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Item Metadata only Assessment of quantum chemical methods for the calculation of homolytic N–F bond dissociation energies(Chemical Data Collections, 2016-11-01) Akhmetova, Nuriya; Kaliyeva, Laura; O'Reilly, Robert J.; Nuriya, AkhmetovaAbstract In this article, the performance of a wide range of conventional and double-hybrid DFT methods (in conjunction with Dunning basis sets of double-, triple- and quadruple-zeta quality), as well as a number of Gaussian-n thermochemical protocols are assessed for their ability to compute accurate homolytic N–F bond dissociation energies (BDEs). Their performance is evaluated against a previously reported set of 31 highly accurate gas-phase N–F BDEs obtained using the benchmark-quality W2w thermochemical protocol (See: R.J. O'Reilly, A. Karton, L. Radom, J. Phys. Chem. A2011, 115, 5496.). Out of all of the DFT/basis set combinations investigated, ωB97 and M06-2X (in conjunction with the aug'-cc-pVDZ basis set) offer the lowest mean absolute deviations (MADs= 2.4 and 2.7kJ mol–1, respectively). Of the Gaussian-n procedures, G3X offers the best performance (MAD= 1.4kJ mol–1), whilst the significantly more economical G3X(MP2)-RAD method also offers excellent performance (MAD= 1.8kJ mol–1).Item Open Access Bacterial expression, purification and in Vitro phosphorylation of full-length ribosomal S6 kinase 2 (RSK2)(PLoS One, 2016-10-01) Utepbergenov, Darkhan; Hennig, Paulina M.; Derewenda, Urszula; Artamonov, Mykhaylo V.; Somlyo, Avril V.; Derewenda, Zygmunt S.Ribosomal S6 kinases (RSK) play important roles in cell signaling through the mitogen-activated protein kinase (MAPK) pathway. Each of the four RSK isoforms (RSK1-4) is a single polypeptide chain containing two kinase domains connected by a linker sequence with regulatory phosphorylation sites. Here, we demonstrate that full-length RSK2 - which is implicated in several types of cancer, and which is linked to the genetic Coffin-Lowry syndrome - can be overexpressed with high yields in Escherichia coli as a fusion with maltose binding protein (MBP), and can be purified to homogeneity after proteolytic removal of MBP by affinity and size-exclusion chromatography. The purified protein can be fully activated in vitro by phosphorylation with protein kinases ERK2 and PDK1. Compared to full-length RSK2 purified from insect host cells, the bacterially expressed and phosphorylated murine RSK2 shows the same levels of catalytic activity after phosphorylation, and sensitivity to inhibition by RSK-specific inhibitor SL0101. Interestingly, we detect low levels of phosphorylation in the nascent RSK2 on Ser386, owing to autocatalysis by the C-terminal domain, independent of ERK. This observation has implications for in vivo signaling, as it suggests that full activation of RSK2 by PDK1 alone is possible, circumventing at least in some cases the requirement for ERK.Item Open Access Carbon Dots Doped with Dysprosium: A Bimodal Nanoprobe for MRI and Fluorescence Imaging(MDPI, 2018-05-18) Atabaev, Timur; Piao, Zhonglie; Molkenova, AnaraIn recent years, functional nanoprobes with multiple imaging modalities have become an emerging field of biomedical research. In this preliminary study, we utilized a facile hydrothermal method for the preparation of magneto-fluorescent bimodal carbon dots doped with dysprosium (Dy-CDs). The prepared Dy-CDs have shown a good colloidal stability in a water solution and strong blue–green fluorescence, with a maximum at 452 nm. In addition, the excellent transverse relaxivity of the prepared Dy-CDs (r2 = 7.42 ± 0.07 mM−1 s −1 ) makes them also suitable for T2-weighted magnetic resonance imaging (MRI). Thus, synthesized Dy-CDs could be potentially utilized for both MRI and fluorescence imaging of living cells.Item Open Access Catalytic hydroboration by an imido-hydrido complex of Mo(IV)(2011) Khalimon, Andrey; Farha, Philip; Kuzmina, Lyudmila G.; Nikonov, Georgii I.The imido-hydrido complex (ArN)Mo(H)(Cl)(PMe3)3 catalyses a variety of hydroboration reactions, including the first example of catalytic addition of HBCat to nitriles to form the bis(borylated) amines RCH2N(BCat)2. The latter species easily undergoes chemoselective coupling with aldehydes R0C(O)H to yield imines RCH2NQC(H)R0Item Open Access Commercial Gold Nanoparticles on Untreated Aluminum Foil: Versatile, Sensitive, and Cost-Effective SERS Substrate(Journal of