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Gupta SK, Gupta AK. Electronic, Thermal, and Vibrational Properties of SiO2/SCN System: A Combined Density Functional Theory and Experimental Study. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022. [DOI: 10.1134/s0036024422030219] [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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2
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Fu W, Xia GJ, Zhang Y, Hu J, Wang YG, Li J, Li X, Li B. Using general computational chemistry strategy to unravel the reactivity of emerging pollutants: An example of sulfonamide chlorination. WATER RESEARCH 2021; 202:117391. [PMID: 34233248 DOI: 10.1016/j.watres.2021.117391] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Increasing number of emerging pollutants in environments requires an effective approach which can facilitate the prediction of reactivity and provide insights into the reaction mechanisms. Computational chemistry is exactly the tool to fulfill this demand with its good performance in theoretical investigation of chemical reactions at molecular level. In this study, chlorination of sulfonamide antibiotics is used as an illustration to present a systematic strategy demonstrating how computational chemistry can be applied to investigate the reaction behavior of emerging pollutants. Sulfonamides is a class of micropollutants that contain the common structure of 4-aminobenzenesulfonmaide while differ in their heterocycles. Based on the calculated conceptual DFT indices, the reactive sites of sulfonamide are successfully predicted, which locate on their common structure of 4-aminobenzenesulfonmaide. Therefore, all sulfonamides follow the similar reaction pathway. Product identification by LTQ-Orbitrap MS further verifies the in silico prediction. Three critical pathways are discovered, i.e., S-N bond cleavage, Cl-substitution onto aniline-N, and the following rearrangement to lose -SO2- group, among which Cl-substitution is the key step due to its lowest free energy barrier. Heterocycles impact the reaction rate by affecting the electronic density of aniline group. In general, the more electron-donating the heterocycle is, the more readily sulfonamides to be chlorinated.
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Affiliation(s)
- Wenjie Fu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Department of Chemistry, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Guang-Jie Xia
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yixiang Zhang
- Theoretical Chemistry Center, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jiahui Hu
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Yang-Gang Wang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jun Li
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Theoretical Chemistry Center, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xiaoyan Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Environmental Science and New Energy Laboratory, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen 518055, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
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3
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Lubkowski J, Vanegas J, Chan WK, Lorenzi PL, Weinstein JN, Sukharev S, Fushman D, Rempe S, Anishkin A, Wlodawer A. Mechanism of Catalysis by l-Asparaginase. Biochemistry 2020; 59:1927-1945. [PMID: 32364696 DOI: 10.1021/acs.biochem.0c00116] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Two bacterial type II l-asparaginases, from Escherichia coli and Dickeya chrysanthemi, have played a critical role for more than 40 years as therapeutic agents against juvenile leukemias and lymphomas. Despite a long history of successful pharmacological applications and the apparent simplicity of the catalytic reaction, controversies still exist regarding major steps of the mechanism. In this report, we provide a detailed description of the reaction catalyzed by E. coli type II l-asparaginase (EcAII). Our model was developed on the basis of new structural and biochemical experiments combined with previously published data. The proposed mechanism is supported by quantum chemistry calculations based on density functional theory. We provide strong evidence that EcAII catalyzes the reaction according to the double-displacement (ping-pong) mechanism, with formation of a covalent intermediate. Several steps of catalysis by EcAII are unique when compared to reactions catalyzed by other known hydrolytic enzymes. Here, the reaction is initiated by a weak nucleophile, threonine, without direct assistance of a general base, although a distant general base is identified. Furthermore, tetrahedral intermediates formed during the catalytic process are stabilized by a never previously described motif. Although the scheme of the catalytic mechanism was developed only on the basis of data obtained from EcAII and its variants, this novel mechanism of enzymatic hydrolysis could potentially apply to most (and possibly all) l-asparaginases.
