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https://www.readbyqxmd.com/read/28649242/an-approach-for-a-synthetic-ctl-vaccine-design-against-zika-flavivirus-using-class-i-and-class-ii-epitopes-identified-by-computer-modeling
#1
Edecio Cunha-Neto, Daniela S Rosa, Paul E Harris, Tim Olson, Alex Morrow, Serban Ciotlos, Charles V Herst, Reid Martin Rubsamen
The threat posed by severe congenital abnormalities related to Zika virus (ZKV) infection during pregnancy has turned development of a ZKV vaccine into an emergency. Recent work suggests that the cytotoxic T lymphocyte (CTL) response to infection is an important defense mechanism in response to ZKV. Here, we develop the rationale and strategy for a new approach to developing cytotoxic T lymphocyte (CTL) vaccines for ZKV flavivirus infection. The proposed approach is based on recent studies using a protein structure computer model for HIV epitope selection designed to select epitopes for CTL attack optimized for viruses that exhibit antigenic drift...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28648259/semisynthesis-and-spectral-characterization-of-5-methylpyranopelargonidin-and-4-methylfuropelargonidin-and-their-separation-and-detection-in-strawberry-fruit-wine
#2
Ondřej Kurka, Lukáš Kučera, Helena Pelantová, Marek Kuzma, Vladimír Havlíček, Petr Bednář
Condensation of anthocyanins and their aglycons with small organic molecules yields more stable natural dyes, e.g. pyranoanthocyanins arising spontaneously in various food products. Reaction of pelargonidin with acetone produces two isomeric anthocyanidin dyes - 5-methylpyranopelargonidin and 4-methylfuropelargonidin. A robust semipreparative liquid chromatographic method was developed to isolate both derivatives from a simple aged solution of pelargonidin in methanol: acetone: 37% aqueous hydrochloric acid (1:1:0...
June 17, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28646663/experimental-determination-of-the-absolute-infrared-absorption-intensities-of-formyl-radical-hco
#3
Sergey V Ryazantsev, Daniil A Tyurin, Vladimir I Feldman
Formyl radical HCO is an important reactive intermediate in combustion, atmospheric and extraterrestrial chemistry. Like in the case of other transients, the lack of knowledge of the absolute IR intensities limits the quantitative spectroscopic studies on this species. We report the first experimental determination of the absorption intensities for the fundamental vibrational bands of HCO. The measurements have been performed using matrix-isolation FTIR spectroscopy. Determination of the values was based on the repeated photodissociation and thermal recovery of the HCO radical using the known value of the absorption coefficient of CO...
June 15, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28644616/importance-of-a-fully-anharmonic-treatment-of-equilibrium-isotope-fractionation-properties-of-dissolved-ionic-species-as-evidenced-by-li-aq
#4
Romain Dupuis, Magali Benoit, Mark E Tuckerman, Merlin Méheut
Equilibrium fractionation of stable isotopes is critically important in fields ranging from chemistry, including medicinal chemistry, electrochemistry, geochemistry, and nuclear chemistry, to environmental science. The dearth of reliable estimates of equilibrium fractionation factors, from experiment or from natural observations, has created a need for accurate computational approaches. Because isotope fractionation is a purely quantum mechanical phenomenon, exact calculation of fractionation factors is nontrivial...
June 23, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28641555/supervised-machine-learning-methods-applied-to-predict-ligand-binding-affinity
#5
Gabriela Sehnem Heck, Val Oliveira Pintro, Richard Rene Pereira, Mauricio Boff de Ávila, Nayara Maria Bernhardt Levin, Walter Filgueira de Azevedo
BACKGROUND: Calculation of ligand-binding affinity is an open problem in computational medicinal chemistry. The ability to computationally predict affinities has a beneficial impact in the early stages of drug development, since it allows a mathematical model to assess protein-ligand interactions. Due to the availability of structural and binding information, machine learning methods have been applied to generate scoring functions with good predictive power. OBJECTIVE: Our goal here is to review recent developments in the application of machine learning methods to predict ligand- binding affinity...
June 22, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28641529/irna-2methyl-identify-rna-2-o-methylation-sites-by-incorporating-sequence-coupled-effects-into-general-pseknc-and-ensemble-classifier
#6
Wang-Ren Qiu, Shi-Yu Jiang, Bi-Qian Sun, Xuan Xiao, Xiang Cheng, Kuo-Chen Chou
OBJECTIVE: Being a kind of post-transcriptional modification (PTCM) in RNA, the 2'-O-methylation modification occurs in the processes of life development and disease formation as well. Accordingly, from the angles of both basic research and drug development, we are facing a challenging problem: given an uncharacterized RNA sequence formed by many nucleotides of A (adenine), C (cytosine), G (guanine), and U (uracil), which one can be of 2-O-methylation modification, and which one cannot? Unfortunately, so far no computational method whatsoever has been developed to address such a problem...
