keyword
MENU ▼
Read by QxMD icon Read
search

computational chemistry

keyword
https://www.readbyqxmd.com/read/28229155/sulfate-radical-oxidation-of-aromatic-contaminants-a-detailed-assessment-of-density-functional-theory-and-high-level-quantum-chemical-methods
#1
Sangavi Pari, Inger A Wang, Haizhou Liu, Bryan M Wong
Advanced oxidation processes that utilize highly oxidative radicals are widely used in water reuse treatment. In recent years, the application of sulfate radical (SO4˙(-)) as a promising oxidant for water treatment has gained increasing attention. To understand the efficiency of SO4˙(-) in the degradation of organic contaminants in wastewater effluent, it is important to be able to predict the reaction kinetics of various SO4˙(-)-driven oxidation reactions. In this study, we utilize density functional theory (DFT) and high-level wavefunction-based methods (including computationally-intensive coupled cluster methods), to explore the activation energies of SO4˙(-)-driven oxidation reactions on a series of benzene-derived contaminants...
February 23, 2017: Environmental Science. Processes & Impacts
https://www.readbyqxmd.com/read/28226222/computer-simulations-of-intrinsically-disordered-proteins
#2
Song-Ho Chong, Prathit Chatterjee, Sihyun Ham
The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and molecular biology that requires a new paradigm to connect structural disorder to function. Molecular dynamics simulations and statistical thermodynamics potentially offer ideal tools for atomic-level characterizations and thermodynamic descriptions of this fascinating class of proteins that will complement experimental studies. However, IDPs display sensitivity to inaccuracies in the underlying molecular mechanics force fields...
February 6, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28221714/photonic-devices-out-of-equilibrium-transient-memory-signal-propagation-and-sensing
#3
Thomas Heuser, Rémi Merindol, Sebastian Loescher, Aileen Klaus, Andreas Walther
Soft photonic materials are important for sensors, displays, or energy management and have become switchable under static equilibrium conditions by integration of responsive polymer features. The next step is to equip such materials with the ability for autonomously dynamic and self-regulating behavior, which would advance their functionality and application possibilities to new levels. Here, this study shows the system integration of a nonlinear, biocatalytic pH-feedback system with a pH-responsive block copolymer photonic gel, and demonstrates autonomous transient memories, remotely controlled signal propagation, and sensing...
February 21, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28221002/computational-biology-and-chemistry-in-mti-emphasis-on-the-prediction-of-some-admet-properties
#4
REVIEW
Maria A Miteva, Bruno O Villoutreix
Our research and teaching group called MTi (Molécules Thérapeutiques in silico) has developed numerous applications available online, thanks to the RPBS platform (Ressource Parisienne en Bioinformatique Structurale), in the field of chemoinformatics, structural bioinformatics and drug design. Since its opening in 2009, over 200 articles/reviews have been reported and involve virtual screening studies, prediction of druggability, analysis of protein-protein interaction inhibitors, development of databases, data mining and knowledge discovery, as well as combined in silico-in vitro work to search for new hits and chemical probes acting on original targets in several therapeutic areas...
February 21, 2017: Molecular Informatics
https://www.readbyqxmd.com/read/28218326/diffusive-confinement-of-free-radical-intermediates-in-the-oh-radical-oxidation-of-semisolid-aerosols
#5
Aaron A Wiegel, Matthew J Liu, William D Hinsberg, Kevin R Wilson, Frances A Houle
Multiphase chemical reactions (gas + solid/liquid) involve a complex interplay between bulk and interface chemistry, diffusion, evaporation, and condensation. Reactions of atmospheric aerosols are an important example of this type of chemistry: the rich array of particle phase states and multiphase transformation pathways produce diverse but poorly understood interactions between chemistry and transport. Their chemistry is of intrinsic interest because of their role in controlling climate. Their characteristics also make them useful models for the study of principles of reactivity of condensed materials under confined conditions...
