1
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Khatun M, Sarkar P, Panda S, Sherpa LT, Anoop A. Nanoclusters and nanoalloys of group 13 elements (B, Al, and Ga): benchmarking of methods and analysis of their structures and energies. Phys Chem Chem Phys 2023; 25:19986-20000. [PMID: 37461397 DOI: 10.1039/d2cp05833b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
We investigated the structural and energetic properties of nanoclusters and nanoalloys composed of group 13 elements (B, Al, and Ga) up to a cluster size of 12. We conducted a comprehensive benchmark analysis of density functional and post-Hartree-Fock methods to identify efficient and accurate approaches for studying these systems using our benchmark dataset (BAlGa16) consisting of sixteen dimers and trimers. We compared different density functionals and post-Hartree-Fock methods using bond length and binding energy as parameters. B2PLYP closely follows CCSD(T) for geometry optimization, while REVPBE, BPBE, and PBE show cost-accuracy balanced performances. MRACPF was used as the reference for benchmarking energies, with NEVPT2 being the most accurate method, followed by CCSD(T) and DLPNO-CCSD(T). M06 and range-separated hybrid functionals perform well. Based on a cost-accuracy analysis, we recommend M06/def2-SVP as the preferred method. Additionally, we explored the structural evolution of pure, binary, and ternary clusters of group 13 elements up to 12 atoms, uncovering global and local minima. Ga clusters exhibited more rectangular faces compared to the predominantly trigonal faces of B and Al clusters. Binary clusters showed B in center positions, while Ga preferred outer positions, confirming the higher cohesion of B. The most favorable size of binary clusters (12) exhibited similar compositions of Al and Ga atoms. Compositions with 16.67-40% B, 16.67-60% Al, and 20-50% Ga were estimated to have negative mixing energies, indicating their relative stability.
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Affiliation(s)
- Maya Khatun
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Pratik Sarkar
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Sunanda Panda
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Lazumla T Sherpa
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Anakuthil Anoop
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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2
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Emenike BU, Farshadmand A, Zeller M, Roman AJ, Sevimler A, Shinn DW. Electrostatic CH-π Interactions Can Override Fluorine Gauche Effects To Exert Conformational Control. Chemistry 2023; 29:e202203139. [PMID: 36286329 DOI: 10.1002/chem.202203139] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Indexed: 11/07/2022]
Abstract
Fluorine gauche effects are conformational properties of 2-fluoroethanes often applied in modern molecular designs. However, the physical origins of fluorine gauche effects are not well understood, with the consensus favoring the established hyperconjugation theory over an emerging electrostatic model. Using a series of model systems, we show that a shift to fluorine gauche effects can be influenced by intramolecular CH⋅⋅⋅π aromatic interactions, a through-space event. Modulating the π-ring (forming the aromatic interaction) with substituent groups resulted in a linear Hammett relationship, thus indicating that the CH⋅⋅⋅π interaction has electrostatic features. For instance, attaching a nitro group (an electron-withdrawing substituent) to the π-ring weakened the CH⋅⋅⋅π interaction and led to a gauche preference, whereas an anti conformer is preferred with amine as substituent. The experimental results performed by using proton NMR spectroscopy are corroborated by gas-phase DFT calculations and solid-state X-ray crystallography.
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Affiliation(s)
- Bright U Emenike
- Department of Chemistry & Physics, State University of New York, Old Westbury, 223 Store Hill Road, Old Westbury, NY 11568, USA
| | - Amiel Farshadmand
- Department of Chemistry & Physics, State University of New York, Old Westbury, 223 Store Hill Road, Old Westbury, NY 11568, USA
| | - Matthias Zeller
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA
| | - Armando J Roman
- Department of Chemistry & Physics, State University of New York, Old Westbury, 223 Store Hill Road, Old Westbury, NY 11568, USA
| | - Arzu Sevimler
- Department of Chemistry & Physics, State University of New York, Old Westbury, 223 Store Hill Road, Old Westbury, NY 11568, USA
| | - David W Shinn
- Department of Mathematics and Science, United States Merchant Marine Academy, 300 Steamboat Road, Kings Point, NY 11024, USA
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3
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Lo CCL, Joaquin D, Moyá DA, Ramos A, Kastner DW, White SM, Christensen BL, Naglich JG, Degnen WJ, Castle SL. Synthesis and evaluation of potent yaku'amide A analogs. Chem Sci 2022; 13:1899-1905. [PMID: 35308852 PMCID: PMC8848768 DOI: 10.1039/d1sc05992k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/02/2022] [Indexed: 11/21/2022] Open
Abstract
Two full-length analogs of the anticancer peptide yaku'amide A (1a) and four partial structures have been synthesized. These analogs were identified by computational studies in which the three E- and Z-ΔIle residues of the natural product were replaced by the more accessible dehydroamino acids ΔVal and ΔEnv. Of the eight possible analogs, modeling showed that the targeted structures 2a and 2b most closely resembled the three-dimensional structure of 1a. Synthesis of 2a and 2b followed a convergent route that was streamlined by the absence of ΔIle in the targets. Screening of the compounds against various cancer cell lines revealed that 2a and 2b mimic the potent anticancer activity of 1a, thereby validating the computational studies. Simplified full-length analogs of yaku'amide A were designed with the aid of computations and then synthesized. The analog that was predicted to most closely resemble the structure of the natural product mimicked its anticancer activity.![]()
