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Thuéry P, Harrowfield J. Anionic uranyl ion complexes with pyrazinetetracarboxylate: Influence of structure-directing cations. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.116118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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2
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Voronin AP, Surov AO, Churakov AV, Parashchuk OD, Rykounov AA, Vener MV. Combined X-ray Crystallographic, IR/Raman Spectroscopic, and Periodic DFT Investigations of New Multicomponent Crystalline Forms of Anthelmintic Drugs: A Case Study of Carbendazim Maleate. Molecules 2020; 25:E2386. [PMID: 32455564 PMCID: PMC7287603 DOI: 10.3390/molecules25102386] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 12/14/2022] Open
Abstract
Synthesis of multicomponent solid forms is an important method of modifying and fine-tuning the most critical physicochemical properties of drug compounds. The design of new multicomponent pharmaceutical materials requires reliable information about the supramolecular arrangement of molecules and detailed description of the intermolecular interactions in the crystal structure. It implies the use of a combination of different experimental and theoretical investigation methods. Organic salts present new challenges for those who develop theoretical approaches describing the structure, spectral properties, and lattice energy Elatt. These crystals consist of closed-shell organic ions interacting through relatively strong hydrogen bonds, which leads to Elatt > 200 kJ/mol. Some technical problems that a user of periodic (solid-state) density functional theory (DFT) programs encounters when calculating the properties of these crystals still remain unsolved, for example, the influence of cell parameter optimization on the Elatt value, wave numbers, relative intensity of Raman-active vibrations in the low-frequency region, etc. In this work, various properties of a new two-component carbendazim maleate crystal were experimentally investigated, and the applicability of different DFT functionals and empirical Grimme corrections to the description of the obtained structural and spectroscopic properties was tested. Based on this, practical recommendations were developed for further theoretical studies of multicomponent organic pharmaceutical crystals.
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Affiliation(s)
- Alexander P. Voronin
- Department of Physical Chemistry of Drugs, G.A. Krestov Institute of Solution Chemistry of RAS, 153045 Ivanovo, Russia; (A.P.V.); (A.O.S.)
| | - Artem O. Surov
- Department of Physical Chemistry of Drugs, G.A. Krestov Institute of Solution Chemistry of RAS, 153045 Ivanovo, Russia; (A.P.V.); (A.O.S.)
| | - Andrei V. Churakov
- Department of Crystal Chemistry and X-ray Diffraction, N.S. Kurnakov Institute of General and Inorganic Chemistry of RAS, 119991 Moscow, Russia;
| | - Olga D. Parashchuk
- Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Alexey A. Rykounov
- Theoretical Department, FSUE “RFNC-VNIITF Named after Academ. E.I. Zababakhin”, 456770 Snezhinsk, Russia;
| | - Mikhail V. Vener
- Department of Quantum Chemistry, D. Mendeleev University of Chemical Technology, 125047 Moscow, Russia
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3
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Sosa-Rivadeneyra MV, Vasquez-Ríos MG, Vargas-Olvera EC, Mendoza M, Varela-Caselis JL, Meza-León RL, Sánchez-Guadarrama MO, Höpfl H. Crystal structures of organic salts of chloranilic acid and 2,2′-bi(3-hydroxy-1,4-naphthoquinone) acting as proton donors to 4,4′-Bipyridine and 1,4-Diazabicyclo[2.2.2]octane: 3D networks with bifurcated N+-H···O−/O or N+-H···O/Cl synthons. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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4
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Ruelas‐Alvarez GY, Cárdenas‐Valenzuela AJ, Cruz‐Enríquez A, Höpfl H, Campos‐Gaxiola JJ, Rodríguez‐Rivera MA, Rodríguez‐Molina B. Exploration of the Luminescence Properties of Organic Phosphate Salts of 3‐Quinoline‐ and 5‐Isoquinolineboronic Acid. Eur J Inorg Chem 2019. [DOI: 10.1002/ejic.201900244] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Glenda Y. Ruelas‐Alvarez
- Facultad de Ingeniería Mochis Universidad Autónoma de Sinaloa Fuente de Poseidón y Prol. A. Flores S/N C.P. 81223 C.U. Los Mochis, Sinaloa México
| | - A. Jaquelin Cárdenas‐Valenzuela
- Facultad de Ingeniería Mochis Universidad Autónoma de Sinaloa Fuente de Poseidón y Prol. A. Flores S/N C.P. 81223 C.U. Los Mochis, Sinaloa México
| | - Adriana Cruz‐Enríquez
- Facultad de Ingeniería Mochis Universidad Autónoma de Sinaloa Fuente de Poseidón y Prol. A. Flores S/N C.P. 81223 C.U. Los Mochis, Sinaloa México
| | - Herbert Höpfl
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas Universidad Autónoma del Estado de Morelos Av. Universidad 1001, C.P. 62209 Cuernavaca México
| | - José J. Campos‐Gaxiola
- Facultad de Ingeniería Mochis Universidad Autónoma de Sinaloa Fuente de Poseidón y Prol. A. Flores S/N C.P. 81223 C.U. Los Mochis, Sinaloa México
