151
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Xiao F, Pignatello JJ. Effects of Post-Pyrolysis Air Oxidation of Biomass Chars on Adsorption of Neutral and Ionizable Compounds. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:6276-6283. [PMID: 27152745 DOI: 10.1021/acs.est.6b00362] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
This study was conducted to understand the effects of thermal air oxidation of biomass chars experienced during formation or production on their adsorptive properties toward various compounds, including five neutral nonpolar and polar compounds and seven weak acids and bases (pKa = 3-5.2) selected from among industrial chemicals and the triazine and phenoxyacetic acid herbicide classes. Post-pyrolysis air oxidation (PPAO) at 400 °C of anoxically prepared wood and pecan shell chars for up to 40 min enhanced the mass-normalized adsorption at pH ∼ 7.4 of all test compounds, especially the weak acids and bases, by up to 100-fold. Both general and specific effects were identified. The general effect results from "reaming" of pores by the oxidative removal of pore wall matter and/or tarry deposits generated during the pyrolysis step. Reaming creates new surface area and enlarges nanopores, which helps relieve steric hindrance to adsorption. The specific effect results from creation of new acidic functionality that provides sites for the formation of very strong, charge-assisted hydrogen bonds (CAHB) with solutes having comparable pKa. The CAHB hypothesis was supported by competition experiments and the finding that weak acid anion adsorption increased with surface carboxyl content, despite electrostatic repulsion from the growing negative charge. The results provide insight into the effects of air oxidation on pollutant retention.
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Affiliation(s)
- Feng Xiao
- Department of Civil Engineering, University of North Dakota , Grand Forks, North Dakota 58202-8115, United States
- Department of Environmental Sciences, The Connecticut Agricultural Experimental Station , New Haven, Connecticut 06504-1106, United States
| | - Joseph J Pignatello
- Department of Environmental Sciences, The Connecticut Agricultural Experimental Station , New Haven, Connecticut 06504-1106, United States
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152
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Bengiat R, Gil M, Klein A, Bogoslavsky B, Cohen S, Dubnikova F, Yardeni G, Zilbermann I, Almog J. Selective recognition of fluoride salts by vasarenes: a key role of a self-assembled in situ dimeric entity via an exceptionally short [O-H-O](-) H-bond. Dalton Trans 2016; 45:8734-9. [PMID: 26804131 DOI: 10.1039/c5dt04171f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A self-assembled supramolecular dimeric entity via an exceptionally short (2.404 Å) and strong (22.9 kcal mol(-1)) [O-H-O](-) hydrogen bond is the key to the special reactivity of vasarenes with fluoride salts. Vasarene is a self-assembled, vase-shaped compound, obtained by the reaction between ninhydrin and phloroglucinol. Analogous compounds are prepared by replacing the phloroglucinol with other polyhydroxy aromatics. Vasarenes show special affinity towards compounds of the type M(+)F(-), where M being a large monovalent cation, producing ion-pair-vasarene adducts. The first step in the proposed mechanism is the dissociation of the M(+)F(-) salt releasing F(-) to the solution, which may provide an explanation as to why only MF salts, which include large monovalent cations, undergo this reaction. From a practical point of view, the ease of their preparation and their special affinity towards fluoride salts make vasarenes potential means for salt separation. The readily formed dimeric structure with the very short [O-H-O](-) negative charge-assisted H-bond (-CAHB) can also be further used as a model in theoretical studies of such systems and understanding their role in biological processes.
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Affiliation(s)
- R Bengiat
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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153
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Suzuki M, Kotyk JFK, Khan SI, Rubin Y. Directing the Crystallization of Dehydro[24]annulenes into Supramolecular Nanotubular Scaffolds. J Am Chem Soc 2016; 138:5939-56. [PMID: 27088651 DOI: 10.1021/jacs.6b01939] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The self-assembly of a series of dehydro[24]annulene derivatives into columnar stacks has been examined for its latent ability to form π-conjugated carbon-rich nanotubular structures through topochemical polymerizations. We have studied the parameters affecting self-assembly, including the nature of the substituent and crystallization conditions, using 10 different dehydro[24]annulene derivatives. In particular, hydrogen-bonding interactions through carbamate groups were found to be especially useful at directing the formation of nanotubular supramolecular assemblies. We have also evaluated the electronic coupling between neighboring dehydroannulene molecules within these supramolecular assemblies. Density functional calculations on the stacked supramolecular nanotube assemblies show that transfer integrals vary considerably between the three columnar assemblies, ranging from moderate to high (59-98 meV for the highest occupied molecular orbitals, 63-97 meV for the lowest unoccupied molecular orbitals), depending on the local molecular topology. In addition, the dehydro[24]annulene derivatives afforded distinct architectures in the crystal, including nanochannel arrays, sheets with solvent-filled pores, and lamellae. This work is an essential step toward a controlled formation of covalently linked carbon-rich nanostructures generated from molecular precursors with a latent diacetylene reactivity.
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Affiliation(s)
- Mitsuharu Suzuki
- Department of Chemistry and Biochemistry, University of California, Los Angeles , 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Juliet F Khosrowabadi Kotyk
- Department of Chemistry and Biochemistry, University of California, Los Angeles , 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Saeed I Khan
- Department of Chemistry and Biochemistry, University of California, Los Angeles , 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Yves Rubin
- Department of Chemistry and Biochemistry, University of California, Los Angeles , 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
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154
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Investigating the properties of muchimangin B through comparisons with related and model structures. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1874-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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155
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Dannenberg JJ. The importance of cooperative interactions and a solid-state paradigm to proteins: what Peptide chemists can learn from molecular crystals. ACTA ACUST UNITED AC 2016; 72:227-73. [PMID: 16581379 DOI: 10.1016/s0065-3233(05)72009-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Proteins and peptides in solution or in vivo share properties with both liquids and solids. More often than not, they are studied using the liquid paradigm rather than that of a solid. Studies of molecular crystals illustrate how the use of a solid paradigm may change the way that we consider these important molecules. Cooperative interactions, particularly those involving H-bonding, play much more important roles in the solid than in the liquid paradigms, as molecular crystals clearly illustrate. Using the solid rather than the liquid paradigm for proteins and peptides includes these cooperative interactions while application of the liquid paradigm tends to ignore or minimize them. Use of the solid paradigm has important implications for basic principles that are often implied about peptide and protein chemistry, such as the importance of entropy in protein folding and the nature of the hydrophobic effect. Understanding the folded states of peptides and proteins (especially alpha-helices) often requires the solid paradigm, whereas understanding unfolded states does not. Both theoretical and experimental studies of the energetics of protein and peptide folding require comparison to a suitable standard. Our perspective on these energetics depends on the reasonable choice of reference. The use of multiple reference states, particularly that of component amino acids in the gas phase, is proposed.