Nanomaterials, 2017-04-27) Gudun, Kristina; Elemessova, Zarina; Khamkhash, Laura; Ralchenko, Ekaterina; Bukasov, RostislavWe introduce low-cost, tunable, hybrid SERS substrate of commercial gold nanoparticles on untreated aluminum foil (AuNPs@AlF). Two or three AuNP centrifugation/resuspension cycles are proven to be critical in the assay preparation.The limits of detection (LODs) for 4-nitrobenzenethiol (NBT) and crystal violet (CV) on this substrate are about 0.12nM and 0.19 nM, respectively, while maximum analytical SERS enhancement factors (AEFs) are about 107. In comparative assays LODs for CV measured on AuNPs@Au film and AuNPs@glass are about 0.35 nM and 2 nM, respectively. The LOD for melamine detected on AuNPs@ Al foil is 27 ppb with 3 orders of magnitude for linear response range. Overall, AuNPs@AlF demonstrated competitive performance in comparison with AuNPs@Au film substrate in SERS detection of CV, NBT, andmelamine. To check the versatility of the AuNPs@AlF substrate we also detectedKNO3 with LODs of 0.7mMand SERS EF around 2 × 103, which is on the same order with SERS EF reported for this compound in the literature.Item Open Access CONTROLLING THE STEREOCHEMISTRY IN 2-OXO-ALDEHYDE-DERIVED UGI ADDUCTS THROUGH THE CINCHONA ALKALOID-PROMOTED ELECTROPHILIC FLUORINATION(Beilstein Journal of Organic Chemistry, 2020-08) Wang, Yuqing; Wang, Gaigai; Peshkov, Anatoly A.; Yao, Ruwei; Hasan, Muhammad; Zaman, Manzoor; Liu, Chao; Kashtanov, Stepan; Pereshivko, Olga P.; Peshkov, Vsevolod A.In this report, we introduce a new strategy for controlling the stereochemistry in Ugi adducts. Instead of controlling stereochemistry directly during the Ugi reaction we have attempted to stereodefine the chiral center at the peptidyl position through the post-Ugi functionalization. In order to achieve this, we chose to study 2-oxo-aldehyde-derived Ugi adducts many of which partially or fully exist in the enol form that lacks the aforementioned chiral center. This in turn led to their increased nucleophilicity as compared to the standard Ugi adducts. As such, the stereocenter at the peptidyl position could be installed and stereodefined through the reaction with a suitable electrophile. Towards this end, we were able to deploy an asymmetric cinchona alkaloid-promoted electrophilic fluorination producing enantioenriched post-Ugi adducts fluorinated at the peptidyl position.Item Metadata only Corrigendum to “Synthesis and anodic electrochemistry of cymanquine and related complexes” [J. Organomet. Chem. 817 (15 August 2016) 15–20](Journal of Organometallic Chemistry, 2017-05-15) Lam, Kevin; Geiger, William E.; Kevin, LamThe authors regret that the oxidation potentials given for compound 5 in the paper are incorrect. The correct values, referenced to ferrocene, are 0.88 V for the first oxidation and 1.14 V for the second oxidation.Item Metadata only A dataset of homolytic C–Cl bond dissociation energies obtained by means of W1w theory(Chemical Data Collections, 2016-08-01) Garifullina, Ainash; Mahboob, Abdulla; O'Reilly, Robert J.; Ainash, GarifullinaAbstract We herein report a dataset of 28 homolytic C–Cl bond dissociation energies (BDEs) (to be known as the CCl28 dataset), obtained using the benchmark-quality W1w thermochemical protocol. This set contains chlorinated organic molecules that consist of either sp3-, sp2- or sp-hybridized C–Cl bonds. The species in this set have C–Cl BDEs (at 298K) that differ by as much as 168.4kJ mol–1, with allyl chloride having the lowest BDE (291.7kJ mol–1) and 1-chloroprop-1-yne having the largest (460.1kJ mol–1). Given the benchmark quality of the CCl28 dataset, it may serve as a useful reference for assessing the performance of more approximate quantum chemical methods, such as density functional theory (DFT) and double-hybrid DFT methods.Item Open Access Detection of Paracetamol in Water and Urea in Artificial Urine with Gold Nanoparticle@Al Foil Cost-efficient SERS Substrate(Nihon Bunseki Kagakkai, 2018) Mukanova, Zhansaya; Gudun, Kristina; Elemessova, Zarina; Khamkhash, Laura; Ralchenko, Ekaterina; Bukasov, RostislavWe demonstrated that a cost-efficient, easy to prepare, hybrid SERS substrate-gold nanoparticles (AuNPs) on untreated Al foil (AlF) can effectively detect pharmaceuticals, such as paracetamol and clinical biomarkers, like urea in artificial urine. The limit of detection (LOD) for paracetamol on AuNPs on AlF is superior (0.1 vs. 1 mM ) to the LOD