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Chaloupecká E, Tyrpekl V, Bártová K, Nishiyama Y, Dračínský M. NMR crystallography of amino acids. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2024; 130:101921. [PMID: 38422809 DOI: 10.1016/j.ssnmr.2024.101921] [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: 11/23/2023] [Revised: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
The development of NMR crystallography methods requires a reliable database of chemical shifts measured for systems with known crystal structure. We measured and assigned carbon and hydrogen chemical shifts of twenty solid natural amino acids of known polymorphic structure, meticulously determined using powder X-ray diffraction. We then correlated the experimental data with DFT-calculated isotropic shieldings. The small size of the unit cell of most amino acids allowed for advanced computations using various families of DFT functionals, including generalized gradient approximation (GGA), meta-GGA and hybrid DFT functionals. We tested several combinations of functionals for geometry optimizations and NMR calculations. For carbon shieldings, the widely used GGA functional PBE performed very well, although an improvement could be achieved by adding shielding corrections calculated for isolated molecules using a hybrid functional. For hydrogen nuclei, we observed the best performance for NMR calculations carried out with structures optimized at the hybrid DFT level. The high fidelity of the calculations made it possible to assign additional signals that could not be assigned based on experiments alone, for example signals of two non-equivalent molecules in the unit cell of some of the amino acids.
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Affiliation(s)
- Ema Chaloupecká
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague 2, Czech Republic
| | - Václav Tyrpekl
- Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague 2, Czech Republic
| | - Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic
| | | | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic.
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2
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Niehaus TA, Prost E, Loriot V, Lépine F, Bergé L, Skupin S. THz to far-infrared spectra of the known crystal polymorphs of phenylalanine. Phys Chem Chem Phys 2024; 26:7329-7334. [PMID: 38353103 DOI: 10.1039/d3cp05805k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
There is renewed interest in the structure of the essential amino acid phenylalanine in the solid state. Three new polymorphs were found in the years 2012 to 2014. Here, we investigate the structure, stability, and energetical ordering of these phases using first-principles simulations at the level of density functional theory incorporating van der Waals interactions. Two of the distinct crystal forms are found to be structurally similar and energetically very close after vibrational free energy corrections have been taken into account. Infrared absorption spectra are likewise calculated and compared to experimental measurements. By combining measurements obtained with a commercial Fourier transform infra-red spectrometer and a homemade air-photonics-based THz time domain spectrometer, we could carry out this comparison in the vibrational frequency region from 1 to 40 THz. The excellent agreement of the line positions and the established energy ranking allow us to identify the most stable polymorph of phenylalanine.
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Affiliation(s)
- Thomas A Niehaus
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France.
| | - Emilien Prost
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France.
| | - Vincent Loriot
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France.
| | - Franck Lépine
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France.
| | - Luc Bergé
- Centre Lasers Intenses et Applications, Université de Bordeaux-CNRS-CEA, 33405 Talence Cedex, France
| | - Stefan Skupin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France.
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3
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Kuila S, Dey S, Singh P, Shrivastava A, Nanda J. Phenylalanine-based fibrillar systems. Chem Commun (Camb) 2023; 59:14509-14523. [PMID: 37987167 DOI: 10.1039/d3cc04138g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Phenylketonuria (PKU) is an inborn metabolic disorder characterized by excess accumulation of phenylalanine (Phe) and its fibril formation, resulting in progressive intellectual disability. Several research groups have approached from various directions to understand the formation of toxic amyloid fibrils from the essential amino acid Phe. Different parameters like the nature of the solvent, pH, Phe concentration, temperature, etc. influence the fibril formation kinetics. In this article, we have summarized all major findings regarding the formation of Phe-based fibrils in aqueous and organic media and discussed how non-covalent interactions are involved in the self-assembly process using spectroscopic and microscopic techniques. The toxicity of Phe-based fibrils is compared with other neurodegenerative peptides. It is noted that the Phe-based fibrils can also induce various globular proteins into toxic fibrils. Later, we discuss the different approaches to inhibit fibril formation and reduce its toxicity. The presence of polyphenolic compounds, drugs, amino acids, nanoparticles, metal ions, crown ethers, and others showed a remarkable inhibitory effect on fibril formation. To the best of our knowledge, this is the first-ever etymological analysis of the Phe-fibrillar system and its inhibition to create a strong database against PKU.
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Affiliation(s)
- Soumen Kuila
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
| | - Sukantha Dey
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
| | - Pijush Singh
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India
| | - Akash Shrivastava
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
| | - Jayanta Nanda
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
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4
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Adhikari RY, Pujols JJ. Highly rigid & transparent supramolecular fibrils of tyrosine. NANO SELECT 2022. [DOI: 10.1002/nano.202200063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Ramesh Y. Adhikari
- Department of Physics & Astronomy Colgate University Hamilton New York USA
| | - Jeiko J. Pujols
- Department of Physics & Astronomy Colgate University Hamilton New York USA
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5
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Liu Q, Wang J, Huang X, Wu H, Zong S, Cheng X, Hao H. Spatiotemporal control of l-phenyl-alanine crystallization in microemulsion: the role of water in mediating molecular self-assembly. IUCRJ 2022; 9:370-377. [PMID: 35546797 PMCID: PMC9067117 DOI: 10.1107/s2052252522003001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 03/18/2022] [Indexed: 06/15/2023]
Abstract
Water confined or constrained in a cellular environment can exhibit a diverse structural and dynamical role and hence will affect the self-assembly behavior of biomolecules. Herein, the role of water in the formation of l-phenyl-alanine crystals and amyloid fibrils was investigated. A microemulsion biomimetic system with controllable water pool size was employed to provide a microenvironment with different types of water, which was characterized by small-angle X-ray scattering, attenuated total reflectance-Fourier transform infrared spectroscopy and differential scanning calorimetry. In a bound water environment, only plate-like l-phenyl-alanine crystals and their aggregates were formed, all of which are anhydrous crystal form I. However, when free water dominated, amyloid fibrils were observed. Free water not only stabilizes new oligomers in the initial nucleation stage but also forms bridged hydrogen bonds to induce vertical stacking to form a fibrous structure. The conformational changes of l-phenyl-alanine in different environments were detected by NMR. Different types of water trigger different nucleation and growth pathways, providing a new perspective for understanding molecular self-assembly in nanoconfinement.
