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Franco VG, Rodríguez SJ, Calaza FC, Passeggi MCG, Ruano GD. Novel mixed self-assembled monolayers of L-cysteine and methanol on gold surfaces under ambient conditions. NANOSCALE 2024; 16:15366-15380. [PMID: 39091174 DOI: 10.1039/d4nr01848f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
In this work, we carried out an experimental and theoretical study on the formation of self-assembled monolayers of L-cysteine molecules on gold surfaces in the presence of methanol as a solvent. We report for the first time L-cysteine and methanol ordered structures forming a mixed self-assembled mono-layer on Au(100) surfaces under ambient conditions. Finger-like ordered structures with a relative height of 0.10-0.20 nm, average width of 2.0 nm and variable lengths were observed using scanning tunneling microscopy under room temperature and ambient pressure conditions. Using X-ray photoemission spectroscopy, it was determined that L-cysteine molecules bind to the gold surface through the sulfur atom of their thiol group in two molecular configurations: neutral and zwitterionic. We found that the finger-like structures are the result of complex interactions of L-cysteine molecules with gold surfaces and L-cysteine molecules with methanol molecules and among all three components of the system (L-cysteine + methanol + gold surfaces). These interactions were detected through attenuated total reflectance-Fourier transform infrared spectroscopy. Furthermore, adsorbate/substrate interactions were studied by employing ab initio calculations using density functional theory, resulting in molecular arrangements formed by chains of L-cysteine pairs surrounded by physisorbed methanol molecules.
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Affiliation(s)
- Vanina Gisela Franco
- Instituto de Física del Litoral (IFIS Litoral), Consejo Nacional de Investigaciones Científicas y Técnicas and Universidad Nacional del Litoral (CONICET-UNL), Güemes 3450, (3000) Santa Fe, Argentina.
- Facultad de Ingeniería Química (FIQ), Universidad Nacional del Litoral (UNL), Santiago del Estero 2829, (3000) Santa Fe, Argentina
| | - Sindy Julieth Rodríguez
- Instituto de Física del Litoral (IFIS Litoral), Consejo Nacional de Investigaciones Científicas y Técnicas and Universidad Nacional del Litoral (CONICET-UNL), Güemes 3450, (3000) Santa Fe, Argentina.
| | - Florencia Carolina Calaza
- Facultad de Ingeniería Química (FIQ), Universidad Nacional del Litoral (UNL), Santiago del Estero 2829, (3000) Santa Fe, Argentina
- Instituto de Desarrollo Tecnológico para la Industria Química (INTEC), Consejo Nacional de Investigaciones Científicas y Técnicas and Universidad Nacional del Litoral (CONICET-UNL), Güemes 3450, (3000) Santa Fe, Argentina
| | - Mario César Guillermo Passeggi
- Instituto de Física del Litoral (IFIS Litoral), Consejo Nacional de Investigaciones Científicas y Técnicas and Universidad Nacional del Litoral (CONICET-UNL), Güemes 3450, (3000) Santa Fe, Argentina.
- Facultad de Ingeniería Química (FIQ), Universidad Nacional del Litoral (UNL), Santiago del Estero 2829, (3000) Santa Fe, Argentina
| | - Gustavo Daniel Ruano
- Centro Atómico Bariloche (CAB), Comisión Nacional de Energía Atómica (CNEA), Av. Exequiel Bustillo 9500, (8400) San Carlos de Bariloche, Argentina
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Avelar S Silva J, Militão Vasconcelos DL, Araújo de Lima R, Cordeiro AJP, Tarso C Freire P. Structural and vibrational analysis of glycyl-L-phenylalanine and phase transition under high-pressure. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 304:123383. [PMID: 37725884 DOI: 10.1016/j.saa.2023.123383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/03/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023]
Abstract
The structural and vibrational properties of the glycyl-L-phenylalanine dipeptide were investigated using vibrational spectroscopy (Raman and infrared) and first-principle calculations. Raman spectroscopy measurements were performed between 100 and 3200 cm-1 and infrared spectroscopy from 100 and 3200 cm-1 under ambient conditions. The conformational analysis of the zwitterionic form of the dipeptide was performed using the B3LYP functional, the 6-311++ base set and the Polarizable Continuum Model of solvation, determining the lowest energy conformation and assigning the vibrational modes. The effect of pressure on the glycyl-1-phenylalanine crystal was investigated using the Raman spectroscopy between 0.0 and -7.1 GPa in the spectral region of 100 - 3200 cm-1. As a result, conformational changes around 1.0 GPa were observed in the lattice modes and in some internal modes, showing a reorganization of the molecule in the crystal. In the decompression process, it was observed that the conformational change is reversible and the original Raman spectrum is recoverd.
