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Bajaj N, Bhatt H, Murli C, Vishwakarma SR, Chitra R, Ravindran TR, Deo MN. Perceptible isotopic effect in 3D-framework of α-glycine at low temperatures. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 204:495-507. [PMID: 29975911 DOI: 10.1016/j.saa.2018.06.087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/22/2018] [Accepted: 06/23/2018] [Indexed: 06/08/2023]
Abstract
Glycine, the most fundamental amino acid, albeit studied for many decades, has kept researchers captivated with interesting structural variations relevant to important biological, astrophysical and technological applications. We report here a noticeable effect of deuteration on the three dimensional hydrogen bonding network of α-glycine using low temperature infrared absorption studies in a wide spectral range, corroborated with Raman scattering studies. These systematic studies in the range 300-4.2 K have demonstrated a relatively compact assembly of glycine molecules in the three dimensional bilayered structure of hydrogenated glycine (gly-h) at low temperatures. This is inferred from a remarkable temperature effect in the weak intra-bilayer hydrogen bond ~ along the b-axis, which strengthens upon cooling. A pronounced increase in the intensity of NH3 torsional and NH stretching modes has been observed. This is accompanied with a large rate of stiffening and softening respectively of these modes upon cooling and a change in slope across 210 K and 80 K. In contrast, the D---O hydrogen bond lengths in fully deuterated isotope (gly-d), as estimated using empirical correlation, show that the weak intra-bilayer hydrogen bond is not strengthened upon cooling down to 180 K, whereas the stronger intra-layer hydrogen bonds in the ac-plane become further strong. The ND3 torsional vibrations show no temperature effect. This implies a relatively stable two dimensional layered structure formed by strongly hydrogen bonded glycine sheets in the ac-plane. Below 180 K, similar qualitative trends have been obtained for the hydrogen bond lengths in the two isotopes. In addition, temperature induced variation of the characteristic "indicator" band of zwitterionic gly-h and gly-d has also been reported.
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Affiliation(s)
- Naini Bajaj
- High Pressure & Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Bhabha Atomic Research Centre, Mumbai, India
| | - Himal Bhatt
- High Pressure & Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India.
| | - Chitra Murli
- High Pressure & Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Bhabha Atomic Research Centre, Mumbai, India
| | - S R Vishwakarma
- High Pressure & Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - R Chitra
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - T R Ravindran
- Materials Science Group, Indira Gandhi Centre for Atomic Research, Kalpakkam, India
| | - M N Deo
- High Pressure & Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Bhabha Atomic Research Centre, Mumbai, India.
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Yamamoto K, Kanematsu Y, Nagashima U, Ueda A, Mori H, Tachikawa M. Multicomponent DFT study of geometrical H/D isotope effect on hydrogen-bonded organic conductor, κ-H 3 (Cat EDT-ST) 2. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.073] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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3
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Yamamoto K, Kanematsu Y, Nagashima U, Ueda A, Mori H, Tachikawa M. Theoretical study of the H/D isotope effect on phase transition of hydrogen-bonded organic conductor κ-H3(Cat-EDT-TTF)2. Phys Chem Chem Phys 2016; 18:29673-29680. [DOI: 10.1039/c6cp05414e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
κ-H3(Cat-EDT-TTF)2 (H-TTF) is a hydrogen-bonded π-electron system. Only its isotopologue, D-TTF, shows the phase transition. We obtained a symmetric single-well effective-PEC for H-TTF and low-barrier effective-PEC for D-TTF.
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Affiliation(s)
- Kaichi Yamamoto
- Graduate School of Nanobioscience
- Yokohama City University
- Yokohama-City
- Japan
| | - Yusuke Kanematsu
- Faculty of Information Sciences
- Hiroshima City University
- Hiroshima
- Japan
| | | | - Akira Ueda
- The Institute for Solid State Physics
- The University of Tokyo
- Kashiwa
- Japan
| | - Hatsumi Mori
- The Institute for Solid State Physics
- The University of Tokyo
- Kashiwa
- Japan
| | - Masanori Tachikawa
- Graduate School of Nanobioscience
- Yokohama City University
- Yokohama-City
- Japan
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4
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Molecular motor-driven abrupt anisotropic shape change in a single crystal of a Ni complex. Nat Chem 2014; 6:1079-83. [PMID: 25411886 DOI: 10.1038/nchem.2092] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 09/19/2014] [Indexed: 11/08/2022]
Abstract
Many molecular machines with controllable molecular-scale motors have been developed. However, transmitting molecular movement to the macroscopic scale remains a formidable challenge. Here we report a single crystal of a Ni complex whose shape changes abruptly and reversibly in response to thermal changes at around room temperature. Variable-temperature single-crystal X-ray diffraction studies show that the crystalline shape change is induced by an unusual 90° rotation of uniaxially aligned oxalate molecules. The oxalate dianions behave as molecular-scale rotors, with their movement propagated through the entire crystalline material via intermolecular hydrogen bonding. Consequently, the subnanometre-scale changes in the oxalate molecules are instantly amplified to a micrometre-scale contraction or expansion of the crystal, accompanied by a thermal hysteresis loop. The shape change in the crystal was clearly detected under an optical microscope. The large directional deformation and prompt response suggest a role for this material in microscale or nanoscale thermal actuators.