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Affiliation(s)
- Qi Liu
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Jingkang Wang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Xin Huang
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Hao Wu
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Shuyi Zong
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Xiaowei Cheng
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Hongxun Hao
- National Engineering Research Center of Industrial Crystallization Technology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
- School of Chemical Engineering and Technology, Hainan University, Haikou 570228, People’s Republic of China
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6
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Gong Y, Wei Y, Gao Y, Pang Z, Zhang J, Qian S. The bending behavior of an L-phenylalanine monohydrate soft crystal via reversible hydrogen bond rupture and remodeling. Phys Chem Chem Phys 2022; 24:3216-3221. [PMID: 35044406 DOI: 10.1039/d1cp05449j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The present study reports a novel L-phenylalanine monohydrate (L-Phe·H2O) soft crystal, which has the potential to be developed as a medical microdevice owing to its flexibility and biosafety. Structure analysis indicated that there were plenty of directional hydrogen bonds distributed along almost every direction of the L-Phe·H2O crystal, which appeared to be a rigid and brittle crystal. However, the L-Phe·H2O crystal could be easily bent heavily and repeatedly. The aim of this study was to systematically investigate the bending mechanism of the L-Phe·H2O soft crystal from the viewpoint of hydrogen bond variations. In situ micro-Raman and in situ micro-infrared spectra showed that the hydrogen bonds ruptured and rearranged during the bending process. According to the micro-X-ray diffraction results, the order of the L-Phe·H2O lattice decreased in the bending region, and the varied lattice could return to its original state after straightening. Additionally, energy calculations suggested that the non-directional Coulomb attraction was the major force maintaining the macroscopic crystal integrity of L-Phe·H2O when it was bent.
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Affiliation(s)
- Yaxiang Gong
- School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Yuanfeng Wei
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Yuan Gao
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Zunting Pang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Jianjun Zhang
- School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Shuai Qian
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
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7
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Allen JL, Sanders TJ, Plathe R, Appadoo D, Horvat J, Lewis RA. Temperature-dependent terahertz spectroscopy of l-phenylalanine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119922. [PMID: 34058666 DOI: 10.1016/j.saa.2021.119922] [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: 02/27/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
Undiluted l-phenylalanine has been cooled to 6K and its transmission spectrum obtained under terahertz radiation from a synchrotron source. Three distinct absorption bands are evident: at 1.37, 2.14, and 2.32THz. Each of these tracks to lower frequency ("redshifts") as the temperature is increased from 6 to 250K. The observed shifts are in the range of 0.1-0.2THz. The form of the temperature dependence is well accounted for by a Bose-Einstein model, from which the zero-temperature frequency of each mode and the characteristic temperature of the associated phonon bath may be estimated. At 6K a fourth band is evident, at 2.65THz. However, the depth of this, touching the noise floor, coupled with the increasing opacity of the sample with temperature for frequencies beyond 2.5THz, makes it difficult to track. The frequencies of all four modes are in good accord with and thus confirm a previous calculation.
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Affiliation(s)
- J L Allen
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia.
| | - T J Sanders
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
| | - R Plathe
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Rd Clayton, VIC 3168, Australia
| | - D Appadoo
- Australian Synchrotron, Australian Nuclear Science and Technology Organisation, 800 Blackburn Rd Clayton, VIC 3168, Australia
| | - J Horvat
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
| | - R A Lewis
- Institute for Superconducting and Electronic Materials and School of Physics, University of Wollongong, NSW 2522, Australia
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8
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Feliciano IO, Silva DP, Piedade MFM, Bernardes CES, Minas da Piedade ME. First and Second Dissociation Enthalpies in Bi-Component Crystals Consisting of Maleic Acid and L-Phenylalanine. Molecules 2021; 26:molecules26185714. [PMID: 34577186 PMCID: PMC8469174 DOI: 10.3390/molecules26185714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
The energetics of the stepwise dissociation of a A:B2 bi-component crystal, according to A:B2(cr) → A:B(cr) + B(cr) and A:B(cr) → A(cr) + B(cr), was investigated using MA:Phe2 and MA:Phe (MA = maleic acid; Phe = L-phenylalanine) as model systems. The enthalpy changes associated with these sequential processes and with the overall dissociation reaction A:B2(cr) → A(cr) + 2B(cr) were determined by solution calorimetry. It was found that they are all positive, indicating that there is a lattice enthalpy gain when MA:Phe2 is formed, either from the individual precursors or by adding Phe to MA:Phe. Single-crystal X-ray diffraction (SCXRD) analysis showed that MA:Phe2 is best described as a protic salt containing a maleate anion (MA−) and two non-equivalent L-phenylalanine units, both linked to MA− by NH···O hydrogen bonds (H-bond): one of these units is protonated (HPhe+) and the other zwitterionic (Phe±). Only MA− and HPhe+ molecules are present in the MA:Phe lattice. In this case, however, NH···O and OH···O H-bonds are formed between each MA− unit and two HPhe+ molecules. Despite these structural differences, the enthalpy cost for the removal of the zwitterionic Phe± unit from the MA:Phe2 lattice to yield MA:Phe is only 0.9 ± 0.4 kJ mol−1 higher than that for the dissociation of MA:Phe, which requires a proton transfer from HPhe+ to MA− and the rearrangement of L-phenylalanine to the zwitterionic, Phe±, form. Finally, a comparison of the dissociation energetics and structures of MA:Phe and of the previously reported glycine maleate (MA:Gly) analogue indicated that parameters, such as the packing coefficient, density, hydrogen bonds formed, or fusion temperature, are not necessarily good descriptors of dissociation enthalpy or lattice enthalpy trends when bi-component crystals with different molecular composition are being compared, even if the stoichiometry is the same.
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Affiliation(s)
- Inês O. Feliciano
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (I.O.F.); (C.E.S.B.)
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal;
| | - Daniela P. Silva
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal;
| | - M. Fátima M. Piedade
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal;
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal;
| | - Carlos E. S. Bernardes
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (I.O.F.); (C.E.S.B.)
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal;
| | - Manuel E. Minas da Piedade
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (I.O.F.); (C.E.S.B.)
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal;
- Correspondence: ; Tel.: +351-217500005
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Joseph V, Levine M. Ronald C.D. Breslow (1931-2017): A career in review. Bioorg Chem 2021; 115:104868. [PMID: 34523507 DOI: 10.1016/j.bioorg.2021.104868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/23/2021] [Indexed: 11/26/2022]
Abstract
Reviewed herein are key research accomplishments of Professor Ronald Charles D. Breslow (1931-2017) throughout his more than 60 year research career. These accomplishments span a wide range of topics, most notably physical organic chemistry, medicinal chemistry, and bioorganic chemistry. These topics are reviewed, as are topics of molecular electronics and origin of chirality, which combine to make up the bulk of this review. Also reviewed briefly are Breslow's contributions to the broader chemistry profession, including his work for the American Chemical Society and his work promoting gender equity. Throughout the article, efforts are made to put Breslow's accomplishments in the context of other work being done at the time, as well as to include subsequent iterations and elaborations of the research.