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Affiliation(s)
- J J Dannenberg
- Department of Chemistry, City University of New York, Hunter College and the Graduate School New York, New York 10021
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156
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Hayashi S, Sugibayashi Y, Nakanishi W. Dynamic and static behavior of the H...π and E...π interactions in EH₂ adducts of benzene π-system (E = O, S, Se and Te), elucidated by QTAIM dual functional analysis. Phys Chem Chem Phys 2016; 18:9948-60. [PMID: 26818845 DOI: 10.1039/c5cp06062a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dynamic and static behavior of the interactions in the EH2 adducts of a benzene π-system (E = O, S, Se and Te) is elucidated by applying QTAIM-DFA (QTAIM dual functional analysis). Two types of H-*-π and E-*-π interactions are detected in the adducts, where the asterisk (*) emphasizes the existence of the bond critical point (BCP) on the interaction in question. Total electron energy densities Hb(rc) are plotted versus Hb(rc) -Vb(rc)/2 [=(ℏ(2)/8m)∇(2)ρb(rc)] at BCPs in QTAIM-DFA, where Vb(rc) are the potential energy densities at BCPs. Data from the fully optimized structures are analyzed by polar (R, θ) coordinate representation. Each plot for an interaction, containing data from the perturbed structures with those of the fully optimized one, shows a specific curve, which provides important information. The plot is expressed by (θp, κp): θp corresponds to the tangent line for the plot and κp is the curvature. θ and θp are measured from the y-axis and y-direction, respectively. Moreover, (R, θ) corresponds to the static nature, (θp, κp) represents the dynamic nature of interactions. While θ classifies the interaction in question, θp characterizes it. Both values are less than 90° for all H-*-π and E-*-π interactions examined in this study; therefore, they are all classified by the pure closed-shell interactions and predicted to have the character of vdW nature. However, it is suggested that E-*-π has the nature of the stronger interaction than the case of H-*-π for dynamic behavior in the same species evaluated at the MP2 and M06-2X levels. The nature of the interactions is well analyzed and specified by applying QTAIM-DFA.
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Affiliation(s)
- Satoko Hayashi
- Department of Material Science and Chemistry, Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan.
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157
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Kakeshpour T, Wu JI, Jackson JE. AMHB: (Anti)aromaticity-Modulated Hydrogen Bonding. J Am Chem Soc 2016; 138:3427-32. [DOI: 10.1021/jacs.5b12703] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tayeb Kakeshpour
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Judy I. Wu
- Department
of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - James E. Jackson
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
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158
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Armanious A, Aeppli M, Jacak R, Refardt D, Sigstam T, Kohn T, Sander M. Viruses at Solid-Water Interfaces: A Systematic Assessment of Interactions Driving Adsorption. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:732-43. [PMID: 26636722 DOI: 10.1021/acs.est.5b04644] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Adsorption to solid-water interfaces is a major process governing the fate of waterborne viruses in natural and engineered systems. The relative contributions of different interaction forces to adsorption and their dependence on the physicochemical properties of the viruses remain, however, only poorly understood. Herein, we systematically studied the adsorption of four bacteriophages (MS2, fr, GA, and Qβ) to five model surfaces with varying surface chemistries and to three dissolved organic matter adlayers, as a function of solution pH and ionic strength, using quartz crystal microbalance with dissipation monitoring. The viruses were selected to have similar sizes and shapes but different surface charges, polarities, and topographies, as identified by modeling the distributions of amino acids in the virus capsids. Virus-sorbent interactions were governed by long-ranged electrostatics and favorable contributions from the hydrophobic effect, and shorter-ranged van der Waals interactions were of secondary importance. Steric effects depended on the topographic irregularities on both the virus and sorbent surfaces. Differences in the adsorption characteristics of the tested viruses were successfully linked to differences in their capsid surface properties. Besides identifying the major interaction forces, this work highlights the potential of computable virus surface charge and polarity descriptors to predict virus adsorption to solid-water interfaces.
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Affiliation(s)
- Antonius Armanious
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL) , Lausanne, CH-1015, Switzerland
| | | | - Ronald Jacak
- Applied Physics Laboratory, Johns Hopkins University , Laurel, Maryland 20723, United States
| | | | - Thérèse Sigstam
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL) , Lausanne, CH-1015, Switzerland
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL) , Lausanne, CH-1015, Switzerland
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159
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Sovago I, Thomas LH, Adam MS, Capelli SC, Wilson CC, Farrugia LJ. High resolution X-ray and neutron diffraction studies on molecular complexes of chloranilic acid and lutidines. CrystEngComm 2016. [DOI: 10.1039/c6ce01065b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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160
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Ruggiero MT, Korter TM. The crucial role of water in shaping low-barrier hydrogen bonds. Phys Chem Chem Phys 2016; 18:5521-8. [DOI: 10.1039/c5cp07760e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Low-barrier hydrogen bonds (LBHBs) are key components in a range of chemical processes, often appearing in metal-mediated catalytic applications.
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161
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You R, Sun H, Yu Y, Lin Z, Qin M, Liu Y. Time-dependent hormesis of chemical mixtures: A case study on sulfa antibiotics and a quorum-sensing inhibitor of Vibrio fischeri. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2016; 41:45-53. [PMID: 26645135 DOI: 10.1016/j.etap.2015.10.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 10/24/2015] [Accepted: 10/29/2015] [Indexed: 06/05/2023]
Abstract
Sulfa antibiotics (SAs) and quorum-sensing inhibitor (QSI) may pose potential ecological risks because mixed using of them has been proposed to inhibit bacteria from generating antibiotic resistance. This study investigated the time-dependent hormesis of single and binary mixtures of QSI and SAs of Vibrio fischeri (V. fischeri) for 0-24 h. Although the low-dose SAs stimulated the expression of LuxR protein, the high-dose SAs could inhibit bacteria growth by competitively binding to dihydropteroate synthase. Moreover, AinR protein was bound to Benzofuran-3(2H)-one (B3O) with low concentration, thus the N-octanoyl homoserine lactone signal molecules (C8) has chance to bind to LuxR protein to promote light emission. The hormesis effect induced by the mixtures could be deduced that SAs promoted the expression of LuxR protein and B3O increases the chance of C8 binding to LuxR. Our findings facilitate new insight into the mechanistic study of hormesis and ecological risks of the chemical mixtures.
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Affiliation(s)
- Ruirong You
- College of Materials Science and Engineering, Fuzhou University, Fujian Province 350108, China; Key Laboratory of Eco-materials Advanced Technology (Fuzhou University), Fujian Province University, China
| | - Haoyu Sun
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Yan Yu
- College of Materials Science and Engineering, Fuzhou University, Fujian Province 350108, China; Key Laboratory of Eco-materials Advanced Technology (Fuzhou University), Fujian Province University, China.
| | - Zhifen Lin
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Key Lab of Chemical Assessment and Sustainability, Shanghai, China; Collaborative Innovation Center for Regional Environmental Quality, Beijing, China.
| | - Mengnan Qin
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Ying Liu
- Shanghai Key Lab of Chemical Assessment and Sustainability, Shanghai, China
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162
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Vodolazhenko MA, Gorobets NY, Zhikol OA, Desenko SM, Shishkin OV. A quantum chemical approach towards understanding stability and tautomerism of 2-imino-2H-pyran derivatives. RSC Adv 2016. [DOI: 10.1039/c6ra08873b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The ring-chain tautomerism of 2-imino-2H-pyran derivatives annelated with an aromatic or aliphatic ring and their transformation into corresponding 2-pyridons were studied based on the relative stabilities of two series of model isomers calculated by the DFT method.
