Investigating the mechanisms of 17<Emphasis Type="Italic">β</Emphasis>-estradiol imprinting by computational prediction and spectroscopic analysis

Molecular dynamics simulations combined with spectroscopic analysis were applied to understand the nature of recognition in molecularly imprinted polymers (MIPs), and for optimizing the MIP formulation. The best monomers for synthesizing imprinted materials for 17β-estradiol (BE2) were selected by evaluating the strength of the template–monomer interaction derived from molecular dynamics simulations. A number of potential functional monomers for BE2 were screened for hydrogen-bonding strength in order to analyze template–monomer interactions favorable for synthesizing noncovalent MIPs, with the simulations revealing that methacrylic acid, 2-(diethylamino)ethyl methacrylate, and methacrylamide provided the highest binding affinity to BE2. These theoretical predictions agree with previously reported results on batch rebinding studies using the corresponding functional monomers for synthesizing a series of MIPs. Molecular analysis such as ¹H NMR was used for experimentally confirming the prevalent template–monomer interactions derived from the modeling results. Molecular dynamics simulations indicating monomer dimerization in the prepolymerization solution correlated with the nature of the porogenic solvent, which was confirmed by NMR studies on hydrogen-bonding interactions of methacrylic acid in different solvents. Furthermore, batch rebinding studies revealed that the specific functionalities of the monomers essential to rebinding are retained after polymerization, which proves that the application of computational methods for modeling the prepolymerization solution provides useful information for optimizing real MIP systems.     

Spectroscopic and electrochemical studies of cocaine–opioid interactions

The drugs of abuse cocaine (C), heroin (H), and morphine (M) have been studied to enable understanding of the occurrence of cocaine–opioid interactions at a molecular level. Electrochemical, Raman, and NMR studies of the free drugs and their mixtures were used to study drug–drug interactions. The results were analyzed using data obtained from quantum-mechanical calculations. For the cocaine–morphine mixture (C–MH), formation of a binary complex was detected; this involved the 3-phenolic group and the heterocyclic oxygen of morphine and the carbonyl oxygen and the methyl protons of cocaine’s methyl ester group. NMR studies conducted simultaneously also revealed C–MH binding geometry consistent with theoretical predictions and with electrochemical and vibrational spectroscopy results. These results provide evidence for the occurrence of a cocaine–morphine interaction, both in the solid state and in solution, particularly for the hydrochloride form. A slight interaction, in solution, was also detected by NMR for the cocaine–heroin mixture. Figure "Schematic representation of the proposed model for cocaine:morphine salt interaction"     

Dynamic rheological characterization of polyamide/modified polyolefin laminates

 In this work dynamic rheological and peel strength measurements on laminates of polyamide and several modified polyolefins were made to evaluate the interfacial compatibilization phenomena. The polyolefins used were a low-density polyethylene, without any treatment and γ-ray irradiated in air, and two copolymers, an ethylene–tert-butyl acrylate–acrylic acid terpolymer and a partially neutralized ethylene–methacrylic acid copolymer containing sodium cations. Multilayer structures containing different amounts of both interfacial surface and volume fraction were studied. Relationships between viscoelastic functions and composition were used to analyze the effect of bulk and surface modification in the polyolefins at the interface with the polyamide. The results show that dynamic rheological measurements of stratified polymers can be used as a tool to investigate interfacial activity in multiphase systems. Received: 2 January 1998/Accepted: 21 March 1998     