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Affiliation(s)
- Jacek Lubkowski
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Juan Vanegas
- Department of Physics, The University of Vermont, Burlington, Vermont 05408, United States
| | - Wai-Kin Chan
- Department of Bioinformatics and Computational Biology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, United States
| | - Philip L Lorenzi
- Department of Bioinformatics and Computational Biology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, United States
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, United States
| | - Sergei Sukharev
- Department of Biology, University of Maryland, College Park, Maryland 20742, United States
| | - David Fushman
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Susan Rempe
- Center for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Andriy Anishkin
- Department of Biology, University of Maryland, College Park, Maryland 20742, United States
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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4
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Wang X, Ye S, Hu W, Sharman E, Liu R, Liu Y, Luo Y, Jiang J. Electric Dipole Descriptor for Machine Learning Prediction of Catalyst Surface-Molecular Adsorbate Interactions. J Am Chem Soc 2020; 142:7737-7743. [PMID: 32297511 DOI: 10.1021/jacs.0c01825] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The challenge of evaluating catalyst surface-molecular adsorbate interactions holds the key for rational design of catalysts. Finding an experimentally measurable and theoretically computable descriptor for evaluating surface-adsorbate interactions is a significant step toward achieving this goal. Here we show that the electric dipole moment can serve as a convenient yet accurate descriptor for establishing structure-property relationships for molecular adsorbates on metal catalyst surfaces. By training a machine learning neural network with a large data set of first-principles calculations, we achieve quick and accurate predictions of molecular adsorption energy and transferred charge. The training model using NO/CO@Au(111) can be extended to study additional substrates such as Au(001) or Ag(111), thus exhibiting extraordinary transferability. These findings validate the effectiveness of the electric dipole descriptor, providing an efficient modality for future catalyst design.
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Affiliation(s)
- Xijun Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China.,Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Sheng Ye
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Wei Hu
- Shandong Provincial Key Laboratory of Molecular Engineering, School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250353, People's Republic of China
| | - Edward Sharman
- Department of Neurology, University of California, Irvine, California 92697, United States
| | - Ran Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Yan Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Yi Luo
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Jun Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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5
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Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2. Sci Rep 2019; 9:20219. [PMID: 31882608 PMCID: PMC6934455 DOI: 10.1038/s41598-019-56078-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 12/04/2019] [Indexed: 12/31/2022] Open
Abstract
We have investigated covalent conjugation of VPPPVPPRRRX′ peptide (where X′ denotes Nε-chloroacetyl lysine) to N-terminal SH3 domain from adapter protein Grb2. Our experimental results confirmed that the peptide first binds to the SH3 domain noncovalently before establishing a covalent linkage through reaction of X′ with the target cysteine residue C32. We have also confirmed that this reaction involves a thiolate-anion form of C32 and follows the SN2 mechanism. For this system, we have developed a new MD-based protocol to model the formation of covalent conjugate. The simulation starts with the known coordinates of the noncovalent complex. When two reactive groups come into contact during the course of the simulation, the reaction is initiated. The reaction is modeled via gradual interpolation between the two sets of force field parameters that are representative of the noncovalent and covalent complexes. The simulation proceeds smoothly, with no appreciable perturbations to temperature, pressure or volume, and results in a high-quality MD model of the covalent complex. The validity of this model is confirmed using the experimental chemical shift data. The new MD-based approach offers a valuable tool to explore the mechanics of protein-peptide conjugation and build accurate models of covalent complexes.
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Lubkowski J, Wlodawer A. Geometric considerations support the double-displacement catalytic mechanism of l-asparaginase. Protein Sci 2019; 28:1850-1864. [PMID: 31423681 DOI: 10.1002/pro.3709] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 11/09/2022]
Abstract
Twenty crystal structures of the complexes of l-asparaginase with l-Asn, l-Asp, and succinic acid that are currently available in the Protein Data Bank, as well as 11 additional structures determined in the course of this project, were analyzed in order to establish the level of conservation of the geometric parameters describing interactions between the substrates and the active site of the enzymes. We found that such stereochemical relationships are highly conserved, regardless of the organism from which the enzyme was isolated, specific crystallization conditions, or the nature of the ligands. Analysis of the geometry of the interactions, including Bürgi-Dunitz and Flippin-Lodge angles, indicated that Thr12 (Escherichia coli asparaginase II numbering) is optimally placed to be the primary nucleophile in the most likely scenario utilizing a double-displacement mechanism, whereas catalysis through a single-displacement mechanism appears to be the least likely.