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Affiliation(s)
- José Avelar S Silva
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60021-970, Fortaleza, CE, Brazil.
| | - Daniel L Militão Vasconcelos
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60021-970, Fortaleza, CE, Brazil; Faculdade de Educação Ciências e Letras do Sertão Central, Universidade Estadual do Ceará, CEP 63.902-098 Quixadá, CE, Brazil
| | - Raphaela Araújo de Lima
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60021-970, Fortaleza, CE, Brazil
| | - Adrya J P Cordeiro
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60021-970, Fortaleza, CE, Brazil
| | - Paulo Tarso C Freire
- Departamento de Física, Universidade Federal do Ceará, Caixa Postal 6030, 60021-970, Fortaleza, CE, Brazil.
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Silva R, Ramiro de Castro AJ, da Silva Filho JG, de Sousa FF, Paraguassu W, Freire PTC, Façanha Filho PF. Pressure-induced phase transition in Glycinium maleate crystal. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 262:120076. [PMID: 34174678 DOI: 10.1016/j.saa.2021.120076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/31/2021] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
The multicomponent glycinium maleate single crystal was grown by the slow evaporation method. The crystal was submitted to pressures ranging from 1 atm to 5.6 GPa and Raman spectroscopy was used as a spectroscopic probe. The modifications of relative intensity bands related to the lattice modes at 0.3 GPa were associated with rearrangements of hydrogen bonds. Moreover, between 1.7 and 4.8 GPa the Raman results indicate that the crystal experience a long structural phase transition, which was confirmed by PCA analysis. DFT calculations gave us more precision in the assignments of modes. The behavior of the internal modes under pressure showed that the maleic acid molecule undergoes greater modifications than glycine amino acid. All observed modifications were reversible when the pressure was released.
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Affiliation(s)
- R Silva
- Centro de Ciências Sociais, Saúde e Tecnologia, CCSST, Universidade Federal do Maranhão, Imperatriz, MA 65900-410, Brazil
| | | | - J G da Silva Filho
- Centro de Ciências Sociais, Saúde e Tecnologia, CCSST, Universidade Federal do Maranhão, Imperatriz, MA 65900-410, Brazil
| | - F F de Sousa
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, PA 66075-110, Brazil
| | - W Paraguassu
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, PA 66075-110, Brazil
| | - P T C Freire
- Departamento de Física, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE 60455-760, Brazil
| | - P F Façanha Filho
- Centro de Ciências Sociais, Saúde e Tecnologia, CCSST, Universidade Federal do Maranhão, Imperatriz, MA 65900-410, Brazil.
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4
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Victor FMS, Rêgo FSC, de Paiva FM, Dos Santos AO, Polian A, Freire PTC, Lima JA, Filho PFF. Pressure-induced phase transitions in DL-glutamic acid monohydrate crystal. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 230:118059. [PMID: 32000059 DOI: 10.1016/j.saa.2020.118059] [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: 06/21/2019] [Revised: 01/06/2020] [Accepted: 01/09/2020] [Indexed: 06/10/2023]
Abstract
DL-glutamic acid monohydrate crystal was synthesized from an aqueous solution by slow evaporation technique. The crystal was submitted to high-pressure (1 atm-14.3 GPa) to investigate its vibrational behavior and the occurrence of phase transitions. We performed Raman spectroscopy as probe and through the analysis of the spectra we discovered three structural phase transitions. The first one occurs around 0.9 GPa. In this phase transition, glutamic acid molecules suffer modifications in their conformations while water molecules are less affected. The second phase transition at 4.8 GPa involves conformational changes related to CO2-, NH3+ units and the water molecules, while the third one, between 10.9 and 12.4 GPa, involves motions of several parts of the glutamic acid as well as the water molecules. Considering the dynamic of high pressure, the second phase of DL-glutamic acid monohydrate crystal presented a better stability compared with the second phase of its polymorphs α and β L-glutamic acid. In addition, water molecules seem to play important role on this structural stability. All changes are reversible.