Protein-induced DNA bending: the role of phosphate neutralisation

An important component of protein–nucleic acid interactions is the formation of salt bridges between cationic amino acid side chains and the anionic phosphate groups of the nucleic acid. We have used molecular mechanics to study the energetic and conformational impact of such interactions. Firstly, crystallographic protein–nucleic acid complexes from the Protein Data Bank were analysed in terms of DNA curvature and the presence of salt bridges. For complexes where the DNA is significantly bent, the contribution of salt bridges to this curvature was modelled by studying the effect of neutralising the appropriate phosphate groups. The number and the distribution of salt bridges vary widely for different DNA binding motifs and appear to have very different effects on DNA. In the case of homeodomain, bZIP and helix–loop–helix proteins, salt bridges induce DNA bending, whereas for prokaryotic helix–turn–helix proteins the number of salt bridges is much smaller and little bending is found. By analysing the components of the DNA deformation energy involved in protein binding we show that salt bridges consistently increase the flexibility of the DNA backbone. Received: 1 September 2000 / Accepted: 5 January 2001 / Published online: 3 May 2001     

The NaDyBr4 complex; its molecular structure and thermodynamic properties

The molecular geometry, vibrational frequencies, relative stabilities, and some thermodynamic properties of different isomers of the NaDyBr₄ complex were determined by computation. We investigated, to our knowledge for the first time for such a complex, the possible effect of the partially filled 4f orbitals on the molecular properties of an MLnX₄ complex by using a “small core” effective core potential of the Stuttgart group. The tridentate complex, with three Na–Br bridges, was found to be the ground-state structure with the bidentate one only about 4–6 kJ/mol higher in energy. The relative abundance of these isomers changes with temperature and at the high-temperature conditions of a metal halide lamp the bidentate isomer is the more abundant isomer.     

The effect of PVP-<Emphasis Type="Italic">b</Emphasis>-PMAA block copolymer on morphologies control of calcium carbonate

A novel double-hydrophilic block copolymer (DHBC) poly(vinyl pyrrolidone)–block–poly(methacrylic acid) (PVP-b-PMAA) was synthesized via reversible addition–fragmentation chain transfer polymerization. The structure of the resulting copolymer was characterized by ¹H nuclear magnetic resonance, and the molecular weight of the block copolymer was determined by gel permeation chromatography. The study of morphological control of calcium carbonate (CaCO₃) has been performed in the presence of the PVP-b-PMAA block copolymer. Various morphologies of CaCO₃ particles such as rhombohedral, multilayered, and aggregated with cavities can be produced by varying the copolymer concentrations. The all-obtained CaCO₃ particles were calcite, which was confirmed by either X-ray diffraction or Fourier transform infrared spectra. Such calcium carbonate/polymer hybrids with complex morphologies may find valuable applications in biomimic mineralization.     

Separation of the vibrational,rotational, and translational motions of polyatomic molecules using curvilinear vibrational coordinates

A new method is suggested for separating the vibrational, rotational, and translational motions of polyatomic molecules using curvilinear vibrational coordinates that are linear with respect to the natural vibrational coordinates. It is shown that, in this case, Coriolis interactions between the vibrational and rotational motions are absent. The solutions of the anharmonic vibrational-rotational problems in the curvilinear and linear vibrational coordinates are compared. The absence of Coriolis interactions between the vibrational and rotational motions in the curvilinear vibrational coordinates is proved numerically. The same conclusion is additionally supported by calculations of the anharmonic vibrational energy levels for the H₂O, H₂S, NO₂, SO₂, and ClO₂ molecules in the linear and curvilinear vibrational coordinates using the Hamiltonian designed in the curvilinear vibrational coordinates with and without Coriolis vibrational-rotational interactions. Volgograd Pedagogical University. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 2, pp. 239–254, March–April, 1995. Translated by I. Izvekova     

Calculation of the vibronic spectra of adenine

The vibrational structure of the absorption spectra of the first two π-π* singlet transitions of adenine is calculated in the Franck-Condon approximation including Herzberg-Teller interactions. The effect of excitation-induced changes in molecular angles on the intensities of the vibrational components is estimated. Structural models of the adenine molecule in the excited states are constructed. The theoretical and absorption spectra of the first π-π* transition are compared. The results of the electronic structure calculations of adenine by different CNDO/S methods are discussed. Translated fromZhumal Struktumoi Khimii, Vol. 38, No. 2, pp. 334–344, March–April, 1997.     

