Purification and characterization of a surfactin-like molecule produced by Bacillus sp. H2O-1 and its antagonistic effect against sulfate reducing bacteria

Abstract Background Bacillus sp. H2O-1, isolated from the connate water of a Brazilian reservoir, produces an antimicrobial substance (denoted as AMS H2O-1) that is active against sulfate reducing bacteria, which are the major bacterial group responsible for biogenic souring and biocorrosion in petroleum reservoirs. Thus, the use of AMS H2O-1 for sulfate reducing bacteria control in the petroleum industry is a promising alternative to chemical biocides. However, prior to the large-scale production of AMS H2O-1 for industrial applications, its chemical structure must be elucidated. This study also analyzed the changes in the wetting properties of different surfaces conditioned with AMS H2O-1 and demonstrated the effect of AMS H2O-1 on sulfate reducing bacteria cells. Results A lipopeptide mixture from AMS H2O-1 was partially purified on a silica gel column and identified via mass spectrometry (ESI-MS). It comprises four major components that range in size from 1007 to 1049 Da. The lipid moiety contains linear and branched β-hydroxy fatty acids that range in length from C13 to C16. The peptide moiety contains seven amino acids identified as Glu-Leu-Leu-Val-Asp-Leu-Leu. Transmission electron microscopy revealed cell membrane alteration of sulfate reducing bacteria after AMS H2O-1 treatment at the minimum inhibitory concentration (5 μg/ml). Cytoplasmic electron dense inclusions were observed in treated cells but not in untreated cells. AMS H2O-1 enhanced the osmosis of sulfate reducing bacteria cells and caused the leakage of the intracellular contents. In addition, contact angle measurements indicated that different surfaces conditioned by AMS H2O-1 were less hydrophobic and more electron-donor than untreated surfaces. Conclusion AMS H2O-1 is a mixture of four surfactin-like homologues, and its biocidal activity and surfactant properties suggest that this compound may be a good candidate for sulfate reducing bacteria control. Thus, it is a potential alternative to the chemical biocides or surface coating agents currently used to prevent SRB growth in petroleum industries.

Electron collisions with the HCOOH...(H2O)n (n=1, 2 and 3) complexes in liquid phase: the influence on the π* shape resonance of formic acid

In this conference we report cross sections for elastic collisions of low-energy electrons with the HCOOH…(H2O)n complexes, with n = 1, 2 and 3. The scattering cross sections were computed with the Schwinger multichannel method [K. Takatsuka and V. McKoy, Phys. Rev. A 24 , 2473 (1981); Phys. Rev. A 30 , 1734 (1984)] with pseudopotentials [M. H. F. Bettega, L. G. Ferreira, and M. A. P. Lima, Phys. Rev. A 47, 1111 (1993)] in the static-exchange and static-exchange plus polarization approximations, for energies from 0.5 eV to 6 eV. We considered some diÆerent hydrogen-bonded structures for the complexes that were generated with classical Monte Carlo simulations [K. Coutinho and S. Canuto, J. Chem. Phys. 113, 9132, (2000)]. The aim of this work is to investigate the effect of the surrounding water molecules on the π* shape resonance of the solute. Previous theoretical and experimental studies carried out in the gas phase reported a π* state for HCOOH at around 1.9 eV. For the n = 1 case and for all complexes, the stabilization of the resonance was observed (it appears at lower energy compared to the value obtained in the gas phase), as reported previously for the CH2O…H2O complexes [T. C. Freitas, M. A. P. Lima, S. Canuto, and M. H. F. Bettega, Phys. Rev. A 80, 062710 (2009)]. This result indicates that the presence of the solvent may affect the processes related to the π* state, such as the molecular dissociation by electron impact. For the n = 2 case we have observed both stabilization and destabilization of the π* resonance, that is associated with the hydrogen bond donor or acceptor role of the water molecules in the complexes. For the n = 3 case, preliminary static-exchange results show the stabilization of the π* state. We propose an explanation of the stabilization/destabilization of the π* state in terms of the polarization of the solute due to the surrounding water molecules and the net charge in the solute.