February 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28217147/automatic-procedure-for-generating-symmetry-adapted-wavefunctions
#6
Marcus Johansson, Valera Veryazov
Automatic detection of point groups as well as symmetrisation of molecular geometry and wavefunctions are useful tools in computational quantum chemistry. Algorithms for developing these tools as well as an implementation are presented. The symmetry detection algorithm is a clustering algorithm for symmetry invariant properties, combined with logical deduction of possible symmetry elements using the geometry of sets of symmetrically equivalent atoms. An algorithm for determining the symmetry adapted linear combinations (SALCs) of atomic orbitals is also presented...
2017: Journal of Cheminformatics
https://www.readbyqxmd.com/read/28212487/interactions-between-membranes-and-metaphilic-polypeptide-architectures-with-diverse-sidechain-populations
#7
Michelle W Lee, Ming Han, Guilherme Volpe Bossa, Carly Snell, Ziyuan Song, Haoyu Tang, Lichen Yin, Jianjun Cheng, Sylvio May, Erik Luijten, Gerard C L Wong
At physiological conditions, most proteins or peptides can fold into relatively stable structures that present on their molecular surfaces specific chemical patterns partially smeared out by thermal fluctuations. These nanoscopically defined patterns of charge, hydrogen bonding, and/or hydrophobicity, along with their elasticity and shape stability (folded proteins have Young's moduli of ~1 × 10(8) Pa), largely determine and limit the interactions of these molecules, such as molecular recognition and allosteric regulation...
February 17, 2017: ACS Nano
https://www.readbyqxmd.com/read/28211697/benchmarking-density-functionals-for-chemical-bonds-of-gold
#8
Kasper P Kepp
Gold plays a major role in nanochemistry, catalysis, and electrochemistry. Accordingly, hundreds of studies apply density functionals to study chemical bonding with gold, yet there is no systematic attempt to assess the accuracy of these methods applied to gold. This paper reports a benchmark against 51 experimental bond enthalpies of AuX systems and seven additional polyatomic and cationic molecules. Twelve density functionals were tested, covering meta functionals, hybrids with variable HF exchange, double-hybrid, dispersion-corrected, and nonhybrid GGA functionals...
February 24, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28210880/can-fe-3-and-al-3-ions-serve-as-cationic-bridges-to-facilitate-the-adsorption-of-anionic-as-v-species-on-humic-acids-a-density-functional-theory-study
#9
Leonid Gorb, Manoj K Shukla
A computational chemistry investigation was undertaken to shed light on the facilitatory role played by Fe(3+) and Al(3+) cations in the adsorption of anionic As(V) species by humic acids through the formation of so-called cationic bridges. Geometric and energetic parameters were obtained using density functional theory at the B3LYP/6-31G(d,p) level in conjunction with the polarizable continuum model (to account for the influence of bulk water). We found that, despite their similar molecular geometries, the adsorption energies of the As(V) species AsO4(3-) and H2AsO(4-) differ when Fe(3+), FeOH(2+), Al(3+), and AlOH(2+) participate in the bridge...
March 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28210731/pressure-driven-phase-transition-mechanisms-revealed-by-quantum-chemistry-l-serine-polymorphs
#10
Denis A Rychkov, Jernej Stare, Elena V Boldyreva
The present study delivers a computational approach for the understanding of the mechanism of phase transitions between polymorphs of small organic molecules. By using state of the art periodic DFT calculations augmented with dispersion corrections and an external stress tensor together with gas-phase cluster calculations, we thoroughly explained the reversible phase transitions of three polymorphs of the model system, namely crystalline l-serine in the pressure range up to 8 GPa. This study has shown that at the macroscopic level the main driving force of the phase transitions is the decrease in the volume of the crystal unit cell, which contributes to the enthalpy difference between the two forms, but not to the difference in their internal crystal energies...
