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computational chemistry

Ayda Nemati Vesali Azar, Seda Keskin
Efficient separation of acetylene (C2 H2 ) from CO2 and CH4 is important to meet the requirement of high-purity acetylene in various industrial applications. Metal organic frameworks (MOFs) are great candidates for adsorption-based C2 H2 /CO2 and C2 H2 /CH4 separations due to their unique properties such as wide range of pore sizes and tunable chemistries. Experimental studies on the limited number of MOFs revealed that MOFs offer remarkable C2 H2 /CO2 and C2 H2 /CH4 selectivities based on single-component adsorption data...
2018: Frontiers in Chemistry
Juan García de la Concepción, Martín Ávalos, Pedro Cintas, José Luis Jiménez
Computational strategies have gained increasing impact in the de novo design of large molecular sets targeted to a desired application. Here, we show that DFT-assisted theoretical analyses of cycloadditions involving mesoionic dipoles and strained cycloalkynes unveil a series of unexplored mesomeric betaines as vastly superior candidates for orthogonal applications. Thus, isosydnones, thiosydnones, and a six-membered homolog in particular, 6-oxo-1,3-oxazinium-4-olate, do exhibit enhanced reactivity with respect to sydnones, the archetypal mesoionic ring employed so far in orthogonal chemistry...
March 13, 2018: Chemistry: a European Journal
Dmitry A Fedorov, Aleksandr O Lykhin, Sergey A Varganov
Accurate prediction of the intersystem crossing rates is important for many different applications in chemistry, physics, and biology. Recently, we implemented the ab initio multiple spawning (AIMS) molecular dynamics method to describe the intersystem crossing processes, where nonradiative transitions between electronic states with different spin multiplicities are mediated by spin-orbit coupling. Our original implementation of the direct AIMS dynamics used the complete active space self-consistent field (CASSCF) method to describe multiple coupled electronic states on which multidimensional Gaussian wave packets were propagated...
March 13, 2018: Journal of Physical Chemistry. A
S Liyanaarachchi, S Muthukumaran, Joshua Kaiser, Paul Rogers, Li Shu, Ho Kyong Shon, V Jegatheesan
Diffusion coefficient of solutes through a porous membrane media is different from diffusion coefficient through a free homogenous media. Porosity, tortuosity and the thickness of the membrane significantly affect the diffusion through a specific thickness of a membrane and therefore it is termed as effective diffusion coefficient (Deff ) which is lower than the actual diffusion coefficient, D. The Deff of single or dual solutes through a porous membrane layer are well documented but not for multiple salts...
March 8, 2018: Journal of Environmental Management
Muhammed Veli, Aydogan Ozcan
We present a cost-effective and portable platform based on contact lenses for non-invasively detecting Staphylococcus aureus, which is part of the human ocular microbiome and resides on the cornea and conjunctiva. Using Staphylococcus aureus-specific antibodies and a surface chemistry protocol that is compatible with human tear, contact lenses are designed to specifically capture Staphylococcus aureus. After the bacteria capture on the lens, and right before its imaging, the captured bacteria are tagged with surface-functionalized polystyrene microparticles...
March 9, 2018: ACS Nano
John Mark Cline, Greg Dugan, John Daniel Bourland, Donna L Perry, Joel D Stitzel, Ashley A Weaver, Chen Jiang, Artak Tovmasyan, Kouros Owzar, Ivan Spasojevic, Ines Batinic-Haberle, Zeljko Vujaskovic
Radiation injury to the lung is the result of acute and chronic free radical formation, and there are currently few effective means of mitigating such injury. Studies in rodents indicate that superoxide dismutase mimetics may be effective in this regard; however, studies in humans or large animals are lacking. We hypothesized that post-exposure treatment with the lipophilic mitochondrial superoxide dismutase mimetic, MnTnHex-2-PyP5+ (hexyl), would reduce radiation-induced pneumonitis and fibrosis in the lungs of nonhuman primates...