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Affiliation(s)
- Jacek Lubkowski
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland
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7
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Niyomsin S, Hirai T, Takahara A, Chirachanchai S. Incorporation of Benzoxazine Pendants in Polymer Chains: A Simple Approach to Add-Up Multi-Responsive Functions. MACROMOL CHEM PHYS 2019. [DOI: 10.1002/macp.201800526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sorapat Niyomsin
- The Petroleum and Petrochemical College; Chulalongkorn University; Bangkok 10330 Thailand
| | - Tomoyasu Hirai
- Institute for Materials Chemistry and Engineering; Kyushu University; 744 Motooka, Nishi-Ku Fukuoka 819-0395 Japan
| | - Atsushi Takahara
- Institute for Materials Chemistry and Engineering; Kyushu University; 744 Motooka, Nishi-Ku Fukuoka 819-0395 Japan
- WPI I2CNER; Kyushu University; 744 Motooka, Nishi-Ku Fukuoka 819-0395 Japan
| | - Suwabun Chirachanchai
- The Petroleum and Petrochemical College; Chulalongkorn University; Bangkok 10330 Thailand
- Center of Excellence on Petrochemical and Materials Technology; Chulalongkorn University; Bangkok 10330 Thailand
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8
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A density functional theory investigation of the fragmentation mechanism of deprotonated asparagine. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.08.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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9
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10
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Hori Y, Ida T, Mizuno M. A comparative theoretical study of the hydride transfer mechanisms during LiAlH 4 and LiBH 4 reductions. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2015.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Thukral K, Vijayan N, Haranath D, Jayaramakrishnan V, Philip J, Sreekanth P, Bhagavannaryana G. Assessment on third order non linearity and other optical analyses of L-Asparagine Monohydrate single crystal: An efficient candidate for harmonic conversions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 151:419-425. [PMID: 26148830 DOI: 10.1016/j.saa.2015.05.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 05/06/2015] [Accepted: 05/21/2015] [Indexed: 06/04/2023]
Abstract
Single crystal of l-Asparagine Monohydrate, an organic material has been successfully grown by slow evaporation solution growth technique at ambient condition. The lattice parameters and its strain of the grown crystal have been evaluated from powder X-ray diffraction and found that it belongs to orthorhombic crystal system. The polarizability has been measured by using the Clausius-Mossotti relation. The crystalline perfection of grown single crystal has been examined by high resolution X-ray diffraction and its imperfection in the diffraction plane was clearly visible by recording topographical image of the plane. From the high resolution XRD, it confirms that the crystal contained high crystalline perfection. The optical behavior was analyzed by photoluminescence and birefringence methods. In the photoluminescence, a broad peak has been observed at 475 nm which suggest that it emits blue light. The decay tendency of the material has also been observed by calculating decay constant. The optical homogeneity has been determined by the dispersion pattern of the material. The two photon absorption coefficient was further calculated by Z-scan, which gives the information about the third order non linear optical behavior of the material. The value of two-photon absorption coefficient is 4.25 × 10(-12)m/W. The thermal parameters like thermal effusivity, thermal diffusivity, specific heat and thermal conductivity was obtained by using photopyroelectric technique. The ferroelectric behavior of the grown specimen was analyzed from PE (polarization VS electric field) loop. The loop suggests that the material was a nearly equivalent to ideal capacitor.
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Affiliation(s)
- Kanika Thukral
- Academy of Scientific and Innovative Research, CSIR-National Physical Laboratory, New Delhi 110012, India; CSIR-National Physical Laboratory, Dr. K.S. Krishnan Road, New Delhi 110 012, India
| | - N Vijayan
- CSIR-National Physical Laboratory, Dr. K.S. Krishnan Road, New Delhi 110 012, India.
| | - D Haranath
- CSIR-National Physical Laboratory, Dr. K.S. Krishnan Road, New Delhi 110 012, India
| | - V Jayaramakrishnan
- Centro De Investigations En Optica Loma del Bosque 115, Colonia Lomas del Campestre, Código Postal 37150 León, Guanajuato, México
| | - J Philip
- Department of Basic Sciences, Amal Jyothi College of Engineering, Kanjirappally, Kottayam 686518, Kerala
| | - P Sreekanth
- Light and Matter Physics Group, Raman Research Institute, Bangalore 560080, India
| | - G Bhagavannaryana
- CSIR-National Physical Laboratory, Dr. K.S. Krishnan Road, New Delhi 110 012, India
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12
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Gerlei KZ, Élő L, Fiser B, Owen MC, Jákli I, Knak Jensen SJ, Csizmadia IG, Perczel A, Viskolcz B. Impairment of a model peptide by oxidative stress: Thermodynamic stabilities of asparagine diamide Cα-radical foldamers. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2013.12.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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13