| | - Mario A. Rodríguez‐Rivera
- Centro de Investigaciones en Óptica A.C. (CIO) Loma del Bosque #115, Col. Lomas del Campestre, C.P. 37150 León Guanajuato México
| | - Braulio Rodríguez‐Molina
- Instituto de Química Universidad Nacional Autónoma de México Ciudad Universitaria, Del. Coyoacán Ciudad de México México
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5
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Liu L, Tan S(J, Horikawa T, Do D, Nicholson D, Liu J. Water adsorption on carbon - A review. Adv Colloid Interface Sci 2017; 250:64-78. [PMID: 29129312 DOI: 10.1016/j.cis.2017.10.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 10/18/2017] [Accepted: 10/22/2017] [Indexed: 10/18/2022]
Abstract
Water adsorption on carbonaceous materials has been studied increasingly in the recent years, not only because of its impact on many industrial processes, but also motivated by a desire to understand, at a fundamental level, the distinctive character of directional interactions between water molecules, and between water molecules and other polar groups, such as the functional groups (FGs) at the surfaces of graphene layers. This paper presents an extensive review of recent experimental and theoretical work on water adsorption on various carbonaceous materials, with the aim of gaining a better understanding of how water adsorption in carbonaceous materials relates to the concentration of FGs, their topology (arrangement of the groups) and the structure of the confined space in porous carbons. Arising from this review we are able to propose mechanisms for water adsorption in carbonaceous materials as the adsorbate density increases. The intricate interplay between the roles of FGs and confinement makes adsorption of water on carbon materials very different from that of other simple molecules.
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6
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Golafale ST, Ingram CW, Holder AA, Chen WY, Zhang ZJ. 1-D calcium, 2-D zinc and 3-D manganese coordination polymers derived from pyrazine-2,3,5,6-tetracarboxylic acid. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2017.07.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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7
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Campos-Gaxiola JJ, García-Grajeda BA, Hernández-Ahuactzi IF, Guerrero-Álvarez JA, Höpfl H, Cruz-Enríquez A. Supramolecular networks in molecular complexes of pyridine boronic acids and polycarboxylic acids: synthesis, structural characterization and fluorescence properties. CrystEngComm 2017. [DOI: 10.1039/c7ce00762k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
3- and 4-pyridineboronic acids have been combined with trimesic and pyromellitic acids to give three molecular complexes.
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Affiliation(s)
| | | | | | - Jorge A. Guerrero-Álvarez
- Centro de Investigaciones Químicas
- Instituto de Investigación en Ciencias Básicas y Aplicadas
- Universidad Autónoma del Estado de Morelos
- Cuernavaca
- Mexico
| | - Herbert Höpfl
- Centro de Investigaciones Químicas
- Instituto de Investigación en Ciencias Básicas y Aplicadas
- Universidad Autónoma del Estado de Morelos
- Cuernavaca
- Mexico
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8
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Bhatt H, Mishra AK, Murli C, Verma AK, Garg N, Deo MN, Sharma SM. Proton transfer aiding phase transitions in oxalic acid dihydrate under pressure. Phys Chem Chem Phys 2016; 18:8065-74. [PMID: 26924455 DOI: 10.1039/c5cp07442h] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oxalic acid dihydrate, an important molecular solid in crystal chemistry, ecology and physiology, has been studied for nearly 100 years now. The most debated issues regarding its proton dynamics have arisen due to an unusually short hydrogen bond between the acid and water molecules. Using combined in situ spectroscopic studies and first-principles simulations at high pressures, we show that the structural modification associated with this hydrogen bond is much more significant than ever assumed. Initially, under pressure, proton migration takes place along this strong hydrogen bond at a very low pressure of 2 GPa. This results in the protonation of water with systematic formation of dianionic oxalate and hydronium ion motifs, thus reversing the hydrogen bond hierarchy in the high pressure phase II. The resulting hydrogen bond between a hydronium ion and a carboxylic group shows remarkable strengthening under pressure, even in the pure ionic phase III. The loss of cooperativity of hydrogen bonds leads to another phase transition at ∼ 9 GPa through reorientation of other hydrogen bonds. The high pressure phase IV is stabilized by a strong hydrogen bond between the dominant CO2 and H2O groups of oxalate and hydronium ions, respectively. These findings suggest that oxalate systems may provide useful insights into proton transfer reactions and assembly of simple molecules under extreme conditions.