March 7, 2018: Antioxidants (Basel, Switzerland)
Uğur Bozkaya, Asli Unal
The accurate computation of ionization potentials (IPs), within 0.10 eV, is one of the most challenging problem in modern computational chemistry. The extended Koopmans' theorem (EKT) provides a systematic direct approach to compute IPs from any level of theory. In this study, the EKT approach is integrated with the coupled- cluster singles and doubles with perturbative triples [CCSD(T)] method for the first time. For efficiency, the density-fitting (DF) approximation is employed for electron repulsion integrals...
March 8, 2018: Journal of Physical Chemistry. A
Pedro Merino, Mattia Ghirardello, Daniela Perrone, Nicola Chinaglia, David Sadaba, Ignacio Delso, Tomas Tejero, Elena Marchesi, Marco Fogagnolo, Karim Rafie, Daan M F van Aalten
A series of glycomimetics of UDP-GlcNAc in which the β-phosphate has been replaced by either an alkyl chain or a triazolyl ring and the sugar moiety has been replaced by a pyrrolidine ring have been synthesized by using different click-chemistry procedures. Their affinity for human O-GlcNAc transferase (hOGT) has been evaluated and both spectroscopically and computationally studied. The binding epitopes of the best ligands have been determined in solution using saturation transfer difference (STD) NMR spectroscopy...
March 7, 2018: Chemistry: a European Journal
Saad Raza, Syed Sikander Azam
Conformational flexibility and generalized structural features are responsible for specific phenomena existing in biological pathways. With advancements in computational chemistry, novel approaches and new methods are required to compare the dynamic nature of biomolecules, which are crucial not only to address dynamic functional relationships but also to gain detailed insights into the disturbance and positional fluctuation responsible for functional shifts. Keeping this in mind, axial frequency distribution (AFD) has been developed, designed, and implemented...
March 6, 2018: Journal of Molecular Modeling
Franco Tassi, Stefano Fazi, Simona Rossetti, Paolo Pratesi, Marco Ceccotti, Jacopo Cabassi, Francesco Capecchiacci, Stefania Venturi, Orlando Vaselli
Volcanic lakes are characterized by physicochemical favorable conditions for the development of reservoirs of C-bearing greenhouse gases that can be dispersed to air during occasional rollover events. By combining a microbiological and geochemical approach, we showed that the chemistry of the CO2- and CH4-rich gas reservoir hosted within the meromictic Lake Averno (Campi Flegrei, southern Italy) are related to the microbial niche differentiation along the vertical water column. The simultaneous occurrence of diverse functional groups of microbes operating under different conditions suggests that these habitats harbor complex microbial consortia that impact on the production and consumption of greenhouse gases...
2018: PloS One
Eric McGivney, Kayleigh Elizabeth Jones, Bandrea Weber, Ann Margaret Valentine, Jeanne M Vanbriesen, Kelvin B Gregory
Quorum sensing (QS) regulates important bacterial behaviors such as virulent protein production and biofilm formation. QS requires that molecular signals are exchanged between cells, extracellularly, where environmental conditions influence signal stability. In this work, we present a novel complexation between metal cations (Ag+ and Cu2+ ) and a QS autoinducer signal, N-hexanoyl-homoserine lactone (HHL). The molecular interactions were investigated using mass spectrometry, attenuated total reflectance-Fourier transform infrared spectroscopy, and computational simulations...
March 6, 2018: ACS Chemical Biology
Michał L Chodkiewicz, Szymon Migacz, Witold Rudnicki, Anna Makal, Jarosław A Kalinowski, Nigel W Moriarty, Ralf W Grosse-Kunstleve, Pavel V Afonine, Paul D Adams, Paulina Maria Dominiak
It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation called DiSCaMB , 'densities in structural chemistry and molecular biology', has been developed...
February 1, 2018: Journal of Applied Crystallography
Jaime Rodríguez-Guerra Pedregal, Pablo Gómez-Orellana, Jean-Didier Pierre Maréchal
Electronic Supporting Information (ESI) occupies a fundamental position in the way scientists report their work. It is a key element in lightening the writing of the core manuscript and makes concise communication easier for the authors. Computational chemistry, as all fields related to structural studies of molecules, tends to generate huge amounts of data that should be inserted in the ESI. ESI reports raising from computational chemistry works generally reach tens of sheets long and include 3D depictions, coordinates, energies and other characteristics of the structures involved in the molecular process understudy...