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Affiliation(s)
| | | | - Oleg A. Zhikol
- SSI “Institute for Single Crystals”
- NAS of Ukraine
- 61001 Kharkiv
- Ukraine
| | - Sergey M. Desenko
- SSI “Institute for Single Crystals”
- NAS of Ukraine
- 61001 Kharkiv
- Ukraine
| | - Oleg V. Shishkin
- SSI “Institute for Single Crystals”
- NAS of Ukraine
- 61001 Kharkiv
- Ukraine
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163
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Guevara-Vela JM, Romero-Montalvo E, Mora Gómez VA, Chávez-Calvillo R, García-Revilla M, Francisco E, Pendás ÁM, Rocha-Rinza T. Hydrogen bond cooperativity and anticooperativity within the water hexamer. Phys Chem Chem Phys 2016; 18:19557-66. [DOI: 10.1039/c6cp00763e] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We propose a hierarchy of H-bond strength in terms of the single and double character of the involved donor and acceptors within different structures of (H2O)6.
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Affiliation(s)
| | - Eduardo Romero-Montalvo
- Institute of Chemistry
- National Autonomous University of Mexico
- Circuito Exterior
- Ciudad Universitaria
- Mexico City
| | - Víctor Arturo Mora Gómez
- Institute of Chemistry
- National Autonomous University of Mexico
- Circuito Exterior
- Ciudad Universitaria
- Mexico City
| | - Rodrigo Chávez-Calvillo
- School of Chemistry
- National Autonomous University of Mexico
- Circuito Exterior
- Ciudad Universitaria
- Mexico City
| | - Marco García-Revilla
- Department of Chemistry
- Division of Natural and Exact Sciences
- University of Guanajuato
- Guanajuato
- Mexico
| | - Evelio Francisco
- Department of Physical and Analytical Chemistry
- University of Oviedo
- Oviedo
- Spain
| | - Ángel Martín Pendás
- Department of Physical and Analytical Chemistry
- University of Oviedo
- Oviedo
- Spain
| | - Tomás Rocha-Rinza
- Institute of Chemistry
- National Autonomous University of Mexico
- Circuito Exterior
- Ciudad Universitaria
- Mexico City
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164
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Chang DH, Ou CL, Hsu HY, Huang GJ, Kao CY, Liu YH, Peng SM, Diau EWG, Yang JS. Cooperativity and Site-Selectivity of Intramolecular Hydrogen Bonds on the Fluorescence Quenching of Modified GFP Chromophores. J Org Chem 2015; 80:12431-43. [PMID: 26583964 DOI: 10.1021/acs.joc.5b02303] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper provides the first example of experimentally characterized hydrogen-bond cooperativity on fluorescence quenching with a modified green fluorescence protein (GFP) chromophore that contains a 6-membered C═N···H-O and a 7-membered C═O···H-O intramolecular H-bonds. Variable-temperature (1)H NMR and electronic absorption and emission spectroscopies were used to elucidate the preference of intra- vs intermolecular H-bonding at different concentrations (1 mM and 10 μM), and X-ray crystal structures provide clues of possible intermolecular H-bonding modes. In the ground state, the 6-membered H-bond is significant but the 7-membered one is rather weak. However, fluorescence quenching is dominated by the 7-membered H-bond, indicating a strengthening of the H-bond in the excited state. The H-bonding effect is more pronounced in more polar solvents, and no intermediates were observed from femtosecond fluorescence decays. The fluorescence quenching is attributed to the occurrence of diabatic excited-state proton transfer. Cooperativity of the two intramolecular H-bonds on spectral shifts and fluorescence quenching is evidenced by comparing with both the single H-bonded and the non-H-bonded counterparts. The H-bond cooperativity does not belong to the conventional patterns of σ- and π-cooperativity but a new type of polarization interactions, which demonstrates the significant interplay of H-bonds for multiple H-bonding systems in the electronically excited states.
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Affiliation(s)
- Deng-Hsiang Chang
- Department of Chemistry, National Taiwan University , Taipei 10617, Taiwan
| | - Chun-Lin Ou
- Department of Chemistry, National Taiwan University , Taipei 10617, Taiwan
| | - Hung-Yu Hsu
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University , Hsinchu 30010, Taiwan
| | - Guan-Jhih Huang
- Department of Chemistry, National Taiwan University , Taipei 10617, Taiwan
| | - Chen-Yi Kao
- Department of Chemistry, National Taiwan University , Taipei 10617, Taiwan
| | - Yi-Hung Liu
- Department of Chemistry, National Taiwan University , Taipei 10617, Taiwan
| | - Shie-Ming Peng
- Department of Chemistry, National Taiwan University , Taipei 10617, Taiwan
| | - Eric Wei-Guang Diau
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University , Hsinchu 30010, Taiwan
| | - Jye-Shane Yang
- Department of Chemistry, National Taiwan University , Taipei 10617, Taiwan
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165
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Cycloaddition of [3]dendralene derivatives to dinitrobenzofuroxan and nitrobenzodifuroxan. Chem Heterocycl Compd (N Y) 2015. [DOI: 10.1007/s10593-015-1794-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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166
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Kaştaş ÇA, Kaştaş G, Gür M, Muğlu H, Büyükgüngör O. Analysis of tautomeric equilibrium in (E)-4,6-dibromo-2-[(4-fluorophenylimino)methyl]-3-methoxyphenol compound. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 151:731-738. [PMID: 26172460 DOI: 10.1016/j.saa.2015.07.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/27/2015] [Accepted: 07/06/2015] [Indexed: 06/04/2023]
Abstract
In this study, the tautomeric equilibrium between the phenol-imine and keto-amine structural forms of (E)-4,6-dibromo-2-[(4-fluorophenylimino)methyl]-3-methoxyphenol compound has been investigated with experimental (XRD, UV-vis and NMR) and theoretical (DFT and TD-DFT) methods. The results clearly show that structural preference of the compound is definitely depended on its state. Namely, the compound exists in phenol-imine form in the solid state while one or both of these forms can be seen in solvent media. For example, the compound prefers phenol-imine form in benzene while both forms exist in EtOH and DMSO solvents. Coexistence of two forms has been quantified with NMR studies, giving a ratio of 11:9 for phenol and keto structures of the compound in acetone-d6 solvent.
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Affiliation(s)
- Çiğdem Albayrak Kaştaş
- Sinop University, Faculty of Arts and Sciences, Department of Chemistry, 57000 Sinop, Turkey.
| | - Gökhan Kaştaş
- Ondokuz Mayıs University, Civil Aviation College, Samsun, Turkey
| | - Mahmut Gür
- Kastamonu University, Faculty of Forest, Forest Industry Engineering, Kastamonu, Turkey
| | - Halit Muğlu
- Kastamonu University, Faculty of Arts and Sciences, Department of Chemistry, Kastamonu, Turkey
| | - Orhan Büyükgüngör
- Ondokuz Mayıs University, Faculty of Arts and Sciences, Department of Physics, 55139 Kurupelit-Samsun, Turkey
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167
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Chu C, Lundeen RA, Sander M, McNeill K. Assessing the Indirect Photochemical Transformation of Dissolved Combined Amino Acids through the Use of Systematically Designed Histidine-Containing Oligopeptides. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:12798-12807. [PMID: 26425803 DOI: 10.1021/acs.est.5b03498] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Photooxidation is an important abiotic transformation pathway for amino acids (AAs) in sunlit waters. Although dissolved free AAs are well studied, the photooxidation of dissolved combined AAs (DCAAs) remains poorly investigated. This study is a systematic investigation of the effect of neighboring photostable AA residues (i.e., aliphatic, cationic, anionic, or aromatic residues) on the environmental indirect photochemical transformation of histidine (His) in His-containing oligopeptides. The pKa values of His residues in the studied oligopeptides were found to be between 4.3 and 8.1. Accordingly, the phototransformation rate constants of the His-containing oligopeptides were highly pH-dependent in an environmentally relevant pH range with higher reactivity for neutral His than for the protonated species. The photostable AA residues significantly modulated the photoreactivity of oligopeptides either through altering the accessibility of His to photochemically produced oxidants or through shifting the pKa values of His residues. In addition, the influence of neighboring photostable AA residues on the sorption-enhanced phototransformation of oligopeptides in solutions containing chromophoric dissolved organic matter (CDOM) was assessed. The constituent photostable AA residues promoted sorption of His-containing oligopeptides to CDOM macromolecules through electrostatic attraction, hydrophobic effects, and/or low-barrier hydrogen bonds, and subsequently increased the apparent phototransformation rate constants by up to 2 orders of magnitude.
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Affiliation(s)
- Chiheng Chu
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), Department of Environmental Systems Science, ETH Zurich , 8092 Zurich, Switzerland
| | - Rachel A Lundeen
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), Department of Environmental Systems Science, ETH Zurich , 8092 Zurich, Switzerland
| | - Michael Sander
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), Department of Environmental Systems Science, ETH Zurich , 8092 Zurich, Switzerland
| | - Kristopher McNeill
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), Department of Environmental Systems Science, ETH Zurich , 8092 Zurich, Switzerland
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168
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Biedermannová L, Schneider B. Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:2192-202. [PMID: 26527137 PMCID: PMC4631476 DOI: 10.1107/s1399004715015679] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/20/2015] [Indexed: 12/22/2022]
Abstract
Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon-donor hydrogen bonds, OH-π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.
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Affiliation(s)
- Lada Biedermannová
- Laboratory of Biomolecular Recognition, Institute of Biotechnology CAS, Videnska 1083, 142 20 Prague, Czech Republic
| | - Bohdan Schneider
- Laboratory of Biomolecular Recognition, Institute of Biotechnology CAS, Videnska 1083, 142 20 Prague, Czech Republic
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169
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Tabayashi K, Takahashi O. Substituent Electron Push–Pull Interaction in Intermolecular Resonance-Assisted Hydrogen Bonds: Thymine/Adenine Base Pair and Their Complexes with Carboxylic Acids. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20150113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
| | - Osamu Takahashi
- Institute for Sustainable Sciences and Development, Hiroshima University
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170
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Ogata Y, Kawashima Y, Takahashi K, Tachikawa M. Theoretical vibrational spectra of OH(-)(H2O)2: the effect of quantum distribution and vibrational coupling. Phys Chem Chem Phys 2015; 17:25505-15. [PMID: 26365920 DOI: 10.1039/c5cp03632a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We performed ab initio path integral molecular dynamics simulations for the hydroxide-water cluster, OH(-)(H2O)2, at 50 K, 100 K, and 150 K to investigate its flexible structure. From our simulations, we found that nuclear quantum effects enhance hydroxide hydrogen atom inversion and the conformational change between isomers occurs by simultaneous rotation of the free hydrogen atom. We propose the importance of including the transition state conformer with C2 symmetry, for the description of this system at temperatures realized in predissociation experiments. Temperature dependence of relative populations of each conformer along with multidimensional vibrational calculations were used to simulate the vibrational spectra and compare with the experimental spectra of Johnson and coworkers. We assign the doublet peaks seen in the experiment at 2500 to 3000 cm(-1), as the mixture of the ionic hydrogen bonded OH stretching overtone, ionic hydrogen bonded OH bending overtone, and the combination band of the ionic hydrogen bonded OH stretch and bend, which are modulated by the van der Waals OO vibrations. We concluded that for OH(-)(H2O)2, the vibrational couplings between the ionic hydrogen bonded motion and floppy modes contribute to the broadening of peaks observed in the 2500 to 3000 cm(-1) region.
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Affiliation(s)
- Yudai Ogata
- Graduate school of Nanobioscience, Yokohama City University, Yokohama 236-0027, Japan.
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171
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Specific features of the extra strong intermolecular hydrogen bonds in crystals: Insights from the theoretical charge density analysis. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.08.053] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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172
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Yang D, Zhao J, Zheng R, Wang Y, Lv J. A DFT/TDDFT investigation of the excited state proton transfer reaction of fisetin chromophore. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 151:368-374. [PMID: 26143329 DOI: 10.1016/j.saa.2015.06.098] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 06/09/2015] [Accepted: 06/25/2015] [Indexed: 06/04/2023]
Abstract
In the present work, 3, 3', 4', 7-tetrahydroxyflavone (fisetin), as one of the most extensive distributed flavonoids, has been investigated on the excited state proton transfer (ESPT) based on the time-dependent density functional theory (TDDFT) method. The calculated absorption and fluorescence spectra based on the TDDFT method are in agreement with the experimental results. Two kinds of structures of fisetin chromophore are found in the first excited (S1) state, which may be due to the proton transfer reactive. Hydrogen bond strengthening has been testified in the S1 state based on comparing staple bond lengths and bond angles involved in hydrogen bonding between the S0 state and the S1 state. In addition, the calculated infrared spectra at the O-H stretching vibrational region and calculated hydrogen bond energy also declare the phenomenon of hydrogen bond strengthening. The frontier molecular orbitals (MOs) analysis and Natural bond orbital (NBO) manifest the intramolecular charge transfer of fisetin chromophore, which reveals the tendency of proton transfer. The potential energy surfaces of the S0 and S1 states are constructed to explain the mechanism of the proton transfer in excited state in detail.
