The atomic force microscope: Can it be used to study biological molecules?

The conditions necessary for studying biological molecules with the atomic force microscope are discussed. It is shown that in order to avoid large substrate deformations the microscope should be operated in its attractive mode where the van der Waals force between the tip and the substrate is ≈ 10⁻¹¹ N and where the tip-substrate separation is of the order of 4–5 Å.     

Teaching Chemistry with Electron Density Models. 2. Can Atomic Charges Adequately Explain Electrostatic Potential Maps?

Electrostatic potential maps generated from quantum mechanical calculations are widely used to teach students about molecular polarity and assign atomic charges (Shusterman, G. P.; Shusterman, A. J. J. Chem. Educ. 1997, 74, 771–776; Hehre, W. J.; Shusterman, A. J.; Nelson, J. E. The Molecular Modeling Workbook for Organic Chemistry: Wavefunction: Irvine, CA, 1998). The assumption that potential equals charge is only valid, however, when comparing atoms of similar size. The proper use of potential maps requires consideration of atomic charge, atomic radius, and the electron configuration (orbital occupancy) of the atom in question. These points are illustrated through the analysis of the potential maps of various halogen-containing molecules.The first article in this series is Shusterman, G. P.; Shusterman, A. J. J. Chem. Educ. 1997, 74, 771.776.     

Can atom-surface potential measurements test atomic structure models?

van der Waals (vdW) atom-surface potentials can be excellent benchmarks for atomic structure calculations. This is especially true if measurements are made with two different types of atoms interacting with the same surface sample. Here we show theoretically how ratios of vdW potential strengths (e.g., C?(K)/C?(Na)) depend sensitively on the properties of each atom, yet these ratios are relatively insensitive to properties of the surface. We discuss how C? ratios depend on atomic core electrons by using a two-oscillator model to represent the contribution from atomic valence electrons and core electrons separately. We explain why certain pairs of atoms are preferable to study for future experimental tests of atomic structure calculations. A well chosen pair of atoms (e.g., K and Na) will have a C? ratio that is insensitive to the permittivity of the surface, whereas a poorly chosen pair (e.g., K and He) will have a ratio of C? values that depends more strongly on the permittivity of the surface.     

Are metal alkoxides linear owing to electrostatic repulsion?

Density functional theory calculations on [LnCp2APh] (Ln = La, Lu; Cp = eta 5-C5H5; A = O, S; Ph = C6H5) suggest that the linearity of the Ln-O-C vectors arises largely as a result of electrostatic repulsion between the alpha carbon and the trivalent metal centre.     

Can purely repulsive soft potentials predict micelle formation correctly?

We determine the free energy of micelle formation for surfactants in a solvent by employing a hybrid semi-grand Monte Carlo simulation scheme in combination with umbrella sampling and configurational bias techniques. We compare results of two surfactant models: one based on Lennard-Jones interactions and one based on the soft repulsive potential that is often used in dissipative particle dynamics (DPD). The free energies of micellization in both models show similar behavior. However, although the critical micelle concentration for the Lennard-Jones systems lies within the experimental range, it is 13 orders of magnitude lower for the soft repulsive model. We discuss the implication for the applicability of soft repulsive potentials for the study of micelle formation.     

Reduction potentials of reagents: II - a tool to anticipate yields of organometallic reactions?

Reduction potentials of four cage-structure halogenated derivatives and five alicyclic and aromatic ketones have been determined by cyclic voltammetry. For the Barbier reaction these parameters are used to anticipate the behaviour of intermediates formed at the metal surface and on which the distribution product depends. Semiquantitative relationships are obtained between these potentials and yields of condensation products.     

Carbons?urederivate. II

Zusammenfassung Durch Vergleich der IR-Spektren von Benzamidiumsalzen, quartärem Benzimidoesterperchlorat und Perchloraten des Benzamids sowie seiner Derivate wird nachgewiesen, daß die Protonierung der Carbonsäureamide am Sauerstoff erfolgt. Dasselbe gilt für die Anlagerung von Borfluorid. — Das protonmagnetische Resonanzspektrum des Maleinsäurehydrazids weist darauf hin, daß die Verbindung die Struktur eines 3,6-Dioxo-1,2,3,6-tetrahydro-pyridazins besitzt.Herrn Prof. Dr. Th. Förster und Herrn Dr. W. Brügel sowie der Direktion der Badischen Anilin- & Soda-Fabrik sind wir zu großem Dank verpflichtet, daß sie uns die Aufnahme der protonmagnetischen Resonanzspektren ermöglicht haben. Herrn Prof. Dr. H. Bredereck danken wir für die Förderung dieser Arbeit.I. Mitteilung: Gompper, R., u. O. Christmann: Chem. Ber. 92, 1935 (1959).Aus der Diplomarbeit P. Altreuther, Technische Hochschule Stuttgart, 1958.     

