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Stylianakis I, Zervos N, Lii JH, Pantazis DA, Kolocouris A. Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory. J Comput Aided Mol Des 2023; 37:607-656. [PMID: 37597063 PMCID: PMC10618395 DOI: 10.1007/s10822-023-00513-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/03/2023] [Indexed: 08/21/2023]
Abstract
We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree-Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol-1), followed by B3LYP (0.69 kcal mol-1) and the HF theories (0.81-1.0 kcal mol-1). As regards the force fields, the lowest errors were observed for the Allinger's force fields MM3-00 (1.28 kcal mol-1), ΜΜ3-96 (1.40 kcal mol-1) and the Halgren's MMFF94 force field (1.30 kcal mol-1) and then for the MM2-91 clones MMX (1.77 kcal mol-1) and MM+ (2.01 kcal mol-1) and MM4 (2.05 kcal mol-1). The DREIDING (3.63 kcal mol-1) and UFF (3.77 kcal mol-1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization.
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Affiliation(s)
- Ioannis Stylianakis
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece
| | - Nikolaos Zervos
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece
| | - Jenn-Huei Lii
- Department of Chemistry, National Changhua University of Education, Changhua City, Taiwan
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Antonios Kolocouris
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece.
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece.
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2
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Brown M, Skelton JM, Popelier PLA. Construction of a Gaussian Process Regression Model of Formamide for Use in Molecular Simulations. J Phys Chem A 2023; 127:1702-1714. [PMID: 36756842 PMCID: PMC9969515 DOI: 10.1021/acs.jpca.2c06566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
FFLUX, a novel force field based on quantum chemical topology, can perform molecular dynamics simulations with flexible multipole moments that change with geometry. This is enabled by Gaussian process regression machine learning models, which accurately predict atomic energies and multipole moments up to the hexadecapole. We have constructed a model of the formamide monomer at the B3LYP/aug-cc-pVTZ level of theory capable of sub-kJ mol-1 accuracy, with the maximum prediction error for the molecule being 0.8 kJ mol-1. This model was used in FFLUX simulations along with Lennard-Jones parameters to successfully optimize the geometry of formamide dimers with errors smaller than 0.1 Å compared to those obtained with D3-corrected B3LYP/aug-cc-pVTZ. Comparisons were also made to a force field constructed with static multipole moments and Lennard-Jones parameters. FFLUX recovers the expected energy ranking of dimers compared to the literature, and changes in C═O and C-N bond lengths associated with hydrogen bonding were found to be consistent with density functional theory.
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Mehmood M, Imtiaz-ud-Din, Abbas S, Azam SS, Ihsan-ul-Haq, Tahir MN, Parvaiz N, Tameez Ud Din A. Bioactive heteroleptic Bismuth(V) carboxylates: Synthetic Stratagem, characterization and binding pattern validation. J Organomet Chem 2020. [DOI: 10.1016/j.jorganchem.2020.121357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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4
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Dubbeldam D, Walton KS, Vlugt TJH, Calero S. Design, Parameterization, and Implementation of Atomic Force Fields for Adsorption in Nanoporous Materials. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201900135] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- David Dubbeldam
- Van 't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 904 1098XH Amsterdam The Netherlands
| | - Krista S. Walton
- School of Chemical & Biomolecular EngineeringGeorgia Institute of Technology311 Ferst Dr. NW Atlanta GA 30332‐0100 USA
| | - Thijs J. H. Vlugt
- Delft University of TechnologyProcess & Energy DepartmentLeeghwaterstraat 39 2628CB Delft The Netherlands
| | - Sofia Calero
- Department of PhysicalChemical and Natural SystemsUniversity Pablo de OlavideSevilla 41013 Spain
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5
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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: 301] [Impact Index Per Article: 50.2] [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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6
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Bouju X, Mattioli C, Franc G, Pujol A, Gourdon A. Bicomponent Supramolecular Architectures at the Vacuum–Solid Interface. Chem Rev 2017; 117:1407-1444. [DOI: 10.1021/acs.chemrev.6b00389] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Xavier Bouju
- CEMES-CNRS, 29 Rue J. Marvig, 31055 Toulouse, France
| | | | - Grégory Franc
- CEMES-CNRS, 29 Rue J. Marvig, 31055 Toulouse, France
| | - Adeline Pujol
- Université de Toulouse, UPS, CNRS, CEMES, 118 route de Narbonne, 31062 Toulouse, France