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Affiliation(s)
- Dapeng Yang
- College of Mathematics and Information Science, North China University of Water Resources and Electric Power, Zhengzhou 450045, China; State Key Laboratory of Molecular Reaction Dynamics, Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Jinfeng Zhao
- State Key Laboratory of Molecular Reaction Dynamics, Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Rui Zheng
- College of Mathematics and Information Science, North China University of Water Resources and Electric Power, Zhengzhou 450045, China
| | - Yusheng Wang
- College of Mathematics and Information Science, North China University of Water Resources and Electric Power, Zhengzhou 450045, China
| | - Jian Lv
- College of Mathematics and Information Science, North China University of Water Resources and Electric Power, Zhengzhou 450045, China
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173
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Computational investigation on the intramolecular resonance-inhibited hydrogen bonding: a new type of interaction versus the RAHB model. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1683-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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174
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Facile synthesis of iodopyridines from N-propargylic β-enaminones via iodine-mediated electrophilic cyclization. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.04.070] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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175
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Wang C, Guan L, Danovich D, Shaik S, Mo Y. The origins of the directionality of noncovalent intermolecular interactions#. J Comput Chem 2015; 37:34-45. [DOI: 10.1002/jcc.23946] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/24/2015] [Accepted: 04/27/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Changwei Wang
- Department of Chemistry; School of Science; China University of Petroleum (East China); Changjiangxi Road 66 266580 Tsingtao China
| | - Liangyu Guan
- Department of Chemistry; Western Michigan University; Kalamazoo Michigan 49008
| | - David Danovich
- Institute of Chemistry and Lise Meitner Minerva Center for Computational Quantum Chemistry; the Hebrew University; Jerusalem 91904 Israel
| | - Sason Shaik
- Institute of Chemistry and Lise Meitner Minerva Center for Computational Quantum Chemistry; the Hebrew University; Jerusalem 91904 Israel
| | - Yirong Mo
- Department of Chemistry; Western Michigan University; Kalamazoo Michigan 49008
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176
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Saha S, Sastry GN. Cooperative or Anticooperative: How Noncovalent Interactions Influence Each Other. J Phys Chem B 2015; 119:11121-35. [DOI: 10.1021/acs.jpcb.5b03005] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Soumen Saha
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500007, Andhra Pradesh, India
| | - G. Narahari Sastry
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500007, Andhra Pradesh, India
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177
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A detailed theoretical investigation on the excited-state intramolecular proton-transfer mechanism of 3-BTHPB chemosensor. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1664-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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178
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Korkmaz U, Bulut A, Bulut İ. 3-Phenylpyridinium hydrogen squarate: experimental and computational study of a nonlinear optical material. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 140:140-149. [PMID: 25590828 DOI: 10.1016/j.saa.2014.12.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 11/20/2014] [Accepted: 12/09/2014] [Indexed: 06/04/2023]
Abstract
The detailed investigation of an organic nonlinear optical (NLO) squarate salt of 3-phenylpyridinium hydrogen squarate (1), C11H10N+·C4HO4(-), was reported in this study. The XRD data indicates that the crystal structure of the title compound is in the triclinic P-1 space group. In the asymmetric unit, the 3-phenylpyridine molecule is protonated by one hydrogen atom donation of squaric acid molecule, forming the salt (1). The X-ray analysis shows that the crystal packing has hydrogen bonding ring pattern of D2(2)(10) (α-dimer) through NH···O interactions. The structural and vibrational properties of the compound were also studied by computational methods of ab initio at DFT/B3LYP/6-31++G(d,p) (2) and HF/6-31++G(d,p) (3) levels of theory. The calculation results on the basis of two models for both the optimized molecular structure and vibrational properties for the 1 are presented and compared with the experimental results. Non-linear optical properties (NLO) of the title compound together with the molecular electrostatic potential (MEP), electronic absorption spectrum, frontier molecular orbitals (FMOs) and conformational flexibility were also studied at the 2 level and the results were reported. In order to evaluate the suitability for NLO applications thermal analysis (TG, DTA and DTG) data of 1 were also obtained.
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Affiliation(s)
- Ufuk Korkmaz
- Department of Physics, Faculty of Arts and Sciences, Ondokuzmayıs University, Kurupelit, 55139 Samsun, Turkey
| | - Ahmet Bulut
- Department of Physics, Faculty of Arts and Sciences, Ondokuzmayıs University, Kurupelit, 55139 Samsun, Turkey
| | - İclal Bulut
- Department of Chemistry, Faculty of Engineering, Ondokuzmayıs University, Kurupelit, 55139 Samsun, Turkey
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179
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Rypkema HA, Sinha A, Francisco JS. Carboxylic Acid Catalyzed Hydration of Acetaldehyde. J Phys Chem A 2015; 119:4581-8. [DOI: 10.1021/jp510704j] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Heather A. Rypkema
- Department of Atmospheric, Oceanic, and Space Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Amitabha Sinha
- Department
of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Joseph S. Francisco
- Department of Chemistry, H.C.
Brown Building, Purdue University, West Lafayette, Indiana 47906, United States
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180
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Moustafa AMA, Huang J, McPhedran KN, Zeng H, El-Din MG. Probing the adsorption of weak acids on graphite using amplitude modulation-frequency modulation atomic force microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:3069-3075. [PMID: 25710305 DOI: 10.1021/la5048968] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Recent thermodynamics calculations and adsorption isotherms showed that the adsorption of a self-assembled layer (SAL) of ionized weak acids to carbon was attributed to the negatively charged hydrogen bonding (-CAHB), yet the direct visualization and characterization of this adsorption behavior have not been reported. Here, an amplitude modulation-frequency modulation atomic force microscopy (AM-FM AFM) technique was applied to discriminate the adsorption of decanoic acids (DA) on highly ordered pyrolytic graphite (HOPG). Thermodynamics calculations revealed that the adsorption of SAL was driven by the formation of -CAHB with negatively charged functional groups of HOPG. Multilayer adsorption could occur over the adsorbed ionized SAL, leading to the development of aggregates. AM-FM AFM imaging showed that the adsorption of the DA molecules forming aggregates occurred only for the HOPG-functionalized steps, while DA molecules were found to adsorb over the entire functionalized HOPG surface after water-plasma treatment, as evident from the frequency shifts identified in AFM images.
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Affiliation(s)
- Ahmed M A Moustafa
- †Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 2W2, Canada
| | - Jun Huang
- ‡Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
| | - Kerry N McPhedran
- †Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 2W2, Canada
| | - Hongbo Zeng
- ‡Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
| | - Mohamed Gamal El-Din
- †Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 2W2, Canada
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181
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Korkmaz U, Bulut A. 2-Pyridinium propanol hydrogen squarate: experimental and computational study of a nonlinear optical material. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt B:1058-1068. [PMID: 25459503 DOI: 10.1016/j.saa.2014.09.130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 09/26/2014] [Accepted: 09/30/2014] [Indexed: 06/04/2023]
Abstract
The experimental and theoretical investigation of a novel organic nonlinear optical (NLO) squarate salt of 2-pyridinium propanol hydrogen squarate (1), C8H12ON(+)·C4HO4(-), were reported in this study. The crystal structure of the title compound was found to crystallize in the triclinic P-1 space group. In the asymmetric unit each squaric acid molecules have donated one H atom to the pyridines N1 and N2 atoms of a 2-pyridine propanol molecule, forming the salt (1). The X-ray analysis clearly indicated that the crystal packing has shown the hydrogen bonding ring pattern of D2(2)(10) (α-dimer) through N-H⋯O interactions. The structural and vibrational properties of the compound were also studied by computational methods of ab initio performed on the compound at DFT/B3LYP/6-31++G(d,p) (2) and HF/6-31++G(d,p) (3) level of theory. The calculation results on the basis of two models for both the optimized molecular structure and vibrational properties for the 1 are presented and compared with the X-ray analysis result. The molecular electrostatic potential (MEP), electronic absorption spectra, frontier molecular orbitals (FMOs), conformational flexibility and non-linear optical properties (NLO) of the title compound were also studied at the 2 level and the results are reported. In order to evaluate the suitability for NLO applications thermal analysis (TG, DTA and DTG) data of 1 were also obtained.