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Copper(II) complexes with cyanoguanidine and o-phenanthroline: Theoretical studies, in vitro antimicrobial activity and alkaline phosphatase inhibitory effect. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2013.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Wu L, Lee G, Chen C, Wang C. Charge Density Distribution and Bond Characterization of 2,2′‐Dipyridylamine (Hdpa): A Combined Study of Experiment and Theory. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201200651] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lai‐Chin Wu
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Gene‐Hsiang Lee
- Instrumental Center, National Taiwan University, Taipei, Taiwan
| | - Chien‐Kai Chen
- Department of Chemistry, Soochow University, Taipei, Taiwan
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15
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Selvaraj ARK, Murugan NA, Ågren H. Solvent Polarity-Induced Conformational Unlocking of Asparagine. J Phys Chem A 2012; 116:11702-8. [DOI: 10.1021/jp307715n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ananda Rama Krishnan Selvaraj
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - N. Arul Murugan
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Hans Ågren
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
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16
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Gilman-Politi R, Harries D. Unraveling the Molecular Mechanism of Enthalpy Driven Peptide Folding by Polyol Osmolytes. J Chem Theory Comput 2011; 7:3816-28. [PMID: 26598272 DOI: 10.1021/ct200455n] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Many polyols and carbohydrates serve in different organisms as protective osmolytes that help to stabilize proteins in their native, functional state, even under a variety of environmental stresses. However, despite their important role, much of the molecular mechanism by which these osmolytes exert their action remains elusive. We have recently shown experimentally that, although polyols and carbohydrates are excluded from protein and peptide interfaces, as also expected for the known entropic "crowding" mechanism, the osmolyte folding action can in fact primarily be enthalpic in nature. To follow this newly resolved enthalpically driven stabilization mechanism, we report here on molecular dynamics simulations of a model peptide that can fold in solution into a β-hairpin. In agreement with experiments, our simulations indicate that sorbitol, a representative polyol, promotes peptide folding by preferential exclusion. At the molecular level, simulations further show that peptide stabilization can be explained by sorbitol's perturbation of the solution hydrogen bonding network in the peptide first hydration shells. Consequently, fewer hydrogen bonds between peptide and solvating water are lost upon folding, and additional internal peptide hydrogen bonds are formed in the presence of sorbitol, while internal peptide and water-associated hydrogen bonds are strengthened, resulting in stabilization of the peptide folded state. We further find that changes in water orientational entropy are reduced upon folding in sorbitol solution, reflecting the struggle of water molecules to maintain optimal hydrogen bonding in the presence of competing polyols. By providing first molecular underpinnings for enthalpically driven osmolyte stabilization of peptides and proteins, this mechanism should allow a better understanding of the variety of physical forces by which protective osmolytes act in biologically realistic solutions.
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Affiliation(s)
- Regina Gilman-Politi
- Institute of Chemistry and The Fritz Haber Center, The Hebrew University , Jerusalem 91904, Israel
| | - Daniel Harries
- Institute of Chemistry and The Fritz Haber Center, The Hebrew University , Jerusalem 91904, Israel
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17
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Prikhodchenko PV, Medvedev AG, Tripol'skaya TA, Churakov AV, Wolanov Y, Howard JAK, Lev O. Crystal structures of natural amino acid perhydrates. CrystEngComm 2011. [DOI: 10.1039/c0ce00481b] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Engels B, Schmidt TC, Gatti C, Schirmeister T, Fink RF. Challenging Problems in Charge Density Determination: Polar Bonds and Influence of the Environment. ELECTRON DENSITY AND CHEMICAL BONDING II 2011. [DOI: 10.1007/430_2010_36] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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19
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Mebs S, Messerschmidt M, Luger P. Experimental charge density of an L-phenylalanine formic acid complex with a short hydrogen bond determined at 25 K. ACTA ACUST UNITED AC 2009. [DOI: 10.1524/zkri.2006.221.9.656] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
The experimental charge density and related atomic and bond topological properties of an L-phenylalanine formic acid complex were derived from a high resolution X-ray data set (sin θ/λ = 1.18 Å–1/d = 0.42 Å) measured at 25 K. The complex consists of a zwitterionic and a cationic phenylalanine molecule with formate as counterion. Special focus was directed on the density distribution in the region of a strong O—H ·· O hydrogen bond (O ·· O = 2.491(1) Å) which is formed between the two phenylalanine units. The obtained results are compared with the 15 previously derived experimental amino acid charge density data, with various theoretical calculations at experimental geometries and with the complete set of topological descriptors based on ab initio calculations of the neutral forms of all 20 amino acids published recently in the literature. A comparison of all available data in this biologically important class of compounds gives an impression about the significance of the quantitative results from experimental and theoretical charge density determinations.
