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https://www.readbyqxmd.com/read/28933853/exchange-hole-dipole-dispersion-model-for-accurate-energy-ranking-in-molecular-crystal-structure-prediction-ii-non-planar-molecules
#1
Sarah R Whittleton, Alberto Otero-de-la-Roza, Erin R Johnson
The crystal structure prediction (CSP) of a given compound from its molecular diagram is a fundamental challenge in computational chemistry with implications in relevant technological fields. A key component of CSP is the method to calculate the lattice energy of a crystal, which allows the ranking of candidate structures. This work is the second part of our investigation to assess the potential of the exchange-hole dipole moment dispersion (XDM) model for crystal structure prediction. In this article, we study the relatively large, non-planar, mostly flexible molecules in the first five blind tests held by the Cambridge Crystallographic Data Centre...
September 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28929771/kinetic-and-thermodynamic-control-in-porphyrin-and-phthalocyanine-self-assembled-monolayers
#2
K W Hipps, Ursula Mazur
Porphyrins and phthalocyanines are ubiquitous in modern science and technology. Their stability, redox properties, and photoresponse make them candidates for numerous applications. Many of these applications rely on thin films, and these are critically dependent on the first monolayer. In this article, we focus on noncovalently bound self-assembled monolayers of porphyrins and phthalocyanines at the solution-solid interface with special emphasis on the kinetic and thermodynamic processes that define the films and their reaction chemistry...
September 20, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28926710/structure-vibrational-frequencies-and-bond-energies-of-the-brhgox-and-brhgxo-species-formed-in-atmospheric-mercury-depletion-events
#3
Yuge Jiao, Theodore Simon Dibble
Photochemistry during the polar Spring leads to atmospheric mercury depletion events (AMDEs): Hg(0), which typically lives for months in the atmosphere, can experience losses of more than 90% in less than a day. These dramatic losses are known to be initiated largely by Br + Hg + M → BrHg• + M, but the fate of BrHg• is a matter of guesswork. It is believed that BrHg• largely reacts with halogen oxides, XO (X = Cl, Br, and I) to form BrHgOX compounds, but these species have never been studied experimentally...
September 19, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28925700/infrared-signature-of-structural-isomers-of-gas-phase-m-n2o-n-m-cu-ag-au-ion-molecule-complexes
#4
Ethan M Cunningham, Alexander S Gentleman, Peter M Beardsmore, Andreas Iskra, Stuart R Mackenzie
Gas-phase metal ion-ligand complexes offer model environments to study molecular interactions which are key to many catalytic processes. Here, we present a combined experimental and computational study of M+(N2O)n [M= Cu, Ag, Au; n = 2-7] complexes. The spectra provide clear evidence for both nitrogen- and oxygen- bound ligands giving rise to a wide range of structural isomers for each complex studied. The evolution of the complex structures observed as well as spectral trends for each metal center are interpreted in terms of a molecular orbital binding picture and resulting calculated ligand binding energies...
September 19, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28922917/diverting-reactive-intermediates-toward-unusual-chemistry-unexpected-anthranil-products-from-davis-beirut-reaction
#5
Jie S Zhu, Jung-Ho Son, Andrew P Teuthorn, Makhluf J Haddadin, Mark J Kurth, Dean J Tantillo
The discovery of a new variation on the Davis-Beirut reaction is described in which an atypical heterocyclic framework (the anthranil or benzo[c]isoxazole framework) is formed as the result of diversion of a key reactive intermediate away from its expected reactivity - a potentially general approach to reaction design and development. Experimental and computational support for the proposed mechanism and origins of altered reactivity are described.
September 19, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28921975/intricacies-of-van-der-waals-interactions-in-systems-with-elongated-bonds-revealed-by-electron-groups-embedding-and-high-level-coupled-cluster-approaches
#6
Ewa Pastorczak, Jun Shen, Michal Hapka, Piotr Piecuch, Katarzyna Pernal
Non-covalent interactions between molecules with stretched intramonomer covalent bonds are a fascinating, yet little studied area. This shortage of information stems largely from the inability of most of the commonly used computational quantum chemistry methods to accurately describe weak long-range and strong non-dynamic correlations at the same time. In this work, we propose a geminal-based approach, abbreviated as EERPA-GVB, capable of describing such systems in a robust manner using relatively inexpensive computational steps...
September 18, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28920628/fluoroquinolones-as-imaging-agents-for-bacterial-infection
#7
Syed Ali Raza Naqvi, Karl Drlica
Diagnosis of deep-seated bacterial infection is difficult, as neither standard anatomical imaging nor radiolabeled, autologous leukocytes distinguish sterile inflammation from infection. Two recent imaging efforts are receiving attention: (1) radioactive derivatives of sorbitol show good specificity with Gram-negative bacterial infections, and (2) success in combining anatomical and functional imaging for cancer diagnosis has rekindled interest in (99m)Tc-fluoroquinolone-based imaging. With the latter, computed tomography (CT) would be combined with single-photon-emission-computed tomography (SPECT) to detect (99m)Tc-fluoroquinolone-bacterial interactions...
