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Yang X, Liu C, Ren P. Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning. J Chem Theory Comput 2024; 20:4065-4075. [PMID: 38742922 PMCID: PMC11187603 DOI: 10.1021/acs.jctc.4c00053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Conformational dynamics play a crucial role in determining the behavior of the biomolecules. Polarizable force fields, such as AMOEBA, can accurately capture electrostatic interactions underlying the conformational space. However, applying a polarizable force field in molecular dynamics (MD) simulations can be computationally expensive, especially in studying long-time-scale dynamics. To overcome this challenge, we incorporated the AMOEBA potential with Milestoning, an enhanced sampling method in this work. This integration allows us to efficiently sample the rare and important conformational states of a biomolecule by using many short and independent molecular dynamics trajectories with the AMOEBA force field. We applied this method to investigate the conformational dynamics of alanine dipeptide, DNA, and RNA A-B form conversion. Well-converged thermodynamic and kinetic properties were obtained, including the free energy difference, mean first passage time, and critical transitions between states. Our results demonstrate the power of integrating polarizable force fields with enhanced sampling methods in quantifying the thermodynamic and kinetic properties of biomolecules at the atomic level.
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Affiliation(s)
- Xudong Yang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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2
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Gorbunov VA, Uliankina AI, Akimenko SS, Myshlyavtsev AV. Tensor renormalization group study of orientational ordering in simple models of adsorption monolayers. Phys Rev E 2023; 108:014133. [PMID: 37583228 DOI: 10.1103/physreve.108.014133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/06/2023] [Indexed: 08/17/2023]
Abstract
A simple lattice model of the orientational ordering in organic adsorption layers that considers the directionality of intermolecular interactions is proposed. The symmetry and the number of rotational states of the adsorbed molecule are the main parameters of the model. The model takes into account both the isotropic and directional contributions to the molecule-molecule interaction potential. Using several special cases of this model, we have shown that the tensor renormalization group (TRG) approach can be successfully used for the analysis of orientational ordering in organic adsorption layers with directed intermolecular interactions. Adsorption isotherms, potential energy, and entropy have been calculated for the model adsorption layers differing in the molecule symmetry and the number of rotational states. The calculated thermodynamic characteristics show that entropy effects play a significant role in the self-assembly of dense phases of the molecular layers. All the results obtained with the TRG have been verified by the standard Monte Carlo method. The proposed model reproduces the main features of the phase behavior of the real adsorption layers of benzoic, terephthalic, and trimesic acids on a homogeneous surface of metal single crystals and graphite.
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Affiliation(s)
- V A Gorbunov
- Department of Chemistry and Chemical Engineering, Omsk State Technical University, 11 Mira Avenue, Omsk 644050, Russian Federation
| | - A I Uliankina
- Department of Chemistry and Chemical Engineering, Omsk State Technical University, 11 Mira Avenue, Omsk 644050, Russian Federation
| | - S S Akimenko
- Department of Chemistry and Chemical Engineering, Omsk State Technical University, 11 Mira Avenue, Omsk 644050, Russian Federation
| | - A V Myshlyavtsev
- Department of Chemistry and Chemical Engineering, Omsk State Technical University, 11 Mira Avenue, Omsk 644050, Russian Federation
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3
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Hassan M, Coutsias EA. Protein secondary structure motifs: A kinematic construction. J Comput Chem 2021; 42:271-292. [PMID: 33306852 DOI: 10.1002/jcc.26448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/02/2020] [Accepted: 09/29/2020] [Indexed: 12/19/2022]
Abstract
The kinematic geometry of protein backbone structures, constrained by either single or multiple hydrogen bonds (H-bonds), possibly in a periodic array, is discussed. These structures include regular secondary structure elements α-helices and β-sheets but also include other short H-bond stabilized irregular structural elements like β-turns. The work here shows that the variations observed in such structures have simple geometrical correlations consistent with constrained motion kinematics. A new classification of the ideal helices is given, in terms of the parameter α, the angle at a Cα atom to its two neighboring Cα 's along the helix, and shown how it can be generalized to include nonideal helices. Specifically, we derive an analytical expression of the backbone dihedrals, (ϕ, ψ), in terms of the parameter α subject to the constraint that the peptide planes are parallel to the helical axis. Helices constructed in this way exhibit near-vertical alignment of the C = O and N - H units and are the canonical objects of this study. These expressions are easily modifiable to include perturbations of parameters relevant to nonplanar peptide units and noncanonical angles. The addition of a second parameter, ε0 , inclination of successive peptide planes along a helix with respect to the helical axis leads to a generalization of the previous expression and provides an efficient parametrization of such structures in terms of coordinates consistent with H-bond parameters. An analogs parametrization of β-turns, using inverse kinematic methods, is also given. Besides offering a unifying viewpoint, our results may find useful applications to protein and peptide design.
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Affiliation(s)
- Mosavverul Hassan
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
| | - Evangelos A Coutsias
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
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Wei W, Luo J, Waldispühl J, Moitessier N. Predicting Positions of Bridging Water Molecules in Nucleic Acid-Ligand Complexes. J Chem Inf Model 2019; 59:2941-2951. [PMID: 30998377 DOI: 10.1021/acs.jcim.9b00163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Over the past two decades, interests in DNA and RNA as drug targets have been growing rapidly. Following the trends observed with protein drug targets, computational approaches for drug design have been developed for this new class of molecules. Our efforts toward the development of a universal docking program, Fitted, led us to focus on nucleic acids. Throughout the development of this docking program, efforts were directed toward displaceable water molecules which must be accurately located for optimal docking-based drug discovery. However, although there is a plethora of methods to place water molecules in and around protein structures, there is, to the best of our knowledge, no such fully automated method for nucleic acids, which are significantly more polar and solvated than proteins. We report herein a new method, Splash'Em (Solvation Potential Laid around Statistical Hydration on Entire Macromolecules) developed to place water molecules within the binding cavity of nucleic acids. This fast method was shown to have high agreement with water positions in crystal structures and will therefore provide essential information to medicinal chemists.