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20
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Quantitative estimates of transferability of the QTAIM descriptors. Case study of the substituted hydropyrimidines. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.03.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Yearley EJ, Zhurova EA, Zhurov VV, Alan Pinkerton A. Experimental electron density studies of non-steroidal synthetic estrogens: Diethylstilbestrol and dienestrol. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2008.03.053] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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22
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Yearley EJ, Zhurova EA, Zhurov VV, Pinkerton AA. Binding of Genistein to the Estrogen Receptor Based on an Experimental Electron Density Study. J Am Chem Soc 2007; 129:15013-21. [DOI: 10.1021/ja075211j] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eric J. Yearley
- Contribution from the Department of Chemistry, University of Toledo, Toledo, Ohio 43606
| | - Elizabeth A. Zhurova
- Contribution from the Department of Chemistry, University of Toledo, Toledo, Ohio 43606
| | - Vladimir V. Zhurov
- Contribution from the Department of Chemistry, University of Toledo, Toledo, Ohio 43606
| | - A. Alan Pinkerton
- Contribution from the Department of Chemistry, University of Toledo, Toledo, Ohio 43606
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23
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Spackman MA, Munshi P, Dittrich B. Dipole Moment Enhancement in Molecular Crystals from X-ray Diffraction Data. Chemphyschem 2007; 8:2051-63. [PMID: 17676648 DOI: 10.1002/cphc.200700339] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Although reliable determination of the molecular dipole moment from experimental charge density analyses on molecular crystals is a challenging undertaking, these values are becoming increasingly common experimental results. We collate all known experimental determinations and use this database to identify broad trends in the dipole moment enhancements implied by these measurements as well as outliers for which enhancements are pronounced. Compelling evidence emerges that molecular dipole moments from X-ray diffraction data can provide a wealth of information on the change in the molecular charge distribution that results from crystal formation. Most importantly, these experiments are unrivalled in their potential to provide this information in such detail and deserve to be exploited to a much greater extent. The considerable number of experimental determinations now available has enabled us to pinpoint those studies that merit further attention, either because they point unequivocally to a considerable enhancement in the crystal (of 50 % or more), or because the experimental determinations suggest enhancements of 100 % or more--much larger than independent theoretical estimates. In both cases further detailed experimental and theoretical studies are indicated.
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Affiliation(s)
- Mark A Spackman
- School of Biomedical, Biomolecular & Chemical Sciences, University of Western Australia, Crawley WA 6009, Australia.
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24
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Mukkamala D, Zhang Y, Oldfield E. A Solid State 13C NMR, Crystallographic, and Quantum Chemical Investigation of Phenylalanine and Tyrosine Residues in Dipeptides and Proteins. J Am Chem Soc 2007; 129:7385-92. [PMID: 17506558 DOI: 10.1021/ja071227y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the results of a solid-state NMR and quantum chemical investigation of the 13C gamma NMR chemical shifts in phenylalanine and tyrosine in dipeptides and proteins. Accurate computation of the experimental shifts is shown to require a good description of local electrostatic field effects, and we find the best results (R2=0.94, rmsd=1.6 ppm, range = 17.1 ppm, N=14) by using a self-consistent reaction field continuum model. There are no obvious correlations with phi, psi, chi 1, or chi2 torsion angles, unlike the results seen with other amino acids. There is, however, a linear relation between computed C gamma atomic charges and shifts for the 14 peptide as well as 18 protein residues investigated. This result is similar to the correlation reported in the 1960s between pi-electron density and 13C shifts for classical 4n + 2 (n=0, 1, 2) pi-electron aromatic species, such as cyclopentadienide and the tropylium cation, and in fact, we found that the shielding/atomic charge correlation seen in the peptides and proteins is virtually identical to that seen with a broad range of aromatic carbocations/carbanions. These results suggest the dominance of an electrostatic field polarization model in which increasing pi electron density results in an increase in C gamma atomic charge and increased shielding (of sigma 11 and sigma 22, perpendicular to the pi orbital) in Phe and Tyr, as well as in the other aromatic species. These results are of general interest since they demonstrate the importance of electrostatic field effects on Phe and Tyr C gamma chemical shifts in peptides and proteins and imply that inclusion of these effects will be necessary in order to interpret the shifts of other aromatic species, such as drug molecules, bound to proteins.
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Affiliation(s)
- Dushyant Mukkamala
- Center for Biophysics and Computational Biology, 607 South Mathews Avenue, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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Checińska L, Mebs S, Hübschle CB, Förster D, Morgenroth W, Luger P. Reproducibility and transferability of topological data: experimental charge density study of two modifications ofl-alanyl-l-tyrosyl-l-alanine. Org Biomol Chem 2006; 4:3242-51. [PMID: 17036112 DOI: 10.1039/b607744g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two crystalline modifications of the tripeptide L-Ala-L-Tyr-L-Ala, which have different solvent molecules in the crystal structure (water and ethanol for modifications 1 and 2), were the subject of experimental charge density studies based on high resolution X-ray data collected at ultra-low temperatures of 9 K (1) and 20 K (2), respectively. The molecular structures and the intermolecular interactions were found to be rather similar in the two crystal lattices, so that this study allowed the reproducibility of the charge density of a given molecule in different (but widely comparable) crystalline environments to be examined. With respect to bond topological and atomic properties, the agreement between the two modifications of the title tripeptide was in the same range as found from the comparison with the previously reported results of tri-L-alanine. It follows that the reproducibility and transferability of quantitative topological data are comparable and that within the accuracy of experimental charge density work the replacement of the central amino acid residue L-Ala by L-Tyr has no significant influence, neither on bond nor on the atomic properties of the oligopeptide main chain. Intermolecular interactions in the form of hydrogen bonds were characterized quantitatively and qualitatively by topological criteria and by mapping the charge density distribution on the Hirshfeld surface.