June 22, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28640604/parametrizaton-of-a-reactive-force-field-reaxff-for-molecular-dynamics-simulations-of-si-nanoparticles
#7
Giovanni Barcaro, Susanna Monti, Luca Sementa, Vincenzo Carravetta
A novel computational approach, based on classical reactive molecular dynamics simulations (RMD) and quantum chemistry (QC) global energy optimizations, is proposed for modelling large Si nanoparticles. The force field parameters, which can describe bond breaking and formation, are derived by reproducing energetic and structural properties of a set of Si clusters increasing in size. These reference models are obtained through a new protocol based on a joint high temperature RMD/low temperature Basin Hopping QC search...
June 22, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28640293/collision-cross-section-predictions-using-2-dimensional-molecular-descriptors
#8
M T Soper-Hopper, A S Petrov, J N Howard, S-S Yu, J G Forsythe, M A Grover, F M Fernández
Traditional methods for deriving computationally-generated collision cross sections for comparisons with ion mobility-mass spectrometry data require 3-dimensional energy-minimized structures and are often time consuming, preventing high throughput implementation. Here, we introduce a method to predict ion mobility collision cross sections of lipids and peptide analogs important in prebiotic chemistry and other fields. Using less than 100 2-D molecular descriptors this approach resulted in prediction errors of less than 2%...
June 22, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28639657/exploring-the-catalytic-mechanism-of-dihydropteroate-synthase-elucidating-the-differences-between-the-substrate-and-inhibitor
#9
Warot Chotpatiwetchkul, Kanokthip Boonyarattanakalin, Duangkamol Gleeson, M Paul Gleeson
Dihydropteroate synthase (DHPS) catalyzes the condensation of 6-hydroxymethyl-7,8-dihydropterin pyrophosphate (DHPPP) with p-aminobenzoic acid (pABA) and is a well validated target for anti-malarial and anti-bacterial drugs. However, in recent years its utility as a therapeutic target has diminished considerably due to multiple mutations. As such, considerable structural biology and medicinal chemistry effort has been expended to understand and overcome this issue. To date no detailed computational analysis of the protein mechanism has been made despite the detailed crystal structures and multiple mechanistic proposals being made...
June 22, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28636685/interfacial-memristors-in-al-lanio3-heterostructures
#10
Bobo Tian, Pavan Nukala, Mohamed Ben Hassine, Xiaolin Zhao, Xudong Wang, Hong Shen, Jianlu Wang, Shuo Sun, Tie Lin, Jinglan Sun, Jun Ge, Rong Huang, Chungang Duan, Thomas Reiss, Maria Varela, Brahim Dkhil, Xiangjian Meng, Junhao Chu
Memristive devices are promising circuit elements that enable novel computational approaches which go beyond the von-Neumann paradigms. Here by tuning the chemistry at the Al-LaNiO3 (LNO) interface, a metal-metal junction, we engineer good switching behavior with good electroresistance (ON-OFF resistance ratios of 100), and repeatable multiple resistance states. The active material responsible for such a behavior is a self-formed sandwich of an AlxOy layer at the interface obtained by grabbing oxygen by Al from LNO...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28636684/balanced-work-function-as-a-driver-for-facile-hydrogen-evolution-reaction-comprehension-and-experimental-assessment-of-interfacial-catalytic-descriptor
#11
Aleksandar R Zeradjanin, Ashokanand Vimalanandan, George Polymeros, Angel A Topalov, Karl J J Mayrhofer, Michael Rohwerder
A major step in the development of (electro)catalysis would be the possibility to estimate accurately the energetics of adsorption processes related to reaction intermediates. Computational chemistry (e.g. using DFT) developed significantly in that direction and allowed the fast prediction of (electro)catalytic activity trends and improved the general understanding of adsorption at electrochemical interfaces. However, building a reliable and comprehensive picture of electrocatalytic reactions undoubtedly requires experimental assessment of adsorption energies...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28636358/transferable-atom-centered-potentials-for-the-correction-of-basis-set-incompleteness-errors-in-density-functional-theory
#12
Alberto Otero-de-la-Roza, Gino A DiLabio
Recent progress in the accurate calculation of non-covalent interactions has enabled density-functional theory (DFT) to model systems relevant in biological and supramolecular chemistry. The application of DFT methods using atom-centered Gaussian basis sets to large systems is limited by the number of basis functions required to accurately model thermochemistry and, in particular, weak intermolecular interactions. Basis-set incompleteness error (BSIE) arising from the use of incomplete basis sets leads to erroneous intermolecular energies, bond dissociation energies, and structures...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28636351/heats-of-formation-of-medium-size-organic-compounds-from-contemporary-electronic-structure-methods
#13
Yury Minenkov, Heng Wang, Zhandong Wang, S Mani Sarathy, Luigi Cavallo
Computational electronic structure calculations are routinely undertaken to predict thermodynamic properties of the various species. However, the application of highly accurate wave function theory methods, such as the "gold standard" coupled cluster approach including single, double and partly triple excitations in perturbative fashion, CCSD(T), to large molecules is limited due to high computational cost. In this work, the promising domain based local pair natural orbital coupled cluster approach, DLPNO-CCSD(T), has been tested to reproduce 113 accurate formation enthalpies of medium-size molecules (few dozens heavy atoms) important for bio- and combustion chemistry via the reaction based Feller-Peterson-Dixon approach...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28636349/water-dynamics-from-the-surface-to-the-interior-of-a-supramolecular-nanostructure
#14
Julia H Ortony, Baofu Qiao, Christina J Newcomb, Timothy J Keller, Liam C Palmer, Elad Deiss-Yehiely, Monica Olvera de la Cruz, Songi Han, Samuel I Stupp
Water within and surrounding the structure of a biological system adopts context-specific dynamics that mediate virtually all of the events involved in the inner workings of a cell. These events range from protein folding and molecular recognition to the formation of hierarchical structures. Water dynamics are mediated by the chemistry and geometry of interfaces where water and biomolecules meet. Here we investigate experimentally and computationally the translational dynamics of vicinal water molecules within the volume of a supramolecular peptide nanofiber measuring 6...