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Affiliation(s)
- F M S Victor
- Universidade Federal do Maranhão, CCSST, Imperatriz, MA 65900-000, Brazil
| | - F S C Rêgo
- Departamento de Física, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE 60455-760, Brazil
| | - F M de Paiva
- Departamento de Física, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE 60455-760, Brazil; Faculdade de Educação, Ciências e Letras de Iguatu, FECLI, Universidade Estadual do Ceará, Iguatu, CE 63502-253, Brazil
| | - A O Dos Santos
- Universidade Federal do Maranhão, CCSST, Imperatriz, MA 65900-000, Brazil
| | - A Polian
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, UMR CNRS 7590, F-75005 Paris, France
| | - P T C Freire
- Departamento de Física, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE 60455-760, Brazil
| | - J A Lima
- Departamento de Física, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE 60455-760, Brazil
| | - P F Façanha Filho
- Universidade Federal do Maranhão, CCSST, Imperatriz, MA 65900-000, Brazil.
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Rêgo FSC, Melo FEA, Nogueira CES, Polian A, Freire PTC, Filho PFF, Lima JA. High pressure Raman scattering of DL‑isoleucine crystals and DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 214:207-215. [PMID: 30785040 DOI: 10.1016/j.saa.2019.01.087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
DL‑isoleucine single crystals were grown by the slow evaporation method at ambient temperature. Their vibrational properties were studied at ambient temperature as a function of pressure by Raman scattering. At ambient conditions the mode assignment was done in terms of the Potential Energy Distribution (PED) through density functional theory calculations. Both nitrogen and neon were used as pressure transmitting media. The pressure-dependent investigation shows modifications in the Raman spectra recorded between 30 and 3200 cm-1 that were interpreted as phase transitions undergone by the crystal between 1.3 and 1.9 GPa and between 3.6 and 5.1 GPa. Finally, stress was simulated on the unit cell of the crystal from ambient up to 5.0 GPa.
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Affiliation(s)
- F S C Rêgo
- Departamento de Física, Universidade Federal do Ceará, C. P. 6030, CEP 60455-760 Fortaleza, CE, Brazil
| | - F E A Melo
- Departamento de Física, Universidade Federal do Ceará, C. P. 6030, CEP 60455-760 Fortaleza, CE, Brazil
| | - C E S Nogueira
- Departamento de Física, Universidade Regional do Cariri, CEP 63010-970 Juazeiro do Norte, CE, Brazil
| | - A Polian
- Institut de Minéralogie de Physique des Matériaux et de Cosmochimie, Sorbonne Université - UPMC Univ Paris 06, UMR CNRS 7590, F-75005 Paris, France
| | - P T C Freire
- Departamento de Física, Universidade Federal do Ceará, C. P. 6030, CEP 60455-760 Fortaleza, CE, Brazil
| | - P F Façanha Filho
- Centro de Ciências Sociais, Saúde e Tecnologia, Universidade Federal do Maranhão, Imperatriz, MA 65900-410, Brazil
| | - J A Lima
- Departamento de Física, Universidade Federal do Ceará, C. P. 6030, CEP 60455-760 Fortaleza, CE, Brazil.
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Fedorov AY, Rychkov DA, Losev EA, Drebushchak TN, Boldyreva EV. Completing the picture of tolazamide polymorphism under extreme conditions: a low-temperature study. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2019; 75:598-608. [PMID: 31062718 DOI: 10.1107/s2053229619005217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 04/16/2019] [Indexed: 11/10/2022]
Abstract
We present the results of an experimental and computational study of structural changes in two polymorphs of tolazamide {systematic name: 1-[(azepan-1-ylamino)carbonyl]-4-methylbenzenesulfonamide}, C14H21N3O3S, on cooling to 100 K and reverse heating. No phase transitions occurred in this temperature range. The anisotropy of the thermal expansion was different for the two polymorphs and differed from that reported previously for the hydrostatic compression. The changes in different intermolecular contacts responsible for the strain anisotropy were analysed. Relative shortening of the contacts was related directly to their initial length and reversely to the steric density around them. Increasing steric density is likely to be the driving force for the conformational ordering of the azepane ring under compression.