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Affiliation(s)
- Vincent Joseph
- Department of Chemical Sciences, Ariel University, Israel
| | - Mindy Levine
- Department of Chemical Sciences, Ariel University, Israel.
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10
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Pokorný V, Štejfa V, Havlín J, Růžička K, Fulem M. Heat Capacities of l-Histidine, l-Phenylalanine, l-Proline, l-Tryptophan and l-Tyrosine. Molecules 2021; 26:4298. [PMID: 34299573 PMCID: PMC8305567 DOI: 10.3390/molecules26144298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 11/16/2022] Open
Abstract
In an effort to establish reliable thermodynamic data for proteinogenic amino acids, heat capacities for l-histidine (CAS RN: 71-00-1), l-phenylalanine (CAS RN: 63-91-2), l-proline (CAS RN: 147-85-3), l-tryptophan (CAS RN: 73-22-3), and l-tyrosine (CAS RN: 60-18-4) were measured over a wide temperature range. Prior to heat capacity measurements, thermogravimetric analysis was performed to determine the decomposition temperatures while X-ray powder diffraction (XRPD) and heat-flux differential scanning calorimetry (DSC) were used to identify the initial crystal structures and their possible transformations. Crystal heat capacities of all five amino acids were measured by Tian-Calvet calorimetry in the temperature interval from 262 to 358 K and by power compensation DSC in the temperature interval from 307 to 437 K. Experimental values determined in this work were then combined with the literature data obtained by adiabatic calorimetry. Low temperature heat capacities of l-histidine, for which no literature data were available, were determined in this work using the relaxation (heat pulse) calorimetry from 2 K. As a result, isobaric crystal heat capacities and standard thermodynamic functions up to 430 K for all five crystalline amino acids were developed.
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Affiliation(s)
- Václav Pokorný
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic; (V.P.); (V.Š.); (K.R.)
| | - Vojtěch Štejfa
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic; (V.P.); (V.Š.); (K.R.)
| | - Jakub Havlín
- Central Laboratories, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic;
| | - Květoslav Růžička
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic; (V.P.); (V.Š.); (K.R.)
| | - Michal Fulem
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Czech Republic; (V.P.); (V.Š.); (K.R.)
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11
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Bera S, Dong X, Krishnarjuna B, Raab SA, Hales DA, Ji W, Tang Y, Shimon LJ, Ramamoorthy A, Clemmer DE, Wei G, Gazit E. Solid-state packing dictates the unexpected solubility of aromatic peptides. CELL REPORTS. PHYSICAL SCIENCE 2021; 2:100391. [PMID: 33928264 PMCID: PMC8063180 DOI: 10.1016/j.xcrp.2021.100391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/11/2021] [Accepted: 03/12/2021] [Indexed: 05/10/2023]
Abstract
The understanding and prediction of the solubility of biomolecules, even of the simplest ones, reflect an open question and unmet need. Short aromatic tripeptides are among the most highly aggregative biomolecules. However, in marked contrast, Ala-Phe-Ala (AFA) was surprisingly found to be non-aggregative and could be solubilized at millimolar concentrations. Here, aiming to uncover the underlying molecular basis of its high solubility, we explore in detail the solubility, aggregation propensity, and atomic-level structure of the tripeptide. We demonstrate an unexpectedly high water solubility of AFA reaching 672 mM, two orders of magnitude higher than reported previously. The single crystal structure reveals an anti-parallel β sheet conformation devoid of any aromatic interactions. This study provides clear mechanistic insight into the structural basis of solubility and suggests a simple and feasible tool for its estimation, bearing implications for design of peptide drugs, peptides materials, and advancement of peptide nanotechnology.
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Affiliation(s)
- Santu Bera
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Xuewei Dong
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Fudan University, Shanghai, 200433, People’s Republic of China
| | - Bankala Krishnarjuna
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Shannon A. Raab
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN 47401, USA
| | - David A. Hales
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN 47401, USA
- Department of Chemistry, Hendrix College, Conway, AR 72032, USA
| | - Wei Ji
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Fudan University, Shanghai, 200433, People’s Republic of China
| | - Linda J.W. Shimon
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - David E. Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, IN 47401, USA
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Fudan University, Shanghai, 200433, People’s Republic of China
| | - Ehud Gazit
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
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12
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Liu C, Guo Z, Feng H, Lin L, Cui Y, Li Y, Tian H. Synthesis of Copolymers Polyethyleneimine-co-Polyphenylalanine as Gene and Drug Codelivery Carrier. Macromol Biosci 2021; 21:e2100033. [PMID: 33689218 DOI: 10.1002/mabi.202100033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/16/2021] [Indexed: 12/26/2022]
Abstract
In this study, a series of hyperbranched copolymers polyethyleneimine-co-polyphenylalanine (PEI-co-PPhe) are synthesized by ring-opening polymerization with phenylalanine-N-carboxyanhydride as monomer and PEI-25k as initiator, using as a gene and drug codelivery carrier. Among them, PEI-co-PPhe (1:170) is selected out from transfection efficiency and cytotoxicity tests. Then, doxorubicin-cis-aconitic anhydride (CAD) and BCl2-shRNA (as a therapeutic gene) are coloaded into the PEI-co-PPhe carrier to form PEI-co-PPhe/Bcl2-shRNA/CAD complexes as a codeliver system. When the mass ratio of PEI-co-PPhe:Bcl2-shRNA:CAD is 5:1:1, the codeliver system has the most obvious synergistic therapeutic effect against B16F10 cells. Confirmed by confocal laser scanning microscope and flow cytometry, compared with drug and gene alone, the codeliver complexes can be endocytosed into B16F10 cells efficiently. As a result, the appropriate length of PPhe grafted on PEI will improve the gene transfer efficiency and decrease cytotoxicity, as well as effective codelivery of gene and drug into cancer cells to be a promising codelivery carrier for cancer therapy.
