A halophilic Chromohalobacter species from estuarine coastal waters as a detoxifier of manganese, as well as a novel bio-catalyst for synthesis of n-butyl acetate

Anthropogenic pollution due to ferro-manganese ore transport by barges through the Mandovi estuary in Goa, India is a major environmental concern. In this study a manganese (Mn) tolerant, moderately halophilic Chromohalobacter sp. belonging to the family Halomonadaceae was isolated from the sediments of a solar saltern adjacent to this Mandovi estuary. Using techniques of Atomic absorption spectroscopy, Scanning electron microscopy-Energy dispersive X-ray spectroscopy, Fourier-transform infrared spectroscopy and Atomic Force Microscopy, the Chromohalobacter sp. was explored for its ability to tolerate and immobilize Mn in amended and unamended media with 20% natural salt concentration (w/v). In aqueous media supplemented with 0.1 mM Mn, the Chromohalobacter sp. was capable of sequestering up to 76% Mn with an average immobilization rate of 8 mg Mn /g /day. Growth rate kinetic analysis using Gompertz mathematical functions was found to model the experimental data well. The model inferred that the maximum growth rate of Chromohalobacter sp. was at 10% natural salt concentration (w/v). The Chromohalobacter sp. was further found to be multimetal tolerant showing high tolerance to Iron (Fe), Nickel (Ni) and Cobalt (Co), (each at 4 mM), and tolerated Manganese (Mn) up to 6 mM. Morphologically, the Chromohalobacter sp. was a non-spore forming, Gram negative motile rod (0.726 μ× 1.33 μ). The adaptative mechanism of Chromohalobacter sp. to elevated Mn concentrations (1 mM) resulted in the reduction of its cell size to 0.339 μ× 0.997 μ and the synthesis of an extracellular slime, immobilizing Mn from the liquid phase forming Manganese oxide, as confirmed by Scanning Electron Microscopy. The expression of Mnx genes for manganese oxidation further substantiated the finding. This bacterial synthesized manganese oxide also displayed catalytic activity (∼50% conversion) for the esterification of butan-1-ol with CH3COOH to yield n-butyl acetate. This Chromohalobacter sp. being indigenous to marine salterns, has adapted to high concentrations of heavy metals and high salinities and can withstand this extremely stressed environment, and thus holds a tremendous potential as an environmentally friendly “green bioremediator” of Mn from euryhaline environments. The study also adds to the limited knowledge about metal-microbe interactions in extreme environments. Further, since Chromohalobacter sp. exhibits commendable catalytic activity for the synthesis of n-butyl acetate, it would have several potential industrial applications

Machine Learning of Molecular Electronic Properties in Chemical Compound Space

The combination of modern scientific computing with electronic structure theory can lead to an unprecedented amount of data amenable to intelligent data analysis for the identification of meaningful, novel, and predictive structure-property relationships. Such relationships enable high-throughput screening for relevant properties in an exponentially growing pool of virtual compounds that are synthetically accessible. Here, we present a machine learning (ML) model, trained on a data base of \textit{ab initio} calculation results for thousands of organic molecules, that simultaneously predicts multiple electronic ground- and excited-state properties. The properties include atomization energy, polarizability, frontier orbital eigenvalues, ionization potential, electron affinity, and excitation energies. The ML model is based on a deep multi-task artificial neural network, exploiting underlying correlations between various molecular properties. The input is identical to \emph{ab initio} methods, \emph{i.e.} nuclear charges and Cartesian coordinates of all atoms. For small organic molecules the accuracy of such a "Quantum Machine" is similar, and sometimes superior, to modern quantum-chemical methods---at negligible computational cost

Effiziente Modellierung der linearen elektronischen Polarisation in Materialien mithilfe atomarer Antwortfunktionen

