1
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Perera AS, Carlson CD, Cheramy J, Xu Y. Infrared and vibrational circular dichroism spectra of methyl β-D-glucopyranose in water: The application of the quantum cluster growth and clusters-in-a-liquid solvation models. Chirality 2023; 35:718-731. [PMID: 37162747 DOI: 10.1002/chir.23576] [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: 02/28/2023] [Revised: 04/10/2023] [Accepted: 04/18/2023] [Indexed: 05/11/2023]
Abstract
The infrared (IR) and vibrational circular dichroism (VCD) spectra of methyl β-D-glucopyranose in water were measured. Both implicit and explicit solvation models were utilized to explain the observed spectra. The vast body of existing experimental and theoretical data suggested that about eight explicit water molecules are needed to account for the solvent effects, supported by the current Quantum Cluster Growth (QCG) analysis. Extensive manual and systematic conformational searches of the molecular target and its water clusters were carried out by using a recently developed conformational searching tool, conformer-rotamer ensemble sampling tool (CREST), and the microsolvation model in the associated QCG code. The Boltzmann averaged IR and VCD spectra of the methyl β-D-glucopyranose-(water)n (n = 8) conformers in the PCM of water provide better agreement with the experimental ones than those with n = 0, 1, and 2. The explicit solvation with eight water molecules was shown to greatly modify the conformational preference of methyl β-D-glucopyranose from its monomeric form. Further analyses show that the result is consistent with the existence of long-lived methyl β-D-glucopyranose monohydrates with the additional explicit water effects being accounted for with the quantum mechanical treatment of the other seven close-by water molecules in the PCM of water.
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Affiliation(s)
| | - Colton D Carlson
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Joseph Cheramy
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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2
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Yamamoto S, Ishiro S, Kessler J, Bouř P. Intense chiral signal from α-helical poly-L-alanine observed in low-frequency Raman optical activity. Phys Chem Chem Phys 2021; 23:26501-26509. [PMID: 34806737 DOI: 10.1039/d1cp04401j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Raman optical activity (ROA) spectral features reliably indicate the structure of peptides and proteins, but the signal is often weak. However, we observed significantly enhanced low-frequency bands for α-helical poly-L-alanine (PLA) in solution. The biggest ROA signal at ∼100 cm-1 is about 10 times stronger than higher-frequency bands described previously, which facilitates the detection. The low-frequency bands of PLA were compared to those of α-helical proteins. For PLA, density functional simulations well reproduced the experimental spectra and revealed that about 12 alanine residues within two turns of the α-helix generate the strong ROA band. Averaging based on molecular dynamics (MD) provided an even more realistic spectrum compared to the static model. The low-frequency bands could be largely related to a collective motion of the α-helical backbone, partially modulated by the solvent. Helical and intermolecular vibrational coordinates have been introduced and the helical unwinding modes were assigned to the strongest ROA signal at 101-128 cm-1. Further analysis indicated that the helically arranged amide and methyl groups are important for the strong chiral signal of PLA, while the local chiral centers CαH contribute in a minor way only. The strong low-frequency ROA can thus provide precious information about the motions of the peptide backbone and facilitate future protein studies.
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Affiliation(s)
- Shigeki Yamamoto
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560-0043, Japan.
| | - Shota Ishiro
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560-0043, Japan.
| | - Jiří Kessler
- 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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3
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Lu H, Qi Y, Zhao Y, Jin N. Effects of Hydroxyl Group on the Interaction of Carboxylated Flavonoid Derivatives with S. Cerevisiae α-Glucosidase. Curr Comput Aided Drug Des 2020; 16:31-44. [PMID: 30345924 PMCID: PMC6967131 DOI: 10.2174/1573409914666181022142553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 08/23/2018] [Accepted: 10/17/2018] [Indexed: 02/07/2023]
Abstract
Introduction Carboxyalkyl flavonoids derivatives are considered as effective inhibitors in reducing post-prandial hyperglycaemia. Methods Combined with Density Functional Theory (DFT) and the theory of Atoms in Molecules (AIM), molecular docking and charge density analysis are carried out to understand the molecular flexibility, charge density distribution and the electrostatic properties of these carboxyalkyl derivatives. Results Results show that the electron density of the chemical bond C14-O17 on B ring of molecule II increases while O17-H18 decreases at the active site, suggesting the existence of weak non-covalent interactions, most prominent of which are H-bonding and electrostatic interaction. When hydroxyl groups are introduced, the highest positive electrostatic potentials are distributed near the B ring hydroxyl hydrogen atom and the carboxyl hydrogen atom on the A ring. It was reported that quercetin has a considerably inhibitory activity to S. cerevisiae α-glucosidase, from the binding affinities, it is suggested that the position and number of hydroxyl groups on the B and C rings are also pivotal to the hypoglycemic activity when the long carboxyalkyl group is introduced into the A ring. Conclusion It is concluded that the presence of three well-defined zones in the structure, both hydrophobicity alkyl, hydrophilicity carboxyl and hydroxyl groups are necessary.