February 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28210619/a-useful-tool-as-a-medical-checkup-in-a-general-population-bioelectrical-impedance-analysis
#11
Mika Enomoto, Hisashi Adachi, Ako Fukami, Eita Kumagai, Sachiko Nakamura, Yume Nohara, Shoko Kono, Erika Nakao, Nagisa Morikawa, Tomoko Tsuru, Akiko Sakaue, Yoshihiro Fukumoto
Accumulation of visceral fat leads to metabolic syndrome and increases risks of cerebro-cardiovascular diseases, which should be recognized and improved at the early stage in general population. Accurate measurement of visceral fat area (VFA) is commonly performed by the abdominal cross-sectional image measured by computed tomography scan, which is, however, limited due to the radiation exposure. The bioelectrical impedance analysis (OMRON, HDS-2000 DUALSCAN(R)) has been recently developed to measure VFA, which is more easily accessible modality...
2017: Frontiers in Cardiovascular Medicine
https://www.readbyqxmd.com/read/28205402/quantum-chemistry-descriptors-for-photosensitizers-based-on-macrocycles
#12
Fernanda Bettanin, Felipe C T Antonio, Kathia M Honorio, Paula Homem-de-Mello
Phthalocyanines, porphyrins, and chlorins have been widely studied as photosensitizers. Both experimental and computational strategies are employed in order to propose new and more active molecules derived from those macrocycles. In this context, there are two main strategies used: (i) the addition of different substituents and (ii) the complexation of the macrocycle with different metallic ions. In this work, we present selected descriptors based on quantum chemistry calculations for forty macrocycles, including some approved drugs...
February 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28205401/computer-aided-drug-design-to-explore-cyclodextrin-therapeutics-and-biomedical-applications
#13
Azizeh Abdolmaleki, Fatemeh Ghasemi, Jahan B Ghasemi
Cyclodextrin (CD) is a subset of the macrocyclic structural class, which is an important class of small organic agents that are useful functional excipients. They have wide range application possibilities in different fields of sciences such as material preparation, medicine, analytical chemistry, and separation processes. They are used widely in pharmaceutical formulations and drug delivery for increasing the water solubility of low soluble drugs and drug candidates. Due to the ring structure, they behave differently than smaller molecules and may be capable of hitting new classes of targets...
February 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28201891/electron-transport-through-a-spin-crossover-junction-perspectives-from-a-wavefunction-based-approach
#14
Sergi Vela, Martin Verot, Emmanuel Fromager, Vincent Robert
The present paper reports the application of a computational framework, based on the quantum master equation, the Fermi's golden Rule, and conventional wavefunction-based methods, to describe electron transport through a spin crossover molecular junction (Fe(bapbpy) (NCS)2, 1, bapbpy = N-(6-(6-(Pyridin-2-ylamino)pyridin-2-yl)pyridin-2-yl)-pyridin-2-amine). This scheme is an alternative to the standard approaches based on the relative position and nature of the frontier orbitals, as it evaluates the junction's Green's function by means of accurate state energies and wavefunctions...
February 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28191571/a-computer-based-prediction-platform-for-the-reaction-of-ozone-with-organic-compounds-in-aqueous-solution-kinetics-and-mechanisms
#15
Minju Lee, Lorenz C Blum, Emanuel Schmid, Kathrin Fenner, Urs von Gunten
Ozonation of secondary wastewater effluents can reduce the discharge of micropollutants by transforming their chemical structures. Therefore, a better understanding of the formation of transformation products during ozonation is important. In this study, a computer-based prediction platform for the kinetics and mechanisms of the reactions of ozone with organic compounds was developed to enable in silico predictions of transformation products. With the developed prediction platform, reaction kinetics expressed as second-order rate constants for the reactions of ozone with selected organic compounds (kO3, M(-1) s(-1)) can be predicted based on an adapted kO3 prediction model from a previous study (Lee et al...