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Affiliation(s)
- Alexey Yu Fedorov
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russian Federation
| | - Denis A Rychkov
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russian Federation
| | - Evgeniy A Losev
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russian Federation
| | - Tatiana N Drebushchak
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russian Federation
| | - Elena V Boldyreva
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russian Federation
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7
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Fu C, Dai C, Du B, Li P, Lei L, Hu F, Jiang Z. Raman spectroscopic study of orthorhombic l -cysteine under pressure up to 20.2 GPa. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.05.061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Shinozaki A, Komatsu K, Kagi H, Fujimoto C, Machida S, Sano-Furukawa A, Hattori T. Behavior of intermolecular interactions in α-glycine under high pressure. J Chem Phys 2018; 148:044507. [PMID: 29390805 DOI: 10.1063/1.5009980] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Pressure-response on the crystal structure of deuterated α-glycine was investigated at room temperature, using powder and single-crystal X-ray diffraction, and powder neutron diffraction measurements under high pressure. No phase change was observed up to 8.7 GPa, although anisotropy of the lattice compressibility was found. No significant changes in the compressibility and the intramolecular distance between non-deuterated α-glycine and deuterated α-glycine were observed. Neutron diffraction measurements indicated the distance of the intermolecular D⋯O bond along with the c-axis increased with compression up to 6.4 GPa. The distance of another D⋯O bond along with the a-axis decreased with increasing pressure and became the shortest intermolecular hydrogen bond above 3 GPa. In contrast, the lengths of the bifurcated N-D⋯O and C-D⋯O hydrogen bonds, which are formed between the layers of the α-glycine molecules along the b-axis, decreased significantly with increasing pressure. The decrease of the intermolecular distances resulted in the largest compressibility of the b-axis, compared to the other two axes. The Hirshfeld analysis suggested that the reduction of the void region size, rather than shrinkage of the strong N-D⋯O hydrogen bonds, occurred with compression.
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Affiliation(s)
- Ayako Shinozaki
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Kazuki Komatsu
- Geochemical Research Center, Graduate School of Science, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Hiroyuki Kagi
- Geochemical Research Center, Graduate School of Science, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Chikako Fujimoto
- Geochemical Research Center, Graduate School of Science, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Shinichi Machida
- CROSS, Neutron Science and Technology Center, IQBRC Building, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Asami Sano-Furukawa
- J-PARC Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
| | - Takanori Hattori
- J-PARC Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
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Neu J, Nemes CT, Regan KP, Williams MRC, Schmuttenmaer CA. Exploring the solid state phase transition in dl-norvaline with terahertz spectroscopy. Phys Chem Chem Phys 2018; 20:276-283. [DOI: 10.1039/c7cp05479c] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Experimental and theoretical demonstration of the power of terahertz spectroscopy to provide novel insights into solid-state phase-transformations in organic materials.
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Affiliation(s)
- Jens Neu
- Department of Chemistry
- Yale University
- New Haven
- USA
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10
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Paiva F, Batista J, Rêgo F, Lima J, Freire P, Melo F, Mendes Filho J, de Menezes A, Nogueira C. Infrared and Raman spectroscopy and DFT calculations of DL amino acids: Valine and lysine hydrochloride. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.07.067] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Rêgo F, Lima J, Freire P, Melo F, Mendes Filho J, Polian A. Raman spectroscopic study of DL valine under pressure up to 20 GPa. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.12.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Zheng C, Qiu Q, Hao L, Li H. Studies on the halogen substituted β-amino acids and their Cu(II) coordination complexes in crystallography. Chem Res Chin Univ 2016. [DOI: 10.1007/s40242-016-5333-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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13
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Minkov VS, Ghazaryan VV, Boldyreva EV, Petrosyan AM. Unusual hydrogen bonding in L-cysteine hydrogen fluoride. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2015; 71:733-41. [PMID: 26243424 DOI: 10.1107/s2053229615013601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/16/2015] [Indexed: 11/10/2022]
Abstract
L-Cysteine hydrogen fluoride, or bis(L-cysteinium) difluoride-L-cysteine-hydrogen fluoride (1/1/1), 2C3H8NO2S(+)·2F(-)·C3H7NO2S·HF or L-Cys(+)(L-Cys···L-Cys(+))F(-)(F(-)...H-F), provides the first example of a structure with cations of the 'triglycine sulfate' type, i.e. A(+)(A···A(+)) (where A and A(+) are the zwitterionic and cationic states of an amino acid, respectively), without a doubly charged counter-ion. The salt crystallizes in the monoclinic system with the space group P2(1). The dimeric (L-Cys···L-Cys(+)) cation and the dimeric (F(-)···H-F) anion are formed via strong O-H···O or F-H···F hydrogen bonds, respectively, with very short O···O [2.4438 (19) Å] and F···F distances [2.2676 (17) Å]. The F···F distance is significantly shorter than in solid hydrogen fluoride. Additionally, there is another very short hydrogen bond, of O-H···F type, formed by a L-cysteinium cation and a fluoride ion. The corresponding O···F distance of 2.3412 (19) Å seems to be the shortest among O-H···F and F-H···O hydrogen bonds known to date. The single-crystal X-ray diffraction study was complemented by IR spectroscopy. Of special interest was the spectral region of vibrations related to the above-mentioned hydrogen bonds.