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Affiliation(s)
- Huining Lu
- Department of Life Sciences and Biological Engineering, Northwest Minzu University, Lanzhou 730124, China
| | - Yanjiao Qi
- Department of Chemical Engineering, Northwest Minzu University, Lanzhou 730124, China.,Key Laboratory for Utility of Environment-Friendly Composite Materials and Biomass in Universities of Gansu Province, Lanzhou, China
| | - Yaming Zhao
- Department of Chemical Engineering, Northwest Minzu University, Lanzhou 730124, China
| | - Nengzhi Jin
- Gansu Province Computing Center, Lanzhou 730000, China
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4
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Del Galdo S, Fusè M, Barone V. The ONIOM/PMM Model for Effective Yet Accurate Simulation of Optical and Chiroptical Spectra in Solution: Camphorquinone in Methanol as a Case Study. J Chem Theory Comput 2020; 16:3294-3306. [PMID: 32250614 PMCID: PMC7222099 DOI: 10.1021/acs.jctc.0c00124] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
This paper deals
with the development and first validation of a
composite approach for the simulation of chiroptical spectra in solution
aimed to strongly reduce the number of full QM computations without
any significant accuracy loss. The approach starts from the quantum
mechanical computation of reference spectra including vibrational
averaging effects and taking average solvent effects into account
by means of the polarizable continuum model. Next, the snapshots of
classical molecular dynamics computations are clusterized and one
reference configuration from each cluster is used to compute a reference
spectrum. Local fluctuation effects within each cluster are then taken
into account by means of the perturbed matrix model. The performance
of the proposed approach is tested on the challenging case of the
optical and chiroptical spectra
of camphorquinone in methanol solution. Although further validations
are surely needed, the results of this first study are quite promising
also taking into account that agreement with experimental data is
reached by just a couple of full quantum mechanical geometry optimizations
and frequency computations.
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Affiliation(s)
- Sara Del Galdo
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Marco Fusè
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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5
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Sterling CM, Bjornsson R. Multistep Explicit Solvation Protocol for Calculation of Redox Potentials. J Chem Theory Comput 2018; 15:52-67. [PMID: 30511855 DOI: 10.1021/acs.jctc.8b00982] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The calculation of molecular redox potentials in aqueous solution presents a challenge to quantum chemistry due to the need to calculate charged, open-shell species experiencing large solvent effects. Traditionally, redox potentials are calculated via the use of density functional theory and continuum solvation methods, but such protocols have been found to often suffer from large errors, particularly in the case of aqueous solution. While explicit solvation models hold promise of higher accuracy to describe solvent effects in general, their complicated use and lack of well-defined, reliable protocols has hindered their adoption. In this study, we present an explicit-solvation-based approach for the calculation of molecular redox potentials. We combine the use of affordable semiempirical QM/MM molecular dynamics (making use of the recently proposed GFN-xTB method by Grimme et al.) for both redox states and use the linear response approximation to relate vertical ionization energies to the adiabatic redox potential. Simulation length, averaging over snapshots, and accounting for bulk and polarization effects are systematically evaluated using phenol as a working example. We find that it is crucial to reliably account for bulk solvation effects in these calculations, as well as polarization effects which we divide up into short-range and long-range contributions. The short-range polarization contribution is accounted for via QM-region expansion, while the long-range contribution is accounted for via Drude-polarizable QM/MM. Our multistep protocol has been coded to be used in a fully automatic way in a local version of Chemshell. It has been evaluated on a test set of oxidation potentials of organic molecules and found to give gas-solution redox shifts with a mean absolute error of 0.13 eV with respect to experiment, compared to mean absolute errors of 0.26 and 0.21 eV with CPCM and SMD continuum models, respectively.
