A comparative study of vibrational dynamics of α- and β-forms of poly(β-hydroxybutyrate)

Normal modes and their dispersion are obtained for planar zig-zag form of poly(β-hydroxybutyrate) using Urey-Bradley force field. A comparison is made with the spectra of its helical form. Apart from detailed assignment of modes, various characteristic features of dispersion curves have been explained as arising due to internal symmetry in energy momentum space. The density-of-states have been used to calculate heat capacity in the temperature range 10-450 K using Debye's formalism.     

Interaction and reaction of the hydroxyl ion with β-d-galactose and its hydrated complex: an ab initio molecular dynamics study

The interaction of OH(-) with the sugar β-d-galactose is studied computationally, with Ab Initio Molecular Dynamics (AIMD) as the prime tool. The main findings are: (1) the OH(-) abstracts a proton from the sugar in a barrier-less process, yielding H(2)O and a Deprotonated beta-d-Galactose anion, (Dep-beta-d-G)(-). (2) This reaction can be reversed when two additional H(2)O molecules are present in the sugar. (3) At 500 K, a ring-opening reaction occurs in (Dep-beta-d-G)(-) within a timescale of 10 ps. The (neutral) sugar itself is stable over this timescale, and well beyond. This indicates that OH(-) can catalyze the degradation of β-d-galactose. Implications of this process are briefly discussed.     

Ab initio molecular dynamics — Applications to the molecular and solid state physics of phosphorus

Summary We review combined molecular dynamics (MD) and density functional (DF) simulations and their applicability in chemistry and physics. This method (also termedab initio MD, first principles MD or Car-Parrinello method) exhibits characteristic strengths and weaknesses, and we demonstrate both in a set of typical example applications from molecular physics (phosphorus clusters) and solid state physics/chemistry (liquid phosphorus). Dynamical, finite temperature, simulations deriving interatomic forces from state-of-the-art density functional calculations represent a substantial advance over both (i) traditional pointwise total energy and electronic band structure calculations and (ii) classical MD simulations with empirical or semi-empirical forces, and have already yielded qualitatively new insights in several fields.     

How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?

The sensitivity of molecular dynamics simulations to variations in the force field has been examined in relation to a set of 36 structures corresponding to 31 proteins simulated by using different versions of the GROMOS force field. The three parameter sets used (43a1, 53a5, and 53a6) differ significantly in regard to the nonbonded parameters for polar functional groups and their ability to reproduce the correct solvation and partitioning behavior of small molecular analogues of the amino acid side chains. Despite the differences in the force field parameters no major differences could be detected in a wide range of structural properties such as the root-mean-square deviation from the experimental structure, radii of gyration, solvent accessible surface, secondary structure, or hydrogen bond propensities on a 5 to 10 ns time scale. The small differences that were observed correlated primarily with the presence of charged residues as opposed to residues that differed most between the parameter sets. The work highlights the variation that can be observed in nanosecond simulations of protein systems and implications of this for force field validation, as well as for the analysis of protein simulations in general.     

Interaction of naproxen with α-, β-, and γ-hydroxypropyl cyclodextrins in solution and in the solid state

Solid combinations of naproxen with amorphous hydroxypropyl derivatives of -, -, and -cyclodextrin with an average substitution degree per anhydroglucose unit of 0.6 were investigated for thermal behaviour (differential scanning calorimetry), drug crystallinity (X-ray diffractometry), and dissolution rate (dispersed amount and rotating disc methods). Phase-solubility analysis and computer-aided molecular modelling were carried out to study the inclusion complexation of naproxen with hydroxypropyl cyclodextrins. The cavity size of the host is a selective factor for the solubilizing effect, complexing ability, and dissolution rate enhancement on naproxen, hydroxypropyl -cyclodextrin being markedly the most effective derivative. No relationship was found between the decrease in crystallinity of the drug dispersed in the amorphous carrier matrix and the geometrical features of the cyclodextrin macrocycle.     

Density functional efficiency in the calculations of vibrational frequencies and molecular structures of β-diketones

Density functional theory (DFT) levels are employed to calculate the vibrational frequencies and geometrical data of β-diketones. We evaluate the relative performance of the different levels by comparing theoretical results to experimental values. The applied DFT levels in this work are B3LYP, BLYP, B3P86, B3PW91, BPW91, G96LYP, BP86, and G96PW91 with the standard 6-31G, 6-31G*, 6-31G**, 6-31+G**, 6-31++G**, 6-311G**, 6-311++G** basis sets. The best results are obtained at the B3LYP, B3PW91, and B3P86 levels.     