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Affiliation(s)
- V S Minkov
- Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation
| | - V V Ghazaryan
- Institute of Applied Problems of Physics, NAS of Armenia, 25 Nersessyan Str., 0014 Yerevan, Armenia
| | - E V Boldyreva
- Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation
| | - A M Petrosyan
- Institute of Applied Problems of Physics, NAS of Armenia, 25 Nersessyan Str., 0014 Yerevan, Armenia
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Görbitz CH. Crystal structures of amino acids: from bond lengths in glycine to metal complexes and high-pressure polymorphs. CRYSTALLOGR REV 2015. [DOI: 10.1080/0889311x.2014.964229] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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15
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Hejny C, Minkov VS. High-pressure crystallography of periodic and aperiodic crystals. IUCRJ 2015; 2:218-29. [PMID: 25866659 PMCID: PMC4392772 DOI: 10.1107/s2052252514025482] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 11/20/2014] [Indexed: 06/02/2023]
Abstract
More than five decades have passed since the first single-crystal X-ray diffraction experiments at high pressure were performed. These studies were applied historically to geochemical processes occurring in the Earth and other planets, but high-pressure crystallography has spread across different fields of science including chemistry, physics, biology, materials science and pharmacy. With each passing year, high-pressure studies have become more precise and comprehensive because of the development of instrumentation and software, and the systems investigated have also become more complicated. Starting with crystals of simple minerals and inorganic compounds, the interests of researchers have shifted to complicated metal-organic frameworks, aperiodic crystals and quasicrystals, molecular crystals, and even proteins and viruses. Inspired by contributions to the microsymposium 'High-Pressure Crystallography of Periodic and Aperiodic Crystals' presented at the 23rd IUCr Congress and General Assembly, the authors have tried to summarize certain recent results of single-crystal studies of molecular and aperiodic structures under high pressure. While the selected contributions do not cover the whole spectrum of high-pressure research, they demonstrate the broad diversity of novel and fascinating results and may awaken the reader's interest in this topic.
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Affiliation(s)
- Clivia Hejny
- Mineralogy and Petrography, University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria
| | - Vasily S. Minkov
- Institute of Solid State Chemistry and Mechanochemistry, Siberian Branch of the Russian Academy of Sciences, 18 Kutateladze Street, Novosibirsk 630128, Russian Federation
- Novosibirsk State University, 2 Pirogov Street, Novosibirsk 630090, Russian Federation
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16
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Kapustin EA, Minkov VS, Boldyreva EV. Sarcosine and betaine crystals upon cooling: structural motifs unstable at high pressure become stable at low temperatures. Phys Chem Chem Phys 2015; 17:3534-43. [PMID: 25536150 DOI: 10.1039/c4cp05094k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The crystal structures of N-methyl derivatives of the simplest amino acid glycine, namely sarcosine (C3H7NO2) and betaine (C5H11NO2), were studied upon cooling by single-crystal X-ray diffraction and single-crystal polarized Raman spectroscopy. The effects of decreasing temperature and increasing hydrostatic pressure on the crystal structures were compared. In particular, we have studied the behavior upon cooling of those structural motifs in the crystals, which are involved in structural rearrangement during pressure-induced phase transitions. In contrast to their high sensitivity to hydrostatic compression, the crystals of both sarcosine and betaine are stable to cooling down to 5 K. Similarly to most α-amino acids, the crystal structures of the two compounds are most rigid upon cooling in the direction of the main structural motif, namely head-to-tail chains (linked via the strongest N-H···O hydrogen bonds and dipole-dipole interactions in the case of sarcosine, or exclusively by dipole-dipole interactions in the case of betaine). The anisotropy of linear strain in betaine does not differ much upon cooling and on hydrostatic compression, whereas this is not the case for sarcosine. Although the interactions between certain structural motifs in sarcosine and betaine weaken as a result of phase transitions induced by pressure, the same interactions strengthen when volume reduction results from cooling.