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Rüter A, Kuczera S, Pochan DJ, Olsson U. Twisted Ribbon Aggregates in a Model Peptide System. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5802-5808. [PMID: 30955339 DOI: 10.1021/acs.langmuir.8b03886] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The model peptides A8K and A10K self-assemble in water into ca. 100 nm long ribbon-like aggregates. These structures can be described as β-sheets laminated into a ribbon structure with a constant elliptical cross-section of 4 by 8 nm, where the longer axis corresponds to a finite number, N ≈ 15, of laminated sheets, and 4 nm corresponds to a stretched peptide length. The ribbon cross-section is strikingly constant and independent of the peptide concentration. High-contrast transmission electron microscopy shows that the ribbons are twisted with a pitch λ ≈ 15 nm. The self-assembly is analyzed within a simple model taking into account the interfacial free energy of the hydrophobic β-sheets and a free energy penalty arising from an increased stretching of hydrogen bonds within the laminated β-sheets, arising from the twist of the ribbons. The model predicts an optimal value N, in agreement with the experimental observations.
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Affiliation(s)
- Axel Rüter
- Division of Physical Chemistry , Lund University , SE-22100 Lund , Sweden
| | - Stefan Kuczera
- Division of Physical Chemistry , Lund University , SE-22100 Lund , Sweden
| | - Darrin J Pochan
- Department of Materials Science and Engineering , University of Delaware , Newark , Delaware 19716 , United States
| | - Ulf Olsson
- Division of Physical Chemistry , Lund University , SE-22100 Lund , Sweden
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Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there? J Comput Aided Mol Des 2018; 33:133-203. [DOI: 10.1007/s10822-018-0111-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 03/09/2018] [Indexed: 10/27/2022]
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Rackers JA, Wang Z, Lu C, Laury ML, Lagardère L, Schnieders MJ, Piquemal JP, Ren P, Ponder JW. Tinker 8: Software Tools for Molecular Design. J Chem Theory Comput 2018; 14:5273-5289. [PMID: 30176213 PMCID: PMC6335969 DOI: 10.1021/acs.jctc.8b00529] [Citation(s) in RCA: 280] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Tinker software, currently released as version 8, is a modular molecular mechanics and dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with OpenMP extensions. It supports a wide variety of force fields, including polarizable models such as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. The package runs on Linux, macOS, and Windows systems. In addition to canonical Tinker, there are branches, Tinker-HP and Tinker-OpenMM, designed for use on message passing interface (MPI) parallel distributed memory supercomputers and state-of-the-art graphical processing units (GPUs), respectively. The Tinker suite also includes a tightly integrated Java-based graphical user interface called Force Field Explorer (FFE), which provides molecular visualization capabilities as well as the ability to launch and control Tinker calculations.
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Affiliation(s)
- Joshua A. Rackers
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Zhi Wang
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Chao Lu
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Marie L. Laury
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Louis Lagardère
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Michael J. Schnieders
- Department of Biomedical Engineering, The University of Iowa, Iowa City, IA 52242, United States
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Paris 06, UMR 7616, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jay W. Ponder
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
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8
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Coupry DE, Addicoat MA, Heine T. Explicit treatment of hydrogen bonds in the universal force field: Validation and application for metal-organic frameworks, hydrates, and host-guest complexes. J Chem Phys 2018; 147:161705. [PMID: 29096468 DOI: 10.1063/1.4985196] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A straightforward means to include explicit hydrogen bonds within the Universal Force Field (UFF) is presented. Instead of treating hydrogen bonds as non-bonded interaction subjected to electrostatic and Lennard-Jones potentials, we introduce an explicit bond with a negligible bond order, thus maintaining the structural integrity of the H-bonded complexes and avoiding the necessity to assign arbitrary charges to the system. The explicit hydrogen bond changes the coordination number of the acceptor site and the approach is thus most suitable for systems with under-coordinated atoms, such as many metal-organic frameworks; however, it also shows an excellent performance for other systems involving a hydrogen-bonded framework. In particular, it is an excellent means for creating starting structures for molecular dynamics and for investigations employing more sophisticated methods. The approach is validated for the hydrogen bonded complexes in the S22 dataset and then employed for a set of metal-organic frameworks from the Computation-Ready Experimental database and several hydrogen bonded crystals including water ice and clathrates. We show that the direct inclusion of hydrogen bonds reduces the maximum error in predicted cell parameters from 66% to only 14%, and the mean unsigned error is similarly reduced from 14% to only 4%. We posit that with the inclusion of hydrogen bonding, the solvent-mediated breathing of frameworks such as MIL-53 is now accessible to rapid UFF calculations, which will further the aim of rapid computational scanning of metal-organic frameworks while providing better starting points for electronic structure calculations.