June 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28635079/oxygen-vacancy-mediated-photocatalysis-of-biocl-reactivity-selectivity-and-perspective
#15
Hao Li, Jie Li, Zhihui Ai, Falong Jia, Lizhi Zhang
Semiconductor photocatalysis is a trustworthy approach to harvest clean solar light for energy conversions, while state-of-the-art catalytic efficiencies are unsatisfactory because of the finite light response and/or robust charge carriers' recombination. Along with the development of modern material characterization techniques and electronic-structure computations, oxygen vacancies (OVs) on real photocatalysts surface, even in infinitesimal concentration, are found to play a more decisive role in determining the kinetics, energetics and mechanisms of photocatalytic reactions...
June 20, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28634602/recent-advances-in-the-computational-chemistry-of-soft-porous-crystals
#16
Guillaume Fraux, François-Xavier Coudert
Here we highlight recent progress in the field of computational chemistry of nanoporous materials, focusing on methods and studies that address the extraordinary dynamic nature of these systems: the high flexibility of their frameworks, the large-scale structural changes upon external physical or chemical stimulation, and the presence of defects and disorder. The wide variety of behavior demonstrated in soft porous crystals, including the topical class of metal-organic frameworks, opens new challenges for computational chemistry methods at all scales...
June 21, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28632384/finite-field-method-for-nonlinear-optical-property-prediction-using-rational-function-approximants
#17
Anand H G Patel, Ahmed A K Mohammed, Peter A Limacher, Paul Woodson Ayers
The finite-field (FF) method is a quick, easy-to-implement tool for the prediction of nonlinear optical properties. Here, we present and explore a novel variant of the FF method, which uses a rational function to fit a molecule's energy with respect to an electric field. Similarly to previous FF methods, factors crucial for the method's accuracy were tuned. These factors include: the number of terms in the function, the distribution of fields used to construct the approximation, and the initial field in the approximation...
June 20, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28632277/variable-temperature-and-high-pressure-crystal-chemistry-of-perovskite-formamidinium-lead-iodide-a-single-crystal-x-ray-diffraction-and-computational-study
#18
Shijing Sun, Zeyu Deng, Yue Wu, Fengxia Wei, Furkan Halis Isikgor, Federico Brivio, Michael W Gaultois, Jianyong Ouyang, Paul D Bristowe, Anthony K Cheetham, Gregor Kieslich
We investigate the variable temperature (100-450 K) and high-pressure (p = ambient - 0.74 GPa) crystal chemistry of the black perovskite formamidinium lead iodide, [(NH2)2CH]PbI3, using single crystal X-ray diffraction. In both cases we find a phase transition to a tetragonal phase. Our experimental results are combined with first principles calculations, providing information about the electronic properties of [(NH2)2CH]PbI3 as well as the most probable orientation of the [(NH2)2CH](+) cations.
June 20, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28631802/aqueous-tantalum-polyoxometalate-reactivity-with-peroxide
#19
Lauren B Fullmer, Christopher E Malmberg, Dylan B Fast, Lindsay A Wills, Paul Ha-Yeon Cheong, Michelle R Dolgos, May Nyman
Peroxide ligation of aqueous metal-oxo clusters provides rich speciation and structural diversity, radiation sensitivity for manipulation with light, and both broadens and shifts pH-range stability. Here we demonstrate peroxide ligation of the polyoxometalate (POM) [Ta6O19](8-). We study in detail solution speciation of the peroxide-substituted cluster, and benchmark it to the peroxide-ligated niobate analogue, [Nb6O10(OH)3(O2)6](5-), whose solid-state structure has been reported. Raman and electrospray ionization mass spectroscopy do not detect any significant differences between the two analogues...
June 20, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28626563/chemistry-with-semi-classical-electrons-reaction-trajectories-auto-generated-by-sub-atomistic-force-fields
#20
Chen Bai, Seyit Kale, Judith Herzfeld
For a century now, "Lewis dots" have been a mainstay of chemical thinking, teaching and communication. However, chemists have assumed that this semi-classical picture of electrons needs to be abandoned for quantitative work, and the recourse in computational simulations has been to the extremes of first principles treatments of electrons on the one hand and force fields that avoid explicit electrons on the other hand. Given both the successes and limitations of these highly divergent approaches, it seems worth considering whether the Lewis dot picture might be made quantitative after all...
June 1, 2017: Chemical Science
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