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.     

Comparison study of several numerical integration schemes used in calculations of density functional theory

Several numerical integration schemes for the evaluation of matrix elements in density functional theory calculations have been studied and compared by computational practice. The best scheme was found to be the combination of the atomic partition function proposed by Becke with the scaled generalized Gauss-Laguerre quadrature formula for radial integration suggested by Yang, which achieve the highest convergence rate to the numerical integration. With the same number of integration points, the accuracy of the calculated results by this scheme is higher by 1 to 2 orders of magnitudes than that by other schemes. The reason for achieving higher accuracy by this scheme has been proposed preliminarily.     

Can the usual validation standard series for quantitative methods,ISO 5725, be also applied for qualitative methods?

Repeatability standard deviation, laboratory standard deviation, and reproducibility standard deviation for quantitative methods according to ISO 5725 series were recently proposed to estimate the precision of qualitative measurements, giving a presence/absence response. In this paper, it is shown that for qualitative methods, the reproducibility standard deviation across laboratories does not reflect the performance of the method as suggested. It is demonstrated that the benefit of the respective laboratory standard deviation is very limited. Alternative performance measures are introduced which are based on another approach also directly linked to ISO 5725. Thereby, meaningful information about the precision of qualitative test methods can be achieved.     

Can octupolar molecules be poled by an external electric field?

Octupolar molecules are generally believed to be of potential use in developing nonlinear optical materials owing to the fact that they do not easily form molecular aggregates. This is often put against the conjectured drawback that electric fields have no poling, or ordering, effect for this class of molecules because of the lack of a permanent ground state dipole moment. In this paper, we analyze this notion in some detail and present results from molecular dynamics computer simulations of an ensemble of a prototypical octupolar molecule, the 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) molecule, dissolved in chloroform. It is found that TATB molecules indeed show rather significant dipole moments in solutions because of the dual action of the thermal motions of the atoms and the strong intermolecular interactions. Applied electric fields accordingly show significant effects on the orientations of the molecular dipole moments. We also find that TATB molecules can aggregate because of the strong hydrogen-bonding interactions between the molecules, though they lack a static permanent dipole moment. Thus, the simulation results for TATB molecules in solution present us with a totally different notion about the collective properties of octupolar molecules. Taking account of quantum chemistry results, we found that the collective molecular nonlinear optical (NLO) properties are enhanced after the onset of the electric field, showing significant anisotropic characteristics.     

Can the speed of sound be used for detecting critical states of fluid mixtures?

The phenomenology of sound speeds in fluid mixtures is examined near and across critical lines. Using literature data for binary and ternary mixtures, it is shown that the ultrasound speed along an isotherm-isopleth passes through a minimum value in the form of an angular (or V-shaped) point at critical states. The relation between critical and pseudo-critical coordinates is discussed. For nonazeotropic fixed-composition fluid mixtures, pseudo-critical temperatures and pressures are found to be lower than the corresponding critical temperatures and pressures. The analysis shows that unstable pseudo-critical states cannot be detected using acoustic methods. The thermodynamic link between sound speeds and isochoric heat capacities is formulated and discussed in terms of p-Vm-T derivatives capable of being calculated using cubic equations of state. Based on the Griffiths-Wheeler theory of critical phenomena, a new specific link between critical sound speeds and critical isochoric heat capacities is deduced in terms of the rate of change of critical pressures and critical temperatures along the p-T projection of the critical locus of binary fluid mixtures. It is shown that the latter link can be used to obtain estimates of critical isochoric heat capacities from the experimental determination of critical speeds of sound. The applicability domain of the new link does not include binary systems at compositions along the critical line for which the rate of change in pressure with temperature changes sign. The new equation is combined with thermodynamic data to provide approximate numerical estimates for the speed of sound in two mixtures of carbon dioxide and ethane at different temperatures along their critical isochores. A clear decrease in the sound speed is found at critical points. A similar behavior is suggested by available critical heat capacity data for several binary fluid mixtures. Using an acoustic technique, the critical temperature and pressure were determined for three different mixtures of methane and propane, and compared with literature data obtained using conventional methods. It is concluded that acoustic-based techniques are reliable to determine, for the most part, critical surfaces of fluid mixtures. The remaining few cases where the present analysis cannot be applied could be tested by the thermodynamic calculation of critical sound speeds using crossover equations of state in conjunction with experimentally determined critical isochoric heat capacities.     