Effect of pH and α-, β- and γ-cyclodextrin on the spectral properties of etoricoxib: spectroscopic and molecular dynamics study

The spectral properties of etoricoxib (ETR) at pH 2.0, 6.0 and 10.0 in the presence of cyclodextrins (CDs) were investigated. The absorption spectrum of ETR in acidic medium exhibited two bands centered at 236 and 273 nm, while in basic medium it exhibited two bands centered at 236 and 285 nm. No change in the spectrum was observed in the presence of CDs. The fluorescence emission spectra of ETR in acidic and basic media exhibited one band at 380 nm and another one at 484 nm. The emission band at 484 nm was enhanced when ETR was complexed with β-CD and γ-CD at pH 2.0, 6.0 and 10.0, while the band at 380 nm was enhanced selectively when ETR was complexed with α-CD at pH 2.0. Molecular dynamics simulations computations revealed that at pH 2.0, the sulfonyl moiety of H₂ETR²⁺ is preferentially included within the α-CD cavity, which is believed to cause the enhancement of the band at 380 nm. Moreover, at pH 6.0 and 10.0, the enhancement of the band at 484 nm was related to the inclusion of the chloropyridinyl and methylpyridinyl groups of the bipyridine moiety of HETR⁺ and ETR within β-CD and γ-CD cavities. Benesi–Hildebrand analysis showed that the ETR/β-CD complex adopts a 1:1 stoichiometry with association constant of K ₁₁?=?64.8 at pH 2.0, K ₁₁?=?105.4 at pH 6.0 and K ₁₁?=?520.5 at pH 10.0.     

The vibrational spectra of amides—II. The force field and isotopic shifts of N,N-dimethyl formamide

The effects of ¹⁶O → ¹⁸O substitution on the vibrational frequencies of N,N-dimethylformamide have been studied. To understand these and the effects of previously measured shift data due to ¹³C, ²H and ¹⁵N ab initio calculations of frequencies and intensities have been carried out at the 3-21G level. Accord between theory and experiment is generally good. A surprising result is the prediction of a weak band near 2000 cm⁻¹ in DMF due to in-plane interaction between the methyl umbrella modes and the anti-symmetric CN stretch. This abnormally high frequency is explained as arising due to the planar trigonal C₃N entity. Previous problems in reproducing isotope shifts are shown to be due to this mode being previously assigned near 1500 cm⁻¹. The effects of suppressing reference to one of a set of internal valence angles involved in a redundancy are explored. It is shown that the principal effect is to add the diagonal quadratic constant for that coordinate to all other quadratic terms involving pairs of the angles involved in the redundancy. This results in large, almost equal, interaction constants amongst this set. Such effects are seen in the present work. The ab initio field is shown to be compatible with ab initio fields of mono N-methyl amides extant in the literature.     

Role of alkylated residues in the tetrapeptide self-assembly—A molecular dynamics study

Designing peptide sequences that self-assemble into well-defined nanostructures can open a new venue for the development of novel drug carriers and molecular contrast agents. Current approaches are often based on a linear block-design of amphiphilic peptides where a hydrophilic peptide chain is terminated by a hydrophobic tail. Here, a new template for a self-assembling tetrapeptide (YXKX, Y = tyrosine, X = alkylated tyrosine, K = lysine) is proposed with two distinct sides relative to the peptide's backbone: alkylated hydrophobic residues on one side and hydrophilic residues on the other side. Using all-atom molecular dynamics simulations, the self-assembly pathway of the tetrapeptide is analyzed for two different concentrations. At both concentrations, tetrapeptides self-assembled into a nanosphere structure. The alkylated tyrosines initialize the self-assembly process via a strong hydrophobic effect and to reduce exposure to the aqueous solvent, they formed a hydrophobic core. The hydrophilic residues occupied the surface of the self-assembled nanosphere. Ordered arrangement of tetrapeptides within the nanosphere with the backbone hydrogen bonding led to a beta sheet formation. Alkyl chain length constrained the size and shape of the nanosphere. This study provides foundation for further exploration of self-assembling structures that are based on peptides with hydrophobic and hydrophilic moieties located on the opposite sides of a peptide backbone.     