The study of matter interacting with external fields is important to understand and design materials with desired (opto)electronic properties. Reliable methods for the accurate and efficient calculation of the dynamic polarizability of molecules and solids are required for modeling a multitude of spectroscopic techniques, including optical absorption and refraction, Raman spectroscopy, and circular dichroism. Efficient prediction of electronic response properties is also necessary for the calculation of van der Waals (vdW) interactions, and coupling between nuclear and electronic degrees of freedom in materials. In principle, explicitly correlated wave function based first-principles techniques could be utilized to determine electronic response properties. However these methods can be only applied to rather small systems and become prohibitively expensive to study complex materials containing thousands of atoms. To address this problem, we developed an efficient non-empirical method for calculating linear response properties of non-metallic molecules and solids based on atomic response functions that describe valence atomic excitations. This is achieved by the synergistic coupling of the Tkatchenko-Scheffler (TS) method, which accurately treats short-range hybridization effects with the Dyson-like self-consistent screening (SCS) equation from classical electrodynamics. The present formulation builds upon and significantly improves an earlier version of the TS+SCS approach, by preserving QHO invariants, satisfying the free-atom dipole oscillator strength sum rule, and using the correct spin-polarized electron densities for the free atoms. Using only the ground state electron density obtained from first-principle density functional theory calculation and accurate free-atom reference data, we obtain a performance of 3.6% for static polarizabilities and 7.6% for vdW coefficients for a large database of gas-phase molecules (∼7500 systems). We further demonstrate the potential of the developed method for the prediction of peculiar scaling laws for vdW interactions in nanostructured materials and interfaces.Die Untersuchung von Wechselwirkungen zwischen Materie und externen Feldern ist bedeutend für das Verständnis (opto-) elektronischer Materialien und das Designen ihrer gewünschter Eigenschaften. Zuverlässige Methoden, um die dynamische Polarisierbarkeit von Molekülen und Festkörpern genau und effizient zu berechnen, wurden für die Modellierung verschiedenster spektroskopischer Techniken, wie z.B. optische Absorption und Brechung, Raman-Spektroskopie und Zirkulardichroismus, benötigt. Die effiziente Vorhersage der elektronischen Antwort ist ebenso für die Berechnung von van-der-Waals(vdW)-Wechselwirkungen und der Kopplung von Elektron- und Kernfreiheitsgraden notwendig. Prinzipiell kann die elektronische Antwort mit Hilfe von explizit korrelierten Wellenfunktionen aus ab-initio Methoden bestimmt werden. Jedoch ist dies nur für sehr kleine Systeme möglich und für das Studium komplexer Materialien mit mehr als 1000 Atomen unerschwinglich. Um dem Problem gerecht zu werden, berechnen wir mit einer effizienten und nicht-empirischen Methode die lineare Antwort von nicht-metallischen Molekülen und Festkörpern auf Grundlage atomarer Antwortfunktionen von Valenzatomanregungen. Dies wird durch die synergistische Kopplung der Tkatchenko-Scheffler-(TS)-Methode erreicht, die akkurat die kurzreichweitige Hybridisierungseffekte mit der Dyson-ähnlichen, selbkonsistenten Abschirmungs(SCS)-Gleichung aus der klassischen Elektrodynamik nähert. Die hier dargestellte Methode baut auf einer früheren Version des TS+SCS-Ansatzes auf und verbessert sie signifikant durch die Erhaltung von QHO-Invarianten, welche die Dipoloszillatorstärken-Summenregel für freie Atome erfüllt und die korrekte spinpolarisierte Elektronendichte der freien Atome verwendet. Wenn lediglich die Grundzustandselektronendichte aus einer ab-initio Dichtefunktionaltheorie-Rechnung und genaue Referenzdaten für die freien Atome verwendet werden, erhalten wir schon eine Genauigkeit von 3.6% für die statische Polarisierbarkeit und von 7.6% für die vdW-Koeffizienten in Bezug auf eine große Datenbank für Moleküle in der Gasphase (∼7500 Systeme). Weiterhin zeigen wir das Potential der von uns entwickelten Methode für die Vorhersage der sehr verschiedenartigen Potenzgesetze der vdW-Wechselwirkungen in nanostrukturierten Materialien und Grenzflächen

