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https://www.readbyqxmd.com/read/30549074/electronic-and-ligating-properties-of-carbocyclic-carbenes-a-theoretical-investigation
#1
Shweta Bhagat, Minhajul Arfeen, Gourav Das, Neha Patel, Prasad V Bharatam
Carbocyclic carbenes (CCCs) are a class of nucleophilic carbenes which are very similar to N-heterocyclic carbenes (NHCs) in terms of their reactivity, but they do not contain a stabilizing heteroatom in their cyclic ring system. In this study, 17 representative known CCCs and 34 newly designed CCCs are evaluated using quantum chemical methods, and the results are compared in terms of their stability, nucleophilicity, and proton affinity (PA) parameters. The results are divided on the basis of ring size of the known and reported CCCs...
December 14, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/30548654/a-fast-scheme-to-calculate-electronic-couplings-between-p3ht-polymer-units-using-diabatic-orbitals-for-charge-transfer-dynamics-simulations
#2
Tao Yu, Florence Fabunmi, Jingsong Huang, Bobby G Sumpter, Jacek Jakowski
We propose a fast and accurate calculation method to compute the electronic couplings between molecular units in a thiophene-ring-based polymer chain mimicking a real organic semiconducting polymer, poly(3-hexylthiophene). Through a unit block diabatization scheme, the method employed minimal number of diabatic orbitals to compute the site energies and electronic couplings, which were validated by comparing with benchmark density functional theory calculations. In addition, by using the obtained electronic couplings, a quantum dynamics simulation was carried out to propagate a hole initially localized in a thiophene-ring unit of the polymer chain...
January 15, 2019: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/30544580/novel-terpenoids-with-potent-cytotoxic-activities-from-resina-commiphora
#3
Bin-Yuan Hu, Da-Peng Qin, Shao-Xiang Wang, Jing-Jing Qi, Yong-Xian Cheng
A novel sesquiterpene dimer, spirocommiphorfuran A ( 1 ); two new cadinane sesquiterpenoids, commiphorenes A ( 2 ) and B ( 3 ); along with three known terpenoids ( 4 ⁻ 6 ), were isolated from Resina Commiphora . The structures of these new compounds were characterized by NMR, HRESIMS, quantum chemical computation, and X-ray diffraction analysis. Compound 1 features a 7-oxabicyclo[2.2.1]heptane-2-ene core, representing the first example of germacrane-type sesquiterpene dimer fused via a spiro ring system. Compound 2 is a novel sesquiterpene with a completely new carbon skeleton, which is characteristic of an additional carbon attaching to the cadinane backbone via a carbon⁻carbon bond...
December 7, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/30544011/does-the-wavelength-dependent-photoisomerization-process-of-the-p%C3%A2-coumaric-acid-come-out-from-the-electronic-state-dependent-pathways
#4
Li Zhao, Jianyong Liu, Panwang Zhou
Similar to the anion photoactive yellow protein (PYP) chromophore, the neutral form of the PYP chromophore was also found to exhibit a the wavelength-dependent photoisomerization quantum yield. The isomerization quantum yield increases with the increasing excitation energy on the S1 state, while decreases when being excited to the S2 state. Does this wavelength dependent product yield come out from the specific reaction pathways of the S1 and S2 states? This would mean that, the relaxation pathway of the S2 state is distinct from that of the S1 state and does not involve twisting motion...
December 5, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/30543247/a-theoretical-study-of-5-6-7-8-tetrahydro-6-hydroxymethylpterin-insight-into-intrinsic-photoreceptor-properties-of-6-substituted-tetrahydropterins
#5
A A Buglak, T A Telegina
Tetrahydropterins are essential biological cofactors, which play a crucial role in DNA and RNA syntheses, NO synthesis, hydroxylation of aromatic amino acids, etc. In the last few years, it has been shown that 6-substituted "unconjugated" tetrahydropterins can also play a photoreceptor chromophoric role in plants and cyanobacteria. However, the nature of the initial light signal transduction act in which H4pterins participate is unknown. Our quantum chemical calculations have shown the possibility of the fast internal conversion of excited states of H4pterins...