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Affiliation(s)
- Chong Liu
- School of Chemistry and Environmental Engineering, Changchun University of Science and Technology, Changchun, 130022, P. R. China
| | - Zhaopei Guo
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Huimin Feng
- School of Chemistry and Environmental Engineering, Changchun University of Science and Technology, Changchun, 130022, P. R. China
| | - Lin Lin
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Yuan Cui
- School of Chemistry and Environmental Engineering, Changchun University of Science and Technology, Changchun, 130022, P. R. China
| | - Yanhui Li
- School of Chemistry and Environmental Engineering, Changchun University of Science and Technology, Changchun, 130022, P. R. China
| | - Huayu Tian
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
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13
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Xue K, Dervisoglu R, Sowa H, Andreas LB. Centerband-Only Detection of Exchange NMR with Natural-Abundance Correction Reveals an Expanded Unit Cell in Phenylalanine Crystals. Chemphyschem 2020; 21:1622-1626. [PMID: 32558171 PMCID: PMC7497148 DOI: 10.1002/cphc.202000517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Indexed: 11/05/2022]
Abstract
The NMR pulse sequence CODEX (centerband-only detection of exchange) is a widely used method to report on the number of magnetically inequivalent spins that exchange magnetization via spin diffusion. For crystals, this rules out certain symmetries, and the rate of equilibration is sensitive to distances. Here we show that for 13 C CODEX, consideration of natural abundance spins is necessary for crystals of high complexity, demonstrated here with the amino acid phenylalanine. The NMR data rule out the C2 space group that was originally reported for phenylalanine, and are only consistent with a larger unit cell containing eight magnetically inequivalent molecules. Such an expanded cell was recently described based on single crystal data. The large unit cell dictates the use of long spin diffusion times of more than 200 seconds, in order to equilibrate over the entire unit cell volume of 1622 Å3 .
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Affiliation(s)
- Kai Xue
- Max Planck Institute for Biophysical ChemistryDepartment of NMR Based Structural BiologyAm Fassberg. 1137077GoettingenGermany
| | - Riza Dervisoglu
- Max Planck Institute for Biophysical ChemistryDepartment of NMR Based Structural BiologyAm Fassberg. 1137077GoettingenGermany
| | - Heidrun Sowa
- Georg-August-University GoettingenDepartment of CrystallographyGoldschmidtstr. 137077GoettingenGermany
| | - Loren B. Andreas
- Max Planck Institute for Biophysical ChemistryDepartment of NMR Based Structural BiologyAm Fassberg. 1137077GoettingenGermany
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14
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Solid-state vibrational circular dichroism studies on the conformation of an amino acid molecule in crystalline state. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140439. [DOI: 10.1016/j.bbapap.2020.140439] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/18/2020] [Accepted: 04/29/2020] [Indexed: 11/20/2022]
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15
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Kadeeja A, Joseph S, Abraham JN. Self-assembly of novel Fmoc-cardanol compounds into hydrogels - analysis based on rheological, structural and thermal properties. SOFT MATTER 2020; 16:6294-6303. [PMID: 32462156 DOI: 10.1039/d0sm00670j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hydrogels of low molecular weight molecules are particularly appealing for various biomedical applications such as drug delivery, tissue engineering, and antitumor therapy due to their excellent biocompatibility, biodegradability, and easy availability. Fmoc-peptide hydrogels form an essential category of these hydrogels. Herein we report a new class of Fmoc hydrogels in which cardanol (3-pentadecyl phenol (PDP)) is covalently linked with fluorenylmethyloxycarbonyl group. Cardanol is a plant-based renewable raw material, readily obtained from Cashew Nut Shell Liquid (CNSL). The long aliphatic chain of pentadecyl phenol helps in bringing a structural incompatibility and generates different nanostructures such as nanospheres, nanotapes, and nanofibers depending on Fmoc substitution and the solvents used. Stable hydrogels were formed from Fmoc-PDP in DMSO/H2O, and the critical aggregation concentration (CAC) and critical gelation concentration (CGC) were determined. The role of non-covalent forces such as hydrogen-bonding, hydrophobicity, and π-π stacking interactions in governing self-assembly to hydrogel formation was studied for Fmoc, DiFmoc and Boc groups attached to PDP. The thermal properties were analyzed, and smectic and nematic phases were identified for the molecules depending on the substitutions involved. Overall the study supports the mechanisms of aggregation and gelation in novel Fmoc-cardanol derivatives.
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Affiliation(s)
- Aliya Kadeeja
- Polymer Science and Engineering Division, CSIR-National Chemical Laboratory, Dr Homibhabha Road, Pune, 411008, India.
| | - Seena Joseph
- Polymer Science and Engineering Division, CSIR-National Chemical Laboratory, Dr Homibhabha Road, Pune, 411008, India.
| | - Jancy Nixon Abraham
- Polymer Science and Engineering Division, CSIR-National Chemical Laboratory, Dr Homibhabha Road, Pune, 411008, India.
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16
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Bera S, Xue B, Rehak P, Jacoby G, Ji W, Shimon LJW, Beck R, Král P, Cao Y, Gazit E. Self-Assembly of Aromatic Amino Acid Enantiomers into Supramolecular Materials of High Rigidity. ACS NANO 2020; 14:1694-1706. [PMID: 31944667 PMCID: PMC7123433 DOI: 10.1021/acsnano.9b07307] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/16/2020] [Indexed: 05/12/2023]
Abstract
Most natural biomolecules may exist in either of two enantiomeric forms. Although in nature, amino acid biopolymers are characterized by l-type homochirality, incorporation of d-amino acids in the design of self-assembling peptide motifs has been shown to significantly alter enzyme stability, conformation, self-assembly behavior, cytotoxicity, and even therapeutic activity. However, while functional metabolite assemblies are ubiquitous throughout nature and play numerous important roles including physiological, structural, or catalytic functions, the effect of chirality on the self-assembly nature and function of single amino acids is not yet explored. Herein, we investigated the self-assembly mechanism of amyloid-like structure formation by two aromatic amino acids, phenylalanine (Phe) and tryptophan (Trp), both previously found as extremely important for the nucleation and self-assembly of aggregation-prone peptide regions into functional structures. Employing d-enantiomers, we demonstrate the critical role that amino acid chirality plays in their self-assembly process. The kinetics and morphology of pure enantiomers is completely altered upon their coassembly, allowing to fabricate different nanostructures that are mechanically more robust. Using diverse experimental techniques, we reveal the different molecular arrangement and self-assembly mechanism of the dl-racemic mixtures that resulted in the formation of advanced supramolecular materials. This study provides a simple yet sophisticated engineering model for the fabrication of attractive materials with bionanotechnological applications.
