1
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Chen D, Gao J, Zheng D, Guo Z, Zhao Z. Gas Phase Conformation of Trisaccharides and Core Pentasaccharide: A Three-Step Tree-Based Sampling and Quantum Mechanical Computational Approach. Molecules 2023; 28:8093. [PMID: 38138582 PMCID: PMC10745714 DOI: 10.3390/molecules28248093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/23/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
As an important component of N-linked glycoproteins, the core pentasaccharide is highly crucial to the potential application prospect of glycoprotein. However, the gas phase conformation study is a challenging one due to the size and complexity of the molecule, together with the necessity to rely on quantum chemistry modeling for relevant energetics and structures. In this paper, the structures of the trisaccharides and core pentasaccharides in N-linked glycans in the gas phase were constructed by a three-step tree-based (TSTB) sampling. Since single point energies of all the conformers are calculated at the temperature of zero, it is necessary to evaluate the stability at a high temperature. We calculate the Gibbs free energies using the standard thermochemistry model (T = 298.15 K). For trimannose, the energetic ordering at 298.15 K can be strongly changed compared to 0 K. Moreover, two structures of trimannose with high energies at 0 K are considered to provide a much better match of IR vibration signatures with the low Gibbs free energies. On this basis, the core pentasaccharide was constructed in three ways. The building configurations of core pentasaccharide were optimized to obtain reasonable low-energy stable conformers. Fortunately, the lowest-energy structure of core pentasaccharide is eventually the minimum at 0 K and 298.15 K. Furthermore, spectrum analysis of core pentasaccharide was carried out. Although poorly resolved, its contour from the experiment was in qualitative correspondence with the computed IR spectrum associated with its minimum free energy structure. A large number of strongly and weakly hydrogen-bonded hydroxyl and acetylamino groups contribute to a highly congested set of overlapping bands. Compared with traditional conformation generators, the TSTB sampling is employed to efficiently and comprehensively obtain preferred conformers of larger saccharides with lower energy.
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Affiliation(s)
- Dong Chen
- School of Physics and Electronics, Henan University, Kaifeng 475004, China; (J.G.); (D.Z.); (Z.G.)
| | - Jianming Gao
- School of Physics and Electronics, Henan University, Kaifeng 475004, China; (J.G.); (D.Z.); (Z.G.)
| | - Danting Zheng
- School of Physics and Electronics, Henan University, Kaifeng 475004, China; (J.G.); (D.Z.); (Z.G.)
| | - Zhiheng Guo
- School of Physics and Electronics, Henan University, Kaifeng 475004, China; (J.G.); (D.Z.); (Z.G.)
| | - Zuncheng Zhao
- School of Physics and Electronics, Henan University, Kaifeng 475004, China; (J.G.); (D.Z.); (Z.G.)
- Henan Province Engineering Research Center of Metal Matrix in situ Composites Based on Aluminum, Magnesium or Copper, Henan University, Kaifeng 475004, China
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2
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Synthesis of Tetrapeptides Containing Dehydroalanine, Dehydrophenylalanine and Oxazole as Building Blocks for Construction of Foldamers and Bioinspired Catalysts. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092611. [PMID: 35565962 PMCID: PMC9102237 DOI: 10.3390/molecules27092611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 11/17/2022]
Abstract
The incorporation of dehydroamino acid or fragments of oxazole into peptide chain is accompanied by a distorted three-dimensional structure and additionally enables the introduction of non-typical side-chain substituents. Thus, such compounds could be building blocks for obtaining novel foldamers and/or artificial enzymes (artzymes). In this paper, effective synthetic procedures leading to such building blocks-tetrapeptides containing glycyldehydroalanine, glycyldehydrophenylalanine, and glycyloxazole subunits-are described. Peptides containing serine were used as substrates for their conversion into peptides containing dehydroalanine and aminomethyloxazole-4-carboxylic acid while considering possible requirements for the introduction of these fragments into long-chain peptides at the last steps of synthesis.