December 13, 2018: Photochemical & Photobiological Sciences
https://www.readbyqxmd.com/read/30543112/solid-state-order-and-charge-mobility-in-5-12-cycloparaphenylenes
#6
Janice B Lin, Evan R Darzi, Ramesh Jasti, Ilhan Yavuz, Kendall N Houk
We report a computational study of mesoscale morphology and charge transport properties of radially π-conjugated cycloparaphenylenes [n]CPPs of various ring sizes (n = 5-12, where n is the number of repeating phenyl units). These molecules are considered as structural constituents of fullerenes and carbon nanotubes. [n]CPP molecules are nested in a unique fashion in the solid state. Molecular dynamics simulations show that while intramolecular structural stability (order) increases with system size, intermolecular structural stability reduces...
December 13, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/30542690/tuning-the-electrochemiluminescent-properties-of-iridium-complexes-of-n-heterocyclic-carbene-ligands
#7
Linh M Quan, Bradley D Stringer, Mohammad A Haghighatbin, Johnny Agugiaro, Gregory J Barbante, David J D Wilson, Conor F Hogan, Peter J Barnard
A series of five heteroleptic Ir(iii) complexes of the general form Ir(dfppy)2(C^C) have been prepared (where dfppy represents 2-(2,4-difluorophenyl)pyridine and C^C represents a bidentate cyclometalated phenyl substituted imidazolylidene ligand). The cyclometalated phenyl ring of the imidazolylidene ligand was either unsubstituted or substituted with electron donating (OMe and Me) or electron withdrawing (Cl and F) groups in the 2 and 4 positions. The synthesised Ir(iii) complexes have been characterised by elemental analysis, NMR spectroscopy, cyclic voltammetry and electronic absorption and emission spectroscopy...
December 13, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/30540313/%C3%AF-hydrogen-bonding-and-aromaticity-a-systematic-interplay-study
#8
A-Reza Nekoei, Morteza Vatanparast
Quantum DFT calculations, corrected for long-range interactions, have been carried out on complex models formed between HF as a proton donor and 2-methylene-2H-indene derivatives as proton acceptors. Using various exocyclic X substitutions, mutual effects of the aromaticity and the strength of the resulting π-hydrogen bond (after its evaluation by AIM methodology) have been investigated. The results show that the aromaticity of 6-membered rings and the hydrogen bond strength increase upon increasing the electron-donating character of the X-substituents...
December 12, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/30534683/using-a-monomer-potential-energy-surface-to-perform-approximate-path-integral-molecular-dynamics-simulation-of-ab-initio-water-at-near-zero-added-cost
#9
Daniel C Elton, Michelle Fritz, Marivi Fernández-Serra
It is now established that nuclear quantum motion plays an important role in determining water's hydrogen bonding, structure, and dynamics. Such effects are important to include in density functional theory (DFT) based molecular dynamics simulation of water. The standard way of treating nuclear quantum effects, path integral molecular dynamics (PIMD), multiplies the number of energy/force calculations by the number of beads required. In this work we introduce a method whereby PIMD can be incorporated into a DFT simulation with little extra cost and little loss in accuracy...
December 10, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/30530072/new-tirucallane-triterpenoids-from-picrasma-quassioides-with-their-potential-antiproliferative-activities-on-hepatoma-cells
#10
Wen-Yu Zhao, Jing-Jie Chen, Chun-Xin Zou, Ying-Ying Zhang, Guo-Dong Yao, Xiao-Bo Wang, Xiao-Xiao Huang, Bin Lin, Shao-Jiang Song
Seven new tirucallane-type triterpenoids (1-7), kumuquassin A-G, along with 20 known analogues (8-27) were isolated from the stems of Picrasma quassioides. The structures and the absolute configurations of new compounds were elucidated by spectroscopic data, electronic circular dichroism (ECD) spectroscopic analyses and quantum ECD calculations. Notably, kumuquassin A (1) contains a rare Δ17, 20 double bond, kumuquassin B (2) is the first example of tirucallane triterpenoid possessing a 5/3 biheterocyclic ring system at the side chain...
November 28, 2018: Bioorganic Chemistry
https://www.readbyqxmd.com/read/30526469/dpp-iv-inhibitory-phenanthridines-ligand-structure-based-design-and-synthesis
#11
Reema Abu Khalaf, Dalal Masalha, Dima Sabbah
BACKGROUND: Lately, diabetes has become a main health concern for millions of people around the world. Dipeptidyl peptidase-IV (DPP-IV) inhibitors have emerged as a new class of oral antidiabetic agents. Formerly, acridines, N4-sulfonamido-succinamic, phthalamic, acrylic and benzoyl acetic acid derivatives, and sulfamoyl-phenyl acid esters were designed and developed as new DPP-IV inhibitors. OBJECTIVE: This study aims to develop a pharmacophore model of DPP-IV inhibitors and to evaluate phenanthridines as a novel scaffold for inhibiting DPP-IV enzyme...
