Phospholipids chiral at phosphorus: Fourier-transform infrared study on the gel-liquid crystalline transition of chiral thiophosphatidylcholine

Fourier-transform infrared spectroscopy (FT-IR) was used to study the structural properties of Rp, Sp, and Rp + Sp isomers of 1,2-dipalmitoyl-sn-glycero-3-thiophosphocholine (DPPsC), in comparison with those of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC). For the vibrational modes of acyl chains, isomers of DPPsC show similar temperature and phase dependence to DPPC. However, the Rp isomer of DPPsC exhibits several unique properties: the CH2 symmetric stretching band is unusually weak, the CH2 asymmetric stretching band is unusually narrow, and the CH2 wagging bands do not disappear completely at temperatures above the main transition. These differences could imply a tighter packing and be responsible for the unique phase-transition property of (Rp)-DPPsC. For the vibrational modes of the thiophosphodiester group, the frequency of the P-O stretching mode of DPPsC suggests that the POS- triad exists predominantly in the mesomeric form. This is in contrast to the structure of nucleoside phosphorothioates where charge localization at sulfur has been demonstrated [Iyengar, R., Eckstein, F., & Frey, P. A. (1984) J. Am. Chem. Soc. 106, 8309-8310]. This suggests that the different biophysical properties between isomers of DPPsC are not due to different charge distribution in the POS- triad or different geometry of charge distribution on the membrane surface. Instead, factors such as size or hydration property of oxygen and sulfur, as well as the different configuration at phosphorus, could be responsible for the differences in the conformation and packing of acyl chains, as revealed by the different properties in the CH2 stretching and wagging modes of DPPsC.     

Vibrational analysis of nucleic acids. V. Force field and conformation-dependent modes of the phosphodiester backbone modeled by diethyl phosphate.

A generalized valence force field is derived for the diethyl phosphate anion [(CH3CH2O)2PO2-] and its deuterium [(CH3CD2O)2PO2-, (CD3CH2O)2PO2- and (CD3CD2O)2PO2-] and carbon-13 [(CH3 13CH2O)2PO2-] derivatives in the stable trans-gauche-gauche-trans conformation. Normal coordinate analysis of the trans-gauche-gauche-trans conformer, which serves as a structural analog of the nucleic acid phosphodiester group, is based on comprehensive infrared and Raman spectroscopic data and vibrational assignments obtained for the diethyl phosphate anion. The generalized valence force field is in good agreement with the scaled ab initio force field of diethyl phosphate and represents significant improvement over earlier modeling of the phosphodiester moiety with dimethyl phosphate. The conformational dependence of skeletal C-C-O-P(O2-)-O-C-C stretching vibrations is also explored. Starting with the trans-gauche-gauche-trans conformation, the frequency dependence of skeletal stretching modes has been obtained by stepwise rotation of the torsion angles of the P-O and C-O bonds corresponding to nucleic acid torsions alpha (P-O5'), beta (O5'-C5'), epsilon (C3'-O3'), and zeta (O3'-P). Both symmetric and antisymmetric phosphoester stretching modes are highly sensitive to P-O and C-O torsions, whereas symmetric and antisymmetric phosphodioxy (PO2-) stretching modes are less sensitive. The present results provide an improved structural basis for understanding previously developed empirical correlations between vibrational marker bands and nucleic acid backbone conformation.     

Theoretical Study On The Reaction Mechanism Of Gecl3ch2ch2cooh+h2o→gecl2ohch2ch2cooh+hcl

The mechanism and dynamical properties for the title reaction have been investigated theoretically. Three reaction pathways have been found. Geometries, vibrational frequencies, infra-red (IR) intensities and relative energies for various stationary points in the three reaction channels have been determined respectively. The corresponding rate constants at the B3LYP/6-31++G(2d,2p) level have been deduced over a wide temperature range of 200–2000 K by using canonical variational transition state theory with small curvature tunnelling effect. Solvent effects are taken into account via the Onsager model of self-constant reaction field at the same level of theory. This preliminary study shows that the complex formation is favoured by the use of water solvent.     

Vibrational CD studies of interchain hydrogen-bonded tripodal peptides.

The solution conformations of three trispeptides--L,L,L-1,3,5-C6H3[CH2NHCOCH(X)-NHBoc++ +]3, X = CH3 (Ala) or CH2CH(CH3)2 (Leu), and L,L,L-N(CH2CH2NHCOCH[CH2-CH(CH3)2]NHBoc)3--have been determined from their ir and vibrational CD (VCD) spectra in the NH stretching and carbonyl stretching regions in apolar solution. The compounds containing L-Leu are shown to occur primarily in a propeller conformation with C3 symmetry that is stabilized by interchain hydrogen bonds. Through application of the coupled oscillator model of VCD, a right-handed sense for the hydrogen-bonded chains in the propeller is deduced, in agreement with previous empirical force field calculations. The spectra also provide evidence for interchain association between two chains, resulting in a C10-ring. For chains not involved in interchain association, the spectra reveal the presence of C7-rings within a chain. The trispeptide containing L-Ala is found to occur primarily in a random form.     