Accurate Predictions of Water Cluster Formation, (H2O)n=2-10

An efficient mixed molecular dynamics/quantum mechanics model has been applied to the water cluster system. The use of the MP2 method and correlation consistent basis sets, with appropriate correction for BSSE, allows for the accurate calculation of electronic and free energies for the formation of clusters of 2−10 water molecules. This approach reveals new low energy conformers for (H2O)n=7,9,10. The water heptamer conformers comprise five different structural motifs ranging from a three-dimensional prism to a quasi-planar book structure. A prism-like structure is favored energetically at low temperatures, but a chair-like structure is the global Gibbs free energy minimum past 200 K. The water nonamers exhibit less complexity with all the low energy structures shaped like a prism. The decamer has 30 conformers that are within 2 kcal/mol of the Gibbs free energy minimum structure at 298 K. These structures are categorized into four conformer classes, and a pentagonal prism is the most stable structure from 0 to 320 K. Results can be used as benchmark values for empirical water models and density functionals, and the method can be applied to larger water clusters.

Pople's Gaussian-3 model chemistry applied to an investigation of (H2O)8 water clusters

The Gaussian-3 method developed by Pople and coworkers has been used to calculate the free energy of neutral octamer clusters of water, (H2O)8. The most energetically stable structures are in excellent agreement with those determined from experiment and those predicted from previous high-level calculations. Cubic structures are favored over noncubic structures over all temperature ranges studied. The D2d cubic structure is the lowest free energy structure and dominates the potential energy and free energy hypersurfaces from 0 K to 298 K.

Do Hydroxyl Radical−Water Clusters, OH(H2O)n, n = 1−5, Exist in the Atmosphere?

It has been speculated that the presence of OH(H2O)n clusters in the troposphere could have significant effects on the solar absorption balance and the reactivity of the hydroxyl radical. We have used the G3 and G3B3 model chemistries to model the structures and predict the frequencies of hydroxyl radical/water clusters containing one to five water molecules. The reaction between hydroxyl radical clusters and methane was examined as a function of water cluster size to gain an understanding of how cluster size affects the hydroxyl radical reactivity.

Prediction of Accurate Anharmonic Experimental Vibrational Frequencies for Water Clusters, (H2O)n, n = 2−5

Accurate anharmonic experimental vibrational frequencies for water clusters consisting of 2−5 water molecules have been predicted on the basis of comparing different methods with MP2/aug-cc-pVTZ calculated and experimental anharmonic frequencies. The combination of using HF/6-31G* scaled frequencies for intramolecular modes and anharmonic frequencies for intermolecular modes gives excellent agreement with experiment for the water dimer and trimer and are as good as the expensive anharmonic MP2 calculations. The water trimer, the cyclic Ci and S4 tetramers, and the cyclic pentamer all have unique peaks in the infrared spectrum between 500 and 800 cm-1 and between 3400 and 3700 cm-1. Under the right experimental conditions these different clusters can be uniquely identified using high-resolution IR spectroscopy.

In search of CS2(H2O)n = 1–4 clusters

Gaussian-3 and MP2/aug-cc-pVnZ methods have been used to calculate geometries and thermochemistry of CS2(H2O)n, where n = 1–4. An extensive molecular dynamics search followed by optimization using these two methods located two dimers, six trimers, six tetramers, and two pentamers. The MP2/aug-cc-pVDZ structure matched best with the experimental result for the CS2(H2O) dimer, showing that diffuse functions are necessary to model the interactions found in this complex. For larger CS2(H2O)n clusters, the MP2/aug-cc-pVDZ minima are significantly different from the MP2(full)/6-31G* structures, revealing that the G3 model chemistry is not suitable for investigation of sulfur containing van der Waals complexes. Based on the MP2/aug-cc-pVTZ free energies, the concentration of saturated water in the atmosphere and the average amount of CS2 in the atmosphere, the concentrations of these clusters are predicted to be on the order of 105CS2(H2O) clusters∙cm−3 and 102 CS2(H2O)2 clusters∙cm−3 at 298.15 K. The MP2/aug-cc-pVDZ scaled harmonic and anharmonic frequencies of the most abundant dimer cluster at 298 K are presented, along with the MP2/aug-cc-pVDZ scaled harmonic frequencies for the CS2(H2O)n structures predicted to be present in a low-temperature molecular beam experiment.