Investigation of selective molecular interactions using two-dimensional Fourier transform IR spectroscopy

A novel method of studying molecular interactions is introduced. It is a method based on the framework of a two-dimensional (2D) infrared (IR) correlation spectroscopy technique with a new data pretreatment strategy. In this method, an additional external perturbation stimulates the system to cause some selective changes in the state, order, and surroundings of system constituents. The overall response of the stimulated system to the applied external perturbation leads to distinctive changes in the measured spectrum, and a series of perturbation-induced dynamic spectra are collected in a systematic manner. Such a set of dynamic spectra are then transformed into a set of 2D correlation spectra by cross-correlation analysis. Temperature was chosen as an external perturbation, and the molecular interaction between 4-aminopyridine (Apy) and methacrylic acid (MAA) was investigated by 2D IR correlation spectroscopy. Synchronous cross peaks exist between the stretching vibration of the C–O group of MAA at 1,298 and 1,202 cm⁻¹ and the C=N group of Apy at 1,531 cm⁻¹, and between the carbonyl group of MAA at 1,705 cm⁻¹ and the amino group of Apy at 3,382 and 3,212 cm⁻¹. The synchronous cross peaks are from orientation of MAA and Apy vibrations generated at the same time; the synchronization of microstructure movements in the molecules indicates that there exists strong interactions between MAA and Apy. According to 2D correlation rules, static electricity and hydrogen-bonding interactions exist between Apy and MAA. Such results were further verified by ¹H-NMR spectroscopy. The successful application demonstrates that 2D IR correlation spectroscopy may be a convenient and effective method in the study of molecular interactions.     

Mapping a Noncovalent Protein–Peptide Interface by Top-Down FTICR Mass Spectrometry Using Electron Capture Dissociation

Noncovalent protein–ligand and protein–protein complexes are readily detected using electrospray ionization mass spectrometry (ESI MS). Furthermore, recent reports have demonstrated that careful use of electron capture dissociation (ECD) fragmentation allows covalent backbone bonds of protein complexes to be dissociated without disruption of noncovalent protein–ligand interactions. In this way the site of protein–ligand interfaces can be identified. To date, protein–ligand complexes, which have proven tractable to this technique, have been mediated by ionic electrostatic interactions, i.e., ion pair interactions or salt bridging. Here we extend this methodology by applying ECD to study a protein–peptide complex that contains no electrostatics interactions. We analyzed the complex between the 21 kDa p53-inhibitor protein anterior gradient-2 and its hexapeptide binding ligand (PTTIYY). ECD fragmentation of the 1:1 complex occurs with retention of protein–peptide binding and analysis of the resulting fragments allows the binding interface to be localized to a C-terminal region between residues 109 and 175. These finding are supported by a solution-phase competition assay, which implicates the region between residues 108 and 122 within AGR2 as the PTTIYY binding interface. Our study expands previous findings by demonstrating that top-down ECD mass spectrometry can be used to determine directly the sites of peptide–protein interfaces. This highlights the growing potential of using ECD and related top-down fragmentation techniques for interrogation of protein–protein interfaces.     

Parametric method for computing the structure of the excited states and the vibronic spectra of complex molecules. Absorption and fluorescence spectra of perylene

The structures of the perylene molecule in the first excited 1¹ 0B_2u state and the band shape (vibrational structure) of its fluorescence and absorption spectra are computed by the parametric method. A fragmentary approach and the molecular fragments H/1C= with the parameters obtained for acenes and polyenes are used to form molecular models in the excited state. It is shown that a model that corresponds to the choice of fragments with the parameters of acenes is the most optimal. The theoretical spectra satisfactorily reproduce both qualitatively and quantitatively, the basic specific features of the vibrational structure of the experimental spectra. Calculation results show high degree of transfer of the parameters of the method in a series of related molecules not only for acenes with “linear” arrangement of the rings (benzene, naphthalene, anthracene, etc.) but also for more complex structures (perylene). It is shown that the parametric method developed is efficient for predicting the vibronic spectra and the structure of the excited states of complex molecules. Translated fromZhurnal Struktumoi Khimii, Vol.40, No. 2, pp. 242–250, March–April, 1999.     