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Affiliation(s)
- Lilianna Checińska
- Department of Crystallography and Crystal Chemistry, University of Łódź, Pomorska 149/153, 90 236, Łódź, Poland
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Zhang Y, Oldfield E. 31P NMR Chemical Shifts in Hypervalent Oxyphosphoranes and Polymeric Orthophosphates. J Phys Chem B 2005; 110:579-86. [PMID: 16471570 DOI: 10.1021/jp054022p] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the first quantum chemical investigation of the solid- and solution-state 31P NMR chemical shifts in models for phosphoryl transfer enzyme reaction intermediates and in polymeric inorganic phosphates. The 31P NMR chemical shifts of five- and six-coordinate oxyphosphoranes containing a variety of substitutions at phosphorus, as well as four-coordinate polymeric orthophosphates and four-coordinate phosphonates, are predicted with a slope of 1.00 and an R2= 0.993 (N = 34), corresponding to a 3.8 ppm (or 2.1%) error over the entire 178.3 ppm experimental chemical shift range, using Hartree-Fock methods. For the oxyphosphoranes, we used either experimental crystallographic structures or, when these were not available, fully geometry optimized molecular structures. For the four-coordinate phosphonates we used X-ray structures together with charge field perturbation, to represent lattice interactions. For the three-dimensional orthophosphates (BPO4, AlPO4, GaPO4 we again used X-ray structures, but for these inorganic systems we employed a self-consistent charge field perturbation approach on large clusters, to deduce peripheral atom charges. For pentaoxyphosphoranes, the solvent effect on 31P NMR chemical shieldings was found to be very small (<0.5 ppm). The 31P NMR chemical shielding tensors in the pentaoxyphosphoranes were in most cases found to be close to axially symmetric and were dominated by changes in the shielding tensor components in the equatorial plane (sigma22 and sigma33). The isotropic shifts were highly correlated (R2= 0.923) with phosphorus natural bonding orbital charges, with the larger charges being associated with shorter axial P-O bond lengths and, hence, more shielding. Overall, these results should facilitate the use of 31P NMR techniques in investigating the structures of more complex systems, such as phosphoryl transfer enzymes, as well as in investigating other, complex oxide structures.
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Affiliation(s)
- Yong Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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Cheng F, Sun H, Zhang Y, Mukkamala D, Oldfield E. A Solid State 13C NMR, Crystallographic, and Quantum Chemical Investigation of Chemical Shifts and Hydrogen Bonding in Histidine Dipeptides. J Am Chem Soc 2005; 127:12544-54. [PMID: 16144402 DOI: 10.1021/ja051528c] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the first solid-state NMR, crystallographic, and quantum chemical investigation of the origins of the 13C NMR chemical shifts of the imidazole group in histidine-containing dipeptides. The chemical shift ranges for Cgamma and Cdelta2 seen in eight crystalline dipeptides were very large (12.7-13.8 ppm); the shifts were highly correlated (R2= 0.90) and were dominated by ring tautomer effects and intermolecular interactions. A similar correlation was found in proteins, but only for buried residues. The imidazole 13C NMR chemical shifts were predicted with an overall rms error of 1.6-1.9 ppm over a 26 ppm range, by using quantum chemical methods. Incorporation of hydrogen bond partner molecules was found to be essential in order to reproduce the chemical shifts seen experimentally. Using AIM (atoms in molecules) theory we found that essentially all interactions were of a closed shell nature and the hydrogen bond critical point properties were highly correlated with the N...H...O (average R2= 0.93) and Nepsilon2...H...N (average R2= 0.98) hydrogen bond lengths. For Cepsilon1, the 13C chemical shifts were also highly correlated with each of these properties (at the Nepsilon2 site), indicating the dominance of intermolecular interactions for Cepsilon1. These results open up the way to analyzing 13C NMR chemical shifts, tautomer states (from Cdelta2, Cepsilon1 shifts), and hydrogen bond properties (from Cepsilon1 shifts) of histidine residue in proteins and should be applicable to imidazole-containing drug molecules bound to proteins, as well.