reported for SERS detection of paracetamol in the literature. For SERS detection of urea in urine, AuNPs on both Al foil and Au film performed much better than AuNPs on glass, in terms of the concentration range, linearity and LOD. However, assay on AuNPs on AlF showed a better semi-logarithmic trendline with R2 = 0.98 than an assay on AuNPs on Au film with R2 = 0.94. They have comparable sensitivity with LOD 0.024 and 0.017 M, respectively. The limit of quantification (LOQ) of the former is 0.026 M, which makes it sufficient for the quantification of urea in urine at both normal and pathophysiological (0.03 – 0.15 M) concentration.Item Open Access DFT/TD-DFT molecular design of porphyrin analogues for use in dye-sensitized solar cells(2008) Balanay, Mannix P.; Kim, Dong HeeDensity functional theory (DFT) and time-dependent DFT calculations have been employed to model Zn meso-tetraphenylporphyrin (ZnTPP) complexes having different b-substituents, in order to design an efficient sensitizer for dye-sensitized solar cells. To calculate the excited states of the porphyrin analogues, at least the TD-B3LYP/6-31G* level of theory is needed to replicate the experimental absorption spectra. Solvation results were found to be invariant with respect to the type of model used (PCM vs. C-PCM). Most of the electronic transitions based on Gouterman’s four-orbital model of ZnTPP-A and ZnTPP-B are p - p* transitions, so that cell efficiency can be enhanced by increasing the p-conjugation and electron-withdrawing capability of the bsubstituent. This proposition was tested by inserting thiophene into the b-substituent of ZnTPP-A to form a new analogue, ZnTPP-C. Compared with ZnTPP-A and ZnTPP-B, ZnTPP-C has a smaller band gap, which brings LUMO closer to the conduction band of TiO2, and a red-shifted absorption spectrum with higher extinction coefficients, especially in the Q-band positionItem Open Access Experimental and theoretical analysis of organic dyes having a double D-π-A configurations for dye-sensitized solar cells(Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy, 2017-02-15) Balanay, Mannix P.; Choi, Kyu Seok; Lee, Sang Hee; Kim, Dong HeeTwo spiro-like organic dyes linked at the thiophene bridge (KS-11 and KS-12) together with the original rod-shaped D-π-A configuration (C1) were designed, synthesized, and characterized based on their electronic structure, and determine the photophysical and photovoltaic properties for its application in dye-sensitized solar cells. Compared to C1, the double D-π-A spiro-like configuration, which consists of two separated light-harvesting moieties, was found to be beneficial to photocurrent generation provided that they are separated properly to prevent intramolecular exciton annihilation. This was observed when KS-11, which is linked at the β-position of the thiophene moiety of D-π-A, was compared with KS-12, where the two D-π-A are linked with an additional thiophene using a α-β linkage. The results show that KS-12 produced a 20% and 17% increase in photovoltaic efficiency under simulated AM 1.5G solar irradiation compared to KS-11 and C1, respectively. This increase in photovoltaic performance is credited mostly to the reduction of recombination effects and the increase in the density of states at the semiconductor surface due to high dye loading and better charge-transfer properties.Item Metadata only Fragmentation of 1,4,2-oxaselenazoles as a route to isoselenocyanates–A high-level CBS-QB3 study(Chemical Data Collections, 2017-08-01) Yertisbayeva, Aigerim; Salkenova, Zarina; Sembayeva, Aliya; O'Reilly, Robert J.; Aigerim, YertisbayevaAbstract In this study, the thermodynamics and barrier heights associated with the fragmentation reactions of a set of fifteen 1,4,2-oxaselenazoles into isoselenocyanates (molecules with promising anticancer activity) and carbonyl derivatives, have been studied using the high-level CBS-QB3 quantum chemical protocol. Of the systems studied, attachment of a CF3-substituent at the C5-position affords the system with the largest gas-phase free energy barrier (190.1kJ mol–1), whilst substitution at the C5-position with two –NMe2 substituents affords a heterocycle with the lowest free energy barrier (67.8kJ mol–1). The presence of solvent (acetonitrile) was shown to reduce the free energy barriers in all cases, with the two systems mentioned above having condensed-phase free energy barriers of 180.8 and 42.0kJ mol–1, respectively.Item Metadata only A high-level G4(MP2) thermochemical study of the relative energies of the N-chlorinated isomers formed upon chlorination of cytosine(Chemical Data Collections, 2017-08-01) Stambekova, Dana; O'Reilly, Robert J.; Dana, StambekovaAbstract Although the relative energies of the various tautomers of cytosine and 5-chlorocytosine have been studied in detail, little is known about the relative energies of the N-chlorinated isomers of cytosine. N-chlorination of cytosine is known to occur when cytosine is exposed to hypochlorous acid, a potent oxidant that is formed during the inflammatory process, and is presumed to have consequences concerning, for example, the structural integrity of DNA and RNA. In this study, the high-level G4(MP2) thermochemical protocol has been employed in studying the relative gas-phase free energies of thirty isomers that may be formed upon N-chlorination of cytosine. Using free energy of solvation corrections obtained by way of continuum models (CPCM and SMD), an approximation of the effect of aqueous solvation on the relative energies of the isomers has also been taken into account. In both the gas- and aqueous-phases, the lowest energy isomer is an exocyclic N-chloroimino derivative.Item Metadata only Homolytic C–Br bond dissociation energies obtained by means of the G4 thermochemical protocol(Chemical Data Collections, 2016-05-01) Kazakbayeva, Zhanna; Zhumagali, Shingis; Mahboob, Abdulla; O'Reilly, Robert J.; Zhanna, KazakbayevaAbstract Knowledge of the energies required to induce homolytic cleavage of the C–Br bonds of brominated organic molecules, a process that affords carbon-centered radicals and Br•, is of fundamental importance. Although some data pertaining to the strength of C–Br bonds can already be found in the literature, the chemical diversity of the species for which bond dissociation energies (BDEs) are available is somewhat limited. In this data article, we report a comprehensive set of homolytic C–Br BDEs, obtained using the G4 thermochemical protocol, for brominated organic molecules with wide structural diversity. The species in this set have C–Br BDEs (at 298K) that differ by as much as 188.3kJmol–1, with α-bromoalanine having the lowest BDE (214.1kJmol–1) and 1-bromobut-1-yne having the largest (402.4kJmol–1). Of particular relevance to biological systems are the BDEs of 8-bromoguanine (345.3kJmol–1), 8-bromoadenine (345.6kJmol–1), 5-bromocytosine (348.8kJmol–1) and 5-bromouracil (350.3kJmol–1).Item Metadata only The hows and whys of peculiar coordination of 4-amino-2,1,3-benzothiadiazole(Polyhedron, 2018-01-08) Sukhikh, T.S.; Komarov, V.Yu.; Konchenko, S.N.; Benassi, E.; T.S., SukhikhAbstract 4-Amino-2,1,3-benzothiadiazole (L) and its model complexes with Cu+, Zn2+, Ag+ and Cd2+ have been computationally investigated in order to reveal the origins of coordination preferences of this multidentate ligand. The computational description is consistent with the analysis of experimental crystal structures of the coordination compounds described earlier and of two new complexes viz. [ZnL(H2O)Cl2] and [CdL2(H2O)2(NO3)2]. Possible coordination types of L are discussed by means of rotational hindrance of NH2 group, relative thermodynamic stability of the complexes and intramolecular interaction analysis. On the basis of our findings, molecular structure – spectral properties relationships of the complexes are revealed. The results obtained for L are compared with those obtained for 8-aminoquinoline, which is structurally similar to L and is known to form a number of metal complexes.Item Open Access Imido–hydrido complexes of Mo(IV): catalysis and mechanistic aspects of hydroboration reactions(2015) Khalimon, Andrey; Farhaa, Philip M.; Nikonov, Georgii I.Imido–hydrido complexes (ArN)Mo(H)(Cl)(PMe3)3 (1) and (ArN)Mo(H)2(PMe3)3 (2) (Ar = 2,6-diisopropylphenyl) catalyse a variety of hydroboration reactions, including the rare examples of addition of HBCat to nitriles to form bis(borylated) amines RCH2N(BCat)2. Stoichiometric reactivity of complexes 1 and 2 with nitriles and HBCat suggest that catalytic reactions proceed via a series of agostic borylamido and borylamino complexes. For complex 1, catalysis starts with addition of nitriles across the Mo–H bond to give (ArN)Mo(Cl)(NvCHR)(PMe3)2; whereas for complex 2 stoichiometric reactions suggest initial addition of HBCat to form the agostic complex