Scaling laws for van der Waals interactions in nanostructured materials

Van der Waals interactions have a fundamental role in biology, physics and chemistry, in particular in the self-assembly and the ensuing function of nanostructured materials. Here we utilize an efficient microscopic method to demonstrate that van der Waals interactions in nanomaterials act at distances greater than typically assumed, and can be characterized by different scaling laws depending on the dimensionality and size of the system. Specifically, we study the behaviour of van der Waals interactions in single-layer and multilayer graphene, fullerenes of varying size, single-wall carbon nanotubes and graphene nanoribbons. As a function of nanostructure size, the van der Waals coefficients follow unusual trends for all of the considered systems, and deviate significantly from the conventionally employed pairwise-additive picture. We propose that the peculiar van der Waals interactions in nanostructured materials could be exploited to control their self-assembly

Theoretical Appraisal of Cyclopropenone: Aggregation and Complexes with Water

Cyclopropenone (HCCOCH, "CPN") is an exotic quasi-aromatic cyclic carbene that abounds in the interstellar medium (ISM). Astronomical observations suggest that (i) stagnate CPN exhibits a tendency to polymerize and that (ii) interactions may occur between CPN and water that is also ubiquitous in the ISM. In this light, density functional theory investigations reveal cooperative hydrogen bonding, which leads to stable polymeric conformations of (CPN)n, tracked up to n = 14. Stable agglomerations with water, however, constitute at best only two CPN and two water molecules, signifying that while CPN exhibits remarkable cooperativity for "cohesive" clustering via hydrogen bonding, this tendency is markedly diminished for "hetero"-interactions. Multifaceted data are employed to probe cogent molecular descriptors, such as structure and energetics of various conformers, vibrational spectroscopic response, molecular electrostatic potential (MESP), effective atomic charges: all these, in unison, describe the evolution of the characteristics upon cluster formation. Salient stretching frequency shifts, as well as charge redistribution gleaned from MESP morphology, have a direct bearing on variegated hydrogen bonding patterns: linear, nonlinear, as well as bifurcated. In particular, characteristic C-H, C═O stretching, and O-H vibrations in the water complexes reveal a "softening" (downshift) of frequencies. While small conformers have markedly distinct MESP variations, the differences become less pronounced with incremental clustering, an effect substantiated by corresponding emergent atomic charges

Data_Sheet_1_A halophilic Chromohalobacter species from estuarine coastal waters as a detoxifier of manganese, as well as a novel bio-catalyst for synthesis of n-butyl acetate.pdf

Anthropogenic pollution due to ferro-manganese ore transport by barges through the Mandovi estuary in Goa, India is a major environmental concern. In this study a manganese (Mn) tolerant, moderately halophilic Chromohalobacter sp. belonging to the family Halomonadaceae was isolated from the sediments of a solar saltern adjacent to this Mandovi estuary. Using techniques of Atomic absorption spectroscopy, Scanning electron microscopy-Energy dispersive X-ray spectroscopy, Fourier-transform infrared spectroscopy and Atomic Force Microscopy, the Chromohalobacter sp. was explored for its ability to tolerate and immobilize Mn in amended and unamended media with 20% natural salt concentration (w/v). In aqueous media supplemented with 0.1 mM Mn, the Chromohalobacter sp. was capable of sequestering up to 76% Mn with an average immobilization rate of 8 mg Mn /g /day. Growth rate kinetic analysis using Gompertz mathematical functions was found to model the experimental data well. The model inferred that the maximum growth rate of Chromohalobacter sp. was at 10% natural salt concentration (w/v). The Chromohalobacter sp. was further found to be multimetal tolerant showing high tolerance to Iron (Fe), Nickel (Ni) and Cobalt (Co), (each at 4 mM), and tolerated Manganese (Mn) up to 6 mM. Morphologically, the Chromohalobacter sp. was a non-spore forming, Gram negative motile rod (0.726 μ× 1.33 μ). The adaptative mechanism of Chromohalobacter sp. to elevated Mn concentrations (1 mM) resulted in the reduction of its cell size to 0.339 μ× 0.997 μ and the synthesis of an extracellular slime, immobilizing Mn from the liquid phase forming Manganese oxide, as confirmed by Scanning Electron Microscopy. The expression of Mnx genes for manganese oxidation further substantiated the finding. This bacterial synthesized manganese oxide also displayed catalytic activity (∼50% conversion) for the esterification of butan-1-ol with CH3COOH to yield n-butyl acetate. This Chromohalobacter sp. being indigenous to marine salterns, has adapted to high concentrations of heavy metals and high salinities and can withstand this extremely stressed environment, and thus holds a tremendous potential as an environmentally friendly “green bioremediator” of Mn from euryhaline environments. The study also adds to the limited knowledge about metal-microbe interactions in extreme environments. Further, since Chromohalobacter sp. exhibits commendable catalytic activity for the synthesis of n-butyl acetate, it would have several potential industrial applications.</p