Vibrational analysis of nucleic acids. I. The phosphodiester group in dimethyl phosphate model compounds: (CH3O)2PO2-, (CD3O)2PO2-, and (13CH3O)2PO2-.

Normal coordinate analyses and vibrational assignments are presented for the dimethyl phosphate anion [(CH3O)2PO2-] and its deuteriomethyl [(CD3O)2PO2-] and carbon-13 [(13CH3O)2PO2-] derivatives in the gauche-gauche conformation. The dimethyl phosphate anion, which is the simplest model for the nucleic acid phosphodiester moiety, exhibits many of the spectral complexities of DNA and RNA and has previously resisted a complete and consistent vibrational analysis. In the present study we make use of new experimental data on the dimethyl phosphate isotopomers, including Raman depolarization measurements, to develop a consistent valence force field for normal modes of the C--O--P--O--C phosphodiester network and its hydrogenic substituents, as well as for stretching and bending modes of the O--P--O network of the anionic phosphodioxy group (PO2-). The force field established for dimethyl phosphate incorporates one significant nonbonded force constant, introduced from ab initio calculations, to account for interaction between the two ester C--O bonds. This study resolves previous problematic assignments for conformation-sensitive symmetric (in-phase) and asymmetric (out-of-phase) skeletal stretching modes of the ester linkages and demonstrates substantial anharmonicity in the hydrogen-stretching vibrations of the methyl substituents. New assignments are proposed for Raman bands of the phosphodioxy group, which may serve as potential indicators of structure and interaction of the DNA phosphates.     

Raman spectroscopy investigation of various saturated monoacid triglycerides

A study of the vibrational behavior of five saturated monoacid triacylglycerides is performed by Raman spectroscopy at room temperature in the 3100-500 cm(-1) spectral range. The splitting of the CO stretching mode leads to conclude on the existence of two or three geometries of CO in the "knot" group OCO. The CO stretching mode seems to be a good tool for distinguishing the polymorphic forms of the studied triglycerides. The assignments of the different CH stretching modes are performed in the 1500-500 cm(-1) spectral range. The I(2845)/I(2880) (in the CH stretching spectral region) and I(1445)/I(1296) intensity ratios (between the maximal intensity I(1445) of the CH(2) scissoring mode and the maximal intensity I(1296) of the skeletal vibration of (CH(2))(n) in-phase twist) seem to depend on the type of polymorphic forms of these molecules.     

Characteristics of molecular hydrogen and CH* radicals in a methane plasma in a magnetically enhanced capacitive RF discharge

The parameters of a methane-containing plasma in an asymmetric RF capacitive discharge in an external magnetic field were studied using optical emission spectroscopy. The power deposited in the discharge was 90 W and the gas pressure and magnetic field were varied in the ranges 1–5 Pa and 50–200 G, respectively. The vibrational and rotational temperatures of hydrogen molecules and CH* radicals were measured as functions of the magnetic field and methane pressure. The ratio between the densities of atomic and molecular hydrogen was estimated. The processes responsible for the excitation of molecular hydrogen and CH* radicals in a methane-containing plasma in an RF capacitive discharge are analyzed.     

Modeling the weak hydrogen bonding of pyrrole and dichloromethane through Raman and DFT study

Raman spectra of neat pyrrole (C(4)H(5)N) and its binary mixtures with dichloromethane (CH(2)Cl(2), DCM) with varying mole fractions of C(4)H(5)N from 0.1 to 0.9 were recorded in order to monitor the influence of molecular interaction on spectral features of selected vibrational bands of pyrrole in the region 600-1600 cm(-1). Only 1369 cm(-1) vibrational band of pyrrole shows a significant change in its peak position in going from neat pyrrole to the complexes. The 1369 cm(-1) band shows (～6 cm(-1)) blue shift upon dilution and the corresponding linewidth shows the maximum shift at C?=?0.5 mole fraction of pyrrole upon dilution which clearly indicates that the concentration fluctuation model plays major role. Quantum chemical calculation using density functional theory (DFT) and ab-initio (MP2 and HF) methods were performed employing high level basis set, 6-311++G(d,p) to obtain the ground state geometry of neat pyrrole and its complexes with DCM in gas phase. Basis set superimpose error (BSSE) correction was also introduced by using the counterpoise method. In order to account for the solvent effect on vibrational features and changes in optimized structural parameters of pyrrole, polarizable continuum model (PCM) (bulk solvations) and PCM (specific plus bulk solvations) calculations were performed. Two possible configurations of pyrrole + DCM complex have been predicted by B3LYP and HF methods, whereas the MP2 method gave only single configuration in which H atom of DCM is bonded to π ring of the pyrrole molecule. This affects significantly the ring vibrations of pyrrole molecule, which was also observed in our experimental results.     