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Affiliation(s)
- Ufuk Korkmaz
- Department of Physics, Faculty of Arts and Sciences, Ondokuzmayıs University, Kurupelit, 55139 Samsun, Turkey
| | - Ahmet Bulut
- Department of Physics, Faculty of Arts and Sciences, Ondokuzmayıs University, Kurupelit, 55139 Samsun, Turkey
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182
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Li X, Gámiz B, Wang Y, Pignatello JJ, Xing B. Competitive sorption used to probe strong hydrogen bonding sites for weak organic acids on carbon nanotubes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:1409-1417. [PMID: 25564729 DOI: 10.1021/es504019u] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We recently proposed that weak acids (AH) adsorb to partially oxidized carbonaceous materials in part by forming strong hydrogen bonds with acidic surface groups, depicted by (A···H···O-surf)(-), known as negative charge-assisted hydrogen bonds, (-)CAHBs. Here we use competition experiments to show that sorption of AH on carbon nanotubes (CNTs) can be described conceptually by a dual specific/nonspecific domain model, where one domain involves (-)CAHB sites that can become saturated. The trends observed in single-solute adsorption, including the stoichiometric release of hydroxide upon sorption of carboxyate or phenolate anions, were consistent with trends in the previous studies and pointed to the formation of (-)CAHB. 3,4-Dinitrophenolate formed (-)CAHBs more efficiently than did 2,6-dichloro-4-nitrophenolate because of alleviation of steric hindrance to approach by the ortho chlorines. Competition against a (-)CAHB-capable target compound was greater when the competitor was also (-)CAHB-capable than when it was not (e.g., benzoate as target vs 3,4-dinitrophenolate or nitrobenzene as competitor; mono-n-butyl phthalate as target vs methyl benzoate or p-tolyl acetate as competitor). Experiments also revealed competition between the nitroaromatic species for π-π electron donor-acceptor sites. The findings will contribute to a better understanding of the adsorption mechanism of ionizable compounds on carbonaceous materials.
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Affiliation(s)
- Xiaoyun Li
- College of Resources and Environment, Northwest A&F University , Yangling, Shaanxi 712100, China
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183
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RAHB concept and σ-skeleton in some oximes of 3-hydroxy fulvene; DFT, AIM, ELF and NBO studies. Struct Chem 2015. [DOI: 10.1007/s11224-015-0562-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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184
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Quantum chemical study on influence of the substitution effect on the structural and electronic properties and intramolecular hydrogen bonding of 2-nitrophenyl hydrosulfide in ground and electronic excited state. Struct Chem 2015. [DOI: 10.1007/s11224-014-0541-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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185
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Korkmaz U, Topçu Y, Taş M, Bulut A. Synthesis, an experimental and quantum chemical computational study: proton sharing in 4-Morpholinium bis(hydrogen squarate). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 134:233-243. [PMID: 25022494 DOI: 10.1016/j.saa.2014.06.100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 06/05/2014] [Accepted: 06/16/2014] [Indexed: 06/03/2023]
Abstract
The experimental and theoretical investigation results of a novel organic squarate salt of 4-Morpholinium bis(hydrogen squarate) (1), C₆H₁₄ON(+)·C₈H₃O₈(-), were reported in this study. The crystal structure of the title compound was found to crystallize in the triclinic P-1 space group. In the crystals of 1 the morpholine ring adopts the chair conformation with the ethyl group in the equatorial and hydrogen atoms in axial positions. The hydrogen squarate anions are linked into a homoconjugated anion, [(HSQ)₂H], by a short symmetric, nonlinear O₈⋯H₂⋯O₂ hydrogen bond of 2.444 (2)Å. The structural and vibrational properties of the compound were also studied by computational methods of ab-initio performed on the compound at DFT/B3LYP/6-31++G(d,p) (2) and HF/6-31++G(d,p) (3) level of theory. The obtained calculation results on the basis of two models for both the optimized molecular structure and vibrational properties for the 1 obtained are presented and compared with the X-ray analysis result. On the other hand the molecular electrostatic potential (MEP), electronic absorption spectra, frontier molecular orbitals (FMOs), conformational flexibility and non-linear optical properties (NLO) of the title compound were also studied at the 2 level and the results are reported. In order to evaluate the suitability for NLO applications thermal analysis (TG, DTA and DTG) data of 1 were also obtained.
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Affiliation(s)
- Ufuk Korkmaz
- Department of Physics, Faculty of Arts and Sciences, Ondokuzmayıs University, 55139 Kurupelit, Samsun, Turkey.
| | - Yıldıray Topçu
- Ondokuz Mayıs University, Faculty of Engineering, Chemical Engineering Department, 55139 Kurupelit, Samsun, Turkey
| | - Murat Taş
- Department of Chemistry, Faculty of Arts and Sciences, Giresun University, 28049 Giresun, Turkey
| | - Ahmet Bulut
- Department of Physics, Faculty of Arts and Sciences, Ondokuzmayıs University, 55139 Kurupelit, Samsun, Turkey
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186
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Schneider TH, Rieger M, Ansorg K, Sobolev AN, Schirmeister T, Engels B, Grabowsky S. Vinyl sulfone building blocks in covalently reversible reactions with thiols. NEW J CHEM 2015. [DOI: 10.1039/c5nj00368g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combination of quantum-chemical calculations, Hirshfeld surface analyses and reactivity studies predicts how to turn vinyl sulfones into electrophiles that react covalently but reversibly with thiols.