| | - André Gourdon
- CEMES-CNRS, 29 Rue J. Marvig, 31055 Toulouse, France
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Della Pia A, Luo D, Blackwell R, Costantini G, Martsinovich N. Molecular self-assembly of substituted terephthalic acids at the liquid/solid interface: investigating the effect of solvent. Faraday Discuss 2017; 204:191-213. [DOI: 10.1039/c7fd00112f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Self-assembly of three related molecules – terephthalic acid and its hydroxylated analogues – at liquid/solid interfaces (graphite/heptanoic acid and graphite/1-phenyloctane) has been studied using a combination of scanning tunnelling microscopy and molecular mechanics and molecular dynamics calculations. Brickwork-like patterns typical for terephthalic acid self-assembly have been observed for all three molecules. However, several differences became apparent: (i) formation or lack of adsorbed monolayers (self-assembled monolayers formed in all systems, with one notable exception of terephthalic acid at the graphite/1-phenyloctane interface where no adsorption was observed), (ii) the size of adsorbate islands (large islands at the interface with heptanoic acid and smaller ones at the interface with 1-phenyloctane), and (iii) polymorphism of the hydroxylated terephthalic acids’ monolayers, dependent on the molecular structure and/or solvent. To rationalise this behaviour, molecular mechanics and molecular dynamics calculations have been performed, to analyse the three key aspects of the energetics of self-assembly: intermolecular, substrate–adsorbate and solvent–solute interactions. These energetic characteristics of self-assembly were brought together in a Born–Haber cycle, to obtain the overall energy effects of formation of self-assembled monolayers at these liquid/solid interfaces.
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Affiliation(s)
- A. Della Pia
- Department of Chemistry
- University of Warwick
- Coventry
- UK
| | - D. Luo
- Department of Chemistry
- University of Warwick
- Coventry
- UK
| | - R. Blackwell
- Department of Chemistry
- University of Sheffield
- Sheffield
- UK
| | - G. Costantini
- Department of Chemistry
- University of Warwick
- Coventry
- UK
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8
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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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9
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Olsen R, Kvamme B, Kuznetsova T. Hydrogen bond lifetimes and statistics of aqueous mono-, di- and tri-ethylene glycol. AIChE J 2016. [DOI: 10.1002/aic.15539] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Richard Olsen
- Dept. of Physics and Technology; University of Bergen; Allégaten 55 Bergen 5007 Norway
| | - Bjørn Kvamme
- Dept. of Physics and Technology; University of Bergen; Allégaten 55 Bergen 5007 Norway
| | - Tatiana Kuznetsova
- Dept. of Physics and Technology; University of Bergen; Allégaten 55 Bergen 5007 Norway
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10
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Kilina S, Kilin D, Tretiak S. Light-Driven and Phonon-Assisted Dynamics in Organic and Semiconductor Nanostructures. Chem Rev 2015; 115:5929-78. [DOI: 10.1021/acs.chemrev.5b00012] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Svetlana Kilina
- Chemistry
and Biochemistry Department, North Dakota State University, Fargo, North Dakota 5810, United States
| | - Dmitri Kilin
- Department
of Chemistry, University of South Dakota, Vermillion, South Dakota 57069, United States
| | - Sergei Tretiak
- Theoretical
Division, Center for Nonlinear Studies (CNLS) and Center for Integrated
Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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11
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Song W, Martsinovich N, Heckl WM, Lackinger M. Thermodynamics of 4,4'-stilbenedicarboxylic acid monolayer self-assembly at the nonanoic acid-graphite interface. Phys Chem Chem Phys 2015; 16:13239-47. [PMID: 24870380 DOI: 10.1039/c4cp01147c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A direct calorimetric measurement of the overall enthalpy change associated with self-assembly of organic monolayers at the liquid-solid interface is for most systems of interest practically impossible. In previous work we proposed an adapted Born-Haber cycle for an indirect assessment of the overall enthalpy change by using terephthalic acid monolayers at the nonanoic acid-graphite interface as a model system. To this end, the sublimation enthalpy, dissolution enthalpy, the monolayer binding enthalpy in vacuum, and a dewetting enthalpy are combined to yield the total enthalpy change. In the present study the Born-Haber cycle is applied to 4,4'-stilbenedicarboxylic acid monolayers. A detailed comparison of these two aromatic dicarboxylic acids is used to evaluate and quantify the contribution of the organic backbone for stabilization of the monolayer at the nonanoic acid-graphite interface.