September 18, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28920597/an-assessment-of-the-random-phase-approximation-functional-and-characteristics-analysis-for-noncovalent-cation-%C3%AF-interactions
#8
He Su, Qiyang Wu, Hongyan Wang, Hui Wang
The binding energy is of great importance in understanding the formation and stability of noncovalent interactions. However, the determination of the binding energy with high precision and efficiency in medium- and long-range noncovalent interactions is still challenging for quantum chemistry. Here, we assess the performance of random-phase approximation (RPA), a fully non-local fifth-rung of the Jacob ladder functional, in determining the binding energy of cation-π systems (cation = Li(+), Na(+), Be(2+), Mg(2+), Al(+), and NH4(+); π = C6H6), which, to the best of our knowledge, has not been investigated...
September 18, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28919707/quantum-mechanics-implementation-in-drug-design-workflows-does-it-really-help
#9
REVIEW
Olayide A Arodola, Mahmoud Es Soliman
The pharmaceutical industry is progressively operating in an era where development costs are constantly under pressure, higher percentages of drugs are demanded, and the drug-discovery process is a trial-and-error run. The profit that flows in with the discovery of new drugs has always been the motivation for the industry to keep up the pace and keep abreast with the endless demand for medicines. The process of finding a molecule that binds to the target protein using in silico tools has made computational chemistry a valuable tool in drug discovery in both academic research and pharmaceutical industry...
2017: Drug Design, Development and Therapy
https://www.readbyqxmd.com/read/28918628/breaking-benzene-aromaticity-computational-insights-into-the-mechanism-of-the-tungsten-containing-benzoyl-coa-reductase
#10
Martin Culka, Simona G Huwiler, Matthias Boll, G Matthias Ullmann
Aromatic compounds are environmental pollutants with toxic and carcinogenic properties. Despite the stability of aromatic rings, bacteria are able to degrade the aromatic compounds into simple metabolites and use them as growth substrates under oxic or even under anoxic conditions. In anaerobic microorganisms, most monocyclic aromatic growth substrates are converted to the central intermediate benzoyl-coenzyme A, which is enzymatically reduced to cyclohexa-1,5-dienoyl-CoA. The strcitly anaerobic bacterium \textit{Geobacter metallireducens} uses the class II benzoyl-CoA reductase complex for this reaction...
September 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28915765/the-parameter-uncertainty-inflation-fallacy
#11
Pascal Pernot
Statistical estimation of the prediction uncertainty of physical models is typically hindered by the inadequacy of these models due to various approximations they are built upon. The prediction errors caused by model inadequacy can be handled either by correcting the model's results or by adapting the model's parameter uncertainty to generate prediction uncertainties representative, in a way to be defined, of model inadequacy errors. The main advantage of the latter approach (thereafter called PUI, for Parameter Uncertainty Inflation) is its transferability to the prediction of other quantities of interest based on the same parameters...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28915446/embracing-chemical-and-structural-diversity-with-uconga-a-universal-conformer-generation-and-analysis-program
#12
Nathaniel R Gunby, Sarah L Masters, Deborah L Crittenden
Molecular properties depend on molecular structure, so the first step in any computational chemistry investigation is to generate all thermally accessible conformers. Typically it is necessary to make a trade-off between the number of conformers to be explored and the accuracy of the method used to calculate their energies. Ab initio potential energy surface scans can, in principle, be applied to any molecule, but their conformational cost scales poorly with both molecular size and dimensionality of the search space...
September 6, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28914473/ethers-on-si-001-a-prime-example-for-the-common-ground-between-surface-science-and-molecular-organic-chemistry
#13
Lisa Pecher, Slimane Laref, Marc Raupach, Ralf Ewald Tonner
Using computational chemistry, we show that the adsorption of ether molecules on Si(001) under ultra-high vacuum conditions can be understood with textbook organic chemistry. The two-step reaction mechanism of (1) dative bond formation between the ether oxygen and a Lewis acidic surface atom and (2) a nucleophilic attack of a nearby Lewis basic surface atom is analysed in detail and found to mirror the acid-catalysed ether cleavage in solution. The O-Si dative bond is found to be the strongest of its kind and reactivity from this state defies the Bell-Evans-Polanyi principle...
September 15, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28913646/computational-investigation-of-the-microstructural-characteristics-and-physical-properties-of-glycerol-based-deep-eutectic-solvents
#14
Tayeb Aissaoui, Yacine Benguerba, Mohamed Khalid AlOmar, Inas M AlNashef
Recently, there has been significant interest in the possibility of using deep eutectic solvents (DESs) as novel green media and alternatives to conventional solvents and ionic liquids (ILs) in many applications. Due to their attractive properties, such as their biodegradability, low cost, easy preparation, and nontoxicity, DESs appear to be very promising solvents for use in the field of green chemistry. This computational study investigated six glycerol-based DESs: DES1 (glycerol:methyl triphenyl phosphonium bromide), DES2 (glycerol:benzyl triphenyl phosphonium chloride), DES3 (glycerol:allyl triphenyl phosphonium bromide), DES4 (glycerol:choline chloride), DES5 (glycerol:N,N-diethylethanolammonium chloride), and DES6 (glycerol:tetra-n-butylammonium bromide)...