How well can density functional methods describe hydrogen bonds to pi acceptors?

We employed four newly developed density functional theory (DFT) methods for the calculation of five pi hydrogen bonding systems, namely, H2O-C6H6, NH3-C6H6, HCl-C6H6, H2O-indole, and H2O-methylindole. We report new coupled cluster calculations for HCl-C6H6 that support the experimental results of Gotch and Zwier. Using the best available theoretical and experimental results for all five systems, our calculations show that the recently proposed MPW1B95, MPWB1K, PW6B95, and PWB6K methods give accurate energetic and geometrical predictions for pi hydrogen bonding interactions, for which B3LYP fails and PW91 is less accurate. We recommend the most recent DFT method, PWB6K, for investigating larger pi hydrogen bonded systems, such as those that occur in molecular recognition, protein folding, and crystal packing.     

Can glandular hair density be a breeding marker for Origanum vulgare subsp. hirtum with high essential oil content?

Origanum vulgare subsp. hirtum (Link) Ietswaart is an essential oil rich plant traditionally used as oregano. Based on the interest of the essential oil producing sector, in 2000 we have started a breeding program of O. vulgare subsp. hirtum. Plant material for our breeding work consists of 6 progeny. Individual evaluation of the plant material was carried out in 2008-2009 with the primary aim of finding mother plants with appropriate morphological features, high essential oil content (> 7%) and with carvacrol as the main essential oil component. Among the survey of morphological characteristics special attention was given to glandular hair density in order to test the usability of it as a morphological marker for screening progeny for high essential oil content. The characteristics of the progeny can be described with high variability ensuring the possibility of a good selection base. Evaluating the morphology, essential oil content and constitution of the individuals, 20 plants were selected on the grounds of their high (7-8.6%) essential oil content, high ratio (70-93%) of carvacrol in the essential oil and typical morphological features of O. vulgare subsp. hirtum. From the results of glandular hair density it can be stated that the correlation between glandular hair density of the upper, middle and lower leaves either on vegetative or generative shoots and essential oil content was never strong enough (correlation coefficient < or = 0.5) to use it exclusively as a morphological marker for individual selection.     

How well can new-generation density functional methods describe stacking interactions in biological systems?

We compare the performance of four recently developed DFT methods (MPW1B95, MPWB1K, PW6B95, and PWB6K) and two previous, generally successful DFT methods (B3LYP and B97-1) for the calculation of stacking interactions in six nucleic acid bases complexes and five amino acid pairs and for the calculation of hydrogen bonding interactions in two Watson-Crick type base pairs. We found that the four newly developed DFT methods give reasonable results for the stacking interactions in the DNA base pairs and amino acid pairs, whereas the previous DFT methods fail to describe interactions in these stacked complexes. We conclude that the new generation of DFT methods have greatly improved performance for stacking interaction as compared to previously available methods. We recommend the PWB6K method for investigating large DNA or protein systems where stacking plays an important role.     

Can TMS and DSS be used as NMR references for cyclodextrin species in aqueous solution?

Tetramethylsilane (TMS) can be included by -cyclodextrin (-CD), and sodium 2,2-dimethylsilapentane-5-sulphonate (DSS) can form inclusion complexes with - and -CD. The NMR chemical shifts are changed considerably as a result of the strong interaction between CD and the guest compound in the inclusion complexes. A downfield shift of as much as 0.63 ppm shift downfield has been observed for the protons of external TMS in CD aqueous solution. In view of this, the question arises of whether TMS and DSS can be used as internal references. DSS in D₂O is suggested as an external reference for aqueous cyclodextrin solution in NMR measurements.     

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.     

Can chiral single walled carbon nanotubes be used as enantiospecific adsorbents?