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Affiliation(s)
- Himal Bhatt
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India.
| | - A K Mishra
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India.
| | - Chitra Murli
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India.
| | - Ashok K Verma
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India.
| | - Nandini Garg
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India.
| | - M N Deo
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India.
| | - Surinder M Sharma
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, 400 085, India.
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9
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Brela MZ, Wójcik MJ, Witek ŁJ, Boczar M, Wrona E, Hashim R, Ozaki Y. Born-Oppenheimer Molecular Dynamics Study on Proton Dynamics of Strong Hydrogen Bonds in Aspirin Crystals, with Emphasis on Differences between Two Crystal Forms. J Phys Chem B 2016; 120:3854-62. [PMID: 27045959 DOI: 10.1021/acs.jpcb.6b01601] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, the proton dynamics of hydrogen bonds for two forms of crystalline aspirin was investigated by the Born-Oppenheimer molecular dynamics (BOMD) method. Analysis of the geometrical parameters of hydrogen bonds using BOMD reveals significant differences in hydrogen bonding between the two crystalline forms of aspirin, Form I and Form II. Analysis of the trajectory for Form I shows spontaneous proton transfer in cyclic dimers, which is absent in Form II. Quantization of the O-H stretching modes allows a detailed discussion on the strength of hydrogen-bonding interactions. The focal point of our study is examination of the hydrogen bond characteristics in the crystal structure and clarification of the influence of hydrogen bonding on the presence of the two crystalline forms of aspirin. In the BOMD method, thermal motions were taken into account. Solving the Schrödinger equation for the snapshots of 2D proton potentials, extracted from MD, gives the best agreement with IR spectra. The character of medium-strong hydrogen bonds in Form I of aspirin was compared with that of weaker hydrogen bonds in aspirin Form II. Two proton minima are present in the potential function for the hydrogen bonds in Form I. The band contours, calculated by using one- and two-dimensional O-H quantization, reflect the differences in the hydrogen bond strengths between the two crystalline forms of aspirin, as well as the strong hydrogen bonding in the cyclic dimers of Form I and the medium-strong hydrogen bonding in Form II.
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Affiliation(s)
- Mateusz Z Brela
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland
| | - Marek J Wójcik
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland
| | - Łukasz J Witek
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland
| | - Marek Boczar
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland
| | - Ewa Wrona
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Krakow, Poland
| | - Rauzah Hashim
- Department of Chemistry, University of Malaya , 50603 Kuala Lumpur, Malaysia
| | - Yukihiro Ozaki
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University , Sanda, Hyogo 669-1337, Japan
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10
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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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11
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D’Ascenzo L, Auffinger P. A comprehensive classification and nomenclature of carboxyl-carboxyl(ate) supramolecular motifs and related catemers: implications for biomolecular systems. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2015; 71:164-75. [PMID: 25827369 PMCID: PMC4383392 DOI: 10.1107/s205252061500270x] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 02/08/2015] [Indexed: 05/13/2023]
Abstract
Carboxyl and carboxylate groups form important supramolecular motifs (synthons). Besides carboxyl cyclic dimers, carboxyl and carboxylate groups can associate through a single hydrogen bond. Carboxylic groups can further form polymeric-like catemer chains within crystals. To date, no exhaustive classification of these motifs has been established. In this work, 17 association types were identified (13 carboxyl-carboxyl and 4 carboxyl-carboxylate motifs) by taking into account the syn and anti carboxyl conformers, as well as the syn and anti lone pairs of the O atoms. From these data, a simple rule was derived stating that only eight distinct catemer motifs involving repetitive combinations of syn and anti carboxyl groups can be formed. Examples extracted from the Cambridge Structural Database (CSD) for all identified dimers and catemers are presented, as well as statistical data related to their occurrence and conformational preferences. The inter-carboxyl(ate) and carboxyl(ate)-water hydrogen-bond properties are described, stressing the occurrence of very short (strong) hydrogen bonds. The precise characterization and classification of these supramolecular motifs should be of interest in crystal engineering, pharmaceutical and also biomolecular sciences, where similar motifs occur in the form of pairs of Asp/Glu amino acids or motifs involving ligands bearing carboxyl(ate) groups. Hence, we present data emphasizing how the analysis of hydrogen-containing small molecules of high resolution can help understand structural aspects of larger and more complex biomolecular systems of lower resolution.
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Affiliation(s)
- Luigi D’Ascenzo
- Architecture et Réactivité de l’ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg, France
| | - Pascal Auffinger
- Architecture et Réactivité de l’ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg, France
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12
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Ingram CW, Kibakaya G, Bacsa J, Mathis,II SR, Holder AA, Rambaran VH, Dennis B, Castaneda E, Robbins JS, John Zhang Z. Complex three-dimensional lanthanide metal–organic frameworks with variable coordination spheres based on pyrazine-2,3,5,6-tetracarboxylate. CrystEngComm 2015. [DOI: 10.1039/c4ce02564d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An open 3-D MOF with complex connectivity of multi-topic pyrazine-2,3,5,6-tetracarboxylate linker and Ln(iii) ions.