September 14, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28910858/overview-of-methods-and-strategies-for-conducting-virtual-small-molecule-screening
#15
REVIEW
Xavier Fradera, Kerim Babaoglu
Virtual screening (VS) in the context of drug discovery is the use of computational methods to discover novel ligands with a desired biological activity from within a larger collection of molecules. These techniques have been in use for many years, there is a wide range of methodologies available, and many successful applications have been reported in the literature. VS is often used as an alternative or a complement to High-throughput screening (HTS) or other methods to identify ligands for target validation or medicinal chemistry projects...
September 14, 2017: Current Protocols in Chemical Biology
https://www.readbyqxmd.com/read/28906074/fully-automated-quantum-chemistry-based-computation-of-spin-spin-coupled-nuclear-magnetic-resonance-spectra-for-molecules
#16
Stefan Grimme, Christoph Bannwarth, Sebastian Dohm, Andreas Hansen, Jana Pisarek, Philipp Pracht, Jakob Seibert, Frank Neese
We present a composite procedure for the quantum chemical computation of spin-spin coupled 1H-NMR spectra for general, flexible molecules in solution. It is based on four main steps, namely, conformer/rotamer ensemble (CRE) generation by the fast tight-binding method GFN-xTB and a newly developed search algorithm, relative free energy and NMR parameter computation, and solution of the spin-Hamiltonian. In this way the NMR-specific nuclear permutation problem is solved and the correct spin-symmetries are obtained...
September 14, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28905070/sodium-cationized-carbohydrate-gas-phase-fragmentation-chemistry-influence-of-glycosidic-linkage-position
#17
Jordan M Rabus, Maha T Abutokaikah, Reginald T Ross, Benjamin J Bythell
We investigate the gas-phase structures and fragmentation chemistry of two isomeric sodium-cationized carbohydrates using combined tandem mass spectrometry, hydrogen/deuterium exchange experiments, and computational methods. Our model systems are the glucose-based disaccharide analytes cellobiose (β-d-glucopyranosyl-(1 → 4)-d-glucose) and gentiobiose (β-d-glucopyranosyl-(1 → 6)-d-glucose). These analytes show substantially different tandem mass spectra. We characterize the rate-determining barriers to both the glycosidic and structurally-informative cross-ring bond cleavages...
September 14, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28902958/nonregenerative-immune-mediated-anemia-associated-with-a-diffuse-large-b-cell-lymphoma-in-a-captive-jaguar-panthera-onca
#18
Monika A Keresztes, Manfred Henrich, Penelope Baloi, Sascha Gerst, Jens-Christian Rudnick, Judith Langenstein, Andreas Moritz, Natali Bauer
An 18-year-old male castrated jaguar (Panthera onca) was presented with anorexia and continuous bleeding from the oral cavity after a history of fighting with the partner animal. Clinical evaluation revealed ulcerating lesions on the gingiva and hard palate and a hematoma on the tongue. Computed tomography of the head and endoscopic examination of the esophagus and stomach were unremarkable. Hematology and clinical chemistry revealed severe nonregenerative anemia, mild thrombocytopenia, and moderate azotemia...
September 13, 2017: Veterinary Clinical Pathology
https://www.readbyqxmd.com/read/28898788/molecular-modelling-and-quantum-biochemistry-computations-of-a-naturally-occurring-bioremediation-enzyme-alkane-hydroxylase-from-pseudomonas-putida-p1
#19
B G de Sousa, J I N Oliveira, E L Albuquerque, U L Fulco, V E Amaro, C A G Blaha
Many species of bacteria involved in degradation of n-alkanes have an important constitutional metabolic enzyme, the alkane hydroxylase called AlkB, specialized in the conversion of hydrocarbons molecules that can be used as carbon and/or energy source. This enzyme plays an important role in the microbial degradation of oil, chlorinated hydrocarbons, fuel additives, and many other compounds. A number of these enzymes has been biochemically characterized in detail because the potential of alkane hydroxylases to catalyse high added-value reactions is widely recognized...
September 1, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28898486/high-pressure-chemistry-and-the-mechanochemical-polymerization-of-5-cyclo-p-phenylene
#20
Lili Qiu, Miriam Peña-Alvarez, Mercedes Taravillo, Paul J Evans, Evan Darzi, Ramesh Jasti, P Mayorga Burrezo, Juan T López Navarrete, Valentín G Baonza, Juan Casado, Miklos Kertesz
We find evidence for the surprising formation of polymeric phases under high pressure for conjugated nanohoop molecules. This paper represents one of the unique cases where the molecular-level effects of pressure in crystalline organic solids is addressed and provides a suitable general approach based on vibrational Raman spectroscopy combining experiments and computations. In particular we studied the structural and supramolecular chemistry of the cyclic conjugated nanohoop molecule, [5]cyclo-para-phenylene under high pressures of 0 to 10 GPa...
September 12, 2017: Chemistry: a European Journal
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