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Affiliation(s)
- Feng Cheng
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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Oldfield E. Quantum chemical studies of protein structure. Philos Trans R Soc Lond B Biol Sci 2005; 360:1347-61. [PMID: 16147526 PMCID: PMC1569496 DOI: 10.1098/rstb.2003.1421] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2003] [Accepted: 09/24/2003] [Indexed: 11/12/2022] Open
Abstract
Quantum chemical methods now permit the prediction of many spectroscopic observables in proteins and related model systems, in addition to electrostatic properties, which are found to be in excellent accord with those determined from experiment. I discuss the developments over the past decade in these areas, including predictions of nuclear magnetic resonance chemical shifts, chemical shielding tensors, scalar couplings and hyperfine (contact) shifts, the isomer shifts and quadrupole splittings in Mössbauer spectroscopy, molecular energies and conformations, as well as a range of electrostatic properties, such as charge densities, the curvatures, Laplacians and Hessians of the charge density, electrostatic potentials, electric field gradients and electrostatic field effects. The availability of structure/spectroscopic correlations from quantum chemistry provides a basis for using numerous spectroscopic observables in determining aspects of protein structure, in determining electrostatic properties which are not readily accessible from experiment, as well as giving additional confidence in the use of these techniques to investigate questions about chemical bonding and chemical reactions.
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Affiliation(s)
- Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, 61801, USA.
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Henn J, Ilge D, Leusser D, Stalke D, Engels B. On the Accuracy of Theoretically and Experimentally Determined Electron Densities of Polar Bonds. J Phys Chem A 2004. [DOI: 10.1021/jp047840a] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Julian Henn
- Institut für Organische Chemie and Institut für Anorganische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Dagmar Ilge
- Institut für Organische Chemie and Institut für Anorganische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Dirk Leusser
- Institut für Organische Chemie and Institut für Anorganische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Dietmar Stalke
- Institut für Organische Chemie and Institut für Anorganische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Bernd Engels
- Institut für Organische Chemie and Institut für Anorganische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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Strohmeier M, Stueber D, Grant DM. Accurate 13C and 15N Chemical Shift and 14N Quadrupolar Coupling Constant Calculations in Amino Acid Crystals: Zwitterionic, Hydrogen-Bonded Systems. J Phys Chem A 2003; 107:7629-42. [DOI: 10.1021/jp0350114] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mark Strohmeier
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850
| | - Dirk Stueber
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850
| | - David M. Grant
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850
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Rovnyak D, Filip C, Itin B, Stern AS, Wagner G, Griffin RG, Hoch JC. Multiple-quantum magic-angle spinning spectroscopy using nonlinear sampling. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2003; 161:43-55. [PMID: 12660110 DOI: 10.1016/s1090-7807(02)00189-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
NMR spectroscopy is a relatively insensitive technique and many biomolecular applications operate near the limits of sensitivity and resolution. A particularly challenging example is detection of the quadrupolar nucleus 17O, due to its low natural abundance, large quadrupole couplings, and low gyromagnetic ratio. Yet the chemical shift of 17O spans almost 1000 ppm in organic molecules and it serves as a potentially unique reporter of hydrogen bonding in peptides, nucleic acids, and water, and as a valuable complement to 13C and 15N NMR. Recent developments including the multiple-quantum magic-angle spinning (MQMAS) experiment have enabled the detection of 17O in biological solids, but very long data acquisitions are required to achieve sufficient sensitivity and resolution. Here, we perform nonlinear sampling in the indirect dimension of MQMAS experiments to substantially reduce the total acquisition time and improve sensitivity and resolution. Nonlinear sampling prevents the use of the discrete Fourier transform; instead, we employ maximum entropy (MaxEnt) reconstruction. Nonlinearly sampled MQMAS spectra are shown to provide high resolution and sensitivity in several systems, including lithium sulfate monohydrate (LiSO(4)-H(2)17O) and L-asparagine monohydrate (H(2)17O). The combination of nonlinear sampling and MaxEnt reconstruction promises to make the application of 17O MQMAS practical in a wider range of biological systems.
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Affiliation(s)
- David Rovnyak
- MIT/Harvard Center for Magnetic Resonance, Massachusetts Institute of Technology, 150 Albany Street, Cambridge, MA 02139, USA
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Abstract
This chapter discusses recent progress in the investigation and use of (13)C, (15)N, and (19)F nuclear magnetic resonance (NMR) chemical shifts and chemical shift tensors in proteins and model systems primarily using quantum chemical (ab initio Hartree-Fock and density functional theory) techniques. Correlations between spectra and structure are made and the techniques applied to other spectroscopic and electrostatic properties as well, including hydrogen bonding, ligand binding to heme proteins, J-couplings, electric field gradients, and atoms-in-molecules theory, together with a brief review of the use of NMR chemical shifts in drug design.