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Affiliation(s)
- Damien E Coupry
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Fakultät für Chemie und Mineralogie, Universität Leipzig, Linnéstr. 2, 04103 Leipzig, Germany
| | - Matthew A Addicoat
- School of Science and Technology, Nottingham Trent University, Clifton Lane, NG11 8NS Nottingham, United Kingdom
| | - Thomas Heine
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Fakultät für Chemie und Mineralogie, Universität Leipzig, Linnéstr. 2, 04103 Leipzig, Germany
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9
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Varfolomeeva VV, Terentev AV. Weak hydrogen bonds in adsorption of nonrigid molecules on graphitized thermal carbon black. J STRUCT CHEM+ 2017. [DOI: 10.1134/s0022476617030180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Moeljadi AMP, Schmid R, Hirao H. Dioxygen binding to Fe-MOF-74: microscopic insights from periodic QM/MM calculations. CAN J CHEM 2016. [DOI: 10.1139/cjc-2016-0284] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Accurate MOF-FF parameter sets were determined for the ferrous and ferric forms of an iron-based metal–organic framework (MOF) called Fe-MOF-74. For this purpose, density functional theory (DFT) calculations were applied to truncated cluster models of Fe-MOF-74, and the DFT-calculated geometries and energy derivatives were used for the force-field parameterization. The resultant parameter sets performed remarkably well in reproducing the experimentally determined structure of the MOF. We also performed periodic quantum mechanics (QM) / molecular mechanics (MM) calculations employing a subtractive scheme called ONIOM, with the optimized MOF-FF parameters used for the MM calculations, in an attempt to evaluate the binding energies between O2 and several Fe-MOF-74 variants. The calculated binding energy for Fe-MOF-74 agreed very well with the experimental value, and QM/MM geometry optimization calculations confirmed that the O2-bound complex has a side-on geometry. Our calculations also predicted that, when the two neighboring iron ions around the O2-binding site are replaced with other metal ions (Mg2+, Ni2+, Zn2+, Co2+, or Mn2+), there are noticeable variations in the binding energy, indicating that these substituted metal ions affect the O2 binding indirectly.
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Affiliation(s)
- Adhitya Mangala Putra Moeljadi
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Rochus Schmid
- Computational Materials Chemistry Group, Chair of Inorganic Chemistry 2, Ruhr-University Bochum, D-44801 Bochum, Germany
| | - Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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11
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Hagler AT. Quantum Derivative Fitting and Biomolecular Force Fields: Functional Form, Coupling Terms, Charge Flux, Nonbond Anharmonicity, and Individual Dihedral Potentials. J Chem Theory Comput 2015; 11:5555-72. [DOI: 10.1021/acs.jctc.5b00666] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- A. T. Hagler
- Department of Chemistry University of Massachusetts, Amherst, Massachusetts 01003, United States
- Shifa Biopharm, Shifa Biomedical Corporation, Malvern, Pennsylvania 19355, United States
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12
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O’Meara MJ, Leaver-Fay A, Tyka M, Stein A, Houlihan K, DiMaio F, Bradley P, Kortemme T, Baker D, Snoeyink J, Kuhlman B. Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta. J Chem Theory Comput 2015; 11:609-22. [PMID: 25866491 PMCID: PMC4390092 DOI: 10.1021/ct500864r] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Interactions between polar atoms are challenging to model because at very short ranges they form hydrogen bonds (H-bonds) that are partially covalent in character and exhibit strong orientation preferences; at longer ranges the orientation preferences are lost, but significant electrostatic interactions between charged and partially charged atoms remain. To simultaneously model these two types of behavior, we refined an orientation dependent model of hydrogen bonds [Kortemme et al. J. Mol. Biol. 2003, 326, 1239] used by the molecular modeling program Rosetta and then combined it with a distance-dependent Coulomb model of electrostatics. The functional form of the H-bond potential is physically motivated and parameters are fit so that H-bond geometries that Rosetta generates closely resemble H-bond geometries in high-resolution crystal structures. The combined potentials improve performance in a variety of scientific benchmarks including decoy discrimination, side chain prediction, and native sequence recovery in protein design simulations and establishes a new standard energy function for Rosetta.
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Affiliation(s)
- Matthew J. O’Meara
- Department of Computer Science, University of North Carolina, 201 S Columbia St. Chapel Hill, North Carolina 27599, United States
| | - Andrew Leaver-Fay
- Department of Biochemistry and Biophysics, University of North Carolina, 120 Mason Farm Rd Chapel Hill, North Carolina 27599, United States
| | - Mike Tyka
- Google Inc., 1600 Amphitheatre Parkway Mountain View, California 94043, United States
| | - Amelie Stein
- Department of Bioengineering and Therapeutic Science, University of California San Francisco, 513 Parnassus Avenue San Francisco, California 94143, United States
| | - Kevin Houlihan
- Department of Biochemistry and Biophysics, University of North Carolina, 120 Mason Farm Rd Chapel Hill, North Carolina 27599, United States
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, 1705 North East Pacific Street Seattle Washington 98195, United States
| | - Philip Bradley
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle Washington 98109, United States
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Science, University of California San Francisco, 513 Parnassus Avenue San Francisco, California 94143, United States
| | - David Baker
- Department of Biochemistry, University of Washington, 1705 North East Pacific Street Seattle Washington 98195, United States
| | - Jack Snoeyink
- Department of Computer Science, University of North Carolina, 201 S Columbia St. Chapel Hill, North Carolina 27599, United States
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina, 120 Mason Farm Rd Chapel Hill, North Carolina 27599, United States
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Hughes TJ, Kandathil SM, Popelier PLA. Accurate prediction of polarised high order electrostatic interactions for hydrogen bonded complexes using the machine learning method kriging. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt A:32-41. [PMID: 24274986 DOI: 10.1016/j.saa.2013.10.059] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Revised: 09/02/2013] [Accepted: 10/15/2013] [Indexed: 06/02/2023]
Abstract
As intermolecular interactions such as the hydrogen bond are electrostatic in origin, rigorous treatment of this term within force field methodologies should be mandatory. We present a method able of accurately reproducing such interactions for seven van der Waals complexes. It uses atomic multipole moments up to hexadecupole moment mapped to the positions of the nuclear coordinates by the machine learning method kriging. Models were built at three levels of theory: HF/6-31G(**), B3LYP/aug-cc-pVDZ and M06-2X/aug-cc-pVDZ. The quality of the kriging models was measured by their ability to predict the electrostatic interaction energy between atoms in external test examples for which the true energies are known. At all levels of theory, >90% of test cases for small van der Waals complexes were predicted within 1 kJ mol(-1), decreasing to 60-70% of test cases for larger base pair complexes. Models built on moments obtained at B3LYP and M06-2X level generally outperformed those at HF level. For all systems the individual interactions were predicted with a mean unsigned error of less than 1 kJ mol(-1).