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Affiliation(s)
- Conrad W. Ingram
- Center for Functional Nanoscale Materials
- Department of Chemistry
- Clark Atlanta University
- Atlanta, USA
| | - Geoffrey Kibakaya
- Center for Functional Nanoscale Materials
- Department of Chemistry
- Clark Atlanta University
- Atlanta, USA
| | - John Bacsa
- Department of Chemistry
- Emory University
- Atlanta, USA
| | - Stephan R. Mathis,II
- Center for Functional Nanoscale Materials
- Department of Chemistry
- Clark Atlanta University
- Atlanta, USA
| | - Alvin A. Holder
- Department of Chemistry and Biochemistry
- Old Dominion University
- Norfolk, USA
| | - Varma H. Rambaran
- Biomedical Engineering Unit
- The University of Trinidad and Tobago
- Arima, West Indies
| | - Brandon Dennis
- Center for Functional Nanoscale Materials
- Department of Chemistry
- Clark Atlanta University
- Atlanta, USA
| | - Esmeralda Castaneda
- Center for Functional Nanoscale Materials
- Department of Chemistry
- Clark Atlanta University
- Atlanta, USA
| | - Julianne S. Robbins
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta, USA
| | - Z. John Zhang
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta, USA
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13
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Stare J, Hadži D. Cooperativity Assisted Shortening of Hydrogen Bonds in Crystalline Oxalic Acid Dihydrate: DFT and NBO Model Studies. J Chem Theory Comput 2014; 10:1817-23. [DOI: 10.1021/ct500167n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jernej Stare
- National
Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Dušan Hadži
- National
Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
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14
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Bagdi PR, Basha RS, Baruah PK, Khan AT. Copper oxide nanoparticle mediated ‘click chemistry’ for the synthesis of mono-, bis- and tris-triazole derivatives from 10,10-dipropargyl-9-anthrone as a key building block. RSC Adv 2014. [DOI: 10.1039/c3ra44869j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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15
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Zhang F, Yan P, Li H, Zou X, Hou G, Li G. Towards full-color-tunable emission of two component Eu(iii)-doped Gd(iii) coordination frameworks by the variation of excitation light. Dalton Trans 2014; 43:12574-81. [DOI: 10.1039/c4dt00837e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Eu(iii)-doped Gd(iii) pyrazine-2,3,5,6-tetracarboxylate alkali–lanthanide metal–organic frameworks (LnMOF) with a unique (411·68·82)(43·62·8)(43) topology present full color-tunable luminescence and white emission by the variation of excitation wavelengths.
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Affiliation(s)
- Fengming Zhang
- Key Laboratory of Functional Inorganic Material Chemistry (MOE)
- School of Chemistry and Materials Science
- Heilongjiang University
- Harbin 150080, P. R. China
- Harbin University of Science and Technology
| | - Pengfei Yan
- Key Laboratory of Functional Inorganic Material Chemistry (MOE)
- School of Chemistry and Materials Science
- Heilongjiang University
- Harbin 150080, P. R. China
| | - Hongfeng Li
- Key Laboratory of Functional Inorganic Material Chemistry (MOE)
- School of Chemistry and Materials Science
- Heilongjiang University
- Harbin 150080, P. R. China
| | - Xiaoyan Zou
- Key Laboratory of Functional Inorganic Material Chemistry (MOE)
- School of Chemistry and Materials Science
- Heilongjiang University
- Harbin 150080, P. R. China
| | - Guangfeng Hou
- Key Laboratory of Functional Inorganic Material Chemistry (MOE)
- School of Chemistry and Materials Science
- Heilongjiang University
- Harbin 150080, P. R. China
| | - Guangming Li
- Key Laboratory of Functional Inorganic Material Chemistry (MOE)
- School of Chemistry and Materials Science
- Heilongjiang University
- Harbin 150080, P. R. China
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16
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Vener MV, Shishkina AV, Rykounov AA, Tsirelson VG. Cl···Cl interactions in molecular crystals: insights from the theoretical charge density analysis. J Phys Chem A 2013; 117:8459-67. [PMID: 23924151 DOI: 10.1021/jp405119x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The structure, IR harmonic frequencies and intensities of normal vibrations of 20 molecular crystals with the X-Cl···Cl-X contacts of different types, where X = C, Cl, and F and the Cl···Cl distance varying from ~3.0 to ~4.0 Å, are computed using the solid-state DFT method. The obtained crystalline wave functions have been further used to define and describe quantitatively the Cl···Cl interactions via the electron-density features at the Cl···Cl bond critical points. We found that the electron-density at the bond critical point is almost independent of the particular type of the contact or hybridization of the ipso carbon atom. The energy of Cl···Cl interactions, E(int), is evaluated from the linking E(int) and local electronic kinetic energy density at the Cl···Cl bond critical points. E(int) varies from 2 to 12 kJ/mol. The applicability of the geometrical criterion for the detection of the Cl···Cl interactions in crystals with two or more intermolecular Cl···Cl contacts for the unique chlorine atom is not straightforward. The detection of these interactions in such crystals may be done by the quantum-topological analysis of the periodic electron density.