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Affiliation(s)
- Cody M Sterling
- Science Institute , University of Iceland , Dunhagi 3 , 107 Reykjavík , Iceland
| | - Ragnar Bjornsson
- Science Institute , University of Iceland , Dunhagi 3 , 107 Reykjavík , Iceland.,Department of Inorganic Spectroscopy , Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany
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6
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Qi YJ, Lu HN, Jin NZ, Zhang JY, Dong JQ. Understanding of the conformational flexibility and electrostatic properties of coumarin derivatives in the active site of S. cerevisiae α-glucosidase. Med Chem Res 2017. [DOI: 10.1007/s00044-017-2086-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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7
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Prasad S, Mandal I, Singh S, Paul A, Mandal B, Venkatramani R, Swaminathan R. Near UV-Visible electronic absorption originating from charged amino acids in a monomeric protein. Chem Sci 2017; 8:5416-5433. [PMID: 28970921 PMCID: PMC5609530 DOI: 10.1039/c7sc00880e] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/18/2017] [Indexed: 11/21/2022] Open
Abstract
Electronic absorption spectra of proteins are primarily characterized over the ultraviolet region (185-320 nm) of the electromagnetic spectrum. While recent studies on peptide aggregates have revealed absorption beyond 350 nm, monomeric proteins lacking aromatic amino acids, disulphide bonds, and active site prosthetic groups are expected to remain optically silent beyond 250 nm. Here, in a joint theoretical and experimental investigation, we report the distinctive UV-Vis absorption spectrum between 250 nm [ε = 7338 M-1 cm-1] and 800 nm [ε = 501 M-1 cm-1] in a synthetic 67 residue protein (α3C), in monomeric form, devoid of aromatic amino acids. Systematic control studies with high concentration non-aromatic amino acid solutions revealed significant absorption beyond 250 nm for charged amino acids which constitute over 50% of the sequence composition in α3C. Classical atomistic molecular dynamics (MD) simulations of α3C reveal dynamic interactions between multiple charged sidechains of Lys and Glu residues present in α3C. Time-dependent density functional theory calculations on charged amino acid residues sampled from the MD trajectories of α3C reveal that the distinctive absorption features of α3C may arise from two different types of charge transfer (CT) transitions involving spatially proximal Lys/Glu amino acids. Specifically, we show that the charged amino (NH3+)/carboxylate (COO-) groups of Lys/Glu sidechains act as electronic charge acceptors/donors for photoinduced electron transfer either from/to the polypeptide backbone or to each other. Further, the sensitivity of the CT spectra to close/far/intermediate range of encounters between sidechains of Lys/Glu owing to the three dimensional protein fold can create the long tail in the α3C absorption profile between 300 and 800 nm. Finally, we experimentally demonstrate the sensitivity of α3C absorption spectrum to temperature and pH-induced changes in protein structure. Taken together, our investigation significantly expands the pool of spectroscopically active biomolecular chromophores and adds an optical 250-800 nm spectral window, which we term ProCharTS (Protein Charge Transfer Spectra), for label free probes of biomolecular structure and dynamics.
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Affiliation(s)
- Saumya Prasad
- Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati 781039 , Assam , India .
| | - Imon Mandal
- Department of Chemical Sciences , Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba , Mumbai 400005 , India .
| | - Shubham Singh
- Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati 781039 , Assam , India .
| | - Ashim Paul
- Department of Chemistry , Indian Institute of Technology Guwahati , Guwahati 781039 , Assam , India
| | - Bhubaneswar Mandal
- Department of Chemistry , Indian Institute of Technology Guwahati , Guwahati 781039 , Assam , India
| | - Ravindra Venkatramani
- Department of Chemical Sciences , Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba , Mumbai 400005 , India .
| | - Rajaram Swaminathan
- Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati 781039 , Assam , India .