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3
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Hägele G, Nazarski RB, Schmitz A, Xing S, Janiak C. 1H NMR spectra, structure, and conformational exchange of S- n-alkyl-tetrahydrothiophenium cations of some ionic liquids. PHOSPHORUS SULFUR 2022. [DOI: 10.1080/10426507.2021.2023149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Gerhard Hägele
- Institut für Anorganische und Strukturchemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Ryszard B. Nazarski
- Department of Physical Chemistry, Faculty of Chemistry, Theoretical and Structural Chemistry Group, University of Lodz, Łódź, Poland
| | - Alexa Schmitz
- Institut für Anorganische und Strukturchemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Shanghua Xing
- Institut für Anorganische und Strukturchemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Christoph Janiak
- Institut für Anorganische und Strukturchemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
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4
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Staś M, Broda MA, Siodłak D. Thiazole-amino acids: influence of thiazole ring on conformational properties of amino acid residues. Amino Acids 2021; 53:673-686. [PMID: 33837859 PMCID: PMC8128816 DOI: 10.1007/s00726-021-02974-0] [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: 12/05/2020] [Accepted: 03/29/2021] [Indexed: 12/29/2022]
Abstract
Post-translational modified thiazole-amino acid (Xaa-Tzl) residues have been found in macrocyclic peptides (e.g., thiopeptides and cyanobactins), which mostly inhibit protein synthesis in Gram + bacteria. Conformational study of the series of model compounds containing this structural motif with alanine, dehydroalanine, dehydrobutyrine and dehydrophenylalanine were performed using DFT method in various environments. The solid-state crystal structure conformations of thiazole-amino acid residues retrieved from the Cambridge Structural Database were also analysed. The studied structural units tend to adopt the unique semi-extended β2 conformation; which is stabilised mainly by N-H⋯NTzl hydrogen bond, and for dehydroamino acids also by π-electron conjugation. The conformational preferences of amino acids with a thiazole ring were compared with oxazole analogues and the role of the sulfur atom in stabilising the conformations of studied peptides was discussed.
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Affiliation(s)
- Monika Staś
- Faculty of Chemistry, University of Opole, 45-052, Opole, Poland.
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo Náměstí 2, 166 10, Praha 6, Czech Republic.
| | | | - Dawid Siodłak
- Faculty of Chemistry, University of Opole, 45-052, Opole, Poland.
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5
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Joaquin D, Lee MA, Kastner DW, Singh J, Morrill ST, Damstedt G, Castle SL. Impact of Dehydroamino Acids on the Structure and Stability of Incipient 3 10-Helical Peptides. J Org Chem 2019; 85:1601-1613. [PMID: 31730750 DOI: 10.1021/acs.joc.9b02747] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A comparative study of the impact of small, medium-sized, and bulky α,β-dehydroamino acids (ΔAAs) on the structure and stability of Balaram's incipient 310-helical peptide (1) is reported. Replacement of the N-terminal Aib residue of 1 with a ΔAA afforded peptides 2a-c that maintained the 310-helical shape of 1. In contrast, installation of a ΔAA in place of Aib-3 yielded peptides 3a-c that preferred a β-sheet-like conformation. The impact of the ΔAA on peptide structure was independent of size, with small (ΔAla), medium-sized (Z-ΔAbu), and bulky (ΔVal) ΔAAs exerting similar effects. The proteolytic stabilities of 1 and its analogs were determined by incubation with Pronase. Z-ΔAbu and ΔVal increased the resistance of peptides to proteolysis when incorporated at the 3-position and had negligible impact on stability when placed at the 1-position, whereas ΔAla-containing peptides degraded rapidly regardless of position. Exposure of peptides 2a-c and 3a-c to the reactive thiol cysteamine revealed that ΔAla-containing peptides underwent conjugate addition at room temperature, while Z-ΔAbu- and ΔVal-containing peptides were inert even at elevated temperatures. These results suggest that both bulky and more accessible medium-sized ΔAAs should be valuable tools for bestowing rigidity and proteolytic stability on bioactive peptides.