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Affiliation(s)
- Concordia C L Lo
- Department of Chemistry and Biochemistry, Brigham Young University Provo UT 84602 USA
| | - Daniel Joaquin
- Department of Chemistry and Biochemistry, Brigham Young University Provo UT 84602 USA
| | - Diego A Moyá
- Department of Chemistry and Biochemistry, Brigham Young University Provo UT 84602 USA
| | - Alexander Ramos
- Department of Chemistry and Biochemistry, Brigham Young University Provo UT 84602 USA
| | - David W Kastner
- Department of Chemistry and Biochemistry, Brigham Young University Provo UT 84602 USA
| | - Stephen M White
- Department of Chemistry and Biochemistry, Brigham Young University Provo UT 84602 USA
| | - Blake L Christensen
- Department of Chemistry and Biochemistry, Brigham Young University Provo UT 84602 USA
| | - Joseph G Naglich
- Bristol Myers Squibb, Research & Early Development, Mechanistic Pharmacology-Leads Discovery & Optimization Rte 206 & Province Line Rd Princeton NJ 08543 USA
| | | | - Steven L Castle
- Department of Chemistry and Biochemistry, Brigham Young University Provo UT 84602 USA
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4
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Mitsikas DA, Glykos NM. A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations. PLoS One 2020; 15:e0243429. [PMID: 33270807 PMCID: PMC7714341 DOI: 10.1371/journal.pone.0243429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/23/2020] [Indexed: 11/19/2022] Open
Abstract
Both molecular mechanical and quantum mechanical calculations play an important role in describing the behavior and structure of molecules. In this work, we compare for the same peptide systems the results obtained from folding molecular dynamics simulations with previously reported results from quantum mechanical calculations. More specifically, three molecular dynamics simulations of 5 μs each in explicit water solvent were carried out for three Asn-Gly-containing heptapeptides, in order to study their folding and dynamics. Previous data, based on quantum mechanical calculations within the DFT framework have shown that these peptides adopt β-turn structures in aqueous solution, with type I’ β-turn being the most preferred motif. The results from our analyses indicate that at least for the given systems, force field and simulation protocol, the two methods diverge in their predictions. The possibility of a force field-dependent deficiency is examined as a possible source of the observed discrepancy.
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Affiliation(s)
- Dimitrios A. Mitsikas
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University campus, Alexandroupolis, Greece
| | - Nicholas M. Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University campus, Alexandroupolis, Greece
- * E-mail:
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Kang YK, Park HS. Conformational preferences of cationic β-peptide in water studied by CCSD(T), MP2, and DFT methods. Heliyon 2020; 6:e04721. [PMID: 32904383 PMCID: PMC7452530 DOI: 10.1016/j.heliyon.2020.e04721] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/14/2020] [Accepted: 08/11/2020] [Indexed: 11/28/2022] Open
Abstract
The conformational preferences of the cationic nylon-3 βNM [(3R,4)-diaminobutanoic acid, dAba] dipeptide in water were explored as the first step to understand the mode of action of polymers of βNM against phylogenetically diverse and intrinsically drug-resistant pathogenic fungi. The CCSD(T), MP2, M06-2X, ωB97X-D, B2PLYP-D3BJ, and DSD-PBEP86-D3BJ levels of theory with various basis sets were assessed for relative energies of the 45 local minima of the cationic Ac-dAba-NHMe located at the SMD M06-2X/6-31+G(d) level of theory in water against the benchmark CCSD(T)/CBS-limit energies in water. The best performance was obtained at the double-hybrid DSD-PBEP86-D3BJ/def2-QZVP level of theory with RMSD = 0.12 kcal/mol in water. The M06-2X/def2-QZVP level of theory predicted reasonably the conformational preference with RMSD = 0.38 kcal/mol in water and may be an alternative level of theory with marginal deviations for the calculation of conformational energies of relatively longer cationic peptides in water. In particular, the H14–helical structures appeared to be the most feasible conformations for the cationic Ac-dAba-NHMe populated at 48–64% by relative free energies in water. The hexamer built from the H14–structure of the cationic Ac-dAba-NHMe adopted a left-handed 314-helix, which has a slightly narrower radius and a longer rise than the regular 314-helix of β-peptides. Hence, the 314-helices of oligomers or polymers of the cationic dAba residues are expected to be the active conformation to exhibit the ability to bridge between charged lipid head groups that might cause a local depression or invagination of the membrane of fungi.
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Affiliation(s)
- Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
| | - Hae Sook Park
- Department of Nursing, Cheju Halla University, Cheju 63092, Republic of Korea
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6
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Koenis MAJ, Xia Y, Domingos SR, Visscher L, Buma WJ, Nicu VP. Taming conformational heterogeneity in and with vibrational circular dichroism spectroscopy. Chem Sci 2019; 10:7680-7689. [PMID: 31803406 PMCID: PMC6844231 DOI: 10.1039/c9sc02866h] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/08/2019] [Indexed: 01/19/2023] Open
Abstract
Genetic fitting algorithm accounting for the uncertainty in computed energies allows a significantly more reliable assignment of stereochemistry and conformational heterogeneity of chiral compounds using vibrational circular dichroism.