February 13, 2017: Environmental Science. Processes & Impacts
https://www.readbyqxmd.com/read/28188808/characterization-of-a-novel-intrinsically-radiopaque-drug-eluting-bead-for-image-guided-therapy-dc-bead-lumi%C3%A2
#16
Koorosh Ashrafi, Yiqing Tang, Hugh Britton, Orianne Domenge, Delphine Blino, Andrew J Bushby, Kseniya Shuturminska, Mark den Hartog, Alessandro Radaelli, Ayele H Negussie, Andrew S Mikhail, David L Woods, Venkatesh Krishnasamy, Elliot B Levy, Bradford J Wood, Sean L Willis, Matthew R Dreher, Andrew L Lewis
We have developed a straightforward and efficient method of introducing radiopacity into Polyvinyl alcohol (PVA)-2-Acrylamido-2-methylpropane sulfonic acid (AMPS) hydrogel beads (DC Bead™) that are currently used in the clinic to treat liver malignancies. Coupling of 2,3,5-triiodobenzaldehyde to the PVA backbone of pre-formed beads yields a uniformly distributed level of iodine attached throughout the bead structure (~150mg/mL) which is sufficient to be imaged under standard fluoroscopy and computed tomography (CT) imaging modalities used in treatment procedures (DC Bead LUMI™)...
February 8, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28186737/metal-like-boronic-organic-frameworks-a-design-and-computation
#17
Xingfa Gao, Xuejiao J Gao
Because of the lack of strong π-interaction in their bonds connecting building units, most of the metal-organic frameworks (MOFs) and covalent-organic frameworks (COFs) achieved so far are insulators or wide-bandgap semiconductors. The design of metal-like frameworks based on known chemical components is a challenge. This work reports that aryl borons can be linked together through isocyanides to form stable and easily accessible low-dimensional boronic-organic frameworks (BOFs). Particularly, the boron atoms in the BOFs behave like transition metals, forming the combined σ-donation and π-backdonation bonds instead of the usual electron-sharing bonds with the isocyanide linkers...
February 10, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28185910/ultrasoft-microwire-neural-electrodes-improve-chronic-tissue-integration
#18
Zhanhong Jeff Du, Christi L Kolarcik, Takashi D Y Kozai, Silvia D Luebben, Shawn A Sapp, Xin Sally Zheng, James A Nabity, X Tracy Cui
: Chronically implanted neural multi-electrode arrays (MEA) are an essential technology for recording electrical signals from neurons and/or modulating neural activity through stimulation. However, current MEAs, regardless of the type, elicit an inflammatory response that ultimately leads to device failure. Traditionally, rigid materials like tungsten and silicon have been employed to interface with the relatively soft neural tissue. The large stiffness mismatch is thought to exacerbate the inflammatory response...
February 6, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28181017/theoretical-studies-of-some-bimolecular-reactions-during-the-decomposition-of-ch3no2-reactions-between-no2-and-nine-intermediates
#19
Ji-Dong Zhang, Li-Li Zhang, Xin-Lu Cheng
Nitromethane (NM, CH3NO2) is a widely studied energetic material, and its decomposition mechanism attracts great interest. In this work, bimolecular reactions between NO2 and nine intermediates generated during the decomposition of NM were investigated by computational chemistry methods. The mechanisms of the reactions were analyzed. The results revealed that these reactions possess small barriers and can easily occur, so they may be responsible for NO2 loss during the decomposition of NM.
February 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28177949/progress-with-structure-activity-relationship-modelling-of-occupational-chemical-respiratory-sensitizers
#20
Martin J Seed, Raymond M Agius
PURPOSE OF REVIEW: This appraises currently available computer-based ('in silico') models relating the molecular structure of low molecular weight compounds to their respiratory sensitization hazard. The present review places focus on the two main applications of such structure--activity relationship (SAR) models: hypotheses on disease mechanisms and toxicological prediction. RECENT FINDINGS: Analyses of the chemical structures of low molecular weight organic compounds known to have caused occupational asthma has led to the development of mechanistic alerts usually based on electrophilic reaction chemistry and protein cross-linking potential...
February 7, 2017: Current Opinion in Allergy and Clinical Immunology
keyword
keyword
64837
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"