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8
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Qi YJ, Lu HN, Zhao YM, Jin NZ. Probing the influence of carboxyalkyl groups on the molecular flexibility and the charge density of apigenin derivatives. J Mol Model 2017; 23:70. [PMID: 28197841 DOI: 10.1007/s00894-017-3221-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 01/11/2017] [Indexed: 12/11/2022]
Abstract
Apigenin is an important flavonoids due to its antidiabetic bioactivity. It was reported experimentally that the 7-substituent derivative of apigenin has higher biological activity than 4'- and 5-substituted derivatives while introducing sole carboxyalkyl group -(CH2)7COOH into the parent structure. Molecular docking studies indicated that the other two derivatives have lower binding affinities than the 7-substituent derivative (-7.52 kcal mol-1), which is considered to be a better inhibitor than the parent molecule. Almost all of the carbon atoms and oxygen atoms are coplaner for all three molecules in solution phase, however, all carboxyalkyl groups bend inside into the parent molecules in the active site, and the jagged geometries of the carbon chains are destroyed correspondingly. In addition, most of the electron densities of the chemical bonds for all molecules are decreased, especially the 7-substituent derivative. In contrast, most of the Laplacian values for three molecules are increased in the active site, which suggests that the charge densities at the bond critical point (bcp) are much more depleted than the solution phase. Dipole moments of derivatives are all increased in the active site, suggesting strong intermolecular interactions. After interacting with the S. cerevisiae α-glucosidase, only the 7-substituent derivative has the lowest energy gap ΔE HOMO-LUMO, which indicates the lowest stability and the highest inhibition activity. Graphical abstract Probing the influence of carboxyalkyl groups on the molecular flexibility and the charge density of apigenin derivatives.
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Affiliation(s)
- Y J Qi
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou, 730124, People's Republic of China.
| | - H N Lu
- Department of Life Sciences and Biological Engineering, Northwest University for Nationalities, Lanzhou, 730124, People's Republic of China
| | - Y M Zhao
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou, 730124, People's Republic of China
| | - N Z Jin
- Gansu Province Computing Center, Lanzhou, 730000, People's Republic of China
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9
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Qi YJ, Lu HN, Liang JX, Zhao YM, Wang XE, Jin NZ. Comparison of the molecular interactions of 7'-carboxyalkyl apigenin derivatives with S. cerevisiae α-glucosidase. Comput Biol Chem 2017; 67:182-193. [PMID: 28131019 DOI: 10.1016/j.compbiolchem.2017.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/09/2016] [Accepted: 01/16/2017] [Indexed: 11/26/2022]
Abstract
As one of the most investigated flavonoids, apigenin, is considered to be a strong α-glucosidase inhibitor. However, the clinical utility of apigenin is limited due to its low solubility. It was reported that the solubility and biological activity can be improved by introducing sole carboxyalkyl group into apigenin, especially the 7'-substitution. With the increase of length of the alkyl chain in carboxyalkyl group, B ring of the apigenin derivative is embedded much more deeply into the binding cavity while the carboxyalkyl stretches to the neighboring cavity. All of the terminal carboxyl groups form hydrogen bonding interactions easily with the surrounding polar amino acids, such as His239, Ser244, Arg312 and Asp349. Thus, the electron density values of the carbonyl in the carboxyl group become higher than the solution status due to the strong molecular interactions. In fact, electron densities of most of the chemical bonds are decreased after molecular docking procedure. On compared with the solution phase, however, dipole moments of most of these molecules are increased, and their vectors are reoriented distinctly in the active sites. It is noticed that all of the Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) are distributed throughout the whole parent apigenin ring in solution phase, whereas the disappeared situation happened on the B rings of some molecules (II-IV) in the active site, leading to higher energy gaps.
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Affiliation(s)
- Y J Qi
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou 730124, PR China.
| | - H N Lu
- Department of Life Sciences and Biological Engineering, Northwest University for Nationalities, Lanzhou 730124, PR China
| | - J X Liang
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou 730124, PR China
| | - Y M Zhao
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou 730124, PR China
| | - X E Wang
- Department of Chemical Engineering, Northwest University for Nationalities, Lanzhou 730124, PR China
| | - N Z Jin
- Gansu Province Computing Center, Lanzhou 730000, PR China
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10
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Kessler J, Yamamoto S, Bouř P. Establishing the link between fibril formation and Raman optical activity spectra of insulin. Phys Chem Chem Phys 2017; 19:13614-13621. [DOI: 10.1039/c7cp01556a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Molecular dynamics and density functional simulations are used to explain changes in Raman optical activity accompanying the formation of insulin fibrils.