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Affiliation(s)
| | - Max Rieger
- University of Würzburg
- Institute of Physical and Theoretical Chemistry
- 97074 Würzburg
- Germany
| | - Kay Ansorg
- University of Würzburg
- Institute of Physical and Theoretical Chemistry
- 97074 Würzburg
- Germany
| | - Alexandre N. Sobolev
- The University of Western Australia
- School of Chemistry and Biochemistry
- Perth
- Australia
| | - Tanja Schirmeister
- University of Mainz
- Institute of Pharmacy and Biochemistry
- 55128 Mainz
- Germany
| | - Bernd Engels
- University of Würzburg
- Institute of Physical and Theoretical Chemistry
- 97074 Würzburg
- Germany
| | - Simon Grabowsky
- The University of Western Australia
- School of Chemistry and Biochemistry
- Perth
- Australia
- Universität Bremen
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187
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Alkorta I, Elguero J, Grabowski SJ. Pnicogen and hydrogen bonds: complexes between PH3X+ and PH2X systems. Phys Chem Chem Phys 2015; 17:3261-72. [DOI: 10.1039/c4cp04840g] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The charge-assisted complexes between PH3X+ and PH2X show three potential minima structures, the pnicogen bonded (I) one being the most stable.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica (CSIC)
- 28006 Madrid
- Spain
| | - José Elguero
- Instituto de Química Médica (CSIC)
- 28006 Madrid
- Spain
| | - Sławomir J. Grabowski
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea UPV/EHU, and Donostia International Physics Center (DIPC)
- 20080 Donostia
- Spain
- IKERBASQUE
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188
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Schmidtmann M, Middlemiss DS, Wilson CC. Isotopomeric polymorphism in a “doubly-polymorphic” multi-component molecular crystal. CrystEngComm 2015. [DOI: 10.1039/c5ce00123d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Isotopomeric polymorphism is observed in complexes of isonicotinamide with oxalic acid, highly unusual here in that each isotopic complex is itself polymorphic, a situation of “double polymorphism”. The four polymorphic forms exhibit different degrees of hydron transfer.
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Affiliation(s)
- Marc Schmidtmann
- Department of Chemistry
- Carl von Ossietzky University of Oldenburg
- Oldenburg, Germany
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189
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Moustafa AMA, McPhedran KN, Moreira J, Gamal El-Din M. Investigation of mono/competitive adsorption of environmentally relevant ionized weak acids on graphite: impact of molecular properties and thermodynamics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:14472-14480. [PMID: 25403017 DOI: 10.1021/es503458t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The thermodynamics of adsorption and competitive interactions of five weak acids on a graphite surface was assessed in alkaline solutions. Adsorption of the acids in mono- and multicompound solutions followed their Freundlich isotherms which suggest a diversity of graphite adsorption sites as confirmed by the presence of carboxylic and phenolic groups observed on graphite surfaces. Thermodynamic calculations assigned the formation of the negatively charged assisted hydrogen bond (-CAHB) between ionized solutes and adsorbent surface groups as the possible adsorption mechanism. However, the similar pKa values of current acids resulted in comparable free energies for -CAHB formation (ΔG(-CAHB)) being less than solvation free energies (ΔGSolv). Thus, additional ΔG is supplemented by increased hydrophobicity due to proton exchange of ionized acids with water (ΔΔG Hydrophobicity). Adsorption capacities and competition coefficients indicated that ΔΔG Hydrophobicity values depend on the neutral and ionized acid Kow. Competitive adsorption implies that multilayer adsorption may occur via hydrophobic bonding with the CH3 ends of the self-assembled layer which affects the acid adsorption capacities in mixtures as compared to monocompound solutions. The determination of adsorption mechanisms will assist in understanding of the fate and bioavailability of emerging and classical weak acids released into natural waters.
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Affiliation(s)
- Ahmed M A Moustafa
- Department of Civil and Environmental Engineering, University of Alberta , Edmonton, Alberta T6G 2W2, Canada
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190
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Belding L, Taimoory SM, Dudding T. Mirroring Enzymes: The Role of Hydrogen Bonding in an Asymmetric Organocatalyzed Aza-Henry Reaction—a DFT Study. ACS Catal 2014. [DOI: 10.1021/cs501062u] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Lee Belding
- Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | | | - Travis Dudding
- Brock University, St. Catharines, Ontario L2S 3A1, Canada
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191
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Kochanek SE, Clymer TM, Pakkala VS, Hebert SP, Reeping K, Firestine SM, Evanseck JD. Intramolecular charge-assisted hydrogen bond strength in pseudochair carboxyphosphate. J Phys Chem B 2014; 119:1184-91. [PMID: 25405523 PMCID: PMC4306500 DOI: 10.1021/jp506796r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Carboxyphosphate,
a suspected intermediate in ATP-dependent carboxylases,
has not been isolated nor observed directly by experiment. Consequently,
little is known concerning its structure, stability, and ionization
state. Recently, carboxyphosphate as either a monoanion or dianion
has been shown computationally to adopt a novel pseudochair conformation
featuring an intramolecular charge-assisted hydrogen bond (CAHB).
In this work, additive and subtractive correction schemes to the commonly
employed open–closed method are used to estimate the strength
of the CAHB. Truhlar’s Minnesota M06-2X functional with Dunning’s
aug-cc-pVTZ basis set has been used for geometry optimization, energy
evaluation, and frequency analysis. The CHARMM force field has been
used to approximate the Pauli repulsive terms in the closed and open
forms of carboxyphosphate. From our additive correction scheme, differential
Pauli repulsion contributions between the pseudochair (closed) and
open conformations of carboxyphosphate are found to be significant
in determining the CAHB strength. The additive correction modifies
the CAHB prediction (ΔEclosed–open) of −14 kcal/mol for the monoanion and −12 kcal/mol
for the dianion to −22.9 and −18.4 kcal/mol, respectively.
Results from the subtractive technique reinforce those from our additive
procedure, where the predicted CAHB strength ranges from −17.8
to −25.4 kcal/mol for the monoanion and from −15.7 to
−20.9 kcal/mol for the dianion. Ultimately, we find that the
CAHB in carboxyphosphate meets the criteria for short-strong hydrogen
bonds. However, carboxyphosphate has a unique energy profile that
does not result in the symmetric double-well behavior of low-barrier
hydrogen bonds. These findings provide deeper insight into the pseudochair
conformation of carboxyphosphate, and lead to an improved mechanistic
understanding of this intermediate in ATP-dependent carboxylases.
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Affiliation(s)
- Sarah E Kochanek
- Center for Computational Sciences and the Department of Chemistry and Biochemistry, Duquesne University , 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282-1530, United States
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192
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Mammino L, Bilonda MK. Computational study of antimalarial pyrazole alkaloids from Newbouldia laevis. J Mol Model 2014; 20:2464. [DOI: 10.1007/s00894-014-2464-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 09/07/2014] [Indexed: 11/27/2022]
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193
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Paul BK, Ganguly A, Guchhait N. Quantum chemical exploration of the intramolecular hydrogen bond interaction in 2-thiazol-2-yl-phenol and 2-benzothiazol-2-yl-phenol in the context of excited-state intramolecular proton transfer: a focus on the covalency in hydrogen bond. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 131:72-81. [PMID: 24820325 DOI: 10.1016/j.saa.2014.03.124] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/25/2014] [Accepted: 03/29/2014] [Indexed: 06/03/2023]
Abstract
The present work demonstrates a computational exploration of the intramolecular H-bond (IMHB) interaction in two model heterocyclic compounds - 2-thiazol-2-yl-phenol (2T2YP) and 2-benzothiazol-2-yl-phenol (2B2YP) by meticulous application of various quantum chemical tools. Major emphasis is rendered on the analysis of IMHB interaction by calculation of electron density ρ(r) and Laplacian ∇(2)ρ(r) at the bond critical point using the Atoms-In-Molecule methodology. Topological features based on ρ(r) suggest that at equilibrium geometry the IMHB interaction develops certain characteristics typical of a covalent interaction. The interplay between aromaticity and Resonance-Assisted H-Bond (RAHB) has also been discussed using both geometrical and magnetic criteria. The occurrence of IMHB interaction in 2T2YP and 2B2YP has also been criticized under the provision of the Natural Bond Orbital (NBO) analysis. The ESIPT phenomenon in the molecular systems is also critically addressed on the lexicon of potential energy surface (PES) analysis.