The flexibility of a molecule has important consequences on its function and application. Vibrational Circular Dichroism (VCD) is intrinsically an excellent experimental technique to get a hold on this flexibility as it is highly sensitive to key conformational details and able to distinguish rapidly interconverting conformers. One of the major challenges in analyzing the spectra by comparison to theoretical predictions is the uncertainty in the computed energies of the multitude of conformations. This uncertainty also affects the reliability of the stereochemical assignment it is normally used for. We present here a novel approach that explicitly takes the energy uncertainties into account in a genetic algorithm based method that fits calculated to the experimental spectra. We show that this approach leads to significant improvements over previously used methodologies. Importantly, statistical validation studies provide quantitative measures for the reliability of relevant parameters used such as the energy uncertainty and the extent to which conformational heterogeneity can be determined. Similarly, quantitative measures can be obtained for the possibility that the flexibility that is introduced in the fit might lead to an incorrect assignment of the stereochemistry. These results break new ground for different techniques based on VCD to elucidate conformational flexibility.
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Affiliation(s)
- Mark A J Koenis
- Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098 XH Amsterdam , The Netherlands .
| | - Yiyin Xia
- Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098 XH Amsterdam , The Netherlands .
| | - Sérgio R Domingos
- Deutsches Elektronen-Synchrotron DESY , Notkestraße 85 , 22607 Hamburg , Germany
| | - Lucas Visscher
- Amsterdam Center for Multiscale Modeling , Division Theoretical Chemistry , Faculty of Sciences , Vrije Universiteit Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Wybren Jan Buma
- Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098 XH Amsterdam , The Netherlands . .,Radboud University , Institute for Molecules and Materials , FELIX Laboratory , Toernooiveld 7c , 6525 ED Nijmegen , The Netherlands
| | - Valentin P Nicu
- Department of Environmental Science, Physics, Physical Education and Sport , Lucian Blaga University of Sibiu , loan Ratiu Street Nr. 7-9 , 550012 Sibiu , Romania .
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Maillard LT, Park HS, Kang YK. Organocatalytic Asymmetric Addition of Aldehyde to Nitroolefin by H-d-Pro-Pro-Glu-NH 2: A Mechanistic Study. ACS OMEGA 2019; 4:8862-8873. [PMID: 31459974 PMCID: PMC6648279 DOI: 10.1021/acsomega.9b00465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/13/2019] [Indexed: 06/10/2023]
Abstract
The mechanism of the asymmetric addition of aldehyde (butanal) to nitroolefin (β-nitrostyrene) catalyzed by H-d-Pro-Pro-Glu-NH2 (dPPE-NH2; 1) was explored using density functional theory methods in chloroform. By conformational search, it was confirmed that catalyst 1 and its enamine intermediate adopted a dominant conformation with a βI structure stabilized by a C10 H-bond between the C=O of d-Pro1 and C-terminal NH2 proton and by an additional H-bond between the side chain and the backbone of Glu3. This βI turn structure was conserved all along the catalytic cycle. Consistently with the kinetic studies, the C-C bond formation between the enamine and electrophile was also confirmed as the rate-determining step. The stereoselectivity results from a re → re prochiral approach of enamine and β-nitrostyrene with a gauche- orientation of the double bonds. Although it was suggested as the possible formation of dihydrooxazine oxide species, this process was confirmed to be kinetically less accessible than the formation of acyclic nitronate. In particular, our calculated results supported that the carboxylic acid group of Glu3 in 1 played a central role by acting as general acid/base all along the catalytic cycle and orienting the asymmetric C-C bond formation.
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Affiliation(s)
- Ludovic T. Maillard
- Institut
des Biomolécules Max Mousseron, UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques
et Biologiques, 15 Avenue
Charles Flahault, 34093 Montpellier Cedex 5, France
| | - Hae Sook Park
- Department
of Nursing, Cheju Halla University, Cheju 63092, Republic of Korea
| | - Young Kee Kang
- Department
of Chemistry, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
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8
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A DFT study on the mechanism of rhodium-catalyzed regioselective hydrothiolation of the allyl amine. MOLECULAR CATALYSIS 2019. [DOI: 10.1016/j.mcat.2019.02.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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9
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Jiang F, Wu HN, Kang W, Wu YD. Developments and Applications of Coil-Library-Based Residue-Specific Force Fields for Molecular Dynamics Simulations of Peptides and Proteins. J Chem Theory Comput 2019; 15:2761-2773. [DOI: 10.1021/acs.jctc.8b00794] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fan Jiang
- Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Hao-Nan Wu
- Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Wei Kang
- Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yun-Dong Wu
- Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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10
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Park HS, Kang YK. Which DFT levels of theory are appropriate in predicting the prolyl cis–trans isomerization in solution? NEW J CHEM 2019. [DOI: 10.1039/c9nj02946j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
DFTs were assessed for the conformational preferences of the peptides containing Pro and its derivatives in chloroform and water.