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Affiliation(s)
- Daniel Joaquin
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Michael A Lee
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - David W Kastner
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Jatinder Singh
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Shardon T Morrill
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Gracie Damstedt
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Steven L Castle
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
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6
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Kupka T, Mnich A, Broda MA. Performance of revised STO(1M)-3G basis set for prediction of 5-fluorocytosine chemical shifts. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:489-498. [PMID: 31013546 DOI: 10.1002/mrc.4879] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/14/2019] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
Nuclear shieldings and chemical shifts of 5-fluorocytosine (5FC) were predicted in the gas phase and DMSO solution modeled by polarizable continuum model using B3LYP density functional and revised STO(1M)-3G basis set. For comparison, eight arbitrary selected basis sets including STO-3G and medium-size Pople-type and larger dedicated Jensen-type ones were applied. The former basis sets were significantly smaller, but the calculated structural parameters, harmonic vibrational frequencies, were very accurate and close to those obtained with larger, polarization-consistent ones. The predicted 13 C and 1 H chemical shieldings of 5FC and cytosine, selected as parent molecule, were acceptable (root mean square for 13 C chemical shifts in DMSO of about 5 ppm and less) though less accurate than those calculated with large basis sets, dedicated for prediction of nuclear magnetic resonance parameters.
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Affiliation(s)
- Teobald Kupka
- Faculty of Chemistry, University of Opole, 48, Oleska Street, 46-052, Opole, Poland
| | - Adrianna Mnich
- Faculty of Chemistry, University of Opole, 48, Oleska Street, 46-052, Opole, Poland
| | - Małgorzata A Broda
- Faculty of Chemistry, University of Opole, 48, Oleska Street, 46-052, Opole, Poland
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7
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Impact of the ΔPhe configuration on the Boc-Gly-ΔPhe-NHMe conformation: experiment and theory. Struct Chem 2019. [DOI: 10.1007/s11224-019-01387-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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8
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Kapusta K, Voronkov E, Okovytyy S, Korobov V, Leszczynski J. Reconstruction of STO-3G Family Basis Set for the Accurate Calculation of Magnetic Properties. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2019. [DOI: 10.1134/s0036024418130174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Luchian R, Vinţeler E, Chiş C, Vasilescu M, Leopold N, Prates Ramalho JP, Chiş V. Conformational Preference and Spectroscopical Characteristics of the Active Pharmaceutical Ingredient Levetiracetam. J Pharm Sci 2017; 106:3564-3573. [PMID: 28842298 DOI: 10.1016/j.xphs.2017.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/01/2017] [Accepted: 08/14/2017] [Indexed: 11/19/2022]
Abstract
The analysis of the possible conformers and the conformational change between solid and liquid states of a particular drug molecule are mandatory not only for describing reliably its spectroscopical properties but also for understanding the interaction with the receptor and its mechanism of action. Therefore, here we investigated the free-energy conformational landscape of levetiracetam (LEV) in gas phase as well as in water and ethanol, aiming to describe the 3-dimensional structure and energetic stability of its conformers. Twenty-two unique conformers were identified, and their energetic stability was determined at density functional theory B3LYP/6-31+G(2d,2p) level of theory. The 6 most stable monomers in water, within a relative free-energy window of 0.71 kcal mol-1 and clearly separated in energy from the remaining subset of 16 conformers, as well as the 3 most stable dimers were then used to compute the Boltzmann populations-averaged UV-Vis and NMR spectra of LEV. The conformational landscape in solution is distinctly different from that corresponding to gas phase, particularly due to the relative orientations of the butanamide group. Aiming to clarify the stability of the possible dimers of LEV, we also investigated computationally the structure of a set of 11 nonhydrated and hydrated homochiral hydrogen-bonded LEV dimers.
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Affiliation(s)
- Raluca Luchian
- Faculty of Physics, Babeş-Bolyai University, 1 Kogălniceanu, RO-400084 Cluj-Napoca, Romania
| | - Emil Vinţeler
- Faculty of Physics, Babeş-Bolyai University, 1 Kogălniceanu, RO-400084 Cluj-Napoca, Romania
| | - Cosmina Chiş
- Pediatric Neurology Department, Children Emergency Hospital, Cluj-Napoca, Romania
| | - Mihai Vasilescu
- Faculty of Physics, Babeş-Bolyai University, 1 Kogălniceanu, RO-400084 Cluj-Napoca, Romania
| | - Nicolae Leopold
- Faculty of Physics, Babeş-Bolyai University, 1 Kogălniceanu, RO-400084 Cluj-Napoca, Romania
| | - João P Prates Ramalho
- Department of Chemistry, School of Science and Technology, University of Évora, Rua Romão Ramalho, 59, 7000-671 Évora, Portugal; CGE-Centro de Geofisica de Evora, University of Évora, Rua Romão Ramalho, 59, 7000-671 Évora, Portugal
| | - Vasile Chiş
- Faculty of Physics, Babeş-Bolyai University, 1 Kogălniceanu, RO-400084 Cluj-Napoca, Romania.