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Affiliation(s)
- Bijan Kumar Paul
- Department of Chemistry, University of Calcutta, 92 A.P.C. Road, Calcutta 700009, India
| | - Aniruddha Ganguly
- Department of Chemistry, University of Calcutta, 92 A.P.C. Road, Calcutta 700009, India
| | - Nikhil Guchhait
- Department of Chemistry, University of Calcutta, 92 A.P.C. Road, Calcutta 700009, India.
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194
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Aluminum-induced entropy in biological systems: implications for neurological disease. J Toxicol 2014; 2014:491316. [PMID: 25349607 PMCID: PMC4202242 DOI: 10.1155/2014/491316] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 07/28/2014] [Indexed: 12/14/2022] Open
Abstract
Over the last 200 years, mining, smelting, and refining of aluminum (Al) in various forms have increasingly exposed living species to this naturally abundant metal. Because of its prevalence in the earth's crust, prior to its recent uses it was regarded as inert and therefore harmless. However, Al is invariably toxic to living systems and has no known beneficial role in any biological systems. Humans are increasingly exposed to Al from food, water, medicinals, vaccines, and cosmetics, as well as from industrial occupational exposure. Al disrupts biological self-ordering, energy transduction, and signaling systems, thus increasing biosemiotic entropy. Beginning with the biophysics of water, disruption progresses through the macromolecules that are crucial to living processes (DNAs, RNAs, proteoglycans, and proteins). It injures cells, circuits, and subsystems and can cause catastrophic failures ending in death. Al forms toxic complexes with other elements, such as fluorine, and interacts negatively with mercury, lead, and glyphosate. Al negatively impacts the central nervous system in all species that have been studied, including humans. Because of the global impacts of Al on water dynamics and biosemiotic systems, CNS disorders in humans are sensitive indicators of the Al toxicants to which we are being exposed.
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195
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Šimůnek P, Padělková Z, Macháček V. Solution and solid-state study of the structure of azo-coupling products from isomeric enaminones possessing tert-butyl group: An unprecedented observation of pure hydrazo form in azo coupled N-alkyl β-enaminones. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.06.069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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196
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Very strong intramolecular hydrogen bonding of 1,2-dithenoylcyclopentadiene; DFT and spectroscopic studies. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.06.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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197
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Electronic structures, intramolecular hydrogen bond interaction, and aromaticity of substituted 4-amino-3-penten-2-one in ground and electronic excited state. Struct Chem 2014. [DOI: 10.1007/s11224-014-0505-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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198
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Korkmaz U, Bulut A. Synthesis, an experimental and quantum chemical computational study of a new nonlinear optical material: 2-picolinium hydrogensquarate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 130:376-385. [PMID: 24813271 DOI: 10.1016/j.saa.2014.04.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 04/04/2014] [Accepted: 04/07/2014] [Indexed: 06/03/2023]
Abstract
The experimental and theoretical investigation results of a novel organic non-linear optical (NLO) organic squarate salt of 2-Picolinium hydrogensquarate (1), C6H8N+·C4HO4-, were reported in this study. The space group of the title compound was found in the monoclinic C2/c space group. It was found that the asymmetric unit consists of one monohydrogen squarate anion together with mono protonated 2-Picolinium, forming the (1) salt. The X-ray analysis clearly indicated that the crystal packing has shown the hydrogen bonding ring pattern of D2(2)(10) (α-dimer) through NH⋯O interactions. The hydrogensquarate anions form α-dimer, while 2-Picolinium molecule interacts through NH⋯O and CH⋯O with the hydrogensquarate anion. The structural and vibrational properties of the compound were also studied by computational methods of ab initio performed on the compound at DFT/B3LYP/6-31++G(d,p) (2) and HF/6-31++G(d,p) (3) level of theory. The calculation results on the basis of two models for both the optimized molecular structure and vibrational properties for the 1 obtained are presented and compared with the X-ray analysis result. On the other the molecular electrostatic potential (MEP), electronic absorption spectra, frontier molecular orbitals (FMOs), conformational flexibility and non-linear optical properties (NLO) of the title compound were also studied at the 2 level and the results are reported. In order to evaluate the suitability for NLO applications thermal analysis (TG, DTA and DTG) data of 1 were also obtained.
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Affiliation(s)
- Ufuk Korkmaz
- Department of Physics, Faculty of Arts and Sciences, Ondokuzmayıs University, Kurupelit 55139, Samsun, Turkey.
| | - Ahmet Bulut
- Department of Physics, Faculty of Arts and Sciences, Ondokuzmayıs University, Kurupelit 55139, Samsun, Turkey
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199
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Auerbach D, Aspenleiter J, Volmer DA. Description of gas-phase ion/neutral interactions in differential ion mobility spectrometry: CV prediction using calibration runs. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1610-1621. [PMID: 24927778 DOI: 10.1007/s13361-014-0934-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/12/2014] [Accepted: 05/12/2014] [Indexed: 06/03/2023]
Abstract
Differential ion mobility spectrometry (DMS) coupled to mass spectrometry is increasingly used in both quantitative analyses of biological samples and as a means of removing background interferences for enhanced selectivity and improved quality of mass spectra. However, DMS separation efficiency using dry inert gases often lacks the required selectivity to achieve baseline separation. Polar gas-phase modifiers such as alcohols are therefore frequently employed to improve selectivity via clustering/declustering processes. The choice of an optimal modifier currently relies on trial and error experiments, making method development a tedious activity. It was the goal of this study to establish a means of CV prediction for compounds using a homologous series of alcohols as gas-phase modifiers. This prediction was based on linear regression of compensation voltages of two calibration runs for the alcohols with the lowest and the highest molecular weights and readily available descriptors such as proton affinity and gas phase acidity of the modifier molecules. All experiments were performed on a commercial quadrupole linear ion trap mass spectrometer equipped with a DMS device between electrospray ionization source and entrance quadrupole lens. We evaluated our approach using a homologous series of 4-alkylbenzoic acids and a selection of 23 small molecules of high chemical diversity. Predicted CV values typically deviated from the experimentally determined values by less than 0.5 V. Several test compounds changed their ion mobility behavior for the investigated gas phase modifiers (e.g., from type B to type A) and thus could thus not be evaluated.
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Affiliation(s)
- David Auerbach
- Institute of Bioanalytical Chemistry, Saarland University, Saarbrücken, Germany
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200
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Esrafili MD, Mohammadian-Sabet F. Halogen-Bond Interactions Enhanced by Charge-Assisted Hydrogen Bonds: An Ab Initio Study. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2014. [DOI: 10.1246/bcsj.20140062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Mehdi D. Esrafili
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh
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