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Affiliation(s)
- Mikhail V Vener
- Department of Quantum Chemistry, Mendeleev University of Chemical Technology, Miusskaya Square 9, 125047 Moscow, Russia.
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17
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Bacchi A, Carcelli M, Pelagatti P. Crystal engineering of flexible metallorganic supramolecular networks. CRYSTALLOGR REV 2012. [DOI: 10.1080/0889311x.2012.712117] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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18
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Vener MV, Egorova AN, Churakov AV, Tsirelson VG. Intermolecular hydrogen bond energies in crystals evaluated using electron density properties: DFT computations with periodic boundary conditions. J Comput Chem 2012; 33:2303-9. [PMID: 22786749 DOI: 10.1002/jcc.23062] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 06/14/2012] [Accepted: 06/19/2012] [Indexed: 11/11/2022]
Abstract
The hydrogen bond (H-bond) energies are evaluated for 18 molecular crystals with 28 moderate and strong O-H···O bonds using the approaches based on the electron density properties, which are derived from the B3LYP/6-311G** calculations with periodic boundary conditions. The approaches considered explore linear relationships between the local electronic kinetic G(b) and potential V(b) densities at the H···O bond critical point and the H-bond energy E(HB). Comparison of the computed E(HB) values with the experimental data and enthalpies evaluated using the empirical correlation of spectral and thermodynamic parameters (Iogansen, Spectrochim. Acta Part A 1999, 55, 1585) enables to estimate the accuracy and applicability limits of the approaches used. The V(b)-E(HB) approach overestimates the energy of moderate H-bonds (E(HB) < 60 kJ/mol) by ~20% and gives unreliably high energies for crystals with strong H-bonds. On the other hand, the G(b)-E(HB) approach affords reliable results for the crystals under consideration. The linear relationship between G(b) and E(HB) is basis set superposition error (BSSE) free and allows to estimate the H-bond energy without computing it by means of the supramolecular approach. Therefore, for the evaluation of H-bond energies in molecular crystals, the G(b) value can be recommended to be obtained from both density functional theory (DFT) computations with periodic boundary conditions and precise X-ray diffraction experiments.
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Affiliation(s)
- M V Vener
- Department of Quantum Chemistry, Mendeleev University of Chemical Technology, Miusskaya Square 9, 125047 Moscow, Russia.
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19
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20
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Liu FH. 5,6-Dimethyl-pyrazine-2,3-dicarb-oxy-lic acid. Acta Crystallogr Sect E Struct Rep Online 2012; 68:o132. [PMID: 22259420 PMCID: PMC3254478 DOI: 10.1107/s1600536811052366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Accepted: 12/05/2011] [Indexed: 11/27/2022]
Abstract
The asymmetric unit of the title compound, C8H8N2O4, consists of one complete molecule and a second molecule generated by the application of twofold axis. The mean planes of the two carboxyl groups attached to the pyrazine ring at neighboring positions are twisted by 10.8 (1) and 87.9 (1)° in the complete molecule and 43.0 (1)° in the symmetry-generated molecule. The crystal packing features O—H⋯N hydrogen bonds, which link the molecules into layers along [101].
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Affiliation(s)
- Fu-Hong Liu
- Basis Department, Jilin Business and Technology College, Hao Yue Road No. 1606, Changchun, Jilin, People's Republic of China
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21
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Montis R, Hursthouse MB. Crystalline adducts of some substituted salicylic acids with 4-aminopyridine, including hydrates and solvates: contact and separated ionic complexes with diverse supramolecular synthons. CrystEngComm 2012. [DOI: 10.1039/c2ce26008e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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22
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Nanubolu JB, Sridhar B, Ravikumar K. Resonance-assisted amide protonation in dutasteride hydrochloride salt. CrystEngComm 2012. [DOI: 10.1039/c2ce06421a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Biliškov N, Kojić-Prodić B, Mali G, Molčanov K, Stare J. A Partial Proton Transfer in Hydrogen Bond O−H···O in Crystals of Anhydrous Potassium and Rubidium Complex Chloranilates. J Phys Chem A 2011; 115:3154-66. [DOI: 10.1021/jp112380f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Nikola Biliškov
- Rudjer Bošković Institute, POB 180, HR-10002 Zagreb, Croatia
| | | | - Gregor Mali
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Dunajska c. 156, SI-1000 Ljubljana
| | | | - Jernej Stare
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
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24
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Bacchi A, Cantoni G, Chierotti MR, Girlando A, Gobetto R, Lapadula G, Pelagatti P, Sironi A, Zecchini M. Water vapour uptake and extrusion by a crystalline metallorganic solid based on half-sandwich Ru(ii) building-blocks. CrystEngComm 2011. [DOI: 10.1039/c0ce00816h] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Zhang XQ, Wu WS, Wang XY, Ma JH. Diisopropyl pyrazine-2,5-dicarboxyl-ate. Acta Crystallogr Sect E Struct Rep Online 2010; 66:o2206. [PMID: 21588578 PMCID: PMC3007933 DOI: 10.1107/s1600536810029314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2010] [Accepted: 07/22/2010] [Indexed: 05/30/2023]
Abstract
The mol-ecule of the title compound, C(12)H(16)N(2)O(4), is located on an inversion center. The carboxyl-ate groups are twisted slightly with respect to the pyrazine ring, making a dihedral angle of 6.4 (3)°.