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Affiliation(s)
- E A Kapustin
- Novosibirsk State University, Pirogov street, 2, Novosibirsk 630090, Russian Federation.
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17
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Minkov VS, Boldyreva EV. Contribution of Weak S–H···O Hydrogen Bonds to the Side Chain Motions in d,l-Homocysteine on Cooling. J Phys Chem B 2014; 118:8513-23. [DOI: 10.1021/jp503154x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vasily S. Minkov
- Novosibirsk State University, 2 Pirogov
str., 630090 Novosibirsk, Russian Federation
- Institute
of Solid State Chemistry and Mechanochemistry Siberian Branch of Russian Academy of Sciences, 18 Kutateladze str., 630128 Novosibirsk, Russian Federation
| | - Elena V. Boldyreva
- Novosibirsk State University, 2 Pirogov
str., 630090 Novosibirsk, Russian Federation
- Institute
of Solid State Chemistry and Mechanochemistry Siberian Branch of Russian Academy of Sciences, 18 Kutateladze str., 630128 Novosibirsk, Russian Federation
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18
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Kapustin EA, Minkov VS, Boldyreva EV. Effect of pressure on methylated glycine derivatives: relative roles of hydrogen bonds and steric repulsion of methyl groups. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2014; 70:517-532. [PMID: 24892599 DOI: 10.1107/s205252061401035x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 05/07/2014] [Indexed: 06/03/2023]
Abstract
Infinite head-to-tail chains of zwitterions present in the crystals of all amino acids are known to be preserved even after structural phase transitions. In order to understand the role of the N-H...O hydrogen bonds linking zwitterions in these chains in structural rearrangements, the crystal structures of the N-methyl derivatives of glycine (N-methylglycine, or sarcosine, with two donors for hydrogen bonding; two polymorphs of N,N-dimethylglycine, DMG-I and DMG-II, with one donor for hydrogen bond; and N,N,N-trimethylglycine, or betaine, with no hydrogen bonds) were studied at different pressures. Methylation has not only excluded the formation of selected hydrogen bonds, but also introduced bulky mobile fragments into the structure. The effects of pressure on the systems of the series were compared with respect to distorting and switching over hydrogen bonds and inducing reorientation of the methylated fragments. Phase transitions with fragmentation of the single crystals into fine powder were observed for partially methylated N-methyl- and N,N-dimethylglycine, whereas the structural changes in betaine were continuous with some peculiar features in the 1.4-2.9 GPa pressure range and accompanied by splitting of the crystals into several large fragments. Structural rearrangements in sarcosine and betaine were strongly dependent on the rate of pressure variation: the higher the rate of increasing pressure, the lower the pressure at which the phase transition occurred.
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Affiliation(s)
- Eugene A Kapustin
- Novosibirsk State University, Pirogov Street, 2, Novosibirsk 630090, Russian Federation
| | - Vasily S Minkov
- Novosibirsk State University, Pirogov Street, 2, Novosibirsk 630090, Russian Federation
| | - Elena V Boldyreva
- Novosibirsk State University, Pirogov Street, 2, Novosibirsk 630090, Russian Federation
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19
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Li S, Chen JM, Lu TB. Synthon polymorphs of 1 : 1 co-crystal of 5-fluorouracil and 4-hydroxybenzoic acid: their relative stability and solvent polarity dependence of grinding outcomes. CrystEngComm 2014. [DOI: 10.1039/c4ce00221k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two synthon polymorphs of 1 : 1 co-crystals of 5-fluorouracil and 4-hydroxybenzoic acid were synthesized, and the crystal structures were determined.
