and corn. These results suggest that SR-FTIRM plus the multivariate analyses can be used to identify spectral features associated with the molecular structure of endosperm from grains with different biodegradation kinetics, especially in relation to protein structure. The Novel synchrotron radiation-based bioanalytical technique provides a new approach for plant seed structural molecular studies at ultraspatial resolution and within intact tissue in relation to nutrient availability.

A study of the high-pressure polymorphs of L-serine using ab initio structures and PIXEL calculations

Polymorphs of L-serine have been studied using ab initio density functional theory for pressures up to 8.1 GPa. The SIESTA code was used to perform geometry optimisations starting from the coordinates derived from high-pressure neutron powder diffraction. Between 0 and 8.1 GPa two phase transitions occur, the first of which takes place between 4.5 and 5.2 GPa and the second between 7.3 and 8.1 GPa. A change in molecular conformation occurs during the I-to-II transition, resulting in a stabilisation in intramolecular energy of 40 kJ mol−1. There is good agreement between the theoretical and experimental coordinates, and the largest root-mean-square deviation between experimental and optimised structures is 0.121 A. Analysis of the effect of pressure on the intermolecular interactions using the PIXEL method showed that none becomes significantly destabilising as the phase-I structure is compressed. It is proposed that the phase transition is driven by attainment of a more stable conformation and from the reduction in the molecular volume. The second phase transition occurs with only a small change in the hydrogen bonding pattern and no substantial difference in molecular conformation. The effect on the energies of attraction between molecules suggests that this transition is driven by the bifurcation of a short OH⋯O interaction.