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Affiliation(s)
- W Song
- Department of Physics, Technische Universität München, James-Franck-Str. 1, 85748 Garching, Germany.
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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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13
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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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Park YI, Postupna O, Zhugayevych A, Shin H, Park YS, Kim B, Yen HJ, Cheruku P, Martinez JS, Park JW, Tretiak S, Wang HL. A new pH sensitive fluorescent and white light emissive material through controlled intermolecular charge transfer. Chem Sci 2015; 6:789-797. [PMID: 28936321 PMCID: PMC5592806 DOI: 10.1039/c4sc01911c] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 09/07/2014] [Indexed: 11/21/2022] Open
Abstract
A new, pH dependent and water-soluble, conjugated oligomer (amino, trimethylammonium oligophenylene vinylene, ATAOPV) was synthesized with a quaternary ammonium salt and an aromatic amine at the two ends of a π-conjugated oligomer, thus creating a strong dipole across the molecule. A unique white light LED is successfully fabricated from a stimuli responsive organic molecule whose emission properties are dominated by the pH value of the solution through controlled intermolecular charge transfer.
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Affiliation(s)
- Y I Park
- Physical Chemistry and Applied Spectroscopy (C-PCS) , Chemistry Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
| | - O Postupna
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
| | - A Zhugayevych
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
| | - H Shin
- Department of Chemistry/Display Research Center , Catholic University of Korea , Bucheon 420-743 , Republic of Korea
| | - Y-S Park
- Physical Chemistry and Applied Spectroscopy (C-PCS) , Chemistry Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
| | - B Kim
- Department of Chemistry/Display Research Center , Catholic University of Korea , Bucheon 420-743 , Republic of Korea
| | - H-J Yen
- Physical Chemistry and Applied Spectroscopy (C-PCS) , Chemistry Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
| | - P Cheruku
- Physical Chemistry and Applied Spectroscopy (C-PCS) , Chemistry Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
| | - J S Martinez
- Center for Integrated Nanotechnologies , Materials Physics and Applications Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA
| | - J W Park
- Department of Chemistry/Display Research Center , Catholic University of Korea , Bucheon 420-743 , Republic of Korea
| | - S Tretiak
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
| | - H-L Wang
- Physical Chemistry and Applied Spectroscopy (C-PCS) , Chemistry Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
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15
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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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16
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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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17
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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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18
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Echeverria J, Monturet S, Joachim C. One-way rotation of a molecule-rotor driven by a shot noise. NANOSCALE 2014; 6:2793-2799. [PMID: 24463579 DOI: 10.1039/c3nr05814j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The shot noise of a tunneling current passing through a molecule-motor can sustain a one-way rotation when populating the molecular excited states by tunneling inelastic excitations. We demonstrate that a ratchet-like ground state rotation potential energy curve is not necessary for the rotation to occur. A relative shift in energy difference between the maxima of this ground state and the minima of the excited states is the necessary condition to get to a unidirectional rotation. The rotor speed of rotation and its rotation direction are both controlled by this shift, indicating the necessity of a careful design of both the ground and excited states of the next generation of molecule-motors to be able to generate a motive power at the nanoscale.