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Affiliation(s)
- Hae Sook Park
- Department of Nursing
- Cheju Halla University
- Cheju 63092
- Republic of Korea
| | - Young Kee Kang
- Department of Chemistry
- Chungbuk National University
- Cheongju
- Republic of Korea
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11
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Braga CB, Silva WGDP, Rittner R. Conformational preferences of N-acetyl-N′-methylprolineamide in different media: a 1H NMR and theoretical investigation. NEW J CHEM 2019. [DOI: 10.1039/c8nj05035j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The conformational preferences and role of non-covalent interactions on the geometries of Ac–Pro–NHMe were elucidated in isolated phase and solution.
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Affiliation(s)
- Carolyne B. Braga
- Institute of Chemistry
- University of Campinas
- Campinas
- São Paulo 13083-970
- Brazil
| | | | - Roberto Rittner
- Institute of Chemistry
- University of Campinas
- Campinas
- São Paulo 13083-970
- Brazil
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12
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Mironov V, Alexeev Y, Mulligan VK, Fedorov DG. A systematic study of minima in alanine dipeptide. J Comput Chem 2018; 40:297-309. [DOI: 10.1002/jcc.25589] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/12/2018] [Accepted: 08/07/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Vladimir Mironov
- Department of Chemistry Lomonosov Moscow State University Leninskie Gory 1/3, Moscow 119991 Russia
| | - Yuri Alexeev
- Argonne National Laboratory Computational Science Division Argonne Illinois 60439
| | - Vikram Khipple Mulligan
- Department of Biochemistry University of Washington, Institute for Protein Design Seattle Washington 98195
| | - Dmitri G. Fedorov
- CD‐FMat National Institute of Advanced Industrial Science and Technology Central 2, Umezono 1‐1‐1, Tsukuba 305‐8568 Japan
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13
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Kang NS, Kang YK. Assessment of CCSD(T), MP2, and DFT methods for the calculations of structures and interaction energies of the peptide backbone with water molecules. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.08.063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Cutini M, Corno M, Ugliengo P. Method Dependence of Proline Ring Flexibility in the Poly-l-Proline Type II Polymer. J Chem Theory Comput 2016; 13:370-379. [PMID: 27976574 DOI: 10.1021/acs.jctc.6b01045] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We studied the sensitivity of the energetic and geometrical features of the proline ring (pyrrolidine) to the quantum mechanical computational approach by adopting the proline monomer, trimer, and polymer, as simplified collagen protein models. Within the Density Functional Theory (DFT) approach, we tested the ability of different functionals (GGA PBE and the hybrid B3LYP), added with a posteriori empirical dispersion corrections (D), to predict the conformational potential energy surface of the five-membered heterocycle pyrrolidine ring for the above models, dictating the collagen main features. We also compared the DFT-D results with those from the recently proposed cost-effective HF-3c method and our variant HF-3c-027, both based on Hartree-Fock Hamiltonian and Gaussian minimal basis set properly corrected for basis set superposition error, structure deficiencies, and dispersion interactions. We found that dispersion interactions are essential to destabilize specific conformers. While the HF-3c and its HF-3c-027 variant are unreliable to predict accurately the energy of the ring conformers, structures are accurate. Indeed, the cost-effective DFT-D//HF-3c-027 approach in which the energetic is from the accurate DFT-D method on HF-3c-027 structures provides energetic in line with that derived by the costly DFT-D//DFT-D approach, paving the way to simulate more realistic collagen models of much larger size. The adoption of either PBE or B3LYP functional for the electronic part of the DFT-D method gives very similar results, recommending the first as the most cost-effective method for simulating large collagen models. The predicted most stable conformation computed for the periodic poly proline (type II) model allows for a higher flexibility, in agreement with experimental studies on collagen protein. The present results open the way to large-scale calculations of the collagen/hydroxyapatite system, crucial for understanding the atomistic details in bones and teeth.
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Affiliation(s)
- Michele Cutini
- Department of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Torino , Via P. Giuria 7, 10125 Turin, Italy
| | - Marta Corno
- Department of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Torino , Via P. Giuria 7, 10125 Turin, Italy
| | - Piero Ugliengo
- Department of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Torino , Via P. Giuria 7, 10125 Turin, Italy
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15
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Baggioli A, Cavallotti CA, Famulari A. Exploring short intramolecular interactions in alkylaromatic substrates. Phys Chem Chem Phys 2016; 18:29616-29628. [PMID: 27753437 DOI: 10.1039/c6cp03323g] [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
From proteins and peptides to semiconducting polymers, aliphatic chains on aromatic groups are recurring motifs in macromolecules from very diverse application fields. Fields in which molecular folding and packing determine the macroscopic physical properties that make such advanced materials appealing in the first place. Within each macromolecule, the intrinsic structure of each unit defines how it interacts with its neighbours, ultimately opening up or denying certain backbone conformations. This eventually also determines how macromolecules interact with each other. This account deals specifically with the conformational problem of many common alkylaromatic units, examining the features of an intramolecular interaction involving a side chain with as few as three methylene groups. A set of 23 model compounds featuring an intramolecular interaction between an aliphatic X-H (X = C, N, O, and S) bond and an aromatic ring was considered. Quantitative computational analysis was made possible, thanks to complete basis set extrapolated CCSD(T) calculations and NCI topological analysis, the latter of which revealed an elaborate network of dispersive and steric interactions leading to somewhat unintuitive and unexpected results, such as the higher energetic stability of certain twisted conformational isomers over those with extended side chains. Vicinal covalent effects from polarizing groups and various heteroatoms, along with the occurrence of non-dispersive phenomena, were also investigated. The conclusions drawn from the investigation include a comprehensive set of guidelines intended to aid in the prediction of the most stable conformation for this class of building blocks. Our findings affect a variety of different research fields, including the tailoring of functional materials for organic electronics and photovoltaics, with insights into a rational treatment of conformational disorder, and the study of protein- and peptide-folding preferences, putting an emphasis on peculiar interactions between the backbone and aromatic residues.