December 10, 2018: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/30525520/effects-of-varying-the-benzannulation-site-and-%C3%AF-conjugation-of-the-cyclometalating-ligand-on-the-photophysics-and-reverse-saturable-absorption-of-monocationic-iridium-iii-complexes
#12
Bingqing Liu, Levi Lystrom, Svetlana Kilina, Wenfang Sun
A series of monocationic iridium(III) complexes, [Ir(C^N)2 (pqu)]+ PF6 - [pqu = 2-(pyridin-2-yl)quinoline, C^N = 2-phenylquinoline (1), 3-phenylisoquinoline (2), 1-phenylisoquinoline (3), benzo[ h]quinoline (4), 2-(pyridin-2-yl)naphthalene (5), 1-(pyridin-2-yl)naphthalene (6), 2-(phenanthren-9-yl)pyridine (7), 2-phenylbenzo[ g]quinoline (8), 2-(naphthalen-2-yl)quinoline (9), and 2-(naphthalen-2-yl)benzo[ g]quinoline (10)], were synthesized in this work. These complexes bear C^N ligands with varied degrees of π conjugation and sites of benzannulation, allowing for elucidation of the effects of the benzannulation site at the C^N ligand on the photophysics of the complexes...
December 10, 2018: Inorganic Chemistry
https://www.readbyqxmd.com/read/30525412/thermal-stability-and-detonation-properties-of-potassium-4-4-bis-dinitromethyl-3-3-azofurazanate-an-environmental-friendly-energetic-three-dimensional-metal-organic-framework
#13
Dezhou Guo, Qi An
Environmentally acceptable alternatives to toxic lead-based primary explosives become increasingly demanding for energetic materials (EMs) because of environmental concerns. Recent experiments suggested that energetic three-dimensional (3D) metal-organic frameworks (MOFs) are promising candidates for the next generation of environmental friendly primary explosives. A new energetic 3D MOF, denoted as potassium 4,4'-bis(dinitromethyl)-3,3'-azofurazanate, was synthesized and suggested as an excellent candidate for green primary explosives...
December 11, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/30524053/energy-conversion-from-environmental-fluctuations-to-coherent-fields-by-cooper-pair-box-quantum-meta-materials
#14
I-Lin Ho, Watson Kuo
Electromagnetic waves propagating in open Cooper-Pair Boxes (CPBs) system is studied by using Maxwell-Bloch equations and Lindblad master equation. The results demonstrate an ensemble of CPBs as highly non-linear meta-material for electromagnetic waves. Incorporating the CPBs in a ring resonator or a Fabry-Perot cavity, one finds that: (1) With weak environmental couplings and CPBs in superconducting phase dominant regime, the non-linearity is enhanced and the system exhibits regular optical hysteresis. (2) With finite environmental couplings and CPBs in charge dominant regime, the Josephson effect and environmental effect can constructively interplay to produce a gain...
November 19, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/30522268/theoretical-evaluation-of-the-reaction-mechanism-of-serine-hydroxymethyltransferase
#15
Jirapat Santatiwongchai, Duangkamol Gleeson, Matthew Paul Gleeson
Serine hydroxymethyltransferase (SHMT) is a pyridoxal phosphate (PLP) dependent enzyme that catalyzes the reversible conversion of serine and tetrahydrofolate (THF) to glycine and 5,10-methylene THF. SHMT is a folate pathway enzyme and is therefore of considerable medical interest since this is an important intervention point for anti-malarial, anti-cancer and anti-bacterial treatments. Despite considerable experimental effort the precise reaction mechanism of SHMT remains unclear. In this study we explore the reaction mechanism of SHMT with its natural substrates to determine the roles of each active site residue and the nature and the sequence of chemical steps...