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Affiliation(s)
- Song Li
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006, China
- School of Life Sciences
- Sun Yat-Sen University
| | - Jia-Mei Chen
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006, China
| | - Tong-Bu Lu
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006, China
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
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20
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Minkov VS, Boldyreva EV. Weak hydrogen bonds formed by thiol groups in N-acetyl-(L)-cysteine and their response to the crystal structure distortion on increasing pressure. J Phys Chem B 2013; 117:14247-60. [PMID: 24102610 DOI: 10.1021/jp4068872] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effect of hydrostatic pressure on single crystals of N-acetyl-l-cysteine was followed at multiple pressure points from 10(-4) to 6.2 GPa with a pressure step of 0.2-0.3 GPa by Raman spectroscopy and X-ray diffraction. Since in the crystals of N-acetyl-l-cysteine the thiol group is involved in intermolecular hydrogen bonds not as a donor only (bonds S-H···O) but also as an acceptor (bonds N-H···S), increasing the pressure does not result in phase transitions. This makes a contrast with the polymorphs of l- and dl-cysteine, in which multiple phase transitions are observed already at relatively low hydrostatic pressures and are related to the changes in the conformation of the thiol side chains only weakly bound to the neighboring molecules in the structure and thus easily switching over the weak S-H···O and S-H···S hydrogen bonds. No phase transitions occur in N-acetyl-l-cysteine with increasing pressure, and changes in cell parameters and volume vs pressure do not reveal any peculiar features. Nevertheless, a more detailed analysis of the changes in intermolecular distances, in particular, of the geometric parameters of the hydrogen bonds based on X-ray single crystal diffraction analysis, complemented by an equally detailed study of the positions of all the significant bands in Raman spectra, allowed us to study the fine details of subtle changes in the hydrogen bond network. Thus, as pressure increases, a continuous shift of the hydrogen atom of the thiol group from one acceptor (a carboxyl group) to another acceptor (a carbonyl group) is observed. Precise single-crystal X-ray diffraction and polarized Raman spectroscopy structural data reveal the formation of a bifurcated S-H···O hydrogen bond with increasing pressure starting with ∼1.5 GPa. The analysis of the vibrational bands in Raman spectra has shown that different donor and acceptor groups start "feeling" the formation of the bifurcated S-H···O hydrogen bond in different pressure ranges. The results are discussed in relation to some of the previously published data on the effect of high pressure on the polymorphs of l-cysteine, dl-cysteine, and glutathione, that show similarity with the effects reported here for N-acetyl-l-cysteine. The results obtained in this work allow one to suggest new models for the pressure-induced structural rearrangements in the whole family of cysteine-containing crystals.
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Affiliation(s)
- Vasily S Minkov
- Novosibirsk State University , 2 Pirogov str., 630090 Novosibirsk, Russian Federation
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21
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Zakharov BA, Boldyreva EV. A high-pressure single-crystal to single-crystal phase transition in DL-alaninium semi-oxalate monohydrate with switching-over hydrogen bonds. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2013; 69:271-280. [PMID: 23719471 DOI: 10.1107/s2052519213011676] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Accepted: 04/29/2013] [Indexed: 06/02/2023]
Abstract
A single-crystal to single-crystal transition in DL-alaninium semi-oxalate monohydrate at a pressure between 1.5 and 2.4 GPa was studied by single-crystal X-ray diffraction and Raman spectroscopy. This is the first example of a single-crystal diffraction study of a high-pressure phase transition in a crystalline amino acid salt hydrate. Selected hydrogen bonds switch over and become bifurcated, whereas the others are compressed continuously. The transition is accompanied by pronounced discontinuities in the cell parameters and volume versus pressure, although no radical changes in the molecular packing are induced. Although, in contrast to DL-alanine, in the crystal structure of the salt there are short O-H···O hydrogen bonds, the structure of the salt is more compressible. At the same time, the structure of DL-alanine does not undergo pressure-induced phase transitions, whereas the structure of DL-alaninium semi-oxalate monohydrate does, and at a relatively low pressure. The anisotropy of lattice strain for the low-pressure phase differs from that on cooling at ambient pressure; interestingly, the anisotropy of the pressure-induced compression of the high-pressure phase is quite similar to the lattice strain of the low-pressure phase on cooling.