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Affiliation(s)
- Eric Oldfield
- Department of Chemistry and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
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Klein RA. Ab initio conformational studies on diols and binary diol-water systems using DFT methods. Intramolecular hydrogen bonding and 1:1 complex formation with water. J Comput Chem 2002; 23:585-99. [PMID: 11939593 DOI: 10.1002/jcc.10053] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Studies on the conformational equilibrium for the following diols, ethane-1,2-diol (12EG, CAS 107-21-1), 2R-D-(-)-propane-1,2-diol (12PG, CAS 4254-14-2), (2S,3S)-L-(+)-butane-2,3-diol (L23BD, CAS 19132-06-0), and (2S,3R)-meso-butane-2,3-diol (m23BD, CAS 5341-95-7), are described using Gaussian ab initio calculations involving density functional theory (DFT) methods. We also report in this article results on the stability and conformation for the 1:1 water-diol complex formed by ethane-1,2-diol, propane-1,2-diol, and L- and meso-butane-2,3-diol. The relative stability of the intramolecular (internal) hydrogen bond in a range of diols (n = 2 to 6), based on ab initio geometry optimization and determination of the -O...H- distance, dOH, and -O-H...O- angle, theta, increases through the sequence 1,2 approximately equals 2,3 < 1,3 < 1,4 approximately equals 1,5 approximately equals 1,6, as judged from the bond linearity and -O...H- separation. Quantum mechanical and topological analysis of possible intramolecular hydrogen bonding in this complete series of diols provides convincing evidence for this in diols in which the hydroxyl groups are separated by three or more carbon atoms, that is, in (n, n+m) diols for m > or = 2, but not for ethane-1,2-diol or other vicinal diols, which do not satisfy Popelier's topological and electron density criteria based on the AIM theory of Bader. Based on these criteria it is unlikely that vicinal diols are in fact capable of forming an intramolecular hydrogen bond, in spite of geometric and spectroscopic data in the literature suggesting otherwise.
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Affiliation(s)
- Roger A Klein
- Institute for Physiological Chemistry, University of Bonn, Federal Republic of Germany.
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Abstract
The hydrogen bond is the most important of all directional intermolecular interactions. It is operative in determining molecular conformation, molecular aggregation, and the function of a vast number of chemical systems ranging from inorganic to biological. Research into hydrogen bonds experienced a stagnant period in the 1980s, but re-opened around 1990, and has been in rapid development since then. In terms of modern concepts, the hydrogen bond is understood as a very broad phenomenon, and it is accepted that there are open borders to other effects. There are dozens of different types of X-H.A hydrogen bonds that occur commonly in the condensed phases, and in addition there are innumerable less common ones. Dissociation energies span more than two orders of magnitude (about 0.2-40 kcal mol(-1)). Within this range, the nature of the interaction is not constant, but its electrostatic, covalent, and dispersion contributions vary in their relative weights. The hydrogen bond has broad transition regions that merge continuously with the covalent bond, the van der Waals interaction, the ionic interaction, and also the cation-pi interaction. All hydrogen bonds can be considered as incipient proton transfer reactions, and for strong hydrogen bonds, this reaction can be in a very advanced state. In this review, a coherent survey is given on all these matters.
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Affiliation(s)
- Thomas Steiner
- Institut für Chemie-Kristallographie, Freie Universität Berlin, Takustrasse 6, Germany.
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Affiliation(s)
- T S Koritsanszky
- Department of Chemistry, University of the Witwatersrand, WITS 2050, Johannesburg, South Africa
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Gogonea V, Suárez D, van der Vaart A, Merz KM. New developments in applying quantum mechanics to proteins. Curr Opin Struct Biol 2001; 11:217-23. [PMID: 11297931 DOI: 10.1016/s0959-440x(00)00193-7] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Algorithmic improvements of quantum mechanical methodologies have increased our ability to study the electronic structure of fragments of a biomolecule (e.g. an enzyme active site) or entire biomolecules. Three main strategies have emerged as ways in which quantum mechanics can be applied to biomolecules. The supermolecule approach continues to be utilized, but it is slowly being replaced by the so-called coupled quantum mechanical/molecular mechanical methodologies. An exciting new direction is the continued development and application of linear-scaling quantum mechanical approaches to biomolecular systems.
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Affiliation(s)
- V Gogonea
- Department of Chemistry, 152 Davey Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
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Gálvez O, Gómez P, Pacios L. Approximate kinetic energy density for intermolecular regions in hydrogen bond dimers. Chem Phys Lett 2001. [DOI: 10.1016/s0009-2614(01)00231-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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