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Affiliation(s)
- Timothy J Hughes
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, United Kingdom; School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Shaun M Kandathil
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, United Kingdom; School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Paul L A Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester M1 7DN, United Kingdom; School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom.
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14
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Carpenter BK, Harvey JN, Glowacki DR. Prediction of enhanced solvent-induced enantioselectivity for a ring opening with a bifurcating reaction path. Phys Chem Chem Phys 2015; 17:8372-81. [DOI: 10.1039/c4cp05078a] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A fully atomistic molecular dynamics simulation predicts enhance induction of enantiomeric excess in the products of a reaction with a bifurcating reaction coordinate, when run in a chiral solvent.
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Affiliation(s)
| | | | - David R. Glowacki
- School of Chemistry
- University of Bristol
- Bristol
- UK
- Department of Computer Science
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15
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Paci JT, Furmanchuk A, Espinosa HD, Schatz GC. Shear and friction between carbon nanotubes in bundles and yarns. NANO LETTERS 2014; 14:6138-6147. [PMID: 25279773 DOI: 10.1021/nl502210r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We perform a detailed density functional theory assessment of the factors that determine shear interactions between carbon nanotubes (CNTs) within bundles and in related CNT and graphene structures including yarns, providing an explanation for the shear force measured in recent experiments (Filleter, T. etal. Nano Lett. 2012, 12, 73). The potential energy barriers separating AB stacked structures are found to be irrelevant to the shear analysis for bundles and yarns due to turbostratic stacking, and as a result, the tube-tube shear strength for pristine CNTs is estimated to be <0.24 MPa, that is, extremely small. Instead, it is pinning due to the presence of defects and functional groups at the tube ends that primarily cause resistance to shear when bundles are fractured in weak vacuum (∼10(-5) Torr). Such defects and groups are estimated to involve 0.55 eV interaction energies on average, which is much larger than single-atom vacancy defects (approximately 0.039 eV). Furthermore, because graphitic materials are stiff they have large coherence lengths, and this means that push-pull effects result in force cancellation for vacancy and other defects that are internal to the CNTs. Another important factor is the softness of cantilever structures relative to the stiff CNTs in the experiments, as this contributes to elastic instability transitions that account for significant dissipation during shear that has been observed. The application of these results to the mechanical behavior of yarns is discussed, providing general guidelines for the manufacture of strong yarns composed of CNTs.
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Affiliation(s)
- Jeffrey T Paci
- Department of Chemistry and ‡Department of Mechanical Engineering, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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16
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Masone D, Grosdidier S. Collective variable driven molecular dynamics to improve protein–protein docking scoring. Comput Biol Chem 2014; 49:1-6. [DOI: 10.1016/j.compbiolchem.2013.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/28/2013] [Accepted: 12/28/2013] [Indexed: 10/25/2022]
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17
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18
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Matsubara T, Takahashi R, Asai S. ONIOM Study of the Mechanism of Olefin Hydrogenation by the Wilkinson’s Catalyst: Reaction Paths and Energy Surfaces of trans- and cis-Forms. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2013. [DOI: 10.1246/bcsj.20120113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Ryohei Takahashi
- Department of Chemistry, Faculty of Science, Kanagawa University
| | - Saori Asai
- Department of Chemistry, Faculty of Science, Kanagawa University
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19
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Sameera WMC, Pantazis DA. A Hierarchy of Methods for the Energetically Accurate Modeling of Isomerism in Monosaccharides. J Chem Theory Comput 2012; 8:2630-45. [PMID: 26592108 DOI: 10.1021/ct3002305] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- W. M. C. Sameera
- Institut Català d’Investigació
Química, Av. Països Catalans 16, 43007 Tarragona, Spain
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für
Bioanorganische Chemie, Stiftstrasse 34-36, 45470 Mülheim an
der Ruhr, Germany
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20
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Filleter T, Yockel S, Naraghi M, Paci JT, Compton OC, Mayes ML, Nguyen ST, Schatz GC, Espinosa HD. Experimental-computational study of shear interactions within double-walled carbon nanotube bundles. NANO LETTERS 2012; 12:732-742. [PMID: 22214436 DOI: 10.1021/nl203686d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The mechanical behavior of carbon nanotube (CNT)-based fibers and nanocomposites depends intimately on the shear interactions between adjacent tubes. We have applied an experimental-computational approach to investigate the shear interactions between adjacent CNTs within individual double-walled nanotube (DWNT) bundles. The force required to pull out an inner bundle of DWNTs from an outer shell of DWNTs was measured using in situ scanning electron microscopy methods. The normalized force per CNT-CNT interaction (1.7 ± 1.0 nN) was found to be considerably higher than molecular mechanics (MM)-based predictions for bare CNTs (0.3 nN). This MM result is similar to the force that results from exposure of newly formed CNT surfaces, indicating that the observed pullout force arises from factors beyond what arise from potential energy effects associated with bare CNTs. Through further theoretical considerations we show that the experimentally measured pullout force may include small contributions from carbonyl functional groups terminating the free ends of the CNTs, corrugation of the CNT-CNT interactions, and polygonization of the nanotubes due to their mutual interactions. In addition, surface functional groups, such as hydroxyl groups, that may exist between the nanotubes are found to play an unimportant role. All of these potential energy effects account for less than half of the ~1.7 nN force. However, partially pulled-out inner bundles are found not to pull back into the outer shell after the outer shell is broken, suggesting that dissipation is responsible for more than half of the pullout force. The sum of force contributions from potential energy and dissipation effects are found to agree with the experimental pullout force within the experimental error.