Exploration of the Potential Energy Surfaces, Prediction of Atmospheric Concentrations, and Prediction of Vibrational Spectra for the HO2···(H2O)n (n = 1−2) Hydrogen Bonded Complexes

The hydroperoxy radical (HO2) plays a critical role in Earth's atmospheric chemistry as a component of many important reactions. The self-reaction of hydroperoxy radicals in the gas phase is strongly affected by the presence of water vapor. In this work, we explore the potential energy surfaces of hydroperoxy radicals hydrogen bonded to one or two water molecules, and predict atmospheric concentrations and vibrational spectra of these complexes. We predict that when the HO2 concentration is on the order of 108molecules·cm-3 at 298 K, that the number of HO2···H2O complexes is on the order of 107molecules·cm-3 and the number of HO2···(H2O)2 complexes is on the order of 106molecules·cm-3. Using the computed abundance of HO2···H2O, we predict that, at 298 K, the bimolecular rate constant for HO2···H2O + HO2 is about 10 times that for HO2 + HO2.

Global Search for Minimum Energy (H2O)n Clusters, n = 3−5

The Gaussian-3 (G3) model chemistry method has been used to calculate the relative ΔG° values for all possible conformers of neutral clusters of water, (H2O)n, where n = 3−5. A complete 12-fold conformational search around each hydrogen bond produced 144, 1728, and 20 736 initial starting structures of the water trimer, tetramer, and pentamer. These structures were optimized with PM3, followed by HF/6-31G* optimization, and then with the G3 model chemistry. Only two trimers are present on the G3 potential energy hypersurface. We identified 5 tetramers and 10 pentamers on the potential energy and free-energy hypersurfaces at 298 K. None of these 17 structures were linear; all linear starting models folded into cyclic or three-dimensional structures. The cyclic pentamer is the most stable isomer at 298 K. On the basis of this and previous studies, we expect the cyclic tetramers and pentamers to be the most significant cyclic water clusters in the atmosphere.

Accurate Predictions of Water Cluster Formation, (H2O)n=2−10

An efficient mixed molecular dynamics/quantum mechanics model has been applied to the water cluster system. The use of the MP2 method and correlation consistent basis sets, with appropriate correction for BSSE, allows for the accurate calculation of electronic and free energies for the formation of clusters of 2−10 water molecules. This approach reveals new low energy conformers for (H2O)n=7,9,10. The water heptamer conformers comprise five different structural motifs ranging from a three-dimensional prism to a quasi-planar book structure. A prism-like structure is favored energetically at low temperatures, but a chair-like structure is the global Gibbs free energy minimum past 200 K. The water nonamers exhibit less complexity with all the low energy structures shaped like a prism. The decamer has 30 conformers that are within 2 kcal/mol of the Gibbs free energy minimum structure at 298 K. These structures are categorized into four conformer classes, and a pentagonal prism is the most stable structure from 0 to 320 K. Results can be used as benchmark values for empirical water models and density functionals, and the method can be applied to larger water clusters.

Structure and thermodynamics of H3O+(H2O)8 clusters: A combined molecular dynamics and quantum mechanics approach

We have studied the structure and stability of (H3O+)(H2O)8 clusters using a combination of molecular dynamics sampling and high-level ab initio calculations. 20 distinct oxygen frameworks are found within 2 kcal/mol of the electronic or standard Gibbs free energy minimum. The impact of quantum zero-point vibrational corrections on the relative stability of these isomers is quite significant. The box-like isomers are favored in terms of electronic energy, but with the inclusion of zero-point vibrational corrections and entropic effects tree-like isomers are favored at higher temperatures. Under conditions from 0 to 298.15 K, the global minimum is predicted to be a tree-like structure with one dangling singly coordinated water molecule. Above 298.15 K, higher entropy tree-like isomers with two or more singly coordinated water molecules are favored. These assignments are generally consistent with experimental IR spectra of (H3O+)(H2O)8 obtained at 150 K.