March 5, 2018: Journal of Chemical Information and Modeling
Arshad Mehmood, Benjamin G Janesko
A method is proposed to predict ions' collision cross-sectional area (CCS) from properties that are already evaluated in standard quantum chemistry software. Computed molecular isodensity surface areas recover the predictions of existing projection approximations. Computed solvent cavity areas give comparable accuracy. This provides a simplified workflow for assigning ion-mobility mass spectra.
March 5, 2018: Journal of Mass Spectrometry: JMS
Marketa Paloncyova, Michal Langer, Michal Otyepka
Carbon dots (CDs), one of the youngest members of the carbon nanostructure family, are now widely experimentally studied for their tunable fluorescence properties, bleaching resistance and biocompatibility. Their interaction with biomolecular systems has also been explored experimentally. However, many atomistic details still remain unresolved. Molecular dynamics (MD) simulations enabling atomistic and femtosecond resolutions simultaneously are a well-established tool of computational chemistry which can provide useful insights into investigated systems...
March 2, 2018: Journal of Chemical Theory and Computation
Anja Massolle, Thomas Dresselhaus, Steffen Eusterwiemann, Carsten Doerenkamp, Hellmut Eckert, Armido Studer, Johannes Neugebauer
We present an efficient and accurate computational procedure to calculate properties measurable by EPR spectroscopy. We simulate a molecular dynamics (MD) trajectory by employing the quantum mechanically derived force field (QMDFF) [S. Grimme, J. Chem. Theory Comput., 2014, 10, 4497] and sample the trajectory at different time steps. For each snapshot EPR properties are calculated with a hybrid density functional theory (DFT) method. EPR spectra are simulated based on the averaged results. We applied the strategy to a number of previously published and novel verdazyl radicals, for which we recorded EPR spectra...
March 2, 2018: Physical Chemistry Chemical Physics: PCCP
Neelaveni Thangavel, Mohammad Al Bratty, Sadique Akhtar Javed, Waquar Ahsan, Hassan Al Hazmi
Design of novel PPAR-γ modulators with better binding efficiency and fewer side effects to treat type 2 diabetes is still a challenge for medicinal chemists. Cost and time efficient computational methods have presently become an integral part of research in nuclear receptors and their ligands, enabling hit to lead identification and lead optimization. This review will focus on cutting-edge technologies used in most recent studies on the design of PPAR- γ agonists and will discuss the chemistry of a few molecules which emerged successful...
February 27, 2018: Current Drug Discovery Technologies
Jan K Szymański, Yousef M Abul-Haija, Leroy Cronin
Millions of years of biological evolution have driven the development of highly sophisticated molecular machinery found within living systems. These systems produce polymers such as proteins and nucleic acids with incredible fidelity and function. In nature, the precise molecular sequence is the factor that determines the function of these macromolecules. Given that the ability to precisely define sequence emerges naturally, the fact that biology achieves unprecedented control over the unit sequence of the monomers through evolved enzymatic catalysis is incredible...
March 1, 2018: Accounts of Chemical Research
Cameron A Smith, Christian A Yates
Many biological and physical systems exhibit behaviour at multiple spatial, temporal or population scales. Multiscale processes provide challenges when they are to be simulated using numerical techniques. While coarser methods such as partial differential equations are typically fast to simulate, they lack the individual-level detail that may be required in regions of low concentration or small spatial scale. However, to simulate at such an individual level throughout a domain and in regions where concentrations are high can be computationally expensive...
February 2018: Journal of the Royal Society, Interface
Niels Sievertsen, Erick M Carreira
Mobile devices such as smartphones are carried in the pockets of university students around the globe and are increasingly cheap to come by. These portable devices have evolved into powerful and interconnected handheld computers, which, among other applications, can be used as advanced learning tools and providers of targeted, curated content. Herein, we describe Apoc Social (Advanced Problems in Organic Chemistry Social), a mobile application that assists both learning and teaching college-level organic chemistry both in the classroom and on the go...
February 1, 2018: Chimia
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