Polarization-Dependent Surface-Enhanced Raman Scattering via Aligned Gold Nanorods in Poly(Vinyl Alcohol) Film

A low-cost and effective surface-enhanced Raman scattering (SERS) substrate consisting of aligned gold nanorods is obtained by stretching the poly(vinyl alcohol) nanorods composite film doped with the probe molecule. The SERS intensity of characteristic vibrational band of the probe is observed obviously dependent on the angle (θ) between incident polarization and major axis of nanorod. The relationship between them manifests a cos² θ dependence. The result is illustrated from both the localized field enhancement and optical antenna effect of gold nanorod. The finite element method calculation is also performed to further confirm the conclusion.     

Reaction Fields in the Environment of Fluorescent Probes: Polarity Profiles in Membranes

Fluorescent probes in biological systems are sensitive to environmental polarity by virtue of their response to the reaction field created by polarization of the dielectric medium. Classically, fluorophore solvatochromism is analyzed in terms of the Lippert equation and later variants, all of which rely upon the original reaction field of Onsager. A recent survey of the solvent dependence of EPR spin-label probes, which are responsive solely to the reaction field in the ground state without the complication of excited states, shows that the reaction field of Block and Walker performs best in describing the polarity dependence. In this model, the step-function transition to the bulk dielectric medium used by Onsager is replaced by a graded transition. Analysis of the Stokes shifts for representative fluorescent membrane probes, such as PRODAN, DANSYL, and anthroyl fatty acid, reveals that, of several different reaction fields (including that of Onsager), the Block-Walker model best describes the dependence on solvent dielectric constant and refractive index for the different probes simultaneously. This is after full allowance is made for all contributions involving polarizability of the fluorophore, a point that is frequently neglected or treated incorrectly in studies using biological fluorescent probes. By using the full range of polar and apolar solvents, it is then possible to establish a common reference for the polarity dependence of different fluorophores and to relate this also to the polarity dependence of biologically relevant spin-label EPR probes. An important application is calibration of the transmembrane polarity profile recorded by fluorescent probes in terms of the high-resolution profile obtained from site-specifically spin-labeled lipid chains.     

Pressure-induced correlation field splitting of vibrational modes: structural and dynamic properties in lipid bilayers and biomembranes.

Correlation field splittings of the vibrational modes of methylene chains in lipid bilayers, isolated lipid molecules in perdeuterated lipid bilayers, crystalline lipid, and interdigitated lipid bilayers have been investigated by pressure-tuning Fourier-transform infrared spectroscopy. The correlation field splittings of these modes are originating from the vibrational coupling interactions between the fully extended methylene chains with different site symmetry along each bilayer leaflet. The interchain-interactions of the methylene chains with the same site symmetry only contribute to frequency shift of the vibrational modes. The magnitude of the correlation field splitting is a measure of the strength of the interchain-interactions, and the relative intensities of the correlation field component bands provide information concerning the relative orientation of the zig-zag planes of the interacting methylene chains. It has been demonstrated in the present work that the correlation field splitting of the CH2 bending and rocking modes commonly observed in the vibrational spectra of lipid bilayers is the result of the intermolecular interchain-interactions among the methylene chains of the neighboring molecules. The intramolecular interchain-interactions between the sn-1 and sn-2 methylene chains within each molecule are weak. The correlation field splitting resulting from the intramolecular interchain-interactions exhibits a much smaller magnitude than that from the intermolecular interchain-interactions and is observed only at very high pressure. Interdigitation of the opposing bilayer leaflets disturbs significantly the intermolecular interchain-interactions and results in dramatic changes in the pressure profiles of the correlation field component bands of both the CH2 bending and rocking modes. The relative intensities of the correlation field component bands of these modes and the magnitude of the splitting are also altered significantly. These results provide further evidence that the correlation field splitting of the CH2 bending and rocking modes in the vibrational spectra of lipid bilayers is due to the intermolecular interchain-interactions. The present work has also demonstrated that the correlation field splitting of the vibrational modes in lipid bilayers is mainly contributed by the intermolecular interchain-interactions among the nearest neighboring molecules and that the long-range correlation interactions beyond the second neighboring molecules are insignificant.     