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10
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Staś M, Bujak M, Broda MA, Siodłak D. Conformational preferences and synthesis of isomers Z and E of oxazole-dehydrophenylalanine. Biopolymers 2017; 106:283-94. [PMID: 27061820 DOI: 10.1002/bip.22852] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 03/30/2016] [Accepted: 04/05/2016] [Indexed: 12/17/2022]
Abstract
Dehydrophenylalanine, ΔPhe, is the most commonly studied α,β-dehydroamino acid. In nature, further modifications of the α,β-dehydroamino acids were found, for example, replacement of the C-terminal amide group by oxazole ring. The conformational properties of oxazole-dehydrophenylalanine residue (ΔPhe-Ozl), both isomers Z and E, were investigated. To determine all possible conformations, theoretical calculations were performed using Ac-(Z/E)-ΔPhe-Ozl(4-Me) model compounds at M06-2X/6-31++G(d,p) level of theory. Ac-(Z/E)-ΔPhe-Ozl-4-COOEt compounds were synthesized and the conformational preferences of each isomer, Z and E, were investigated using FTIR and NMR-NOE in solutions of increasing polarity (CHCl3 , DMSO-d6). The solid-state low-temperature structures of Ac-(Z)-ΔPhe-Ozl-4-COOEt and its intermediate analog Ac-(Z)-ΔPhe-Ozn(4-OH)-4-COOEt were also determined. In a weakly polar environment, the ΔPhe-Ozl residue has a tendency to adopt the conformation β2 with the calculated φ and ψ angles of -127° and 0° for the isomer Z and -170° and 26° for the isomer E. The increase of environment polarity favors the helical conformation α and the beta-turn like conformation β, but the conformation β2 seems to be still accessible. The (E)-ΔPhe-Ozl residue can be obtained from the isomer Z in photoisomerization reaction. However, hydroxyl-oxazoline-dehydrophenylalanine ΔPhe-Ozn(4-OH) decomposes in such conditions. Alternatively, (E)-ΔPhe-NH2 can be applied as a substrate in the Hantzsch reaction. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 283-294, 2016.
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Affiliation(s)
- Monika Staś
- Faculty of Chemistry, University of Opole, Oleska 48, Opole, 45-052, Poland
| | - Maciej Bujak
- Faculty of Chemistry, University of Opole, Oleska 48, Opole, 45-052, Poland
| | - Małgorzata A Broda
- Faculty of Chemistry, University of Opole, Oleska 48, Opole, 45-052, Poland
| | - Dawid Siodłak
- Faculty of Chemistry, University of Opole, Oleska 48, Opole, 45-052, Poland
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11
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Nazarski RB, Justyna K, Leśniak S, Chrostowska A. A Benefit of Using the IDSCRF- over UFF-Radii Cavities and Why Joint Correlations of NMR Chemical Shifts Can Be Advantageous: Condensed Pyridines as an IEF-PCM/GIAO/DFT Case Study. J Phys Chem A 2016; 120:9519-9528. [PMID: 27933911 DOI: 10.1021/acs.jpca.6b10457] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein, an advantage of the use of IDSCRF- over UFF-radii-based solute cavities in GIAO/DFT calculations is presented for the 13C and especially 15N NMR chemical shifts made for several bicyclic aromatic nitrogen heterocycles in CDCl3 solution treated within the classical IEF-PCM solvation scheme. Successful application of the IDSCRF-radii in the non 1:1 joint multinuclear 1H/13C and particularly 1H/13C/15N correlations of the measured δH,C(,N) values to those obtained theoretically is also documented for a series of test systems (-268 ≤ δN ≤ -72 ppm). The experimentally yet unknown δN's were found in this way for the title compounds via a trinuclear eq 1 determined for an optimally chosen value of the multiplication factor of initial raw δH data (mH = 10). Such a simultaneous analysis of the δH,C(,N) data is proposed as a novel method to study the solution structure of the other similar conformationally homogeneous (bio)organic compounds. The issue of small spurious imaginary vibrational frequencies computed for a few molecular systems using the Gaussian 09 default UFF-radii is briefly considered as well.