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Affiliation(s)
- Boris A Zakharov
- Institute of Solid State Chemistry and Mechanochemistry SB RAS, Kutateladze Str. 18, Novosibirsk 630128, Russian Federation.
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22
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Zakharov BA, Losev EA, Boldyreva EV. Polymorphism of “glycine–glutaric acid” co-crystals: the same phase at low temperatures and high pressures. CrystEngComm 2013. [DOI: 10.1039/c3ce27013k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Tumanov NA, Boldyreva EV. X-ray diffraction and Raman study of DL-alanine at high pressure: revision of phase transitions. ACTA CRYSTALLOGRAPHICA SECTION B: STRUCTURAL SCIENCE 2012; 68:412-23. [DOI: 10.1107/s0108768112028972] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 06/26/2012] [Indexed: 11/10/2022]
Abstract
The effect of pressure on DL-alanine has been studied by X-ray powder diffraction (up to 8.3 GPa), single-crystal X-ray diffraction and Raman spectroscopy (up to ∼ 6 GPa). No structural phase transitions have been observed. At ∼ 1.5–2 GPa, cell parameters b and c become accidentally equal to each other, but the space-group symmetry does not change. There is no phase transition between 1.7 and 2.3 GPa, contrary to what has been reported earlier [Belo et al. (2010). Vibr. Spectrosc.
54, 107–111]. The presence of the second phase transition, which was claimed to appear within the pressure range from 6.0 to 7.3 GPa (Belo et al., 2010), is also argued. The changes in the Raman spectra have been shown to be continuous in all the pressure ranges studied.
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Zakharov BA, Kolesov BA, Boldyreva EV. Effect of pressure on crystalline L- and DL-serine: revisited by a combined single-crystal X-ray diffraction at a laboratory source and polarized Raman spectroscopy study. ACTA CRYSTALLOGRAPHICA SECTION B: STRUCTURAL SCIENCE 2012; 68:275-86. [DOI: 10.1107/s0108768112015960] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Accepted: 04/12/2012] [Indexed: 11/11/2022]
Abstract
Information on the effect of pressure on hydrogen bonds, which could be derived from single-crystal X-ray diffraction at a laboratory source and polarized Raman spectroscopy, has been compared. L-Serine and DL-serine were selected for this case study. The role of hydrogen bonds in pressure-induced phase transitions in the first system and in the structural stability of the second one are discussed. Non-monotonic distortion of selected hydrogen bonds in the pressure range below ∼ 1–2 GPa, a change in the compression mechanism at ∼ 2–3 GPa, and the evidence of formation of bifurcated N—H...O hydrogen bonds in DL-serine at ∼ 3–4 GPa are considered.
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25
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26
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Brittain HG. Polymorphism and Solvatomorphism 2010. J Pharm Sci 2012; 101:464-84. [DOI: 10.1002/jps.22788] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 09/18/2011] [Accepted: 09/22/2011] [Indexed: 01/06/2023]
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27
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Minkov VS, Boldyreva EV, Drebushchak TN, Görbitz CH. Stabilizing structures of cysteine-containing crystals with respect to variations of temperature and pressure by immobilizing amino acid side chains. CrystEngComm 2012. [DOI: 10.1039/c2ce25241d] [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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28
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Franz M, Fischer BM, Walther M. Probing structure and phase-transitions in molecular crystals by terahertz time-domain spectroscopy. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.05.061] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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29
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Minkov VS, Boldyreva EV. L-Cysteinium semioxalate: a new monoclinic polymorph or a hydrate? Acta Crystallogr C 2011; 67:o139-42. [DOI: 10.1107/s0108270111009760] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 03/15/2011] [Indexed: 11/10/2022] Open
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30
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Funnell NP, Marshall WG, Parsons S. Alanine at 13.6 GPa and its pressure-induced amorphisation at 15 GPa. CrystEngComm 2011. [DOI: 10.1039/c1ce05487b] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Cai W, Katrusiak A. Enantiomeric crystallization of (±)-trans-1,2-diaminocyclohexane under pressure. CrystEngComm 2011. [DOI: 10.1039/c1ce05553d] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Marelli E, Casati N, Gozzo F, Macchi P, Simoncic P, Sironi A. High pressure modification of organic NLO materials: large conformational re-arrangement of 4-aminobenzophenone. CrystEngComm 2011. [DOI: 10.1039/c1ce05742a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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