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Affiliation(s)
- Alberto Baggioli
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
| | - Carlo A Cavallotti
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
| | - Antonino Famulari
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
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16
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Kang YK, Yoo IK. Propensities of peptides containing the Asn-Gly segment to form β-turn and β-hairpin structures. Biopolymers 2016; 105:653-64. [DOI: 10.1002/bip.22863] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/21/2016] [Accepted: 04/25/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Young Kee Kang
- Department of Chemistry and BK21 PLUS Research Team; Chungbuk National University; Cheongju Chungbuk 28644 Republic of Korea
| | - In Kee Yoo
- Department of Chemistry and BK21 PLUS Research Team; Chungbuk National University; Cheongju Chungbuk 28644 Republic of Korea
- LG Research Park, LG Household & Health Care; Daejeon 34114 Republic of Korea
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17
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Kaminský J, Jensen F. Conformational Interconversions of Amino Acid Derivatives. J Chem Theory Comput 2016; 12:694-705. [PMID: 26691979 DOI: 10.1021/acs.jctc.5b00911] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Exhaustive conformational interconversions including transition structure analyses of N-acetyl-l-glycine-N-methylamide as well as its alanine, serine, and cysteine analogues have been investigated at the MP2/6-31G** level, yielding a total of 142 transition states. Improved estimates of relative energies were obtained by separately extrapolating the Hartree-Fock and MP2 energies to the basis set limit and adding the difference between CCSD(T) and MP2 results with the cc-pVDZ basis set to the extrapolated MP2 results. The performance of eight empirical force fields (AMBER94, AMBER14SB, MM2, MM3, MMFFs, CHARMM22_CMAP, OPLS_2005, and AMOEBAPRO13) in reproducing ab initio energies of transition states was tested. Our results indicate that commonly used class I force fields employing a fixed partial charge model for the electrostatic interaction provide mean errors in the ∼10 kJ/mol range for energies of conformational transition states for amino acid conformers. Modern reparametrized versions, such as CHARMM22_CMAP, and polarizable force fields, such as AMOEBAPRO13, have slightly lower mean errors, but maximal errors are still in the 35 kJ/mol range. There are differences between the force fields in their ability for reproducing conformational transitions classified according to backbone/side-chain or regions in the Ramachandran angles, but the data set is likely too small to draw any general conclusions. Errors in conformational interconversion barriers by ∼10 kJ/mol suggest that the commonly used force field may bias certain types of transitions by several orders of magnitude in rate and thus lead to incorrect dynamics in simulations. It is therefore suggested that information for conformational transition states should be included in parametrizations of new force fields.
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Affiliation(s)
- Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Frank Jensen
- Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus C, Denmark
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Kang YK, Park HS. Propensities to form the β-turn and β-hairpin structures of d-Pro-Gly and Aib- d-Ala containing peptides: a computational study. NEW J CHEM 2016. [DOI: 10.1039/c6nj00614k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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19
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Kann N, Johansson JR, Beke-Somfai T. Conformational properties of 1,4- and 1,5-substituted 1,2,3-triazole amino acids – building units for peptidic foldamers. Org Biomol Chem 2015; 13:2776-85. [PMID: 25605623 PMCID: PMC4718141 DOI: 10.1039/c4ob02359e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/02/2015] [Indexed: 01/22/2023]
Abstract
Peptidic foldamers have recently emerged as a novel class of artificial oligomers with properties and structural diversity similar to that of natural peptides, but possessing additional interesting features granting them great potential for applications in fields from nanotechnology to pharmaceuticals. Among these, foldamers containing 1,4- and 1,5-substitued triazole amino acids are easily prepared via the Cu- and Ru-catalyzed click reactions and may offer increased side chain variation, but their structural capabilities have not yet been widely explored. We here describe a systematic analysis of the conformational space of the two most important basic units, the 1,4-substitued (4Tzl) and the 1,5-substitued (5Tzl) 1,2,3-triazole amino acids, using quantum chemical calculations and NMR spectroscopy. Possible conformations of the two triazoles were scanned and their potential minima were located using several theoretical approaches (B3LYP/6-311++G(2d,2p), ωB97X-D/6-311++G(2d,2p), M06-2X/6-311++G(2d,2p) and MP2/6-311++G(2d,2p)) in different solvents. BOC-protected versions of 4Tzl and 5Tzl were also prepared via one step transformations and analyzed by 2D NOESY NMR. Theoretical results show 9 conformers for 5Tzl derivatives with relative energies lying close to each other, which may lead to a great structural diversity. NMR analysis also indicates that conformers preferring turn, helix and zig-zag secondary structures may coexist in solution. In contrast, 4Tzl has a much lower number of conformers, only 4, and these lack strong intraresidual interactions. This is again supported by NMR suggesting the presence of both extended and bent conformers. The structural information provided on these building units could be employed in future design of triazole foldamers.