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Affiliation(s)
- Jiří Kessler
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences
- 16610 Prague
- Czech Republic
- Department of Physical and Macromolecular Chemistry
| | - Shigeki Yamamoto
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Osaka 560-0043
- Japan
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences
- 16610 Prague
- Czech Republic
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11
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Exploring molecular flexibility and the interactions of Quercetin derivatives in the active site of α-glucosidase using molecular docking and charge density analysis. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Dračínský M, Bouř P, Hodgkinson P. Temperature Dependence of NMR Parameters Calculated from Path Integral Molecular Dynamics Simulations. J Chem Theory Comput 2016; 12:968-73. [PMID: 26857802 DOI: 10.1021/acs.jctc.5b01131] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The influence of temperature on NMR chemical shifts and quadrupolar couplings in model molecular organic solids is explored using path integral molecular dynamics (PIMD) and density functional theory (DFT) calculations of shielding and electric field gradient (EFG) tensors. An approach based on convoluting calculated shielding or EFG tensor components with probability distributions of selected bond distances and valence angles obtained from DFT-PIMD simulations at several temperatures is used to calculate the temperature effects. The probability distributions obtained from the quantum PIMD simulations, which includes nuclear quantum effects, are significantly broader and less temperature dependent than those obtained with conventional DFT molecular dynamics or with 1D scans through the potential energy surface. Predicted NMR observables for the model systems were in excellent agreement with experimental data.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry , Flemingovo nám. 2, 16610 Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry , Flemingovo nám. 2, 16610 Prague, Czech Republic
| | - Paul Hodgkinson
- Department of Chemistry, Durham University , South Road, DH1 3LE Durham, United Kingdom
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13
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Melcrová A, Kessler J, Bouř P, Kaminský J. Simulation of Raman optical activity of multi-component monosaccharide samples. Phys Chem Chem Phys 2016; 18:2130-42. [DOI: 10.1039/c5cp04111b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Determination of the saccharide structure in solution is a laborious process that can be significantly enhanced by chiral optical spectroscopies.
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Affiliation(s)
- Adéla Melcrová
- Institute of Organic Chemistry and Biochemistry
- 166 10 Prague
- Czech Republic
- J. Heyrovský Institute of Physical Chemistry
- 182 23 Prague
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry
- 166 10 Prague
- Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry
- 166 10 Prague
- Czech Republic
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry
- 166 10 Prague
- Czech Republic
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14
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Luber S, Iannuzzi M, Hutter J. Raman spectra from ab initio molecular dynamics and its application to liquid S-methyloxirane. J Chem Phys 2014; 141:094503. [DOI: 10.1063/1.4894425] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Štěpánek P, Bouř P. Multi-scale modeling of electronic spectra of three aromatic amino acids: importance of conformational averaging and explicit solute-solvent interactions. Phys Chem Chem Phys 2014; 16:20639-49. [PMID: 25158079 DOI: 10.1039/c4cp02668c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electronic transitions in the ultraviolet and visible spectral range can reveal a wealth of information about biomolecular geometry and interactions, such as those involved in protein folding. However, the modeling that provides the necessary link between spectral shapes and the structure is often difficult even for seemingly simple systems. To understand as to how conformational equilibria and solute-solvent interaction influence spectral intensities, we collected absorption (UV-vis), electronic circular dichroism (ECD), and magnetic circular dichroism (MCD) spectra of phenylalanine (Phe), tyrosine (Tyr) and tryptophan (Trp) zwitterions in aqueous solutions, and compared them with quantum-chemical simulations. These aromatic amino acids provide a relatively strong signal in the accessible wavelength range. At the same time, they allow for a relatively accurate modeling. Energies and intensities of spectral bands were reproduced by the time-dependent density functional theory (TD DFT). The solvent was approximated by a continuum as well as clusters containing solvent molecules from the first hydration sphere. The ECD signal was found to be strongly dependent on molecular conformation, and the dependence was much weaker in UV-vis and MCD spectra. All spectral intensities, however, were significantly affected by the solvent approximation; especially for ECD and MCD the usual polarizable continuum solvent model did not yield satisfactory spectral shapes. On the other hand, averaging of the clusters obtained from molecular dynamics simulations provided an unprecedented agreement with the experiment. Proper modeling of the interactions with the environment thus makes the information about the molecular structure, as obtained from the electronic spectra, more accurate and reliable.