Dispersion Interactions with Density-Functional Theory: Benchmarking Semiempirical and Interatomic Pairwise Corrected Density Functionals

We present a comparative assessment of the accuracy of two different approaches for evaluating dispersion interactions: interatomic pairwise corrections and semiempirical meta-generalized-gradient-approximation (meta-GGA)-based functionals. This is achieved by employing conventional (semi)local and (screened-)hybrid functionals, as well as semiempirical hybrid and nonhybrid meta-GGA functionals of the M06 family, with and without interatomic pairwise Tkatchenko Scheffler corrections. All of those are tested against the benchmark S22 set of weakly bound systems a representative larger molecular complex (dimer of NiPc molecules), and a representative dispersively bound solid (hexagonal boron nitride). For the 522 database, we also compare our results with those obtained from the pairwise correction of Grimme (DFT-D3) and nonlocal Langreth Lundqvist furtctionals (vdW-DF1 and vdW-DF2). We find that the semiempirical kinetic-energy-density dependence introduced in the M06 functionals mimics some of the nonlocal correlation needed to describe dispersion. However, long-range contributions are still missing. Pair-wise interatomic corrections, applied to conventional semilocal or hybrid functionals, or to M06 functionals, provide for a satisfactory level of accuracy irrespectively of the underlying functional. Specifically, screened-hybrid functionals such as the.Heyd Scuseria Ernzerhof (HSE) approach reduce self-interaction errors in systems possessing both localized and delocalized orbitals and can be applied to both finite and extended systems. Therefore, they serve as a useful underlying functional for dispersion corrections

Theoretical Appraisal of Cyclopropenone: Aggregation and Complexes with Water

Cyclopropenone (HCCOCH, “CPN”) is an exotic quasi-aromatic cyclic carbene that abounds in the interstellar medium (ISM). Astronomical observations suggest that (i) stagnate CPN exhibits a tendency to polymerize and that (ii) interactions may occur between CPN and water that is also ubiquitous in the ISM. In this light, density functional theory investigations reveal cooperative hydrogen bonding, which leads to stable polymeric conformations of (CPN)n, tracked up to n = 14. Stable agglomerations with water, however, constitute at best only two CPN and two water molecules, signifying that while CPN exhibits remarkable cooperativity for “cohesive” clustering via hydrogen bonding, this tendency is markedly diminished for “hetero”-interactions. Multifaceted data are employed to probe cogent molecular descriptors, such as structure and energetics of various conformers, vibrational spectroscopic response, molecular electrostatic potential (MESP), effective atomic charges: all these, in unison, describe the evolution of the characteristics upon cluster formation. Salient stretching frequency shifts, as well as charge redistribution gleaned from MESP morphology, have a direct bearing on variegated hydrogen bonding patterns: linear, nonlinear, as well as bifurcated. In particular, characteristic C–H, CO stretching, and O–H vibrations in the water complexes reveal a “softening” (downshift) of frequencies. While small conformers have markedly distinct MESP variations, the differences become less pronounced with incremental clustering, an effect substantiated by corresponding emergent atomic charges