December 6, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/30521341/selectivity-map-for-molecular-beam-epitaxy-of-advanced-iii-v-quantum-nanowire-networks
#16
Pavel Aseev, Alexandra Fursina, Frenk Boekhout, Filip Krizek, Joachim E Sestoft, Francesco Borsoi, Sebastian Heedt, Guanzhong Wang, Luca Binci, Sara Martí-Sánchez, Timm Swoboda, René Koops, Emanuele Uccelli, Jordi Arbiol, Peter Krogstrup, Leo P Kouwenhoven, Philippe Caroff
Selective area growth is a promising technique to enable fabrication of scalable III-V nanowire networks required to test proposals for Majorana-based quantum computing devices. However, the contours of the growth parameter window resulting in selective growth remain undefined. Herein, we present a set of experimental techniques which unambiguously establish the parameter space window resulting in selective III-V nanowire networks growth by molecular beam epitaxy. Selectivity maps are constructed for both GaAs and InAs compounds based on in situ characterization of growth kinetics on GaAs(001) substrates, where the difference in group III adatom desorption rates between the III-V surface and the amorphous mask area is identified as the primary mechanism governing selectivity...
December 6, 2018: Nano Letters
https://www.readbyqxmd.com/read/30516769/exploring-the-ultrafast-dynamics-of-a-diarylethene-derivative-using-sub-10-fs-laser-pulses
#17
Arkadiusz Jarota, Ewa Pastorczak, Walid Tawfik, Bing Xue, Rafał Kania, Halina Abramczyk, Takayoshi Kobayashi
A diarylethene derivative, 1,2-bis(2,4-dimethyl-5-phenyl-3-thienyl)perfluorocyclopentene (DMP), is a photoswitch molecule utilizing a reversible aromatic ring-opening reaction. The quantum yield of the ring-opening reaction is however remarkably low. We investigate the origin of this behaviour by means of ultrafast transient absorption spectroscopy utilizing sub-10 fs pulses, which is an invaluable tool for simultaneously studying both the electronic and the vibrational molecular dynamics. Namely, a noncollinear optical parametric amplifier (NOPA) generating sub-10 fs pulses in the spectral range 605-750 nm is employed...
December 5, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/30511862/criegee-intermediate-reaction-with-alcohol-is-enhanced-by-a-single-water-molecule
#18
Yen-Hsiu Lin, Cangtao Yin, Wei-Hong Lin, Yu-Lin Li, Kaito Takahashi, Jim Jr-Min Lin
The role of water in gas phase reactions has gained considerable interests. Here we report a direct kinetic measurement of the reaction of syn-CH3CHOO (a Criegee intermediate or carbonyl oxide) with methanol at various relative humidity (RH = 0-80%) under near ambient conditions (298 K, 250-755 Torr). The data indicate that a single water molecule expedites the reaction by upto a factor of 3. The rate coefficient of the corresponding reaction, syn-CH3CHOO + CH3OH + H2O → products, has been determined to be (2...
December 4, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30508759/revealing-structural-involvement-of-chromophores-in-algal-light-harvesting-complexes-using-symmetry-adapted-perturbation-theory
#19
Zi S D Toa, Jacob C Dean, Gregory D Scholes
The attribution of quantum beats observed in the time-resolved spectroscopy of photosynthetic light-harvesting antennae to nontrivial quantum coherences has sparked a flurry of research activity beginning a decade ago. Even though investigations into the functional aspects of photosynthetic light-harvesting were supported by X-ray crystal structures, the non-covalent interactions between pigments and their local protein environment that drive such function has yet to be comprehensively explored. Using symmetry-adapted perturbation theory (SAPT), we have comprehensively determined the magnitude and compositions of these non-covalent interactions involving light-harvesting chromophores in two quintessential photosynthetic pigment-protein complexes - peridinin chlorophyll-a protein (PCP) from dinoflagellate Amphidinium carterae and phycocyanin 645 (PC645) from cryptophyte Chroomonas mesostigmatica...
November 19, 2018: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/30508317/the-effective-conjugation-length-is-responsible-for-the-red-green-spectral-tuning-in-the-cyanobacteriochrome-slr1393g3
#20
Christian Wiebeler, Aditya Gopalakrishna Rao, Wolfgang Gärtner, Igor Schapiro
The origin of the spectral shift from a red- to a green-absorbing form in a cyanobacteriochrome, Slr1393g3, is identified by application of combined quantum mechanics/molecular mechanics simulations. This protein, related to classical phytochromes, carries the open-chain tetrapyrrole chromophore phycocyanobilin. Our calculations reveal that the effective conjugation length in the chromophore becomes shorter upon conversion from the red to the green form. This is related to the planarity of the entire chromophore...
December 3, 2018: Angewandte Chemie
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