Interpolymer complexes of copolymers of vinyl ether of diethylene glycol with poly(acrylic acid)

 The complex formation reactions of poly(vinyl ether of diethylene glycol) as well as vinyl ether of diethylene glycol–vinyl butyl ether copolymers with poly(acrylic acid) have been studied in aqueous and alcohol solutions. The formation of interpolymer complexes which were stabilized by hydrogen bonds was shown. The effects of molecular weight of poly(acrylic acid) and the nature of the nonionic polymer on the composition and stability of interpolymer complexes were clarified. The critical pH values of complexation were determined for different systems with various molecular weights and hydrophobic–hydrophilic balances. The stability of the interpolymer complexes formed in aqueous and alcohol solutions with respect to dimethylformamide addition was evaluated. The role of hydrophobic interactions and the presence of active groups on stability of the interpolymer complexes is discussed. Received: 23 July 2001 Accepted: 27 September 2001     

Density functional theory and topological analysis on the hydrogen bonds in cysteine–propanoic acid complexes

The complexes formed via hydrogen bonding interactions between cysteine and propanoic acid have been studied at the density three-parameter hybrid functional DFT-B3LYP/6-311++G(d,p) level regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis was employed to elucidate the interaction characteristics in cysteine–propanoic acid (Cys–Prop) complexes. More than 10 kinds of hydrogen bonds (H-bonds) including intra- and inter-molecular H-bonds have been found in Cys–Prop complexes. The results show that both the strength of H-bonds and the deformation are important factors for the stability of Cys–Prop complexes. The strongest H-bonds (O2H^A···O1^B and O2H^A···O1^B) exist in the most stable Cys–Prop complex. The stronger H-bonds formed between hydroxyl and O (or N) atom usually stronger than those involve C (or S) atom. Relationships between the electron density (ρ) of BCP and H-bond length as well as the Fock matrix element (F _ij) has also been investigated and used to study the nature of H-bonds. Moreover, the results show that the change of the bond length linearly correlates with the corresponding frequency shift.     

Carbohydrate–protein interactions and their biosensing applications

Carbohydrate recognition is clearly present throughout nature, playing a major role in the initial attachment of one biological entity to another. The important question is whether these prevalent interactions could provide a real suitable alternative to the use of antibodies or nucleic acid for detection and identification. Currently, examples of carbohydrates being employed in biological detection systems are limited. The challenges of using carbohydrate recognition for detection mainly come from the weak affinity of carbohydrate–protein interactions, the lack of versatile carbohydrate scaffolds with well-defined structures, and the less developed high-information-content, real-time, and label-free assay technology. In this review, we focus on discussing the characteristics of carbohydrate–protein interactions in nature and the methods for carbohydrate immobilization based on surface coupling chemistry in terms of their general applicability for developing carbohydrate- and lectin-based label-free sensors. Furthermore, examples of innovative design of multivalent carbohydrate–protein interactions for sensor applications are given. We limit our review to show the feasibility of carbohydrate and lectin as recognition elements for label-free sensor development in several representative cases to formulate a flexible platform for their use as recognition elements for real-world biosensor applications.     

Band shape in vibrational spectra and interactions of polar molecules in liquids

The structure and shape of bands in the Raman vibrational spectra of polar molecules in liquids are analyzed. The possibility of using these data to examine interactions of molecules as well as their vibrational and orientational dynamics is shown. Translated from Zhumal Struktumoi Khimii, Vol. 38, No. 2, pp. 270–281, March–April, 1997.     