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Affiliation(s)
- Santu Bera
- School
of Molecular Cell Biology and Biotechnology, George S. Wise Faculty
of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Bin Xue
- Collaborative
Innovation Center of Advanced Microstructures, National Laboratory
of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, Jiangsu 210093, People’s Republic of China
| | - Pavel Rehak
- Department
of Chemistry, University of Illinois at
Chicago, Chicago, Illinois 60607, United States
| | - Guy Jacoby
- The
Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel
| | - Wei Ji
- School
of Molecular Cell Biology and Biotechnology, George S. Wise Faculty
of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Linda J. W. Shimon
- Department
of Chemical Research Support, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Roy Beck
- The
Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel
| | - Petr Král
- Department
of Chemistry, University of Illinois at
Chicago, Chicago, Illinois 60607, United States
- Department
of Biopharmaceutical Sciences, University
of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Yi Cao
- Collaborative
Innovation Center of Advanced Microstructures, National Laboratory
of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, Jiangsu 210093, People’s Republic of China
| | - Ehud Gazit
- School
of Molecular Cell Biology and Biotechnology, George S. Wise Faculty
of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
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17
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Al Rahal O, Hughes CE, Williams PA, Logsdail AJ, Diskin‐Posner Y, Harris KDM. Polymorphism of
l
‐Tryptophan. Angew Chem Int Ed Engl 2019; 58:18788-18792. [DOI: 10.1002/anie.201908247] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/11/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Okba Al Rahal
- School of ChemistryCardiff University Park Place Cardiff Wales CF10 3AT UK
| | - Colan E. Hughes
- School of ChemistryCardiff University Park Place Cardiff Wales CF10 3AT UK
| | - P. Andrew Williams
- School of ChemistryCardiff University Park Place Cardiff Wales CF10 3AT UK
| | - Andrew J. Logsdail
- School of ChemistryCardiff University Park Place Cardiff Wales CF10 3AT UK
| | - Yael Diskin‐Posner
- Department of Chemical Research SupportWeizmann Institute of Science Rehovot 76100 Israel
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18
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Al Rahal O, Hughes CE, Williams PA, Logsdail AJ, Diskin‐Posner Y, Harris KDM. Polymorphism of
l
‐Tryptophan. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908247] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Okba Al Rahal
- School of ChemistryCardiff University Park Place Cardiff Wales CF10 3AT UK
| | - Colan E. Hughes
- School of ChemistryCardiff University Park Place Cardiff Wales CF10 3AT UK
| | - P. Andrew Williams
- School of ChemistryCardiff University Park Place Cardiff Wales CF10 3AT UK
| | - Andrew J. Logsdail
- School of ChemistryCardiff University Park Place Cardiff Wales CF10 3AT UK
| | - Yael Diskin‐Posner
- Department of Chemical Research SupportWeizmann Institute of Science Rehovot 76100 Israel
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19
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Červinka C, Fulem M. Cohesive properties of the crystalline phases of twenty proteinogenic α-aminoacids from first-principles calculations. Phys Chem Chem Phys 2019; 21:18501-18515. [PMID: 31411212 DOI: 10.1039/c9cp03102b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cohesive properties (lattice and cohesive energy of the crystal and corresponding sublimation enthalpy) of the complete set of twenty enantiopure anhydrous proteinogenic amino acids are investigated using first-principles calculations. In contrast to neutral amino acid molecules in the vapor phase, all amino acids form crystals in their zwitterionic form. Therefore, reliable ab initio calculations of the proton transfer energy are an indispensable step of such calculations. Simplifying procedures, designed to rationalize the computational cost of the quasi-harmonic approximation, which proves too demanding if performed fully at the given quantum level of theory, are presented and tested. For this purpose, atomic multipoles (up to the quadrupoles) for the amoeba force field are parametrized for all amino acid zwitterions. While the calculated lattice energies of the amino acids range from 235-458 kJ mol-1 in absolute value, the proton transfer energies typically amount to 100-220 kJ mol-1, which translates to sublimation enthalpies ranging from 117-202 kJ mol-1, appreciably exceeding the sublimation enthalpy values common for nonionic molecular crystals. Critically assessed experimental data on sublimation enthalpies are used as a benchmark for comparison of the data calculated in this work. Cohesive properties of most amino acids calculated in this work, combining the PBE-D3(BJ)/PAW and CCSD(T)-F12/aug-cc-pVDZ levels of theory used for predictions of the lattice energies and of the proton transfer energies, respectively, exhibit a reasonable agreement with the experiment. At the same time, this work contains the first published data on cohesive properties for several enantiopure amino acids.
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Affiliation(s)
- Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
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20
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Sato H, Takimoto K, Kawamura I, Aisawa S. Application of Solid-State Vibrational Circular Dichroism for Intercalation Compounds of Layered Double Hydroxide and Amino Acids: Conformation of an Intercalated Phenylalanine. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20190161] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hisako Sato
- Department of Chemistry, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Kazuyoshi Takimoto
- Department of Chemistry, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Izuru Kawamura
- Graduate School of Engineering, Yokohama National University, Hodogaya-ku, Yokohama, Kanagawa 240-8501, Japan
| | - Sumio Aisawa
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, 4-3-5 Ueda, Morioka, Iwate 020-8551, Japan
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21
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Ning Li, Ayoubi MA, Chen H, Wang J, Wang W. Co-hydrogelation of Dendritic Surfactant and Amino Acids in Their Common Naturally-occurring Forms: A Study of Morphology and Mechanisms. COLLOID JOURNAL 2019. [DOI: 10.1134/s1061933x19030098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Cuppen HM, Smets MMH, Krieger AM, van den Ende JA, Meekes H, van Eck ERH, Görbitz CH. The Rich Solid-State Phase Behavior of l-Phenylalanine: Disappearing Polymorphs and High Temperature Forms. CRYSTAL GROWTH & DESIGN 2019; 19:1709-1719. [PMID: 30872978 PMCID: PMC6410616 DOI: 10.1021/acs.cgd.8b01655] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/13/2018] [Indexed: 06/02/2023]
Abstract
After years of controversy over the solid state structure of the essential amino acid l-phenylalanine, four different polymorphic forms were published recently. The common form I has symmetry P21 with four molecules in the asymmetric unit (Z' = 4), similar to form III, but with a different arrangement of molecular bilayers. Form II, obtained from the hydrate at very low humidity, is unrelated to forms I and III, as is the high-density form IV. The present investigation demonstrates that this prototype aromatic amino acid has two additional high-temperature phases Ih and IIIh obtained from form I and form III above 458 and 440 K, respectively, when flipping between two alternative side-chain conformations becomes dynamic and causes pairs of molecules, initially crystallographically independent, to become equivalent above a sharp transition temperature. These abrupt and reversible phase changes occur with a reduction of Z' from 4 (low T) to 2 (high T) and modified crystal symmetry. We furthermore experienced an example of disappearing polymorph for form I which after growing form III in one of our laboratories could no longer be crystallized at room temperature. In contrast, form III crystals may be irreversibly converted to form I crystals as a result of sliding of molecular bilayers in the crystal at elevated temperature. No conversions between the high-temperature forms Ih and IIIh were found. The remarkable crystallographic results are here corroborated by Molecular Dynamics and metadynamics simulations of the form I - form III system.