Single-walled carbon nanotubes can exist in chiral forms and can adsorb a range of molecules. We use atomistic simulations to consider whether enantiopure carbon nanotubes might be effective enantiospecific adsorbents for chiral molecules. We examine the adsorption of both enantiomers of trans-1,2-dimethylcyclopropane and trans-1,2-dimethylcyclohexane in a range of chiral nanotubes. Our simulations indicate that these molecules are strongly adsorbed in nanotubes, that is, they have large heats of adsorption, but the energy differences between adsorbed enantiomers are negligible. We argue that this result is generic for chiral organic molecules adsorbed in carbon nanotubes, suggesting that these materials will not be effective enantiospecific adsorbents.     

Can functionalized cucurbituril bind actinyl cations efficiently? A density functional theory based investigation

The feasibility of using cucurbituril host molecule as a probable actinyl cation binders candidate is investigated through density functional theory based calculations. Various possible binding sites of the cucurbit[5]uril host molecule to uranyl are analyzed and based on the binding energy evaluations, μ(5)-binding is predicted to be favored. For this coordination, the structure, vibrational spectra, and binding energies are evaluated for the binding of three actinyls in hexa-valent and penta-valent oxidation states with functionalized cucurbiturils. Functionalizing cucurbituril with methyl and cyclohexyl groups increases the binding affinities of actinyls, whereas fluorination decreases the binding affinities as compared to the native host molecule. Surprisingly hydroxylation of the host molecule does not distinguish the oxidation state of the three actinyls.     

How to obtain accurate results with molecular iodine and density functional theory?

Molecular iodine is found in many organic synthetic methodologies, both as reagent and as catalyst. Naturally, many groups have carried out computational studies involving this element. However, the choice of computational method proves to be more challenging than for other non-metals. We quantify herein the errors that some common theory levels can introduce in terms of both structural and energetic deviations. We also evaluate multiple post hoc corrections, namely, vibrational entropy, dispersion, and counter-poise corrections. Our results indicate the triple- $$ basis sets are essential to obtain quality results and that post hoc corrections are overall detrimental.     

Should negative electron affinities be used for evaluating the chemical hardness?

Despite recent advances in computing negative electron affinities using density-functional theory, it is an open issue as to whether it is appropriate to use negative electron affinities, instead of zero electron affinity, to compute the chemical hardness of atoms and molecules with metastable anions. We seek to answer this question using the accepted empirical rules linking the chemical hardness to the atomic size and the polarizability; we also propose a new correlation with the C6 London dispersion coefficient. For chemical reactivity in the gas phase, it seems to make no difference whether negative, or zero, electron affinities are used for systems with metastable anions. For reactions in solution the evidence that is presently available is insufficient to establish a preference. In addressing this issue, we noted that electron affinity data from which atomic chemical hardness values are computed are out of date; an update to Pearson's classic 1988 table [Inorg. Chem., 1988, 27, 734-740] is thus provided.     

The entrance complex, transition state, and exit complex for the F + H2O → HF + OH reaction. Definitive predictions. Comparison with popular density functional methods

Following the H + H(2) and F + H(2) reactions, the fluorine atom - water system has the potential to become one of the best understood chemical reactions. Stationary points for the F + H(2)O potential energy surface have been located with the "Gold Standard" CCSD(T) method using the Dunning correlation consistent basis sets through quintuple zeta. The CCSD(T)/cc-pV5Z barrier height is prediced to be 2.5 kcal mol(-1), less than previous estimates of 4-7 kcal mol(-1). From higher level theoretical studies of the prototypical F + H(2) reaction, this barrier should be less than 0.5 kcal mol(-1) above the exact, nonrelativistic classical barrier height. 41 of the 49 DFT methods applied to F + H(2)O predict no barrier at all. The eight DFT methods that do predict a barrier show exothermicities that are somewhat too small. The CCSD(T)/cc-pV5Z entrance complex is bound by 3.4 kcal mol(-1) relative to separated F + H(2)O. The analogous exit complex is bound by 5.9 kcal mol(-1) relative to separated HF + OH.