Mo(H)2(PMe3)3(η3-NAr-HBcat)Item Metadata only Lipase-mediated regioselective modifications of macrolactonic sophorolipids(Tetrahedron, 2017-04-06) Sembayeva, Aliya; Berhane, Beniam; Carr, Jason A.; Aliya, SembayevaAbstract Chemoenzymatic synthesis and modification of well-defined macrolactonic sophorolipid (SLML) analogues via a series of successive regioselective de-esterification/transesterification reactions is investigated. Of the lipases screened, Candida antartica lipase- B (Novozyme-435) successfully deacylated the C-6′ acetoxy group of natural and peracylated SLMLs. Subsequent transesterification with acylating agents (esters of fatty acids) was successful only with the C-6′ deacetylated natural SLML providing an avenue to well-defined analogues of varying amphilicity. The macrolactonic motif was essential for enzymatic recognition of the sophorose rings of these complex glycolipids. In the absence of the lactonic motif, the peracylated sophorose rings are not deacylated, rather the carboxyl end of the non-lactonic forms that was preferentially transesterified. All macrolactonic derivatives were characterized by IR, 1H, 13C, 1H-1H and 1H-13C NMR spectroscopy, as well as HRMS where applicable.Item Metadata only Molecular engineering of donor–acceptor co-polymers for bulk heterojunction solar cells(Computational and Theoretical Chemistry, 2015-03-01) Balanay, Mannix P.; Kim, Dong Hee; Mannix P., BalanayAbstract We report a computational modeling, based on DFT and TD-DFT methodologies, on the structural, electronic, and optical properties of different donor–acceptor co-polymer system in bulk heterojunction solar cells. The donor moieties that were considered were the derivatives of thienocyclopentathiophene, fluorene, and thienobenzothiophene. We utilized for the acceptor groups the moieties of thieno[3,4-b]pyrrole-4,6-dione; thieno[3,4-b] thiophene-4,6-dione; tetrafluoro-1,3-dihydrothieno[3,4-c]thiophene and its non-fluorinated counterpart; various electron-donating substituents within the fused π-conjugated polymer system; and 3-fluoroselenophenothiophene. Among the donor–acceptor combination, the best in terms of molecular energy levels, energetic driving force, maximum absorption, calculated open-circuit voltage, reorganization energies, ionization potential, and electron affinity are poly[(bisthieno(bisthieno[3,2-b:2′,3′-d]thiophene)- alt-(5-alkyl-4H-thieno[3,4-c]pyrrole-4,6(5H)-dione)] and poly[(4,8-dimethyl[1,3] oxazolo[5,4-f][1,3]benzoxazole)- alt-(thieno[3,4-d]pyrimidine)].Item Open Access Monitoring of vegetation drying by Brillouin and Raman spectroscopies(Nazarbayev University School of Science and Technology, 2017-05-01) Rakymzhan, Adiya; Yakupov, Talgat A.; Yelemessova, Zarina; Bukasov, Rostislav; Yakovlev, Vladislav V.; Utegulov, Zhandos N.Raman and Brillouin spectroscopic provide with a powerful way to non-invasively assess both chemical and physical (viscoelastic) properties. In this report, Brillouin microspectroscopy was used for real time analysis of elastic properties of Populus and Geranium leaves, while Raman spectroscopy and imaging were employed for assessment of their chemical variation during drying. When used together, those techniques can improve our understanding of mechanochemical changes of plants in response to environmental stress and pathogens at microscopic (cellular) level. Our results have demonstrated for the first time the ability of multimodal assessment of elasticity modulus, hydraulic conductance and interatomic vibrational modes in plants as emerging new markers for real time quantitative assessment of agricultural crops.Item Open Access Multiple coupling of silanes with imido complexes of Mo(2014) Khalimon, Andrey; McLeod, Nicolas A.; Ignatov, Stanislav K.; Okhapkin, Andrey I.; Kuzmina, Lyudmila G.; Howardd, Judith A. K.; Nikonov, Georgii I.The bis(imido) complexes (tBuNv)2Mo(PMe3)(L) (L = PMe3, C2H4) react with up to three equivalents of silane PhSiH3 to give the imido-bridged disilyl silyl Mo(VI) complex (tBuN){μ-tBuN(SiHPh)2}Mo(H)(SiH2Ph)- (PMe3)2 (3) studied by NMR, IR and X-ray diffraction. NMR data supported by DFT calculations show that complex 3 is an unusual example of a silyl hydride of Mo(VI), without significant Si⋯H interaction. Mechanistic NMR studies revealed that silane addition proceeds in a stepwise manner via a series of Si–H⋯M agostic and silanimine complexes whose structures were further elucidated by DFT calculations