On tautomerism of the cytosine molecule

Tautomerism of the cytosine molecule is discussed in connection with recent experimental matrix-isolation infrared spectroscopic measurements and recent ab initio calculations of relative stabilities of tautomers and of IR spectra for different tautomeric forms of the compound. Experimental IR spectra in the N-H and O-H stretching regions and in the C = O stretching region are presented for cytosine and for its several derivatives considered as model compounds. This experimental evidence, as well as the quantum-mechanical calculations (including both electron correlation and zero-point vibrational contributions), clearly indicate that two tautomers of cytosine, i.e. the amino-hydroxy and amino-oxo forms with the hydrogen atom at the N(1) position, exist in equilibrium when the cytosine molecule is isolated in an inert environment. The effect of the environment on the relative stabilities of several tautomers is also discussed briefly.     

Vibrational (FT-IR and FT-Raman) spectral investigations of 7-aminoflavone with density functional theoretical simulations

FT-Raman and FT-IR spectra of the 7-aminoflavone have been recorded and analysed. The detailed interpretation of the vibrational spectra has been carried out with the aid of normal coordinate analysis following the scaled quantum mechanical force field methodology. The various intramolecular interactions that are responsible for stabilisation of the molecule were revealed by natural bond orbital analysis. The obtained vibrational wavenumbers and optimised geometric parameters were observed to be in good agreement with the experimental data. The carbonyl stretching vibrations have been lowered due to conjugation and hydrogen bonding in the molecules.     

Chiroptical properties of 2,2’‐bioxirane

The two enantiomers of 2,2′‐bioxirane were synthesized, and their chiroptical properties were thoroughly investigated in various solvents by polarimetry, vibrational circular dichroism (VCD), and Raman optical activity (ROA). Density functional theory (DFT) calculations at the B3LYP/aug‐cc‐pVTZ level revealed the presence of three conformers (G₊, G_?, and cis) with Gibbs populations of 51, 44, and 5% for the isolated molecule, respectively. The population ratios of the two main conformers were modified for solvents exhibiting higher dielectric constants (G_? form decreases whereas G₊ form increases). The behavior of the specific optical rotation values with the different solvents was correctly reproduced by time‐dependent DFT calculations using the polarizable continuum model (PCM), except for the benzene for which explicit solvent model should be necessary. Finally, VCD and ROA spectra were perfectly reproduced by the DFT/PCM calculations for the Boltzmann‐averaged G₊ and G_? conformers.     

Aggregation of chlorophylls in monolayers. VI. Infrared study of the CH stretching bands of chlorophyll a and of chlorophyll b in monolayers

The CH vibrational stretch bands of chlorophyll (Chl) in monolayers, obtained by the Langmuir-Blodgett technique have been studied by infrared spectroscopy. Compared to a solution or to a multilayer which shows three to four bands, the spectra of Chl a or Chl b molecules in monolayers have revealed more than seven bands, which are assigned to the various CH groups in the molecule. In contrast to solutions or to multilayer samples which give featureless bands, each band of the monolayers is composed of many components which are modified when the system is perturbed either by drying or by hydration techniques. The separation between the components of the CH aliphatic bands is typical of crystalline field splitting and the modification of the intensities of these components is associated with the movement of the phytyl chain of the chlorophyll molecules. The CH aromatic stretch bands have been observed; the displacement and variation of the intensities of these bands are associated with deformation of the porphyrin ring. The CH band of the formyl group on Chl b has also been observed. The displacement and variation of the intensity of this band are related to the association that this group makes with the surrounding molecules and with the displacement of the porphyrin ring.     

Interaction of ferricytochrome c with zwitterionic phospholipid bilayers: a Raman spectroscopic study

The vibrational Raman spectra of both pure L-alpha-dipalmitoylphosphatidylcholine (DPPC) liposomes and DPPC multilayers reconstituted with ferricytochrome c under varying conditions of pH and ionic strength are reported as a function of temperature. Total integrated band intensities and relative peak height intensity ratios, two spectral scattering parameters used to determine bilayer disorder, are invariant to changes in pH and ionic strength but exhibit a sensitivity to the bilayer concentration of the ferricytochrome c. Protein concentrations were estimated by comparing the 1636 cm-1 resonance Raman line of known ferricytochrome c solutions to intensity values for the reconstituted multilayer samples. Temperature-dependent profiles of the 3100-2800 cm-1 C-H stretching, 1150-1000 cm-1 C-C stretching, 1440 cm-1 CH2 deformation, and 1295 cm-1 CH2 twisting mode regions characteristic of acyl chain vibrations reflect bilayer perturbations due to the weak interactions of ferricytochrome c. The DPPC multilamellar gel to liquid-crystalline phase transition temperature, TM, defined by either the C-H stretching mode I2935/I2880 or the C-C stretching mode I1061/I1090 peak height intensity ratios, is decreased by approximately 4 degrees C for the approximately 10(-4) M ferricytochrome c reconstituted DPPC liposomes. Other spectral features, such as the increase in the 2935 cm-1 C-H stretching mode region and the enhancement of higher frequency CH2 twisting modes, which arise in bilayers containing approximately 10(-4) M protein, are interpreted in terms of protein penetration into the hydrophobic region of the bilayer.     