Synthesis of new liquid crystalline compounds containing an α,β-unsaturated ketone and β-chloroketone groups in the side chain

A number of new liquid crystalline compounds containing an ,-unsaturated ketone or -chloro ketone moiety in the side chain were synthesized. The key intermediates in the synthesis were 1-(4-hydroxy-phenyl)-2-octen-1-one and 3-chloro-1-(4-hydroxyphenyl)octan-1-one which were prepared from 5-(4-hydroxy-phenyl)-3-pentyl-4,5-dihydroisoxazole and 3-hydroxy-1-(4-hydroxyphenyl)octan-1-one, respectively.Translated from Zhurnal Organicheskoi Khimii, Vol. 40, No. 10, 2004, pp. 1526–1531.Original Russian Text Copyright © 2004 by V. Kovganko, N. Kovganko, Bezborodov.     

A micro-heterometric determination of traces of iron (III) in alloys and salts with α-nitroso β-naphthol

Ferric iron constituting approximately 0.01% — 0.1% may be determined by a heterometric titration with α-nitroso-β-naphthol. The solution may contain 99.9% or more of calcium, barium, magnesium, aluminium, chromium, manganese, nickel, cadmium or lead salts. No previous separation is necessary. The α-nitroso-β-naphthol is dissolved in alcohol. The analysed solution must be acidified. No complexing agents are necessary. Citrate or tartrate must be absent. The maximum optical density values which are obtained at the end of the titration are proportional to the amount of iron which is analysed. These maximum values are entirely unaffected by the concentrated salt solutions. The heterometric sensitivity of the reaction between iron and α-nitroso-β-naphthol is three times higher in 50% alcoholic solution than in water. The titration takes about one hour. The error is 0.0—4%.     

Concurrent display of both α- and β-turns in a model peptide

This article describes a model peptide that concurrently displays both α- and β-turns, as demonstrated by structural investigations using single crystal X-ray crystallography and solution-state NMR studies. The motif reported herein has the potential for the design of novel conformationally ordered synthetic oligomers with structural architectures distinct from those classically observed.     

Excimer emission of caffeine with α- and β-cyclodextrins: spectral and molecular modelling studies

Excimer emission of caffeine with α-CD and β-CD were studied by UV-visible, fluorescence, time-resolved fluorescence, FTIR, ¹H NMR and molecular modelling techniques. Changes in the absorbance and fluorescence and lifetime of the caffeine with cyclodextrin (CD) solutions indicate (i) caffeine shows dual emission in the CD solutions, (ii) normal emission originates from a monomer and the longer wavelength emission is due to excimer and (iii) in both CDs caffeine forms 1:2 inclusion complex. Carbonyl stretching frequency moved to higher wave numbers and broadening of the N–H stretching band indicated the formation of inclusion complex. The resonance of the methyl protons of caffeine show remarkable upfield or downfield shift in the ¹H NMR, which indicates imidazole ring of the caffeine entrapped in the CD cavities. Investigations of energetic, thermodynamic and electronic properties of PM3 computational calculations confirmed the stability of the inclusion complex.     

Studies on nitramide and its methyl derivatives with ab initio calculations——Ⅳ.The harmonic force field and vibrational spectra of dimethylnitramine and its isotopic derivatives

The complete harmonic vibrational force field of dimethylnitramine has been calculatedat the Hartree-Fock level using 4-21G basis set.The harmonic force field was then scaled with scalefactors previously derived from N-methylnitramine,and the vibrational spectrum of dimethylnitraminewas computed.This apriori prediction,made with no reference to observations on dimethylnitramine,agrees with the experimental IR spectrum in gas phase with a mean deviation of 8.4 cm~(-1).Some of thescale factors were reoptimized by fitting of the computed force field to experimental data.The newset of scale factors reduced the mean deviation to 4.5 cm~(-1),and was used to predict the vibrationalspectrum of deuterated form of dimethylnitramine(-6D).Dipole moment derivatives were also cal-culated and used to predict infrared intensities which are comparable with experimental values.     

Invited Lecture. Ferroelectric liquid crystalline polymers and related model compounds with a low–moderate degree of polymerization

Abstract

Ferroelectric liquid crystalline polymers (FLCPs) with a low-moderate degree of polymerization were synthesized. These had a comb structure; the main chain was polyacrylate and the side chain consisted of a flexible spacer, a core and an optically active chiral end group. They exhibited electro-optic switching times ranging from a few milliseconds to a few seconds in the S*_c phase. As the molecular weight M _n increased, the range of the S*_c shifted to higher temperatures. At a given temperature, the switching time increased with M _n .