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Affiliation(s)
- Xiao-Qing Zhang
- College of Materials Science and Engineering, Huaqiao University, Xiamen, Fujian, 361021, People’s Republic of China
| | - Wen-Shi Wu
- College of Materials Science and Engineering, Huaqiao University, Xiamen, Fujian, 361021, People’s Republic of China
| | - Xin-Yu Wang
- College of Materials Science and Engineering, Huaqiao University, Xiamen, Fujian, 361021, People’s Republic of China
| | - Jian-Hua Ma
- College of Materials Science and Engineering, Huaqiao University, Xiamen, Fujian, 361021, People’s Republic of China
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27
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Allen FH, Bruno IJ. Bond lengths in organic and metal-organic compounds revisited: X-H bond lengths from neutron diffraction data. ACTA CRYSTALLOGRAPHICA SECTION B: STRUCTURAL SCIENCE 2010; 66:380-6. [PMID: 20484809 DOI: 10.1107/s0108768110012048] [Citation(s) in RCA: 273] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 03/30/2010] [Indexed: 11/10/2022]
Abstract
The number of structures in the Cambridge Structural Database (CSD) has increased by an order of magnitude since the preparation of two major compilations of standard bond lengths in mid-1985. It is now of interest to examine whether this huge increase in data availability has implications for the mean bond-length values published in the late 1980s. Those compilations reported mean X-H bond lengths derived from rather sparse information and for rather few chemical environments. During the intervening years, the number of neutron studies has also increased, although only by a factor of around 2.25, permitting a new analysis of X-H bond-length distributions for (a) organic X = C, N, O, B, and (b) a variety of terminal and homometallic bridging transition metal hydrides. New mean values are reported here and are compared with earlier results. These new overall means are also complemented by an analysis of X-H distances at lower temperatures (T < or = 140 K), which indicates the general level of librational effects in X-H systems. The study also extends the range of chemical environments for which statistically acceptable mean X-H bond lengths can be obtained, although values from individual structures are also collated to further extend the chemical range of this compilation. Updated default 'neutron-normalization' distances for use in hydrogen-bond and deformation-density studies are also proposed for C-H, N-H and O-H, and the low-temperature analysis provides specific values for certain chemical environments and hybridization states of X.
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Affiliation(s)
- Frank H Allen
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England.
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28
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Lee HM, Kumar A, Kołaski M, Kim DY, Lee EC, Min SK, Park M, Choi YC, Kim KS. Comparison of cationic, anionic and neutral hydrogen bonded dimers. Phys Chem Chem Phys 2010; 12:6278-87. [PMID: 20405079 DOI: 10.1039/b925551f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Short Strong Hydrogen Bonds (SSHBs) play an important role in many fields of physics, chemistry and biology. Since it is known that SSHBs exist in many biological systems, the role of hydrogen bonding motifs has been particularly interesting in enzyme catalysis, bio-metabolism, protein folding and proton transport phenomena. To explore the characteristic features of neutral, anionic and cationic hydrogen bonds, we have carried out theoretical studies of diverse homogeneous and heterogeneous hydrogen bonded dimers including water, peroxides, alcohols, ethers, aldehydes, ketones, carboxylic acids, anhydrides, and nitriles. Geometry optimization and harmonic frequency calculations are performed at the levels of Density Functional Theory (DFT) and Møller-Plesset second order perturbation (MP2) theory. First principles Car-Parrinello molecular dynamics (CPMD) simulations are performed to obtain IR spectra derived from velocity- and dipole-autocorrelation functions. We find that the hydrogen bond energy is roughly inversely proportional to the fourth power of the r(O/N-H) distance. Namely, the polarization of the proton accepting O/N atom by the proton-donating H atom reflects most of the binding energy in these diverse cation/anion/neutral hydrogen bonds. The present study gives deeper insight into the nature of hydrogen-bonded dimers including SSHBs.