Laser-induced fluorescence determination of thallium in sediments

A simple dissolution procedure is decribed for sediments to be analyzed for thallium by Laser-Excited Atomic Fluorescence Spectrometry (LEAFS). It simply uses a nitric – hydrofluoric acid mixture at room temperature (a “cold dissolution” procedure as opposed to the hot acid digestion) followed by a dilution with water (as opposed to the tedious steps of separation and preconcentration). Excellent accuracy (91–106% recoveries) and precision (4–10% relative standard deviation) were demonstrated by the use of five sediment reference materials of diverse origins. The detection limit was estimated to be 0.5 ng/g of thallium. Additionally, a hot plate digestion procedure, using an in-house designed semi-enclosed Teflon beaker, was also investigated; its analytical results agreed with certified values and confirmed the adequacy of the cold dissolution technique. The method is being applied to study the sediment – water interactions in lake environments. Received: 30 December 1996 / Revised: 20 March 1997 / Accepted: 30 March 1997     

Studies of chemical fixation effects in human cell lines using Raman microspectroscopy

The in vitro study of cellular species using Raman spectroscopy has proven a powerful non-invasive modality for the analysis of cell constituents and processes. This work uses micro-Raman spectroscopy to study the chemical fixation mechanism in three human cell lines (normal skin, normal bronchial epithelium, and lung adenocarcinoma) employing fixatives that preferentially preserve proteins (formalin), and nucleic acids (Carnoy’s fixative and methanol–acetic acid). Spectral differences between the mean live cell spectra and fixed cell spectra together with principal components analysis (PCA), and clustering techniques were used to analyse and interpret the spectral changes. The results indicate that fixation in formalin produces spectral content that is closest to that in the live cell and by extension, best preserves the cellular integrity. Nucleic acid degradation, protein denaturation, and lipid leaching were observed with all fixatives and for all cell lines, but to varying degrees. The results presented here suggest that the mechanism of fixation for short fixation times is complex and dependent on both the cell line and fixative employed. Moreover, important spectral changes occur with all fixatives that have consequences for the interpretation of biochemical processes within fixed cells. The study further demonstrates the potential of vibrational spectroscopy in the characterization of complex biochemical processes in cells at a molecular level.     

Acid-base interactions in the methanesulfonic acid-propylene carbonate system

The methanesulfonic acid (MSA)—propylene carbonate (PC) system with component concentrations of 0–100% was studied at 30°C using the Multiple Attenuated Total Reflection (MATR) IR spectroscopy. The formation of a strong 1∶1 molecular complex of MSA with PC was established. In the presence of an excess of the acid, a second MSA molecule adds to this complex to give the molecular complex (2MSA)·PC. When excess propylene carbonate is used, the MSA·PC complex is solvated by a propylene carbonate molecule. No protonation of the base or formation of complexes with a strong symmetrical H bond was observed. Continuous absorption was not detected in IR spectra of the solutions. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 313–318 February, 1999.     

Parametric method in the theory of vibronic spectra of complex molecules. Excited state structure and fluorescence spectrum of stilbene

The parameters of the adiabatic model of the stilbene molecule in the excited state and the vibrational structure of the fluorescence spectrum are calculated by the parametric method of the theory of vibronic spectra of complex molecules. The first and second orders of theory are used. The molecular models are constructed by the fragment method. Satisfactory agreement with experiment is obtained. The parameters of molecular fragments are shown to be highly transferable. The model and the spectrum max be refined in the second order of theory using only one additional parameter for CCC angles (optimal values were obtained). The parametric method under discussion makes it possible to predict variations of structural parameters due to excitation and to calculate the vibrational structure of the electronic spectra of complex molecules, including characteristic variations of the spectra in series of related molecules (stilbene-di-phenylpolyenes). This method surpasses all previous procedures (in particular, the correlation method) in completeness and accuracy of results. Translated fromZhurnal Strukturnoi Khinii, Vol. 41, No. 2, pp. 369–378, March–April, 2000.