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Affiliation(s)
- Jorge Echeverria
- Nanosciences Group & MANA Satellite, CEMES/CNRS, 29 rue Jeanne Marvig, 31055 Toulouse, France.
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19
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20
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Dubbeldam D, Torres-Knoop A, Walton KS. On the inner workings of Monte Carlo codes. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.819102] [Citation(s) in RCA: 202] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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21
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Song W, Martsinovich N, Heckl WM, Lackinger M. Born-Haber cycle for monolayer self-assembly at the liquid-solid interface: assessing the enthalpic driving force. J Am Chem Soc 2013; 135:14854-62. [PMID: 24003869 DOI: 10.1021/ja407698t] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The driving force for self-assembly is the associated gain in free energy with decisive contributions from both enthalpy and entropy differences between final and initial state. For monolayer self-assembly at the liquid-solid interface, solute molecules are initially dissolved in the liquid phase and then become incorporated into an adsorbed monolayer. In this work, we present an adapted Born-Haber cycle for obtaining precise enthalpy values for self-assembly at the liquid-solid interface, a key ingredient for a profound thermodynamic understanding of this process. By choosing terephthalic acid as a model system, it is demonstrated that all required enthalpy differences between well-defined reference states can be independently and consistently assessed by both experimental and theoretical methods, giving in the end a reliable value of the overall enthalpy gain for self-assembly of interfacial monolayers. A quantitative comparison of enthalpy gain and entropy cost reveals essential contributions from solvation and dewetting, which lower the entropic cost and render monolayer self-assembly a thermodynamically favored process.
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Affiliation(s)
- Wentao Song
- Deutsches Museum , Museumsinsel 1, 80538 Munich, Germany
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22
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Li J, Wang F, Cheng X, Li X. Reactive Molecular Dynamics Simulation on Thermal Decomposition of n‐Heptane. CHINESE J CHEM PHYS 2013. [DOI: 10.1063/1674-0068/26/02/211-219] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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23
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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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24
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Mayo ML, Hogle D, Yilmaz B, Köse ME, Kilina S. Morphology and dispersion of polycarbazole wrapped carbon nanotubes. RSC Adv 2013. [DOI: 10.1039/c3ra44136a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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25
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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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26
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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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27
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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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28
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Liu C, Zhao DX, Yang ZZ. Direct evaluation of individual hydrogen bond energy in situ in intra- and intermolecular multiple hydrogen bonds system. J Comput Chem 2011; 33:379-90. [PMID: 22170234 DOI: 10.1002/jcc.21975] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 09/15/2011] [Accepted: 09/28/2011] [Indexed: 11/11/2022]
Abstract
The results of evaluating the individual hydrogen bond (H-bond) strength are expected to be helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies. Unfortunately, there is few obvious and unambiguous means of evaluating the energy of a single H-bond within a multiple H-bonds system. We present a local analytic model, ABEEMσπ H-bond energy (HBE) model based on ab initio calculations (MP2) as benchmark, to directly and rapidly evaluate the individual HBE in situ in inter- and intramolecular multiple H-bonds system. This model describes the HBE as the sum of electrostatic and van der Waals (vdW) interactions which all depend upon the geometry and environment, and the ambient environment of H-bond in the model is accounted fairly. Thus, it can fairly consider the cooperative effect and secondary effect. The application range of ABEEMσπ HBE model is rather wide. This work has discussed the individual H-bond in DNA base pair and protein peptide dimers. The results indicate that the interactions among donor H atom, acceptor atom as well as those atoms connected to them with 1,2 or 1,3 relationships are all important for evaluating the HBE, although the interaction between the donor H atom and the acceptor atom is large. Furthermore, our model quantitatively indicates the polarization ability of N, O, and S in a new style, and gives the percentage of the polarization effect in HBE, which can not be given by fixed partial charge force field.
