Basis set superposition error-counterpoise corrected potential energy surfaces : application to hydrogen peroxide ... X (X=F-, Cl-, Br-, Li+, Na+) complexes

Møller-Plesset (MP2) and Becke-3-Lee-Yang-Parr (B3LYP) calculations have been used to compare the geometrical parameters, hydrogen-bonding properties, vibrational frequencies and relative energies for several X- and X+ hydrogen peroxide complexes. The geometries and interaction energies were corrected for the basis set superposition error (BSSE) in all the complexes (1-5), using the full counterpoise method, yielding small BSSE values for the 6-311 + G(3df,2p) basis set used. The interaction energies calculated ranged from medium to strong hydrogen-bonding systems (1-3) and strong electrostatic interactions (4 and 5). The molecular interactions have been characterized using the atoms in molecules theory (AIM), and by the analysis of the vibrational frequencies. The minima on the BSSE-counterpoise corrected potential-energy surface (PES) have been determined as described by S. Simón, M. Duran, and J. J. Dannenberg, and the results were compared with the uncorrected PES

How does basis set superposition error change the potential surfaces for hydrogen-bonded dimers?

We describe a simple method to automate the geometric optimization of molecular orbital calculations of supermolecules on potential surfaces that are corrected for basis set superposition error using the counterpoise (CP) method. This method is applied to the H-bonding complexes HF/HCN, HF/H2O, and HCCH/H2O using the 6-31G(d,p) and D95 + + (d,p) basis sets at both the Hartree-Fock and second-order Møller-Plesset levels. We report the interaction energies, geometries, and vibrational frequencies of these complexes on the CP-optimized surfaces; and compare them with similar values calculated using traditional methods, including the (more traditional) single point CP correction. Upon optimization on the CP-corrected surface, the interaction energies become more negative (before vibrational corrections) and the H-bonding stretching vibrations decrease in all cases. The extent of the effects vary from extremely small to quite large depending on the complex and the calculational method. The relative magnitudes of the vibrational corrections cannot be predicted from the H-bond stretching frequencies alone

Destabilizing Mutations Alter the Hydrogen Exchange Mechanism in Ribonuclease A

The effect of strongly destabilizing mutations, I106A and V108G of Ribonuclease A (RNase A), on its structure and stability has been determined by NMR. The solution structures of these variants are essentially equivalent to RNase A. The exchange rates of the most protected amide protons in RNase A (35ºC), the I106A variant (35ºC), and the V108G variant (10ºC) yield stability values of 9.9, 6.0, and 6.8 kcal/mol, respectively, when analyzed assuming an EX2 exchange mechanism. Thus, the destabilization induced by these mutations is propagated throughout the protein. Simulation of RNase A hydrogen exchange indicates that the most protected protons in RNase A and the V108G variant exchange via the EX2 regime, whereas those of I106A exchange through a mixed EX1 1 EX2 process. It is striking that a single point mutation can alter the overall exchange mechanism. Thus, destabilizing mutations joins high temperatures, high pH and the presence of denaturating agents as a factor that induces EX1 exchange in proteins. The calculations also indicate a shift from the EX2 to the EX1 mechanism for less protected groups within the same protein. This should be borne in mind when interpreting exchange data as a measure of local stability in less protected regions

Predicting origins of passerines migrating through Canadian migration monitoring stations using stable-hydrogen isotope analyses of feathers: a new tool for bird conservation

The Canadian Migration Monitoring Network (CMMN) consists of standardized observation and migration count stations located largely along Canada’s southern border. A major purpose of CMMN is to detect population trends of migratory passerines that breed primarily in the boreal forest and are otherwise poorly monitored by the North American Breeding Bird Survey (BBS). A primary limitation of this approach to monitoring is that it is currently not clear which geographic regions of the boreal forest are represented by the trends generated for each bird species at each station or group of stations. Such information on “catchment areas” for CMMN will greatly enhance their value in contributing to understanding causes of population trends, as well as facilitating joint trend analysis for stations with similar catchments. It is now well established that naturally occurring concentrations of deuterium in feathers grown in North America can provide information on their approximate geographic origins, especially latitude. We used stable hydrogen isotope analyses of feathers (δ²Hf) from 15 species intercepted at 22 CMMN stations to assign approximate origins to populations moving through stations or groups of stations. We further constrained the potential catchment areas using prior information on potential longitudinal origins based upon bird migration trajectories predicted from band recovery data and known breeding distributions. We detected several cases of differences in catchment area of species passing through sites, and between seasons within species. We discuss the importance of our findings, and future directions for using this approach to assist conservation of migratory birds at continental scales.

First CRDS-measurements of water vapour continuum in the 940nm absorption band

Measurements of near-infrared water vapour continuum using continuous wave cavity ring down spectroscopy (cw- CRDS) have been performed at around 10611.6 and 10685:2 cm1. The continuum absorption coefficients for N2- broadening have been determined for two temperatures and wavenumbers. These results represent the first near-IR continuum laboratory data determined within the complex spectral environment in the 940nm water vapour band and are in reasonable agreement with simulations using the semiempirical CKD formulation.