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Affiliation(s)
- Nina Kann
- Department of Chemical and Biological Engineering , Chalmers University of Technology , SE-41296 Göteborg , Sweden . ; ; http://www.chalmers.se/chem/ ; Fax: +46-31-7723858 ; Tel: +46 (0)31 772 3029, +46 (0)31 772 3070
| | - Johan R. Johansson
- AstraZeneca R&D Mölndal , RIA IMED , Medicinal Chemistry , SE-43183 Mölndal , Sweden .
| | - Tamás Beke-Somfai
- Department of Chemical and Biological Engineering , Chalmers University of Technology , SE-41296 Göteborg , Sweden . ; ; http://www.chalmers.se/chem/ ; Fax: +46-31-7723858 ; Tel: +46 (0)31 772 3029, +46 (0)31 772 3070
- Research Centre for Natural Sciences , Hungarian Academy of Sciences , Pázmány Péter sétány 1 , H-1125 Budapest , Hungary
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Abstract
The conformational behaviour of Ac-Gly-NHMe and its fluorinated [CF3-C(O)-Gly-NHMe] and N-methyl[Ac-Gly-N(Me)2] derivatives is investigated in nonpolar, polar and polar protic solutions by NMR and IR spectroscopies and theoretical calculations.
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Affiliation(s)
- R. A. Cormanich
- EastChem School of Chemistry
- University of St Andrews
- St Andrews
- UK
- Chemistry Institute
| | - R. Rittner
- Chemistry Institute
- State University of Campinas
- Campinas
- Brazil
| | - M. Bühl
- EastChem School of Chemistry
- University of St Andrews
- St Andrews
- UK
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Kang YK, Park HS. Assessment of CCSD(T), MP2, DFT-D, CBS-QB3, and G4(MP2) methods for conformational study of alanine and proline dipeptides. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.03.067] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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22
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Dub PA, Henson NJ, Martin RL, Gordon JC. Unravelling the mechanism of the asymmetric hydrogenation of acetophenone by [RuX2(diphosphine)(1,2-diamine)] catalysts. J Am Chem Soc 2014; 136:3505-21. [PMID: 24524727 DOI: 10.1021/ja411374j] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The mechanism of catalytic hydrogenation of acetophenone by the chiral complex trans-[RuCl2{(S)-binap}{(S,S)-dpen}] and KO-t-C4H9 in propan-2-ol is revised on the basis of DFT computations carried out in dielectric continuum and the most recent experimental observations. The results of these collective studies suggest that neither a six-membered pericyclic transition state nor any multibond concerted transition states are involved. Instead, a hydride moiety is transferred in an outer-sphere manner to afford an ion-pair, and the corresponding transition state is both enantio- and rate-determining. Heterolytic dihydrogen cleavage proceeds neither by a (two-bond) concerted, four-membered transition state, nor by a (three-bond) concerted, six-membered transition state mediated by a solvent molecule. Instead, cleavage of the H-H bond is achieved via deprotonation of the η(2)-H2 ligand within a cationic Ru complex by the chiral conjugate base of (R)-1-phenylethanol. Thus, protonation of the generated (R)-1-phenylethoxide anion originates from the η(2)-H2 ligand of the cationic Ru complex and not from NH protons of a neutral Ru trans-dihydride complex, as initially suggested within the framework of a metal-ligand bifunctional mechanism. Detailed computational analysis reveals that the 16e(-) Ru amido complex [RuH{(S)-binap}{(S,S)-HN(CHPh)2NH2}] and the 18e(-) Ru alkoxo complex trans-[RuH{OCH(CH3)(R)}{(S)-binap}{(S,S)-dpen}] (R = CH3 or C6H5) are not intermediates within the catalytic cycle, but rather are off-loop species. The accelerative effect of KO-t-C4H9 is explained by the reversible formation of the potassium amidato complexes trans-[RuH2{(S)-binap}{(S,S)-N(K)H(CHPh)2NH2}] or trans-[RuH2{(S)-binap}{(S,S)-N(K)H(CHPh)2NH(K)}]. The three-dimensional (3D) cavity observed within these molecules results in a chiral pocket stabilized via several different noncovalent interactions, including neutral and ionic hydrogen bonding, cation-π interactions, and π-π stacking interactions. Cooperatively, these interactions modify the catalyst structure, in turn lowering the relative activation barrier of hydride transfer by ~1-2 kcal mol(-1) and the following H-H bond cleavage by ~10 kcal mol(-1), respectively. A combined computational study and analysis of recent experimental data of the reaction pool results in new mechanistic insight into the catalytic cycle for hydrogenation of acetophenone by Noyori's catalyst, in the presence or absence of KO-t-C4H9.