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Affiliation(s)
- Han Myoung Lee
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, 790-784 Pohang, South Korea
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29
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Rimaz M, Noroozi Pesyan N, Khalafy J. Tautomerism and isotopic multiplets in the 13C NMR spectra of partially deuterated 3-arylpyrimido[4,5-c]pyridazine-5,7(6H,8H)-diones and their sulfur analogs--evidence for elucidation of the structure backbone and tautomeric forms. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48:276-285. [PMID: 20169579 DOI: 10.1002/mrc.2573] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The tautomerism of the synthesized 3-arylpyrimido[4,5-c]pyridazine-5,7(6H,8H)-diones (1a-d) and 3-aryl-7-thioxo-7,8-dihydro-6H-pyrimido[4,5-c]pyridazine-5-ones (2a-d) was studied in dimethyl sulfoxide (DMSO)-d(6). (1)H NMR spectra of 1a-d showed a clustered water molecule in the structure backbone that is attached by strong intermolecular H bonding. The relation between the temperature and H bonding of the clustered water molecule with 1a was also studied as representative. The relation between the electronegativity (chi) of the substituent on phenyl ring and the chemical shifts of clustered water protons in 1a-d was also studied. All of 1a-d and also 2d compounds existed in lactam (I) form, whereas 2a-c compounds have two distinguished tautomers in DMSO-d(6) [lactam (I) and lactim (II) forms]. The solvent-substrate proton exchange was examined in compounds 1a-d and 2a-d by adding one drop of D(2)O. All compounds (except 1d) showed proton/deuterium exchange of the clustered water protons in DMSO by adding one drop of D(2)O. Some compounds (but not all of them) that are easily soluble in DMSO-d(6) containing D(2)O showed isotopic splitting (beta-isotope effect) in their (13)C NMR spectra. Among them, compound 1a was the best evidence to help the spectral assignments and structure determination of predominant tautomer by carbon-13 splitting (beta-isotope effect).
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Affiliation(s)
- Mehdi Rimaz
- Department of Chemistry, Faculty of Science, Urmia University, 57159 Urmia, Iran
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30
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Thuéry P, Masci B. Lanthanide–organic assemblies with pyrazinetetracarboxylic and benzophenone-3,3′,4,4′-tetracarboxylic acids. CrystEngComm 2010. [DOI: 10.1039/c002054k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Zhao LH, Quan YP, Yang AH, Cui JZ, Gao HL, Lu FL, Shi W, Cheng P. Syntheses and crystal structures of two new nickel(II) complexes with pyrazine-2,3,5,6-tetracarboxylate. CrystEngComm 2009. [DOI: 10.1039/b820663e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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32
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Abstract
Crystal engineering, the design of molecular solids, is the synthesis of functional solid-state structures from neutral or ionic building blocks, using intermolecular interactions in the design strategy. Hydrogen bonds, coordination bonds, and other less directed interactions define substructural patterns, referred to in the literature as supramolecular synthons and secondary building units. Crystal engineering has considerable overlap with supramolecular chemistry, X-ray crystallography, materials science, and solid-state chemistry and yet it is a distinct discipline in itself. The subject goes beyond the traditional divisions of organic, inorganic, and physical chemistry, and this makes for a very eclectic blend of ideas and techniques. The purpose of this Review is to highlight some current challenges in this rapidly evolving subject. Among the topics discussed are the nature of intermolecular interactions and their role in crystal design, the sometimes diverging perceptions of the geometrical and chemical models for a molecular crystal, the relationship of these models to polymorphism, knowledge-based computational prediction of crystal structures, and efforts at mapping the pathway of the crystallization reaction.
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Affiliation(s)
- Gautam R Desiraju
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India.
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33
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Bourne SA, Moitsheki LJ. Hybrid inorganic–organic layered structures of [AuCl4]− and protonated bipyridyl derivatives. Polyhedron 2008. [DOI: 10.1016/j.poly.2007.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Ln[(μ2-H)(H-mpdc)2](H-mpdc)2: Lanthanide infinite architectures with symmetric OHO hydrogen bonds (mpdc=2,6-dimethylpyridine-3,5-dicarboxylate). J Mol Struct 2007. [DOI: 10.1016/j.molstruc.2006.11.047] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Vener MV, Manaev AV, Egorova AN, Tsirelson VG. QTAIM study of strong H-bonds with the O-H...a fragment (A=O, N) in three-dimensional periodical crystals. J Phys Chem A 2007; 111:1155-62. [PMID: 17253671 DOI: 10.1021/jp067057d] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The relationship between the d(H...A) distance (A=O, N) and the topological properties at the H...A bond critical point of 37 strong (short) hydrogen bonds occurring in 26 molecular crystals are analyzed using the quantum theory of atoms in molecules (QTAIM). Ground-state wave functions of the three-dimensional periodical structures representing the accurate experimental geometries calculated at the B3LYP/6-31G** level of approximation were used to obtain the QTAIM electron density characteristics. The use of an electron-correlated method allowed us to reach the quantitatively correct values of electron density rhob at the H...A bond critical point. However, quite significant differences can appear for small absolute values of the Laplacian (<0.5 au). The difference between the H...O and H...N interactions is described using the rhob versus d(H...A) dependence. It is demonstrated that the values of parameters in this dependence are defined by the nature of the heavy atom forming the H...A bond. An intermediate (or transit) region separating the shared and closed-shell interactions is observed for the H-bonded crystals in which the bridging proton can move from one heavy atom to another. The crystalline environment changes the location of the bridging proton in strong H-bonded systems; however, the d(O-H)/d(H...O) ratio is approximately the same for both the gas-phase complexes and molecular crystals with a linear or near-linear O-H...O bond.