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Affiliation(s)
- Herma M. Cuppen
- Radboud
University Nijmegen, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Mireille M. H. Smets
- Radboud
University Nijmegen, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Annika M. Krieger
- Radboud
University Nijmegen, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Joost A. van den Ende
- Radboud
University Nijmegen, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Hugo Meekes
- Radboud
University Nijmegen, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Ernst R. H. van Eck
- Radboud
University Nijmegen, Institute for Molecules
and Materials, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
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23
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Bera S, Mondal S, Rencus-Lazar S, Gazit E. Organization of Amino Acids into Layered Supramolecular Secondary Structures. Acc Chem Res 2018; 51:2187-2197. [PMID: 30095247 DOI: 10.1021/acs.accounts.8b00131] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The unique physiochemical properties and multiscale organization of layered materials draw the attention of researchers across a wide range of scientific disciplines. Layered structures are commonly found in diverse biological systems where they fulfill various functions. A prominent example of layered biological materials is the organization of proteins and polypeptides into the archetypal aggregated amyloidal structures. While the organization of proteins into amyloid structures was initially associated with various degenerative disorders, it was later revealed that proteins not related to any disease could also form identical layered assemblies. Thus, it appears that the ability of peptides and proteins to produce amyloid-like aggregates represents a generic property of polyamides to assemble into higher order fibrillar structures. In the aggregated state, the peptide backbone forms β-sheet structures which are further organized into layered arrangements. We have recently extended the identified amyloidogenic building blocks to include not only peptides or proteins, but also single amino acids and other metabolites. High resolution spectroscopy and crystallography analyses confirm the clear potential of amino acids and other metabolites to form layered amyloid-like aggregates showing biophysical and biochemical properties similar to protein amyloids. Therefore, the generic propensity of peptides and proteins backbones to assemble into layered organizations may emanate from their basic building block, the amino acid. In this Account, we aim to introduce the concept of supramolecular β-sheet organization of single amino acids and to present an analysis of their layered-structure organization based on single crystal structures. We demonstrate that, despite the different side-chains that considerably vary in their chemical properties, all coded amino acids display a layer-like assembly stabilized by α-amine to α-carboxyl H-bonds, resembling supramolecular β-sheet structures, while the side-chains determine the higher order organization of the layers. Our work presents the first analysis of the β-sheet propensity of single amino acids in their unbound form, indicating an evolutionary predisposition. We classify the amino acids β-sheet propensity on the basis of the interlayer separation distance in the crystal packing, which correlates well with previously reported classifications based on various criteria, such as hydrophobicity, steric bulkiness, and folding. In addition, we demonstrate that the relative direction of α-amine to α-carboxyl H-bonding pattern provides critical insights regarding the stabilization of parallel versus antiparallel β-sheet structures by the various amino acids. Taken together, our analysis of amino acid crystals provides substantial information regarding protein folding and dynamics and could serve as basic rules set for the design of potential building blocks for molecular self-assembly to produce functional materials of tunable properties, an important objective of bottom-up nanotechnology.
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Affiliation(s)
- Santu Bera
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Sudipta Mondal
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Sigal Rencus-Lazar
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
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24
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Famiano MA, Boyd RN, Kajino T, Onaka T, Mo Y. Amino Acid Chiral Selection Via Weak Interactions in Stellar Environments: Implications for the Origin of Life. Sci Rep 2018; 8:8833. [PMID: 29891867 PMCID: PMC5995967 DOI: 10.1038/s41598-018-27110-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 05/25/2018] [Indexed: 11/12/2022] Open
Abstract
Magnetochiral phenomena may be responsible for the selection of chiral states of biomolecules in meteoric environments. For example, the Supernova Amino Acid Processing (SNAAP) Model was proposed previously as a possible mode of magnetochiral selection of amino acids by way of the weak interaction in strong magnetic fields. In earlier work, this model was shown to produce an enantiomeric excess (ee) as high as 0.014% for alanine. In this paper we present the results of molecular quantum chemistry calculations from which ees are determined for the α-amino acids plus isovaline and norvaline, which were found to have positive ees in meteorites. Calculations are performed for both isolated and aqueous states. In some cases, the aqueous state was found to produce larger ees reaching values as high as a few percent under plausible conditions.
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Affiliation(s)
- Michael A Famiano
- Department of Physics and Joint Institute for Nuclear Astrophysics, Western Michigan Univ., 1903 W. Michigan Avenue, Kalamazoo, MI, 49008-5252, USA. .,National Astronomical Observatory of Japan, 2-21-1 Mitaka, Tokyo, 181-8588, Japan.