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Affiliation(s)
- Ryszard B Nazarski
- Department of Theoretical and Structural Chemistry, Faculty of Chemistry, University of Łódź , Pomorska 163, 90-236 Łódź, Poland
| | - Katarzyna Justyna
- Department of Organic and Applied Chemistry, Faculty of Chemistry, University of Łódź , Tamka 12, 91-403 Łódź, Poland.,Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, IPREM, UMR CNRS 5254, Université de Pau et des Pays de l'Adour , 2 av. Président Pierre Angot, 64053 Pau Cedex 9, France
| | - Stanisław Leśniak
- Department of Organic and Applied Chemistry, Faculty of Chemistry, University of Łódź , Tamka 12, 91-403 Łódź, Poland
| | - Anna Chrostowska
- Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, IPREM, UMR CNRS 5254, Université de Pau et des Pays de l'Adour , 2 av. Président Pierre Angot, 64053 Pau Cedex 9, France
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12
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Kupka T, Stachów M, Stobiński L, Kaminský J. DFT study of zigzag (n, 0) single-walled carbon nanotubes: 13C NMR chemical shifts. J Mol Graph Model 2016; 67:14-9. [DOI: 10.1016/j.jmgm.2016.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 04/14/2016] [Accepted: 04/19/2016] [Indexed: 10/21/2022]
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13
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Grande-Aztatzi R, Formoso E, Mujika JI, Ugalde JM, Lopez X. Phosphorylation promotes Al(iii) binding to proteins: GEGEGSGG as a case study. Phys Chem Chem Phys 2016; 18:7197-207. [DOI: 10.1039/c5cp06379e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aluminum, the third most abundant element in the Earth's crust and one of the key industrial components of our everyday life, has been associated with several neurodegenerative diseases due to its ability to promote neurofilament tangles and β-amyloid peptide aggregation.
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Affiliation(s)
- Rafael Grande-Aztatzi
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia Internacional Physics Center (DIPC)
- 20080 Donostia
- Spain
| | - Elena Formoso
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia Internacional Physics Center (DIPC)
- 20080 Donostia
- Spain
| | - Jon I. Mujika
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia Internacional Physics Center (DIPC)
- 20080 Donostia
- Spain
| | - Jesus M. Ugalde
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia Internacional Physics Center (DIPC)
- 20080 Donostia
- Spain
| | - Xabier Lopez
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia Internacional Physics Center (DIPC)
- 20080 Donostia
- Spain
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14
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Nazarski RB, Wałejko P, Witkowski S. Multi-conformer molecules in solutions: an NMR-based DFT/MP2 conformational study of two glucopyranosides of a vitamin E model compound. Org Biomol Chem 2016; 14:3142-58. [DOI: 10.1039/c5ob01865j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Overall geometries of both glucosyl derivatives of PMC were found on the basis of their NMR spectra in CDCl3and relatedδH,C/nJHHIEF-PCM(UFF,CHCl3)/DFT calculational results.