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Affiliation(s)
- Petr Štěpánek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 166 10 Prague, Czech Republic.
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16
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Dračínský M, Hodgkinson P. Effects of quantum nuclear delocalisation on NMR parameters from path integral molecular dynamics. Chemistry 2014; 20:2201-7. [PMID: 24435841 DOI: 10.1002/chem.201303496] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Indexed: 11/06/2022]
Abstract
The influence of nuclear delocalisation on NMR chemical shifts in molecular organic solids is explored using path integral molecular dynamics (PIMD) and density functional theory calculations of shielding tensors. Nuclear quantum effects are shown to explain previously observed systematic deviations in correlations between calculated and experimental chemical shifts, with particularly large PIMD-induced changes (up to 23 ppm) observed for carbon atoms in methyl groups. The PIMD approach also enables isotope substitution effects on chemical shifts and J couplings to be predicted in excellent agreement with experiment for both isolated molecules and molecular crystals. An approach based on convoluting calculated shielding or coupling surfaces with probability distributions of selected bond distances and valence angles obtained from PIMD simulations is used to calculate isotope effects.
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Affiliation(s)
- Martin Dračínský
- Department of Chemistry, Durham University, South Road, DH1 3LE Durham (UK); Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610 Prague (Czech Republic).
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17
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Dračínský M, Möller HM, Exner TE. Conformational Sampling by Ab Initio Molecular Dynamics Simulations Improves NMR Chemical Shift Predictions. J Chem Theory Comput 2013; 9:3806-15. [PMID: 26584127 DOI: 10.1021/ct400282h] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Car-Parrinello molecular dynamics simulations were performed for N-methyl acetamide as a small test system for amide groups in protein backbones, and NMR chemical shifts were calculated based on the generated ensemble. If conformational sampling and explicit solvent molecules are taken into account, excellent agreement between the calculated and experimental chemical shifts is obtained. These results represent a landmark improvement over calculations based on classical molecular dynamics (MD) simulations especially for amide protons, which are predicted too high-field shifted based on the latter ensembles. We were able to show that the better results are caused by the solute-solvents interactions forming shorter hydrogen bonds as well as by the internal degrees of freedom of the solute. Inspired by these results, we propose our approach as a new tool for the validation of force fields due to its power of identifying the structural reasons for discrepancies between the experimental and calculated data.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences , Flemingovo náměstí 2, 166 10 Prague, Czech Republic.,Department of Chemistry, Durham University , DH1 3LE Durham, United Kingdom
| | - Heiko M Möller
- Department of Chemistry, University of Konstanz , 78457 Konstanz, Germany
| | - Thomas E Exner
- Department of Chemistry, University of Konstanz , 78457 Konstanz, Germany.,Theoretical Medicinal Chemistry and Biophysics, Institute of Pharmacy, Eberhard Karls University Tübingen , Auf der Morgenstelle 8, 72076 Tübingen, Germany
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Přecechtělová J, Munzarová ML, Vaara J, Novotný J, Dračínský M, Sklenář V. Toward Reproducing Sequence Trends in Phosphorus Chemical Shifts for Nucleic Acids by MD/DFT Calculations. J Chem Theory Comput 2013; 9:1641-56. [DOI: 10.1021/ct300488y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
| | | | - Juha Vaara
- NMR Research Group, Department of Physics,
University of Oulu, P.O. Box 3000, FIN-90014 Oulu, Finland
| | | | - Martin Dračínský
- NMR Laboratory, Institute of
Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v. v. i., Flemingovo nám.
2, CZ-16610 Prague 6, Czech Republic
- Department of Chemistry, Durham University, Durham, DH13LE, United Kingdom
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Dračínský M, Hodgkinson P. A molecular dynamics study of the effects of fast molecular motions on solid-state NMR parameters. CrystEngComm 2013. [DOI: 10.1039/c3ce40612a] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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