Vibronic Spectra of Jet-Cooled 2-Aminopurine center dot H2O Clusters Studied by UV Resonant Two-Photon Ionization Spectroscopy and Quantum Chemical Calculations

For understanding the major- and minor-groove hydration patterns of DNAs and RNAs, it is important to understand the local solvation of individual nucleobases at the molecular level. We have investigated the 2-aminopurine center dot H2O. monohydrate by two-color resonant two-photon ionization and UV/UV hole-burning spectroscopies, which reveal two isomers, denoted A and B. The electronic spectral shift delta nu of the S-1 <- S-0 transition relative to bare 9H-2-aminopurine (9H-2AP) is small for isomer A (-70 cm(-1)), while that of isomer B is much larger (delta nu = 889 cm(-1)). B3LYP geometry optimizations with the TZVP basis set predict four cluster isomers, of which three are doubly H-bonded, with H2O acting as an acceptor to a N-H or -NH2 group and as a donor to either of the pyrimidine N sites. The "sugar-edge" isomer A is calculated to be the most stable form with binding energy D-e = 56.4 kJ/mol. Isomers B and C are H-bonded between the -NH2 group and pyrimidine moieties and are 2.5 and 6.9 kJ/mol less stable, respectively. Time-dependent (TD) B3LYP/TZVP calculations predict the adiabatic energies of the lowest (1)pi pi* states of A and B in excellent agreement with the observed 0(0)(0) bands; also, the relative intensities of the A and B origin bands agree well with the calculated S-0 state relative energies. This allows unequivocal identification of the isomers. The R2PI spectra of 9H-2AP and of isomer A exhibit intense low-frequency out-of-plane overtone and combination bands, which is interpreted as a coupling of the optically excited (1)pi pi* state to the lower-lying (1)n pi* dark state. In contrast, these overtone and combination bands are much weaker for isomer B, implying that the (1)pi pi* state of B is planar and decoupled from the (1)n pi* state. These observations agree with the calculations, which predict the (1)n pi* above the (1)pi pi* state for isomer B but below the (1)pi pi* for both 9H-2AP and isomer A.

Observations of middle atmospheric H2O and O3 during the 2010 major sudden stratospheric warming by a network of microwave radiometers

In this study, we present middle atmospheric water vapor (H2O) and ozone (O3) measurements obtained by ground-based microwave radiometers at three European locations in Bern (47° N), Onsala (57° N) and Sodankylä (67° N) during Northern winter 2009/2010. In January 2010, a major sudden stratospheric warming (SSW) occurred in the Northern Hemisphere whose signatures are evident in the ground-based observations of H2O and O3. The observed anomalies in H2O and O3 are mostly explained by the relative location of the polar vortex with respect to the measurement locations. The SSW started on 26 January 2010 and was most pronounced by the end of January. The zonal mean temperature in the middle stratosphere (10 hPa) increased by approximately 25 Kelvin within a few days. The stratospheric vortex weakened during the SSW and shifted towards Europe. In the mesosphere, the vortex broke down, which lead to large scale mixing of polar and midlatitudinal air. After the warming, the polar vortex in the stratosphere split into two weaker vortices and in the mesosphere, a new, pole-centered vortex formed with maximum wind speed of 70 m s−1 at approximately 40° N. The shift of the stratospheric vortex towards Europe was observed in Bern as an increase in stratospheric H2O and a decrease in O3. The breakdown of the mesospheric vortex during the SSW was observed at Onsala and Sodankylä as a sudden increase in mesospheric H2O. The following large-scale descent inside the newly formed mesospheric vortex was well captured by the H2O observations in Sodankylä. In order to combine the H2O observations from the three different locations, we applied the trajectory mapping technique on our H2O observations to derive synoptic scale maps of the H2O distribution. Based on our observations and the 3-D wind field, this method allows determining the approximate development of the stratospheric and mesospheric polar vortex and demonstrates the potential of a network of ground-based instruments.