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Ueda A, Yamada S, Isono T, Kamo H, Nakao A, Kumai R, Nakao H, Murakami Y, Yamamoto K, Nishio Y, Mori H. Hydrogen-Bond-Dynamics-Based Switching of Conductivity and Magnetism: A Phase Transition Caused by Deuterium and Electron Transfer in a Hydrogen-Bonded Purely Organic Conductor Crystal. J Am Chem Soc 2014; 136:12184-92. [DOI: 10.1021/ja507132m] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Akira Ueda
- The
Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Shota Yamada
- The
Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
- Department
of Physics, Faculty of Science, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Takayuki Isono
- The
Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Hiromichi Kamo
- The
Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
| | - Akiko Nakao
- Comprehensive Research
Organization for Science and Society (CROSS), Tokai, Ibaraki 319-1106, Japan
| | - Reiji Kumai
- CMRC and Photon
Factory, Institute of Materials Structure Science, High Energy Accelerator
Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Hironori Nakao
- CMRC and Photon
Factory, Institute of Materials Structure Science, High Energy Accelerator
Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Youichi Murakami
- CMRC and Photon
Factory, Institute of Materials Structure Science, High Energy Accelerator
Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Kaoru Yamamoto
- Department
of Applied Physics, Okayama University of Science, Okayama 700-0005, Japan
| | - Yutaka Nishio
- Department
of Physics, Faculty of Science, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Hatsumi Mori
- The
Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
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Moncada F, González SA, Reyes A. First principles investigation of hydrogen isotope effects in [XSO4–H–SO4X]−(X = H, K) complexes. Mol Phys 2010. [DOI: 10.1080/00268971003781589] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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7
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Levin AA, Dolin SP, Mikhailova TY. Quantum chemistry of hydrogen-bonded materials. Ferroelectrics and antiferroelectrics. RUSS J GEN CHEM+ 2008. [DOI: 10.1134/s1070363208030427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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de Souza JM, Freire PTC, Bordallo HN, Argyriou DN. Structural isotopic effects in the smallest chiral amino acid: observation of a structural phase transition in fully deuterated alanine. J Phys Chem B 2007; 111:5034-9. [PMID: 17439273 DOI: 10.1021/jp070366z] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A first study of possible changes instigated by deuteration in amino acids was carried out using neutron diffraction, inelastic neutron scattering, and Raman scattering in l-alanine, C2H4(NH2)COOH. Careful analysis of the structural parameters shows that deuteration of l-alanine engenders significant geometric changes as a function of temperature, which can be directly related to the observation of new lattice vibration modes in the Raman spectra. The combination of the experimental data suggests that C2D4(ND2)COOD undergoes a structural phase transition (or a structural rearrangement) at about 170 K. Considering that this particular amino acid is a hydrogen-bonded system with short hydrogen bonds (O...H approximately 1.8 A), we evoke the Ubbelohde effect to conclude that substitution of hydrogen for deuterium gives rise to changes in the hydrogen-bonding interactions. The structural differences suggest distinct relative stabilities for the hydrogenous and deuterated l-alanine.
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Dolin S, Levin A, Polyakov E, Khrulev A, Mikhailova T. Hydrogen-bonded materials based on organic tautomeric molecules: Theoretical treatment. J Mol Struct 2006. [DOI: 10.1016/j.molstruc.2005.09.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Matsuo T, Ohama M, Mochida T, Sugawara T. Coherent tunneling of proton in the intramolecular hydrogen bond of crystalline bromo-hydroxyphenalenone at low temperature. J Mol Struct 2004. [DOI: 10.1016/j.molstruc.2004.03.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Bessonette PWR, White MA. Why is there no low-temperature phase transition in NaOH? J Chem Phys 1999. [DOI: 10.1063/1.478246] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Kume Y, Muraoka H, Yamamuro O, Matsuo T. Deuteration-induced phase transition in ammonium hexachloroplumbate. J Chem Phys 1998. [DOI: 10.1063/1.475806] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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