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Affiliation(s)
- Tobin Filleter
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3111, USA
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21
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Minenkov Y, Occhipinti G, Heyndrickx W, Jensen VR. The Nature of the Barrier to Phosphane Dissociation from Grubbs Olefin Metathesis Catalysts. Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201100932] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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KANG CONGMIN, LIN ZHENYANG. STRUCTURES AND ENERGETICS OF PORPHYRIN-FULLERENE SUPRAMOLECULAR COMPLEXES. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633606002568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this paper, the structures and energetics of porphyrin-fullerene supramolecular complexes have been investigated theoretically via molecular mechanics calculations on complexes having different porphyrins. The results of the calculations allow us to delineate the effect of the substituents on the porphyrin ring on the porphyrin-fullerene interaction energies. The calculations also allow us to understand how the van der Waals force affects the structures of the 2:1, 2:2, and 3:1 supramolecular complexes.
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Affiliation(s)
- CONGMIN KANG
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China
- College of Chemical Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, 266042, P. R. China
| | - ZHENYANG LIN
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China
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23
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Zheng M, Xiong B, Luo C, Li S, Liu X, Shen Q, Li J, Zhu W, Luo X, Jiang H. Knowledge-Based Scoring Functions in Drug Design: 3. A Two-Dimensional Knowledge-Based Hydrogen-Bonding Potential for the Prediction of Protein–Ligand Interactions. J Chem Inf Model 2011; 51:2994-3004. [DOI: 10.1021/ci2003939] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Bing Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Cheng Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Shanshan Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xian Liu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Qianchen Shen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jing Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Weiliang Zhu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xiaomin Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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24
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Kolocouris A. The effect of spiroadamantane substitution on the conformational preferences of N-Me pyrrolidine and N-Me piperidine: a description based on dynamic NMR spectroscopy and ab initio correlated calculations. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.08.071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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25
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Minenkov Y, Occhipinti G, Jensen VR. Metal−Phosphine Bond Strengths of the Transition Metals: A Challenge for DFT. J Phys Chem A 2009; 113:11833-44. [DOI: 10.1021/jp902940c] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yury Minenkov
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
| | - Giovanni Occhipinti
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
| | - Vidar R. Jensen
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
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26
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Lii JH, Allinger NL. The important role of lone-pairs in force field (MM4) calculations on hydrogen bonding in alcohols. J Phys Chem A 2008; 112:11903-13. [PMID: 18942820 DOI: 10.1021/jp804581h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An expanded treatment of hydrogen bonding has been developed for MM4 force field calculations, which is an extension from the traditional van der Waals-electrostatic model. It adds explicit hydrogen-bond angularity by the inclusion of lone-pair directionality. The vectors that account for this directionality are placed along the hydrogen acceptor and its chemically intuitive electron pairs. No physical lone-pairs are used in the calculations. Instead, an H-bond angularity function, and a lone-pair directionality function, are incorporated into the hydrogen-bond term. The inclusion of the lone-pair directionality results in improved accuracy in hydrogen-bonded geometries and interaction energies. In this work is described hydrogen bonding in alcohols, and also in water and hydrogen fluoride dimer. The extension to other compounds such as aldehydes, ketones, amides, and so on is straightforward and will be discussed in future work. The conformational energies of ethylene glycol are discussed.
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Affiliation(s)
- Jenn-Huei Lii
- Department of Chemistry, University of Georgia, Athens, Georgia 30602-2526, USA
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27
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Matsubara T, Sugimoto H, Aida M. A Theoretical Insight into the Interaction of Fatty Acids Involved in Royal Jelly with the Human Estrogen Receptor β. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2008. [DOI: 10.1246/bcsj.81.1258] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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28
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OBATA S, GOTO H. Conformational Polymorphism Analysis of Aspirin Crystal with a Crystal Calculation Method. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2008. [DOI: 10.2477/jccj.h2016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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29
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Levashov VA, Billinge SJL, Thorpe MF. Quantum correction to the pair distribution function. J Comput Chem 2007; 28:1865-82. [PMID: 17405116 DOI: 10.1002/jcc.20713] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We report a numerical technique that allows the quantum effects of zero-point motion to be incorporated into Pair Distribution Functions calculated classically for molecules using Monte Carlo or Molecular Dynamics simulations. We establish the basis for this approximation using a diatomic molecule described by a Morse potential. The correction should significantly improve the agreement between modeled and experimental data, and facilitate conclusions about inter- and intra-molecular motion and flexibility. We describe a similar approach to obtain the energy and the specific heat.
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Affiliation(s)
- V A Levashov
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
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30
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Altmann J, Govender M, Ford * T. Ab initioand DFT calculations of some weakly bound dimers and complexes. I. The dimers of ammonia and phosphine. Mol Phys 2005. [DOI: 10.1080/00268470412331333555] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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Morozov AV, Kortemme T. Potential functions for hydrogen bonds in protein structure prediction and design. ADVANCES IN PROTEIN CHEMISTRY 2005; 72:1-38. [PMID: 16581371 DOI: 10.1016/s0065-3233(05)72001-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Hydrogen bonds are an important contributor to free energies of biological macromolecules and macromolecular complexes, and hence an accurate description of these interactions is important for progress in biomolecular modeling. A simple description of the hydrogen bond is based on an electrostatic dipole-dipole interaction involving hydrogen-donor and acceptor-acceptor base dipoles, but the physical nature of hydrogen bond formation is more complex. At the most fundamental level, hydrogen bonding is a quantum mechanical phenomenon with contributions from covalent effects, polarization, and charge transfer. Recent experiments and theoretical calculations suggest that both electrostatic and covalent components determine the properties of hydrogen bonds. Likely, the level of rigor required to describe hydrogen bonding will depend on the problem posed. Current approaches to modeling hydrogen bonds include knowledge-based descriptions based on surveys of hydrogen bond geometries in structural databases of proteins and small molecules, empirical molecular mechanics models, and quantum mechanics-based electronic structure calculations. Ab initio calculations of hydrogen bonding energies and geometries accurately reproduce energy landscapes obtained from the distributions of hydrogen bond geometries observed in protein structures. Orientation-dependent hydrogen bonding potentials were found to improve the quality of protein structure prediction and refinement, protein-protein docking, and protein design.