Can Nonpolar Polyisobutylenes be Measured by Electrospray Ionization Mass Spectrometry? Anion-Attachment Proved to be an Appropriate Method

Polyisobutylenes (PIBs) with different end-groups including chlorine, exo-olefin, hydroxyl, and methyl prepared from aliphatic and aromatic initiators were studied by electrospray ionization mass spectrometry (ESI-MS). Independently of the end-groups, presence or absence of aromatic initiator moiety, these PIB derivatives were capable of forming adduct ions with NO₃ ^– and Cl^– ions, thus allowing the direct characterization of these compounds in the negative ion mode of ESI-MS. To obtain [PIB + NO₃]^– and [PIB + Cl]^– adduct ions with appreciable intensities, addition of polar solvents such as acetone, 2-propanol, or ethanol to the dichloromethane solution of PIBs was necessary. Furthermore, increasing both the polarity (by increasing the acetone content) and the ion-source temperature give rise to enhanced intensities for both [PIB + NO₃]^– and [PIB + Cl]^– ions. Energy-dependent collision induced dissociation studies (CID) revealed that increasing the collision voltages resulted in the shift of the apparent molecular masses to higher ones. CID studies also showed that dissociation of the [PIB + Cl]^– ions requires higher collision energy than that of [PIB + NO₃]^–. In addition, Density Functional Theory calculations were performed to gain insights into the nature of the interactions between the highly non-polar PIB chains and anions NO₃ ^– and Cl^– as well as to determine the zero-point corrected electronic energies for the formation of [PIB + NO₃]^– and [PIB + Cl]^– adduct ions.

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Can ortho-para transitions for water be observed?

The spectrum of water can be considered as the juxtaposition of the spectra of two molecules, with different total nuclear spin: ortho-H2O, and para-H2O. No transitions have ever been observed between the two different nuclear-spin isotopomers. The interconversion time is unknown and it is widely assumed that interconversion is forbidden without some other intervention. However, weak nuclear spin-rotation interaction occurs and can drive ortho to para transitions. Ab initio calculations show that the hyperfine nuclear spin-rotational coupling constants are about 30 kHz. These constants are used to explore the whole vibration-rotation spectrum with special emphasis on the coupling between nearby levels. Predictions are made for different spectral regions where the strongest transitions between ortho and para levels of water could be experimentally observed.     

Molecular electronegativity in density functional theory (II) --Direct calculation of group electronegativity and the atomic charges in a group

On the basis of a more precise expression of the atomic effective electronegativity deduced from the density functional theory and electronegativity equalization principle, a new scheme for calculating the group electronegativity and the atomic charges in a group is proposed and programed, and various parameters of electronegativity and hardness are given for some common atoms. Through calculation, analysis and comparison of more than one hundred groups, it is shown that the results from this scheme are reasonable and may be extended.     

Heated goethite and natural hematite: Can Raman spectroscopy be used to differentiate them?

Minerals have been used as pigments for thousands of years. Red and yellow pigments are generally associated with iron oxides or, specifically, hematite (α-Fe₂O₃) and goethite (α-FeOOH). It is well known that, under heating, goethite dehydrates forming hematite. An interesting question yet to be answered is whether the pre-historical artists used this knowledge to obtain other shades of red and yellow or used the raw mineral directly.Raman spectroscopy was employed to address this question and XRD, TEM and TG were used as supporting techniques. Ex situ and in situ Raman spectra were obtained and it was observed that in the 250–300 °C temperature range, broad hematite features appears as a consequence of goethite dehydration. In the spectra of the heated sample a band at 657 cm⁻¹ is of particular interest, as it is much more intense than in natural hematite; the possibility that it could be assigned as a magnetite band was discarded. At higher temperatures (900–1000 °C) the disordered structure is perfected and a Raman spectrum similar to a crystalline natural hematite sample is obtained.Temperatures in the 600–700 °C range can be easily reached, thus disordered hematite could be obtained from goethite heating even in ancient times, however, heat is not the only agent able to produce disordered hematite, since grinding, biodegradation and weathering can produce the same effect. Raman spectra obtained from weathered samples are also representative of disordered hematite.The data here reported indicate that it is not possible to differentiate heated goethite from other disordered hematites.     

To be,or not to be…Electrochemist?

Journal of Solid State Electrochemistry -     

Can enantiomers be separated in achiral chromatographic systems?

Consideration of chromatography of a nonracemic mixture on an achiral sorbent from a stereochemical point of view allows the claim that partial separation of the excess enantiomer zone from the racemate zone is possible only with analytes capable of self-associating under the conditions of the chromatographic column. It is from these positions that features of this process can be explained and conditions for its maximal proceeding formulated.     

Can ring strain be realized in momentum space?

An increased electron momentum density (EMD) at low momentum is proposed to be an indicator of ring strain, with the nature of the function tending toward a maximum. A p-space Hirshfeld atomic partitioning scheme is applied for analyzing the effect of strain on molecular EMDs. The Hirshfeld momentum densities for a strained system show an increase in the population for the carbons with the hydrogens becoming more positive in comparison with an unstrained reference molecule. The manifestation of strain in cage-like hydrocarbons such as tetrahedrane, cubane, prismane, etc. as well as their nitrogen-substituted analogues is clearly seen in terms of EMDs.     