Some Thoughts about Bond Energies,Bond Lengths,and Force Constants

The bond energy (BE) of a polyatomic molecule cannot be measured and, therefore, determination of BEs can only be done within a model using a set of assumptions. The bond strength is reflected by the intrinsic BE (IBE), which is related to the intrinsic atomization energy (IAE) and which represents the energy of dissociation under the provision that the degree of hybridization is maintained for all atoms of the molecule. IBE and BE differ in the case of CC and CH bonds by the promotion, the hybridization, and the charge reorganization energy of carbon. Since the latter terms differ from molecule to molecule, IBE and BE are not necessarily parallel and the use of BEs from thermochemical models can be misleading. The stretching force constant is a dynamical quantity and, therefore, it is related to the bond dissociation energy (BDE). Calculation and interpretation of stretching force constants for local internal coordinate modes are discussed and it is demonstrated that the best relationship between BDEs and stretching force constants is obtained within the model of adiabatic internal modes. The valence stretching force constants are less suitable since they are related to an artificial bond dissociation process with geometrical relaxation effects suppressed, which leads to an intrinsic BDE (IBDE). In the case of AX_n molecules, symmetric coordinates can be used to get an appropriate stretching force constant that is related to the BE. However, in general stretching force constants determined for symmetry coordinates do not reflect the strength of a particular bond since the related dissociation processes are strongly influenced by the stability of the products formed.     

Combined Force-Torque Spectroscopy of Proteins by Means of Multiscale Molecular Simulation

Assessing the structural properties of large proteins is important to gain an understanding of their function in, e.g., biological systems or biomedical applications. We propose a method to examine the mechanical properties of proteins subject to applied forces by means of multiscale simulation. Both stretching and torsional forces are considered, and these may be applied independently of each other. As a proof of principle, we apply torsional forces to a coarse-grained continuum model of the antibody protein immunoglobulin G using fluctuating finite element analysis and use it to identify the area of strongest deformation. This region is essential to the torsional properties of the molecule as a whole because it represents the softest, most deformable domain. Zooming in, this part of the molecule is subjected to torques and stretching forces using molecular dynamics simulations on an atomistically resolved level to investigate its torsional properties. We calculate the torsional resistance as a function of the rotation of the domain while subjecting it to various stretching forces. From this, we assess how the measured twist-torque profiles develop with increasing stretching force and show that they exhibit torsion stiffening, in qualitative agreement with experimental findings. We argue that combining the twist-torque profiles for various stretching forces effectively results in a combined force-torque spectroscopy analysis, which may serve as a mechanical signature for a biological macromolecule.     

Lipid hydration: headgroup CH moieties are involved in water binding

To explore the interaction potential of phospholipids, we have studied the hydration of diacyl phosphatidylcholine (PC) and methylphosphocholine (MePC), a pertinent model compound, by ir spectroscopy. Related ab initio Hartree-Fock calculations were performed for MePC. Water is considered ideal as a relevant probe molecule. Spectroscopic data for MePC reveal a strong influence of bound hydration water not only on the phosphate groups but also onto the putatively apolar CH(n) groups. The same could be demonstrated for deuterated dimyristoyl PC taken as a "complete" lipid molecule: both headgroup methyl and methylene moieties are gradually, but remarkably affected by hydration, as evidenced by strong wavenumber upshifts of C-H stretching vibration bands. These findings may originate in directed interactions of the CH(n) groups with bound water molecules, but hydration-driven conformational changes of PC headgroups could also occur. The results of the ab initio calculations rationalize the first explanation by predicting a substantial contribution of specific C-H...OH(2) interactions, mainly characterized by a dramatic loss of electron density of the sigma* antibonding molecular orbitals of C-H bonds. Hence, the propensity of the lipid headgroup methyl and methylene groups to act as donor sites in hydrogen bonding must no longer be ignored when considering the interaction potential of PCs.