| | - Richard N Boyd
- National Astronomical Observatory of Japan, 2-21-1 Mitaka, Tokyo, 181-8588, Japan.,Department of Physics, Department of Astronomy, The Ohio State Univ., Columbus, OH, 43210, USA
| | - Toshitaka Kajino
- National Astronomical Observatory of Japan, 2-21-1 Mitaka, Tokyo, 181-8588, Japan.,Department of Astronomy, Graduate School of Science, Univ. of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,School of Physics and Nuclear Energy Engineering, Beihang Univ. (Beijing Univ. of Aeronautics and Astronautics), Beijing, 100083, P.R. China
| | - Takashi Onaka
- Department of Astronomy, Graduate School of Science, Univ. of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yirong Mo
- Department of Chemistry, Western Michigan Univ., 1903 W. Michigan Avenue, Kalamazoo, MI, 49008-5252, USA
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25
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Sharma A, Tiwari P, Dutt Konar A. The dominant role of side chains in supramolecular double helical organisation in synthetic tripeptides. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.01.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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26
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Tiwari P, Biswas S, Verma R, Sharma A, Dutt Konar A. Porous Biomaterials via Side Chain-Side Chain Interactions of Tyrosine Analogue of Pyridine Carboxamides. ChemistrySelect 2018. [DOI: 10.1002/slct.201702304] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Priyanka Tiwari
- Department of Chemistry and School of Pharmaceutical Sciences; Rajiv Gandhi Technological University; Bhopal 462033, MP
| | - Soumava Biswas
- Department of Chemistry; IISER Bhopal; Bhopal Bypass Road, Bhauri Bhopal 462066
| | - Ritu Verma
- Department of Chemistry and School of Pharmaceutical Sciences; Rajiv Gandhi Technological University; Bhopal 462033, MP
| | - Ankita Sharma
- Department of Chemistry and School of Pharmaceutical Sciences; Rajiv Gandhi Technological University; Bhopal 462033, MP
| | - Anita Dutt Konar
- Department of Chemistry and School of Pharmaceutical Sciences; Rajiv Gandhi Technological University; Bhopal 462033, MP
- Department of Chemistry; IISER Bhopal; Bhopal Bypass Road, Bhauri Bhopal 462066
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27
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Sögütoglu LC, Lutz M, Meekes H, de Gelder R, Vlieg E. Polymorphism and Modulation of Para-Substituted l-Phenylalanine. CRYSTAL GROWTH & DESIGN 2017; 17:6231-6238. [PMID: 29234239 PMCID: PMC5721337 DOI: 10.1021/acs.cgd.7b00747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/21/2017] [Indexed: 06/07/2023]
Abstract
The crystal structure of para-methyl-l-phenylalanine at 230 K resembles that of the para-fluorinated analogue from the literature but is commensurately modulated with seven molecules in the asymmetric unit (Z' = 7). At 100 K, the superstructure loses its modulation, leading to a unit cell with Z' = 1, with clear disorder in the phenyl ring orientations. The methyl-substituent in para-methyl-l-phenylalanine has, in contrast to fluorine, no polar interactions with protons of neighboring molecules, which might allow for the well-defined modulation of the crystal structure at 230 K.
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Affiliation(s)
- Leyla-Cann Sögütoglu
- Radboud
University, Institute for Molecules and
Materials, Heyendaalseweg
135, 6525 AJ, Nijmegen, The Netherlands
| | - Martin Lutz
- Crystal
and Structural Chemistry, Bijvoet Center for Biomolecular Research,
Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Hugo Meekes
- Radboud
University, Institute for Molecules and
Materials, Heyendaalseweg
135, 6525 AJ, Nijmegen, The Netherlands
| | - René de Gelder
- Radboud
University, Institute for Molecules and
Materials, Heyendaalseweg
135, 6525 AJ, Nijmegen, The Netherlands
| | - Elias Vlieg
- Radboud
University, Institute for Molecules and
Materials, Heyendaalseweg
135, 6525 AJ, Nijmegen, The Netherlands
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28
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Xu W, Zhu Q, Hu CT. The Structure of Glycine Dihydrate: Implications for the Crystallization of Glycine from Solution and Its Structure in Outer Space. Angew Chem Int Ed Engl 2017; 56:2030-2034. [DOI: 10.1002/anie.201610977] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/25/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Wenqian Xu
- X-ray Science Division; Advanced Photon Source; Argonne National Laboratory; Argonne IL 60439 USA
| | - Qiang Zhu
- Department of Physics and Astronomy; High Pressure Science and Engineering Center; University of Nevada Las Vegas; Las Vegas NV 89154 USA
- Department of Geosciences; Stony Brook University; Stony Brook NY 11794 USA
| | - Chunhua Tony Hu
- Department of Chemistry; New York University; 100 Washington Square East New York NY 10003 USA
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29
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Xu W, Zhu Q, Hu CT. The Structure of Glycine Dihydrate: Implications for the Crystallization of Glycine from Solution and Its Structure in Outer Space. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610977] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Wenqian Xu
- X-ray Science Division; Advanced Photon Source; Argonne National Laboratory; Argonne IL 60439 USA
| | - Qiang Zhu
- Department of Physics and Astronomy; High Pressure Science and Engineering Center; University of Nevada Las Vegas; Las Vegas NV 89154 USA
- Department of Geosciences; Stony Brook University; Stony Brook NY 11794 USA
| | - Chunhua Tony Hu
- Department of Chemistry; New York University; 100 Washington Square East New York NY 10003 USA
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30
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Ramalhete SM, Foster JS, Green HR, Nartowski KP, Heinrich M, Martin PC, Khimyak YZ, Lloyd GO. Halogen effects on the solid-state packing of phenylalanine derivatives and the resultant gelation properties. Faraday Discuss 2017; 203:423-439. [DOI: 10.1039/c7fd00108h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Phenylalanine is an important amino acid both biologically, essential to human health, and industrially, as a building block of artificial sweeteners. Our interest in this particular amino acid and its derivatives lies with its ability to form gels in a number of solvents. We present here the studies of the influence of halogen addition to the aromatic ring on the gelation properties and we analyse the crystal structures of a number of these materials to elucidate the trends in their behaviour based on the halogen addition to the aromatic group and the interactions that result.
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Affiliation(s)
| | - Jamie S. Foster
- Institute of Chemical Sciences
- School of Engineering and Physical Sciences
- Heriot-Watt University
- Edinburgh
- UK
| | - Hayley R. Green
- Institute of Chemical Sciences
- School of Engineering and Physical Sciences
- Heriot-Watt University
- Edinburgh
- UK
| | - Karol P. Nartowski
- School of Pharmacy
- University of East Anglia
- Norwich
- UK
- Department of Drug Form Technology
| | - Margaux Heinrich
- Institute of Chemical Sciences
- School of Engineering and Physical Sciences
- Heriot-Watt University
- Edinburgh
- UK
| | | | | | - Gareth O. Lloyd
- Institute of Chemical Sciences
- School of Engineering and Physical Sciences
- Heriot-Watt University
- Edinburgh
- UK
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Görbitz CH, Karen P, Dušek M, Petříček V. An exceptional series of phase transitions in hydrophobic amino acids with linear side chains. IUCRJ 2016; 3:341-353. [PMID: 28461895 PMCID: PMC5391856 DOI: 10.1107/s2052252516010472] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 06/28/2016] [Indexed: 05/06/2023]
Abstract
The solid-state phase transitions and intermediate structures of S-2-amino-butanoic acid (l-2-aminobutyric acid), S-2-aminopentanoic acid (l-norvaline), S-2-aminohexanoic acid (l-norleucine) and l-methionine between 100 and 470 K, identified by differential scanning calorimetry, have been characterized in a comprehensive single-crystal X-ray diffraction investigation. Unlike other enantiomeric amino acids investigated until now, this group featuring linear side chains displays up to five distinct phases. The multiple transitions between them involve a number of different processes: alteration of the hydrogen-bond pattern, to our knowledge the first example of this observed for an amino acid, sliding of molecular bilayers, seen previously only for racemates and quasiracemates, concerted side-chain rearrangements and abrupt as well as gradual modifications of the side-chain disorder. Ordering of l-norleucine upon cooling even proceeds via an incommensurately modulated structure. l-Methionine has previously been described as being fully ordered at room temperature. An accurate refinement now reveals extensive disorder for both molecules in the asymmetric unit, while two previously unknown phases occur above room temperature.