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Affiliation(s)
- Alexandre V Morozov
- Center for Studies in Physics and Biology, Rockefeller University, New York, New York 10021
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32
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Carrasco N, González-Nilo F, Rezende MC. Relative solvation and strength of polycyano- and polynitromethanes in water: a study with molecular dynamics simulations. J PHYS ORG CHEM 2004. [DOI: 10.1002/poc.867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Masia M, Rey R. Computational Study of γ-Butyrolactone and Li+/γ-butyrolactone in Gas and Liquid Phases. J Phys Chem B 2004. [DOI: 10.1021/jp046979i] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marco Masia
- Departament de Física i Enginyeria Nuclear, Universitat Politécnica de Catalunya, Campus Nord B4-B5, Barcelona 08034, Spain
| | - Rossend Rey
- Departament de Física i Enginyeria Nuclear, Universitat Politécnica de Catalunya, Campus Nord B4-B5, Barcelona 08034, Spain
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34
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Morozov AV, Kortemme T, Tsemekhman K, Baker D. Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proc Natl Acad Sci U S A 2004; 101:6946-51. [PMID: 15118103 PMCID: PMC406446 DOI: 10.1073/pnas.0307578101] [Citation(s) in RCA: 195] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2003] [Accepted: 02/25/2004] [Indexed: 11/18/2022] Open
Abstract
Hydrogen bonding is a key contributor to the exquisite specificity of the interactions within and between biological macromolecules, and hence accurate modeling of such interactions requires an accurate description of hydrogen bonding energetics. Here we investigate the orientation and distance dependence of hydrogen bonding energetics by combining two quite disparate but complementary approaches: quantum mechanical electronic structure calculations and protein structural analysis. We find a remarkable agreement between the energy landscapes obtained from the electronic structure calculations and the distributions of hydrogen bond geometries observed in protein structures. In contrast, molecular mechanics force fields commonly used for biomolecular simulations do not consistently exhibit close correspondence to either quantum mechanical calculations or experimentally observed hydrogen bonding geometries. These results suggest a route to improved energy functions for biological macromolecules that combines the generality of quantum mechanical electronic structure calculations with the accurate context dependence implicit in protein structural analysis.
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Affiliation(s)
- Alexandre V Morozov
- Departments of Biochemistry and Chemistry, University of Washington, Seattle, WA 98195, USA
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35
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Karamertzanis PG, Pantelides CC. Ab initio crystal structure prediction?I. Rigid molecules. J Comput Chem 2004; 26:304-24. [PMID: 15622548 DOI: 10.1002/jcc.20165] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A new methodology for the prediction of molecular crystal structures using only the atomic connectivity of the molecule under consideration is presented. The approach is based on the global minimization of the lattice enthalpy of the crystal. The modeling of the electrostatic interactions is accomplished through a set of distributed charges that are optimally and automatically selected and positioned based on results of quantum mechanical calculations. A four-step global optimization algorithm is used for the identification of the local minima of the lattice enthalpy surface. A parallelized implementation of the algorithm permits a much more extensive search of the solution space than has hitherto been possible, allowing the identification of crystal structures in less frequently occurring space groups and with more than one molecule in the asymmetric unit. The algorithm has been applied successfully to the prediction of the crystal structures of 3-aza-bicyclo(3.3.1)nonane-2,4-dione (P2(1)/a, Z' = 1), allopurinol (P2(1)/c, Z' = 1), 1,3,4,6,7,9-hexa-azacycl(3.3.3)azine (Pbca, Z' = 2), and triethylenediamine (P6(3)/m, Z' = 1). In all cases, the experimentally known structure is among the most stable predicted structures, but not necessarily the global minimum.
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Affiliation(s)
- Panagiotis G Karamertzanis
- Centre for Process Systems Engineering, Department of Chemical Engineering and Chemical Technology, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
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36
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Lii JH, Chen KH, Grindley TB, Allinger NL. Alcohols, ethers, carbohydrates, and related compounds. III. The 1,2-dimethoxyethane system. J Comput Chem 2003; 24:1490-503. [PMID: 12868112 DOI: 10.1002/jcc.10270] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Ethylene glycol, its dimethyl ether, and some related compounds have been studied using the MM4 molecular mechanics force field. The MM4 calculated structural and energetic results have been brought into satisfactory agreement with a considerable number of experimental data and MP2/6-311++G(2d,2p) ab initio calculations. The heats of formation of these compounds are also well calculated. The MM4 ethylene glycol conformations in particular are in good agreement, both geometrically and in terms of energy, with those from the ab initio calculations. The corresponding dimethyl ether is of special interest, because it has been suggested that the trans-gauche conformation is unusually stable due to the hydrogen bonding of a hydrogen on a methyl group with the more distant oxygen. It is shown in the present work that while this conformation is more stable than might have been expected, the energy is adequately calculated by MM4 without using any hydrogen bonding between the Cbond;H bond and the oxygen. If such hydrogen bonding occurs, it amounts to no more than about 0.5 kcal/mol in energy, and is too small to detect with certainty. Additionally, energetic relationships in trans-1,2-dimethoxycyclohexane, 1,3,5,7-tetraoxadecalin, and 3-methoxytetrahydropyran have been studied, and the calculated results are compared with experimental information, which is adequately reproduced.