Evaluation of suitable spectral intervals for near-IR laboratory detection of water vapour continuum absorption

The water vapour continuum absorption is an important component of molecular absorption of radiation in atmosphere. However, uncertainty in knowledge of the value of the continuum absorption at present can achieve 100% in different spectral regions leading to an error in flux calculation up to 3-5 W/m2 global mean. This work uses line-by-line calculations to reveal the best spectral intervals for experimental verification of the CKD water vapour continuum models in the currently least studied near-infrared spectral region. Possible sources of errors in continuum retrieval taken into account in the simulation include the sensitivity of laboratory spectrometers and uncertainties in the spectral line parameters in HITRAN-2004 and Schwenke-Partridge database. It is shown that a number of micro-windows in near-IR can be used at present for laboratory detection of the water vapour continuum with estimated accuracy from 30 to 5%.

Pure water vapor continuum measurements between 3100 and 4400 cm1: Evidence for water dimer absorption in near atmospheric conditions

Despite the potentially important role that water dimers may play in the Earth’s energy balance, there is still a lack of firm evidence for absorption of radiation by dimers in near-atmospheric conditions. We present results of the first high-resolution laboratory measurements of the water vapor continuum absorption within the 3100–4400 cm1 spectral region at a range of near-room temperatures. The analysis indicates a large contribution of dimer absorption to the water vapor continuum, significantly in excess of that predicted by other modern representations of the continuum. The temperature dependence agrees well with that expected for dimers.

Hydrogen-bonded interpolymer complexes. Formation, structure and applications

Noncovalent interactions play key roles in many natural processes leading to the self-assembly of molecules with the formation of supramolecular structures. One of the most important forces responsible for self-assembly is hydrogen bonding, which also plays an important role in the self-assembly of synthetic polymers in aqueous solutions. Proton-accepting polymers can associate with proton-donating polymers via hydrogen bonding in aqueous solutions and form polymer-polymer or interpolymer complexes. There has been an increased interest among researchers in hydrogen-bonded interpolymer complexes since the first pioneering papers were published in the early 1960s. Several hundred research papers have been published on various aspects of complex formation reactions in solutions and interfaces, properties of interpolymer complexes and their potential applications. This book focuses on the latest developments in the area of interpolymer complexation via hydrogen bonding. It represents a collection of original and review articles written by recognized experts from Germany, Greece, Kazakhstan, Poland, Romania, Russia, UK, Ukraine, and the USA. It highlights many important applications of interpolymer complexes, including the stabilization of colloidal systems, pharmaceuticals, and nanomaterials.

Laser granulometry of Holocene estuarine silts: effects of hydrogen peroxide treatment

The Holocene estuarine silts of the Severn Estuary Levels (southwest Britain) are representative of their kind in northwest Europe. They contain two broad types of plant material: particles codeposited with mineral grains from the estuarine water body, and extraneous debris (stems of indigenous prior plants; post depositional root matter) which is difficult to remove completely by physical means. Treatment with hydrogen peroxide before laser granulometry removes all plant material regardless of kind, drastically reduces values for the mean grain size and median size relative to untreated samples, but has little effect on the mode, except for a restricted group of bimodal-platykurtic, medium-coarse silts. It is concluded that, in the case of sediments of the general kind examined, no advantages acrue from the treatment of samples with hydrogen peroxide prior to analysis. Although a discrete rather than continuous variable, values of the mode obtained from untreated sediments are suggested to be acceptable for most purposes where a measure of central tendency is required.

Solvent Effects on the Formation of Nanoparticles and Multilayered Coatings Based on Hydrogen-Bonded Interpolymer Complexes of Poly(acrylic acid) with Homo- and Copolymers of N-Vinyl Pyrrolidone

The formation of hydrogen-bonded interpolymer complexes between poly(acrylic acid) and poly(N-vinyl pyrrolidone) as well as amphiphilic copolymers of N-vinyl pyrrolidone with vinyl propyl ether has been studied in aqueous and organic solutions. It was demonstrated that introduction of vinyl propyl ether units into the macromolecules of the nonionic polymer enhances their ability to form complexes in aqueous solutions due to more significant contribution of hydrophobic effects. The complexation was found to be a multistage process that involves the formation of primary polycomplex particles, which further aggregate to form spherical nanoparticles. Depending on the environmental factors (pH, solvent nature), these nanoparticles may either form stable colloidal solutions or undergo further aggregation, resulting in precipitation of interpolymer complexes. In organic solvents, the intensity of complex formation increases in the following order: methanol < ethanol < isopropanol < dioxane. The multilayered coatings were developed using layer-by-layer deposition of interpolymer complexes on glass surfaces. It was demonstrated that the solvent nature affects the efficiency of coating deposition.