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Affiliation(s)
- Ryszard B. Nazarski
- University of Łódź
- Faculty of Chemistry
- Department of Theoretical and Structural Chemistry
- 90-236 Łódź
- Poland
| | - Piotr Wałejko
- University of Białystok
- Institute of Chemistry
- 15-245 Białystok
- Poland
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15
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Jiang J, Ma Z, Castle SL. Bulky α,β-dehydroamino acids: their occurrence in nature, synthesis, and applications. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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16
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Vinţeler E, Stan NF, Luchian R, Căinap C, Ramalho JPP, Chiş V. Conformational landscape and low lying excited states of imatinib. J Mol Model 2015; 21:84. [DOI: 10.1007/s00894-015-2639-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/22/2015] [Indexed: 11/28/2022]
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17
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Jankowska M, Kupka T, Stobiński L, Kaminský J. DFT studies on armchair (5, 5) SWCNT functionalization. Modification of selected structural and spectroscopic parameters upon two-atom molecule attachment. J Mol Graph Model 2015; 55:105-14. [DOI: 10.1016/j.jmgm.2014.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/19/2014] [Accepted: 11/07/2014] [Indexed: 12/01/2022]
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18
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Crisma M, De Zotti M, Formaggio F, Peggion C, Moretto A, Toniolo C. Handedness preference and switching of peptide helices. Part II: Helices based on noncodedα-amino acids. J Pept Sci 2015; 21:148-77. [DOI: 10.1002/psc.2743] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 12/19/2014] [Accepted: 12/19/2014] [Indexed: 12/27/2022]
Affiliation(s)
| | - Marta De Zotti
- Department of Chemistry; University of Padova; Padova Italy
| | - Fernando Formaggio
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | | | - Alessandro Moretto
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | - Claudio Toniolo
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
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19
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Wałęsa R, Ptak T, Siodłak D, Kupka T, Broda MA. Experimental and theoretical NMR studies of interaction between phenylalanine derivative and egg yolk lecithin. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2014; 52:298-305. [PMID: 24639342 DOI: 10.1002/mrc.4064] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/18/2014] [Accepted: 02/28/2014] [Indexed: 06/03/2023]
Abstract
The interaction of phenylalanine diamide (Ac-Phe-NHMe) with egg yolk lecithin (EYL) in chloroform was studied by (1)H and (13)C NMR. Six complexes EYL-Ac-Phe-NHMe, stabilized by N-H···O or/and C-H···O hydrogen bonds, were optimized at M06-2X/6-31G(d,p) level. The assignment of EYL and Ac-Phe-NHMe NMR signals was supported using GIAO (gauge including atomic orbital) NMR calculations at VSXC and B3LYP level of theory combined with STO-3Gmag basis set. Results of our study indicate that the interaction of peptides with lecithin occurs mainly in the polar 'head' of the lecithin. Additionally, the most probable lecithin site of H-bond interaction with Ac-Phe-NHMe is the negatively charged oxygen in phosphate group that acts as proton acceptor.
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Affiliation(s)
- Roksana Wałęsa
- Faculty of Chemistry, University of Opole, Oleska 48 Str., 45-052, Opole, Poland
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Radula-Janik K, Kupka T, Ejsmont K, Daszkiewicz Z, Sauer SPA. Halogen effect on structure and 13C NMR chemical shift of 3,6-disubstituted-N-alkyl carbazoles. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:630-5. [PMID: 23922027 DOI: 10.1002/mrc.3992] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Revised: 07/10/2013] [Accepted: 07/10/2013] [Indexed: 05/26/2023]
Abstract
Structures of selected 3,6-dihalogeno-N-alkyl carbazole derivatives were calculated at the B3LYP/6-311++G(3df,2pd) level of theory, and their (13) C nuclear magnetic resonance (NMR) isotropic shieldings were predicted using density functional theory (DFT). The model compounds contained 9H, N-methyl and N-ethyl derivatives. The relativistic effect of Br and I atoms on nuclear shieldings was modeled using the spin-orbit zeroth-order regular approximation (ZORA) method. Significant heavy atom shielding effects for the carbon atom directly bonded with Br and I were observed (~-10 and ~-30 ppm while the other carbon shifts were practically unaffected). The decreasing electronegativity of the halogen substituent (F, Cl, Br, and I) was reflected in both nonrelativistic and relativistic NMR results as decreased values of chemical shifts of carbon atoms attached to halogen (C3 and C6) leading to a strong sensitivity to halogen atom type at 3 and 6 positions of the carbazole ring. The predicted NMR data correctly reproduce the available experimental data for unsubstituted N-alkylcarbazoles.
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Affiliation(s)
- Klaudia Radula-Janik
- Faculty of Chemistry, Opole University, 48, Oleska Street, 45-052, Opole, Poland
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