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Affiliation(s)
- Jenn-Huei Lii
- Department of Chemistry, Computational Center for Molecular Structure and Design, Chemistry Annex, University of Georgia, Athens, Georgia 30602-2526, USA
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37
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Langley CH, Allinger NL. Molecular Mechanics (MM4) and ab Initio Study of Amide−Amide and Amide−Water Dimers. J Phys Chem A 2003. [DOI: 10.1021/jp021764z] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Charles H. Langley
- Department of Chemistry, Chemistry Annex, The University of Georgia, Athens, Georgia 30602-2526
| | - Norman L. Allinger
- Department of Chemistry, Chemistry Annex, The University of Georgia, Athens, Georgia 30602-2526
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38
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Klein RA. Ab initio conformational studies on diols and binary diol-water systems using DFT methods. Intramolecular hydrogen bonding and 1:1 complex formation with water. J Comput Chem 2002; 23:585-99. [PMID: 11939593 DOI: 10.1002/jcc.10053] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Studies on the conformational equilibrium for the following diols, ethane-1,2-diol (12EG, CAS 107-21-1), 2R-D-(-)-propane-1,2-diol (12PG, CAS 4254-14-2), (2S,3S)-L-(+)-butane-2,3-diol (L23BD, CAS 19132-06-0), and (2S,3R)-meso-butane-2,3-diol (m23BD, CAS 5341-95-7), are described using Gaussian ab initio calculations involving density functional theory (DFT) methods. We also report in this article results on the stability and conformation for the 1:1 water-diol complex formed by ethane-1,2-diol, propane-1,2-diol, and L- and meso-butane-2,3-diol. The relative stability of the intramolecular (internal) hydrogen bond in a range of diols (n = 2 to 6), based on ab initio geometry optimization and determination of the -O...H- distance, dOH, and -O-H...O- angle, theta, increases through the sequence 1,2 approximately equals 2,3 < 1,3 < 1,4 approximately equals 1,5 approximately equals 1,6, as judged from the bond linearity and -O...H- separation. Quantum mechanical and topological analysis of possible intramolecular hydrogen bonding in this complete series of diols provides convincing evidence for this in diols in which the hydroxyl groups are separated by three or more carbon atoms, that is, in (n, n+m) diols for m > or = 2, but not for ethane-1,2-diol or other vicinal diols, which do not satisfy Popelier's topological and electron density criteria based on the AIM theory of Bader. Based on these criteria it is unlikely that vicinal diols are in fact capable of forming an intramolecular hydrogen bond, in spite of geometric and spectroscopic data in the literature suggesting otherwise.
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Affiliation(s)
- Roger A Klein
- Institute for Physiological Chemistry, University of Bonn, Federal Republic of Germany.
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39
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Hay BP, Dixon DA, Vargas R, Garza J, Raymond KN. Structural criteria for the rational design of selective ligands. 3. Quantitative structure-stability relationship for iron(III) complexation by tris-catecholamide siderophores. Inorg Chem 2001; 40:3922-35. [PMID: 11466050 DOI: 10.1021/ic001380s] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present an extended MM3 model for catecholamide ligands and their Fe(3+) complexes and the application of this model to understand how ligand architecture effects Fe(3+) binding affinity. Force field parameters were fit to geometries and energies from electronic structure calculations, and to crystal structure data. Optimized geometries are reported for phenol, acetamide, the phenol-phenol dimer, the acetamide-phenol dimer, and N-methylsalicylamide (HMSA) at the BLYP/DZVP2/A2 level of theory. Optimized geometries and relative energies are reported for the pseudo-octahedral ground state and the trigonal planar transition state of [Fe(CAT)(3)](3)(-) at the VWN/DZVP2/A1 level of theory. The MM3 model is validated by comparison of calculated structures with crystal structures containing 1,2-dihydroxybenzene (H(2)CAT) and 2,3-dihydroxy-N-methylbenzamide (H(2)MBA) fragments, crystal structures of [Fe(CAT)(3)](3)(-) and tris-catecholamide Fe(3+) complexes, and comparison of MM3 (6.8 kcal/mol) and VWN (5.9 kcal/mol) barriers for intramolecular octahedral inversion in [Fe(CAT)(3)](3)(-). The MM3 model also rationalizes the higher inversion barrier (14 to 18 kcal/mol) reported for [Ga(N,N-diisopropylterephthalamide)(3)](3)(-) ([Ga(DIPTA)(3)](3)(-)). Conformational searches were performed on enterobactin (H(6)ENT), 1,3,5-tris(2,3-dihydroxybenzamidomethyl)-2,4,6-triethylbenzene (H(6)EMECAM), 1,3,5-tris(2,3-dihydroxybenzamidomethyl)-2,4,6-trimethylbenzene (H(6)MMECAM), 1,3,5-tris(2,3-dihydroxybenzamidomethyl)benzene (H(6)MECAM), and 1,5,9-N,N',N' '-tris(2,3-dihydroxybenzoyl)cyclotriazatridecane (H(6)-3,3,4-CYCAM) and Fe(3+) complexes with each of these ligands. A conformational search also was done on the Fe(3+) complex with the 2,2',2' '-tris(2,3-dihydroxybenzamido)triethylammonium cation (H(7)TRENCAM(+)). The relationship between calculated steric energies and measured thermodynamic quantities is discussed, and linear correlations between formation constants and steric energy differences are reported. Extrapolation to zero strain predicts formation constants 8 +/- 5 orders of magnitude higher than that exhibited by ENT (10(49)) are possible. This prediction is supported by a formation constant of 10(63) estimated from the formation constant of [Fe(2,3-dihydroxy-N,N-dimethylbenzamide)(3)](3)(-) ([Fe(DMBA)(3)](3)(-)) by considering the entropic consequences of connecting three DMBA ligands to a rigid backbone. Structural criteria for the identification of improved tris-catecholate ligand architectures are presented.