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Affiliation(s)
| | - Pavel Karen
- Department of Chemistry, University of Oslo, N-0315 Oslo, Norway
| | - Michal Dušek
- Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, 182 21 Praha 8, Czech Republic
| | - Václav Petříček
- Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, 182 21 Praha 8, Czech Republic
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Singh V, Snigdha K, Singh C, Sinha N, Thakur AK. Understanding the self-assembly of Fmoc-phenylalanine to hydrogel formation. SOFT MATTER 2015; 11:5353-5364. [PMID: 26059479 DOI: 10.1039/c5sm00843c] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Hydrogels of low molecular weight molecules are important in biomedical applications. Multiple factors are responsible for hydrogel formation, but their role in governing self-assembly to hydrogel formation is poorly understood. Herein, we report the hydrogel formation of fluorenylmethyloxycarbonyl phenylalanine (FmocF) molecule. We used physical and thermal stimuli for solubilizing FmocF above the critical concentration to induce gel formation. The key role of Fmoc, Fmoc and phenylalanine covalent linkage, flexibility of phe side chain, pH, and buffer ions in self-assembly of FmocF to gel formation is described. We found that the collective action of different non-covalent interactions play a role in making FmocF hydrogel. Using powder diffraction and infrared spectroscopy, we also report a new polymorphic form of FmocF after transitioning to hydrogel. In addition, we are proposing a model for drug release from FmocF hydrogel.
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Affiliation(s)
- Virender Singh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India.
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Görbitz CH, Karen P. Twin displacive phase transitions in amino acid quasiracemates. J Phys Chem B 2015; 119:4975-84. [PMID: 25794326 DOI: 10.1021/acs.jpcb.5b01483] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three quasiracemates, L-norleucine:D-methionine, L-norvaline:D-norleucine, and L-norvaline:D-methionine, were crystallized to see how they differ from regular racemates in terms of crystal structure (studied by single-crystal X-ray diffraction) and of thermally induced phase transitions (studied by differential scanning calorimetry). Two types of transitions are detected between 100 and 450 K and structurally characterized: (1) displacive transitions of the molecular bilayers that form the crystal and (2) continuous or discontinuous disordering transitions in the amino acid side chains. Uniquely for the quasiracemates, the displacive transition proceeds in two close steps as only one surface of each molecular bilayer slides at first, upon forming an intermediate phase, while the other surface follows at a slightly higher temperature. Altogether, 18 new single-crystal structure-refinement data sets are reported for these three quasiracemates.
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Affiliation(s)
| | - Pavel Karen
- Department of Chemistry, University of Oslo, N-0315 Oslo, Norway
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Williams PA, Hughes CE, Harris KDM. L-Lysine: Exploiting Powder X-ray Diffraction to Complete the Set of Crystal Structures of the 20 Directly Encoded Proteinogenic Amino Acids. Angew Chem Int Ed Engl 2015; 54:3973-7. [DOI: 10.1002/anie.201411520] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Indexed: 11/07/2022]
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35
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Williams PA, Hughes CE, Harris KDM. L-Lysine: Exploiting Powder X-ray Diffraction to Complete the Set of Crystal Structures of the 20 Directly Encoded Proteinogenic Amino Acids. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411520] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Hughes CE, Williams PA, Keast VL, Charalampopoulos VG, Edwards-Gau GR, Harris KDM. New in situ solid-state NMR techniques for probing the evolution of crystallization processes: pre-nucleation, nucleation and growth. Faraday Discuss 2015; 179:115-40. [DOI: 10.1039/c4fd00215f] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The application of in situ techniques for investigating crystallization processes promises to yield significant new insights into fundamental aspects of crystallization science. With this motivation, we recently developed a new in situ solid-state NMR technique that exploits the ability of NMR to selectively detect the solid phase in heterogeneous solid–liquid systems (of the type that exist during crystallization from solution), with the liquid phase “invisible” to the measurement. As a consequence, the technique allows the first solid particles produced during crystallization to be observed and identified, and allows the evolution of different solid phases (e.g., polymorphs) present during the crystallization process to be monitored as a function of time. This in situ solid-state NMR strategy has been demonstrated to be a powerful approach for establishing the sequence of solid phases produced during crystallization and for the discovery of new polymorphs. The most recent advance of the in situ NMR methodology has been the development of a strategy (named “CLASSIC NMR”) that allows both solid-state NMR and liquid-state NMR spectra to be measured (essentially simultaneously) during the crystallization process, yielding information on the complementary changes that occur in both the solid and liquid phases as a function of time. In this article, we present new results that highlight the application of our in situ NMR techniques to successfully unravel different aspects of crystallization processes, focusing on: (i) the application of a CLASSIC NMR approach to monitor competitive inclusion processes in solid urea inclusion compounds, (ii) exploiting liquid-state NMR to gain insights into co-crystal formation between benzoic acid and pentafluorobenzoic acid, and (iii) applications of in situ solid-state NMR for the discovery of new solid forms of trimethylphosphine oxide and l-phenylalanine. Finally, the article discusses a number of important fundamental issues relating to practical aspects, the interpretation of results and the future scope of these techniques, including: (i) an assessment of the smallest size of solid particle that can be detected in in situ solid-state NMR studies of crystallization, (ii) an appraisal of whether the rapid sample spinning required by the NMR measurement technique may actually influence or perturb the crystallization behaviour, and (iii) a discussion of factors that influence the sensitivity and time-resolution of in situ solid-state NMR experiments.
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