Can nanofiltration be fully predicted by a model?

There is an increasing need for model-based tools to design membrane processes for new industrial applications or to optimise existing membrane installations. The advantage of such tools is that costs can be saved by reducing the number of expermiments. In this study, the requirements for a membrane filtration model, suitable for practical use, are summarised. It is investigated to what extent it is possible to set-up such a model with the current available literature and knowledge. A membrane filtration model has been set-up based on the Maxwell–Stefan transport equations. A Freundlich equation is used to describe the membrane charge by means of adsorption of ions. With the model the permeate flux and rejections of multi-component liquid feeds can be calculated as a function of membrane properties (mean pore size, porosity, thickness, surface charge characteristic) and feed pressure. With two NF-membranes (Desal 5DK and a prototype capillary type 2 membrane) rejection experiments have been carried out with glucose, single salt solutions (NaCl, CaCl₂, Na₂SO₄) and ternary ion mixtures of these salts. With the model the experimental flux-rejection curves can be fitted reasonably well. However, each salt mixture needs its own set of fitted parameters for the membrane charge isotherms. Furthermore, the fitted membrane charges are in contradiction with values from the literature obtained by electrokinetic measurements. Obviously, the membrane charge parameters have lost their physical meaning and are used to compensate for physical phenomena not included in the model. Extending the model with an electrostatic free energy term will be a step forward in development. Further research is needed to fulfil all requirements for the wide scope of industrial applications.     

Can glycoprofiling be helpful in detecting prostate cancer?

Glycans are chains of carbohydrates attached to proteins (glycoproteins and proteoglycans) or lipids (glycolipids). Glycosylation is a post-translational modification and glycans have a wide range of functions in the human body including involvement in oncological diseases. Change in a glycan structure can not only indicate the presence of a pathological process but, more importantly, in some cases also its stage. Thus, a glycan analysis has the potential to be an effective and reliable tool in cancer diagnostics. Lectins are proteins responsible for natural biorecognition of glycans; even carbohydrate moieties still attached to proteins or whole cells can be recognised by lectins, which makes them an ideal candidate for designing label-free biosensors for glycan analysis. This review seeks to summarise evidence that the glycoprofiling of biomarkers by lectin-based biosensors can be of significant help in detecting prostate cancer.     

Can gas chromatography combustion isotope ratio mass spectrometry be used to quantify organic compound abundance?

Quantifying the concentrations of organics such as phospholipid fatty acids (PLFAs) and n‐alkanes and measuring their corresponding ¹³ C/¹² C isotope ratios often involves two separate analyses; (1) quantification by gas chromatography flame ionisation detection (GC‐FID) or gas chromatography/mass spectrometry (GC/MS), and (2) ¹³ C‐isotope abundance analysis by gas chromatography/combustion/isotope ratio mass spectrometry (GC‐C‐IRMS). This requirement for two separate analyses has obvious disadvantages in terms of cost and time. However, there is a history of using the data output of isotope ratio mass spectrometers to quantify various components; including the N and C concentrations of solid materials and CO₂ concentrations in gaseous samples. Here we explore the possibility of quantifying n‐alkanes extracted from sheeps' faeces and fatty acid methyl esters (FAMEs) derivatised from PLFAs extracted from grassland soil, using GC‐C‐IRMS. The results were compared with those from GC‐FID analysis of the same extracts. For GC‐C‐IRMS the combined area of the masses for all the ions (m/z 44, 45 and 46) was collected, referred to as 'area all', while for the GC‐FID analysis the peak area data were collected. Following normalisation to a common value for added internal standards, the GC‐C‐IRMS 'area all' values and the GC‐FID peak area data were directly compared. Strong linear relationships were found for both n‐alkanes and FAMEs. For the n‐alkanes the relationships were 1:1 while, for the FAMEs, GC‐C‐IRMS overestimated the areas relative to the GC‐FID results. However, with suitable reference material 1:1 relationships were established. The output of a GC‐C‐IRMS system can form the basis for the quantification of certain organics including FAMEs and n‐alkanes. Copyright © 2011 John Wiley & Sons, Ltd.     

Can the transition from tunneling to hopping in molecular junctions be predicted by theoretical calculation?

The electron transport mechanism changes from tunneling to hopping as molecular length increases. To validate the theoretical simulation after the transition point and clarify influence of electronic structures on the transition, we calculated the conductance of a series of conjugated molecules by density functional theory together with the nonequilibrium Green's function. We found that the highest occupied molecular orbital energy level, transmission spectrum, and the reorganization energy are good indicators for the transition of the electron transport mechanism. The calculated resistances of short junctions (<50 Å, before the transition point) are consistent with the experimental result, following the tunneling mechanism. However, the theoretical predication failed for long molecules, indicating the limitation of the theoretical framework of elastic scattering when the electron transport mechanism changes to hopping. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011