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Affiliation(s)
- B P Hay
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
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40
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Sorensen JB, Lewin AH, Bowen JP. Ab initio and molecular mechanics (MM3) calculations of protonated-neutral diamine hydrogen bonds. J Org Chem 2001; 66:4105-14. [PMID: 11397141 DOI: 10.1021/jo000610h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ab initio calculations of cation-neutral diamine complexes have been carried out at the MP2/6-311+G** level. The geometry and energetics of the charge-reinforced hydrogen bond are analyzed with respect to the alkyl substitution of both the protonated and neutral nitrogen atoms, and these results have been used to improve the quality of the MM3(2000) force field. In addition, specialized hydrogen bond parameters optimized for MM3(2000) are presented. These parameters allow very accurate gas-phase modeling of the charge-neutral diamine environment. Molecular mechanics calculations can model effectively protonated amine-neutral amine hydrogen bonds in the gas phase and solution (continuum dielectric) through a combination of charge-dipole interactions and explicit hydrogen-bonding terms.
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Affiliation(s)
- J B Sorensen
- The Computational Center for Molecular Structure and Design, Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
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41
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Bjerkeseth LH, Bakke JM, Uggerud E. Inter- and intramolecular O–H⋯π hydrogen bonding in the methanol–ethene complex and syn -7-norbornenol, probed by IR, 1 H NMR and quantum chemistry. J Mol Struct 2001. [DOI: 10.1016/s0022-2860(01)00563-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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42
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Bouchoux G, Choret N, Berruyer-Penaud F. Protonation Thermochemistry of α,ω-Alkyldiamines in the Gas Phase: A Theoretical Study. J Phys Chem A 2001. [DOI: 10.1021/jp003753g] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Guy Bouchoux
- Département de Chimie, Laboratoire des Mécanismes Réactionnels, UMR CNRS 7651, Ecole Polytechnique, 91128 Palaiseau Cedex, France, and Laboratoire de Chimie Physique, Groupe de Chimie Théorique, UMR CNRS 8000, Bâtiment 490, Université Paris Sud, 91405 Orsay Cedex, France
| | - Nadège Choret
- Département de Chimie, Laboratoire des Mécanismes Réactionnels, UMR CNRS 7651, Ecole Polytechnique, 91128 Palaiseau Cedex, France, and Laboratoire de Chimie Physique, Groupe de Chimie Théorique, UMR CNRS 8000, Bâtiment 490, Université Paris Sud, 91405 Orsay Cedex, France
| | - Florence Berruyer-Penaud
- Département de Chimie, Laboratoire des Mécanismes Réactionnels, UMR CNRS 7651, Ecole Polytechnique, 91128 Palaiseau Cedex, France, and Laboratoire de Chimie Physique, Groupe de Chimie Théorique, UMR CNRS 8000, Bâtiment 490, Université Paris Sud, 91405 Orsay Cedex, France
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French AD, Kelterer AM, Cramer CJ, Johnson GP, Dowd MK. A QM/MM analysis of the conformations of crystalline sucrose moieties. Carbohydr Res 2000; 326:305-22. [PMID: 10890277 DOI: 10.1016/s0008-6215(00)00051-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Both ab initio quantum mechanics (QM) and molecular mechanics (MM) were used to produce a hybrid energy surface for sucrose that simultaneously provides low energies for conformations that are observed in crystal structures and high energies for most unobserved structures. HF/6-31G* QM energies were calculated for an analogue based on tetrahydropyran (THP) and tetrahydrofuran (THF). Remaining contributions to the potential energy of sucrose were calculated with MM. To do this, the MM surface for the analogue was subtracted from the MM surface for the disaccharide, and the QM surface for the analogue was added. Prediction of the distribution of observable geometries was enhanced by reducing the strength of the hydrogen bonding. Reduced hydrogen-bonding strength is probably useful because many crystalline sucrose moieties do not have intramolecular hydrogen bonds between the fructose and glucose residues. Therefore, hydrogen bonding does not play a large role in determining the molecular conformation. On the hybrid energy surface that was constructed with a dielectric constant of 3.5, the average potential energy of 23 sucrose moieties from crystal structures is 1.16 kcal/mol, and the population of observed structures drops off exponentially as the energy increases.
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Affiliation(s)
- A D French
- Southern Regional Research Center, Agricultural Research Service, US Department of Agriculture, New Orleans, LA 70179-0687, USA.
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Mooij WTM, van Eijck BP, Kroon J. Transferable ab Initio Intermolecular Potentials. 2. Validation and Application to Crystal Structure Prediction. J Phys Chem A 1999. [DOI: 10.1021/jp991640v] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wijnand T. M. Mooij
- Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Bouke P. van Eijck
- Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Jan Kroon
- Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Lii JH, Ma B, Allinger NL. Importance of selecting proper basis set in quantum mechanical studies of potential energy surfaces of carbohydrates. J Comput Chem 1999. [DOI: 10.1002/(sici)1096-987x(19991130)20:15<1593::aid-jcc1>3.0.co;2-a] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Norrman K, McMahon TB. Intramolecular Solvation of Carboxylate Anions in the Gas Phase. J Phys Chem A 1999. [DOI: 10.1021/jp9908202] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K. Norrman
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada
| | - T. B. McMahon
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada
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Barrows SE, Storer JW, Cramer CJ, French AD, Truhlar DG. Factors controlling relative stability of anomers and hydroxymethyl conformers of glucopyranose. J Comput Chem 1998. [DOI: 10.1002/(sici)1096-987x(19980730)19:10<1111::aid-jcc1>3.0.co;2-p] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Barrows SE, Storer JW, Cramer CJ, French AD, Truhlar DG. Factors controlling relative stability of anomers and hydroxymethyl conformers of glucopyranose. J Comput Chem 1998. [DOI: 10.1002/(sici)1096-987x(19980730)19:10%3c1111::aid-jcc1%3e3.0.co;2-p] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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