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Affiliation(s)
- M V Vener
- Department of Quantum Chemistry, Mendeleev University of Chemical Technology, Miusskaya Square 9, Moscow 125047, Russia
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37
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Srinivas D, Gonnade R, Ravindranathan S, Sanjayan GJ. A hybrid foldamer with unique architecture from conformationally constrained aliphatic–aromatic amino acid conjugate. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.08.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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38
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Liang L, Yao P, Jiang M, Zhang G, Yan Y. Interactions of apo cytochrome C with alternating copolymers of maleic acid and alkene. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:10662-70. [PMID: 16262334 DOI: 10.1021/la050973i] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Apo cytochrome c (apo cyt c) tends to aggregate at alkali pH. Poly(isobutylene-alt-maleic acid) (PIMA) is soluble molecularly, whereas poly(1-tetradecene-alt-maleic acid) (PTMA) forms particles that tend to dissociate by increasing pH and decreasing concentration. Dynamic light scattering and surface plasmon resonance are used to investigate the interactions of PIMA and PTMA with apo cyt c at different pH values to understand the mechanism of the interactions. When the positive or negative charges are in excess, the copolymer-protein complex particles can be stabilized by the charges on the surface. When the ratio of the positive to negative charges is close to the stoichiometric value, precipitation occurs. At pH 11.8, both PTMA and apo cyt c carry negative charges, but the hydrophobic interaction makes them form complexes. A competition exists between the interaction of the copolymer with apo cyt c and the self-aggregation of PTMA or apo cyt c alone. The interaction of PIMA or PTMA with apo cyt c at neutral and alkali pH destroys the aggregation of PTMA or apo cyt c and forms new complex particles.
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Affiliation(s)
- Li Liang
- Department of Macromolecular Science, Fudan University, Shanghai, China
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39
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Liang L, Yao P, Jiang M. Structural Transformation of Apocytochrome c Induced by Alternating Copolymers of Maleic Acid and Alkene. Biomacromolecules 2005; 6:2748-55. [PMID: 16153115 DOI: 10.1021/bm050250d] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Apocytochrome c interacts with two copolymers: poly(isobutylene-alt-maleic acid) (PIMA) and poly(1-tetradecene-alt-maleic acid) (PTMA). The interaction leads to apocytochrome c, a conformational change from random coil to alpha-helical structure. The alpha-helix content is influenced by the copolymer concentration, the length of alkyl chain of the copolymers, and pH of the medium. The electrostatic attraction between the copolymer and protein is an indispensable factor for the folding of the protein at acid pH. The hydrophobic interaction is an important factor over the entire pH range, especially when both the copolymer and protein carry negative charges at alkaline pH. The electrostatic and hydrophobic attractions between the copolymer and protein exclude water molecules, promoting the formation of hydrogen bonds within the helical structure. On the other hand, the hydrogen bonds formed between the ionized carboxyl of the copolymer and the amide of the protein partly restrain the formation of hydrogen bonds within the helical structure when the copolymer concentration is higher at pH 6.5 and 10.5.
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Affiliation(s)
- Li Liang
- Department of Macromolecular Science and Key Laboratory of Molecular Engineering of Polymer, Fudan University, Shanghai 200433, China
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Abstract
Short hydrogen bonds are present in many chemical and biological systems. It is well known that these short hydrogen bonds are found in the active site of enzymes and aid enzyme catalysis. This study aims to systematically characterize all short hydrogen bonds from a nonredundant dataset of protein structures. The study has revealed that short hydrogen bonds are commonly found in proteins and are widely present in different regions of the protein chain, such as the backbone or side chain, and in different secondary structural regions such as helices, strands and turns. The frequency of occurrence of donors and acceptors from the charged side chains as well as from the neutral backbone atoms is equally high. This suggests that short hydrogen bonds in proteins occur either due to increased strength or due to geometrical constraints and this has been illustrated from several examples.
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