Spontaneous polarizations P _s , apparent cone angles 2θ, electro-optic switching times τ and rotational viscosities η of some polyoxyethylene FLCPs and corresponding low molecular weight ferroelectric liquid crystal materials (FLCs) were also measured. This is the first report of polyoxyethylene FLCPs. There was no significant difference in P _s and 2θ, which shows that the arrangement of the side chains in the FLCP is similar to that of the molecules in ordinary FLC. On the contrary, τ and η for the FLCPs were 10²–10³ times as large as those for FLCs. The rotational viscosity of the FLCP was mainly dependent on the side chain structure rather than on the spacer. Therefore collisions between adjacent side chains cause large η values in FLCPs rather than hindrance to side chain gyration due to the spacer group. By combining FLCPs with ITO-coated plastic substrates, a large area matrix driven display has been made. Although an improvement in switching time is still needed, a flexible and lightweight display like a sheet of paper will be available in the near future.     

Fourier transform Raman studies of materials and compounds of biological importance—II. The effect of moisture on the molecular structure of the alpha and beta anomers of d-glucose

The effects of small amounts of water added to the alpha and beta anomers of d-glucose have been investigated. The monohydrate of alpha-d-glucose was formed under these conditions and its FT-Raman spectrum has been recorded for the first time. The combination of crystallographic data and vibrational spectroscopy, based on the study of alpha and beta d-glucose, with special emphasis on conformation and configuration sensitive modes, enabled band assignments to be made for the monohydrate of alpha-d-glucose.     

A correction function to determine the β-fusion heat in a mixture of α- and β-PP

Blends of known amounts of α- and β-PP crystals were prepared from pure α- and pure β-PPsamples. Their fusion behaviours were studied by differential scanning calorimetry (DSC).The fusion heats of the α- and β-crystals were approximated from the DSC curves and compared with those calculated on the basis of the compositions of the blends. A correction function was found which improved the accuracy of the respective fusion heats significantly from the DSC analysis. The correction function can be used to determine the respective fusion heats of a PP sample which contains an unknown mixture of the α- and β-crystals. This revised version was published online in July 2006 with corrections to the Cover Date.     

Characterization of the inclusion complex of β-cyclodextrin with sorbic acid in the solid state and in aqueous solution

Crystal structure of β-cyclodextrin (β-CD) complexes with sorbic acid, usually as food preservative, has been determined by single-crystal X-ray diffraction at 113 K. The space group of β-cyclodextrin-sorbic acid complex is P1 with unit cell dimensions of a = 15.284(3) Å, b = 15.402(3) Å, c = 17.981(4) Å, α = 99.67(3)°, β = 112.83(3)°, γ = 102.48(3)° and Z = 1. The result indicates that the β-CD molecules form head-to-head dimers which pack in the intermediate mode. Each dimer contains two guest molecules whose methyl groups are located at the dimer interface while the carboxyl groups protrude from the β-CD primary faces. Water molecules (25.5) are distributed outside the cyclodextrin cavity over 31 sites. Furthermore, nuclear magnetic resonance spectroscopy (¹H NMR) has been employed to investigate the inclusion behavior between the host β-CD and guest sorbic acid in aqueous solution. The results obtained enabled us to structurally characterize the β-CD inclusion complex with sorbic acid.     

Optical-optical double-resonance spectroscopy of high vibrational levels of the Na2 A 1Σu+ state in a molecular beam

High vibrational bands of the Na₂ A-X system are investigated in a molecular beam by two-step excitation at separate interaction regions. With a first laser A-state levels are optically pumped; they decay radiatively and populate high vibrational levels of the ground state (e.g. υ′' = 31). A second laser excitation starting from these prepared levels allows the investigation of high vibrational levels of the A state, for example υ′ = 66, 67, 68, 69 and υ′ = 70. From analysis of the υ′ = 66, …, 70-υ′' = 31 bands we obtain B(υ) and G(υ) and, including the data of others, we determined a new RKR potential curve for the A ¹Σ_u⁺ state, extending the experimentally determined potential from υ′ = 44 to υ′ = 70 (78% of the well depth).     

Vibrational spectra of β-lactams—III. potassium 2-azetidinone-1-sulfonate and its isotopic compounds

The IR and Raman spectra of potassium 2-azetidinone-1-sulfonate and its three deuterated and two ¹⁵N-substituted compounds have been recorded, and the observed bands have been assigned on the basis of the isotope effects and the normal coordinate analysis. Comparison of the force constants for the amide group among 2-azetidinone, 1-methyl-2-azetidinone and potassium 2-azetidinone-1-sulfonate indicates that there is a correlation between these constants and the ease of hydrolysis which was determined by NMR spectroscopy, depending on the amide resonance.