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Affiliation(s)
- Pavel A Dub
- Chemistry Division, MS J582, and ‡Theoretical Division, MS B268, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States
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Johansson JR, Hermansson E, Nordén B, Kann N, Beke-Somfai T. δ-Peptides from RuAAC-Derived 1,5-Disubstituted Triazole Units. European J Org Chem 2014. [DOI: 10.1002/ejoc.201400018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Kang YK, Park HS. Conformational preferences of the 2-methylproline residue and its role in stabilizing β-turn and polyproline II structures of peptides. NEW J CHEM 2014. [DOI: 10.1039/c4nj00072b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Buczek A, Broda MA. DFT study of N–H···O hydrogen bond between model dehydropeptides and water molecule. Mol Phys 2013. [DOI: 10.1080/00268976.2013.847979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Sundararajan M. Quantum Chemical Challenges for the Binding of Simple Alkanes to Supramolecular Hosts. J Phys Chem B 2013; 117:13409-17. [DOI: 10.1021/jp405113j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Mahesh Sundararajan
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
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Parchaňský V, Kapitán J, Kaminský J, Šebestík J, Bouř P. Ramachandran Plot for Alanine Dipeptide as Determined from Raman Optical Activity. J Phys Chem Lett 2013; 4:2763-2768. [PMID: 26706714 DOI: 10.1021/jz401366j] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Accessible values of the φ and ψ torsional angles determining peptide main chain conformation are traditionally displayed in the form of Ramachandran plots. The number of experimental methods making it possible to determine such conformational distribution is limited. In the present study, Raman optical activity (ROA) spectra of Ac-Ala-NHMe were measured and fit by theoretical curves. This revealed the most favored conformers and a large part of the potential energy surface (PES) of this model dipeptide. Such experimental PES compares well to quantum chemical computations, whereas molecular dynamics (MD) modeling reproduces it less faithfully. The surface shape is consistent with the temperature dependence of the spectra, as observed experimentally and predicted by MD. Despite errors associated with spectral modeling and the measurement, the results are likely to facilitate future applications of ROA spectroscopy.
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Affiliation(s)
- Václav Parchaňský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences , Flemingovo náměstí 2, 16610 Prague, Czech Republic
- Department of Analytical Chemistry, Institute of Chemical Technology , Technická 5, 16628 Prague, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University Olomouc , 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences , Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences , Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences , Flemingovo náměstí 2, 16610 Prague, Czech Republic
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Tsipis AC, Gkarmpounis DN, Kefalidis CE, Papamichael EM, Theodorou LG. Modeling the cysteamine catalyzed cysteine proteinases using DFT: mechanistic insights into the hydrolysis of acetyl-p-nitroanilide. NEW J CHEM 2013. [DOI: 10.1039/c3nj00769c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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30
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Hong YJ, Tantillo DJ. C–H⋯π interactions as modulators of carbocation structure – implications for terpene biosynthesis. Chem Sci 2013. [DOI: 10.1039/c3sc50571e] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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31
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Fabregat G, Ballano G, Casanovas J, Laurent AD, Armelin E, del Valle LJ, Cativiela C, Jacquemin D, Alemán C. Design of hybrid conjugates based on chemical similarity. RSC Adv 2013. [DOI: 10.1039/c3ra42191k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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32
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Teklebrhan RB, Owens NW, Xidos JD, Schreckenbach G, Wetmore SD, Schweizer F. Conformational Preference of Fused Carbohydrate-Templated Proline Analogues—A Computational Study. J Phys Chem B 2012; 117:199-205. [DOI: 10.1021/jp310690c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robel B. Teklebrhan
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2,
Canada
| | - Neil W. Owens
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2,
Canada
| | - James D. Xidos
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2,
Canada
| | - Georg Schreckenbach
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2,
Canada
| | - Stacey D. Wetmore
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Frank Schweizer
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2,
Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba R3A 1R9, Canada
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Gao W, Jiao J, Feng H, Xuan X, Chen L. Natures of benzene-water and pyrrole-water interactions in the forms of σ and π types: theoretical studies from clusters to liquid mixture. J Mol Model 2012. [DOI: 10.1007/s00894-012-1659-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Kang YK, Byun BJ. Strength of CH···π interactions in the C-terminal subdomain of villin headpiece. Biopolymers 2012; 97:778-88. [DOI: 10.1002/bip.22062] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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35
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Park HS, Byun BJ, Motooka D, Kawahara K, Doi M, Nakazawa T, Kobayashi Y, Kang YK. Conformational preferences of 4-chloroproline residues. Biopolymers 2012; 97:629-41. [DOI: 10.1002/bip.22054] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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36
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Suramitr S, Piriyagagoon A, Wolschann P, Hannongbua S. Theoretical study on the structures and electronic properties of oligo(p-phenylenevinylene) carboxylic acid and its derivatives: effects of spacer and anchor groups. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1209-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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37
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Profant V, Baumruk V, Li X, Šafařík M, Bouř P. Tracking of the Polyproline Folding by Density Functional Computations and Raman Optical Activity Spectra. J Phys Chem B 2011; 115:15079-89. [DOI: 10.1021/jp207706p] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Václav Profant
- Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Vladimír Baumruk
- Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Xiaojun Li
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Martin Šafařík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
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Lee JY, Kang NS, Kang YK. Binding free energies of inhibitors to iron porphyrin complex as a model for Cytochrome P450. Biopolymers 2011; 97:219-28. [PMID: 22113809 DOI: 10.1002/bip.22009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Accepted: 11/04/2011] [Indexed: 12/25/2022]
Abstract
The binding free energies of the inhibitor-heme model complexes are calculated using the density functional methods and the implicit solvation models in water, where the 16 structurally diverse compounds with a spectrum of IC(50) values from 0.05 (clotrimazole) to 1000 (piroxicam) μM are chosen as inhibitors for Cytochrome P450 3A4 (CYP3A4). CYP3A4 is the most predominant constituent of the human hepatic CYP enzymes that play a role in metabolizing structurally diverse xenobiotics. The observed free energy change for each inhibitory binding, ΔG inh0, is obtained from its IC(50) value. The total binding free energy (ΔG b0) of each inhibitor-heme model complex is calculated by the sum of its relative free energy (ΔG(0) ) in the gas phase and solvation free energy to the water-heme model complex. The UB3LYP/LanL2DZ level of theory provides the correct relative stabilities of the high- and low-spin states for the penta- and hexa-coordinated ferric complexes, respectively. The optimized distances of the inhibitor nitrogen (or water oxygen) and the methyl mercaptide S to the ferric iron of the inhibitor-heme model complexes at the same level of theory are consistent with the values of the corresponding X-ray structures, except for the econazole complex. The correlation coefficient r(2) values of 0.91 and 0.75 are obtained from the ΔG b0-ΔG inh0 and ΔG(0) -ΔG inh0 plots, respectively, at the UM06/LanL2DZ:CPCM_UB3LYP/LanL2DZ//UB3LYP/LanL2DZ level of theory in water. This indicates that the total binding free energies calculated for the inhibitor-heme model complexes can be a good descriptor in interpreting the inhibitor binding to CYP3A4 and the relative free energies in the gas phase are mainly responsible for the total binding free energies in water, although the desolvation can be a factor to affect the binding affinity of the inhibitors to CYP3A4. From the theozyme analysis of the X-ray structures for ketoconazole- and metyrapone-CYP3A4 complexes, the interaction free energy of the neighboring residues with each inhibitor in the active site is calculated to be about -3 kcal mol(-1) in water, whose the interaction energy and the desolvation free energy change are about -5 and 2 kcal mol(-1) , respectively.
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Affiliation(s)
- Joo Yun Lee
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
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Motooka D, Kawahara K, Nakamura S, Doi M, Nishi Y, Nishiuchi Y, Kang YK, Nakazawa T, Uchiyama S, Yoshida T, Ohkubo T, Kobayashi Y. The triple helical structure and stability of collagen model peptide with 4(s)-hydroxyprolyl-pro-gly units. Biopolymers 2011; 98:111-21. [DOI: 10.1002/bip.21730] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 10/09/2011] [Accepted: 10/13/2011] [Indexed: 12/22/2022]
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Revilla-López G, Laurent AD, Perpète EA, Jacquemin D, Torras J, Assfeld X, Alemán C. Key Building Block of Photoresponsive Biomimetic Systems. J Phys Chem B 2011; 115:1232-42. [DOI: 10.1021/jp108341a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Guillem Revilla-López
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal 647, 08028 Barcelona, Spain
| | - Adele D. Laurent
- Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France
| | - Eric A. Perpète
- Unité de Chimie Physique Théorique et Structurale (2742), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Denis Jacquemin
- Unité de Chimie Physique Théorique et Structurale (2742), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Juan Torras
- Departament d’Enginyeria Química, EUETII, Universitat Politècnica de Catalunya, Pça Rei 15, Igualada 08700, Spain
| | - Xavier Assfeld
- Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal 647, 08028 Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C’, C/Pasqual i Vila s/n, Barcelona E-08028, Spain
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Byun BJ, Kang YK. Conformational preferences and pK(a) value of selenocysteine residue. Biopolymers 2011; 95:345-53. [PMID: 21213257 DOI: 10.1002/bip.21581] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Revised: 12/20/2010] [Accepted: 12/22/2010] [Indexed: 12/25/2022]
Abstract
The conformational preferences of the L-selenocysteine (Sec) dipeptides with selenol and selenolate groups (Ac-Sec-NHMe and Ac-Sec(-) -NHMe, respectively) and the apparent (i.e., macroscopic) pK(a) value of the Sec residue have been studied using the dispersion-corrected density functionals M06-2X and B2PLYP-D with the implicit solvation method in the gas phase and in water. In the gas phase, the backbone-to-backbone and/or side chain-to-backbone hydrogen bonds are found to contribute in stabilizing the most preferred conformations for the Sec and Sec(-) residues, as seen for the Cys and Cys(-) residues. However, the polyproline II-like conformations prevail over the conformations with the backbone-to-backbone hydrogen bonds in water because of the weakened hydrogen bonds by the favorable direct interactions between the backbone CO and HN groups and water molecules. The Sec and Sec(-) residues are found to adopt more various conformations than the Cys and Cys(-) residues in water, although the most preferred conformations of the neutral and/or anionic forms of the two residues are similar each other in the gas phase and in water. Using the statistically weighted free energies of the Sec and Sec(-) dipeptides in the gas phase and their solvation free energies, the pK(a) value of the Sec residue is estimated to be 5.47 at 25°C, which is in good agreement with the experimental value of 5.43 ± 0.02. It is found that the lower pK(a) value of the selenol side chain for the Sec residue by ∼3 units than the thiol side chain for the Cys residue is ascribed to the higher gas-phase acidity of the Sec residue.
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Affiliation(s)
- Byung Jin Byun
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
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