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Affiliation(s)
- Cui Liu
- Chemistry and Chemical Engineering Faculty, Liaoning Normal University, Dalian 116029, China
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29
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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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30
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GUAN QINGMEI, YANG ZHONGZHI. STUDY ON COMPLEXES OF TRYPSIN AND ITS INHIBITORS BY MEANS OF ATOM-BOND ELECTRONEGATIVITY EQUALIZATION METHOD FUSED INTO MOLECULAR MECHANICS (ABEEM/MM). JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633607003520] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Trypsin is one of the most important enzymes and plays important roles in the regulation of biological processes. The newly developed trypsin–inhibitor interaction potential model based on atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) was employed to study complexes of trypsin and its inhibitors. Some structural properties, including root-mean-square deviations (RMSD) of bond length, bond angle and key dihedral, and coordinated RMS Shifts of atoms and hydrogen bond, were studied using ABEEM/MM method and compared with OPLS-AA force-field. At the same time, comparative study on the charges of the hydrogen atoms at the tail of the ligand was also discussed in order to investigate the effect of hydrogen bond between trypsin and its ligand. This work demonstrates that ABEEM/MM model can well reproduce good structures for these trypsin–inhibitor complexes with rather small RMSD of bond length, bond angles, key dihedrals, and RMS Shifts of atomic coordinates with respect to the experimental crystal structures, compared with the results from the OPLS-AA method. The charges obtained by ABEEM/MM model are in good accordance with those from an ab initio calculation. Moreover, both the polarization and the salt-bridge effects have been taken into account. It is shown that ABEEM charges can properly describe the electrostatic interactions between the protein trypsin and its inhibitors.
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Affiliation(s)
- QING-MEI GUAN
- Department of Chemistry, Liaoning Normal University, Dalian 116029, P. R. China
| | - ZHONG-ZHI YANG
- Department of Chemistry, Liaoning Normal University, Dalian 116029, P. R. China
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31
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Eder G, Kloft S, Martsinovich N, Mahata K, Schmittel M, Heckl WM, Lackinger M. Incorporation dynamics of molecular guests into two-dimensional supramolecular host networks at the liquid-solid interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:13563-13571. [PMID: 21951230 DOI: 10.1021/la203054k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The objective of this work is to study both the dynamics and mechanisms of guest incorporation into the pores of 2D supramolecular host networks at the liquid-solid interface. This was accomplished by adding molecular guests to prefabricated self-assembled porous monolayers and the simultaneous acquisition of scanning tunneling microscopy (STM) topographs. The incorporation of the same guest molecule (coronene) into two different host networks was compared, where the pores of the networks either featured a perfect geometric match with the guest (for trimesic acid host networks) or were substantially larger than the guest species (for benzenetribenzoic acid host networks). Even the moderate temporal resolution of standard STM experiments in combination with a novel injection system was sufficient to reveal clear differences in the incorporation dynamics in the two different host networks. Further experiments were aimed at identifying a possible solvent influence. The interpretation of the results is aided by molecular mechanics (MM) and molecular dynamics (MD) simulations.
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Affiliation(s)
- Georg Eder
- TUM School of Education and Center for NanoScience (CeNS), Tech. Univ. Munich, Schellingstrasse 33, 80799 Munich, Germany
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32
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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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33
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Ren P, Wu C, Ponder JW. Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules. J Chem Theory Comput 2011; 7:3143-3161. [PMID: 22022236 PMCID: PMC3196664 DOI: 10.1021/ct200304d] [Citation(s) in RCA: 337] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 Å. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.
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Affiliation(s)
- Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Chuanjie Wu
- Department of Chemistry, and Department of Biochemistry … Molecular Biophysics, Washington University, St. Louis, MO 63130
| | - Jay W. Ponder
- Department of Chemistry, and Department of Biochemistry … Molecular Biophysics, Washington University, St. Louis, MO 63130
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34
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Dong Q, Zhou S. Novel nonlinear knowledge-based mean force potentials based on machine learning. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2011; 8:476-486. [PMID: 20820079 DOI: 10.1109/tcbb.2010.86] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The prediction of 3D structures of proteins from amino acid sequences is one of the most challenging problems in molecular biology. An essential task for solving this problem with coarse-grained models is to deduce effective interaction potentials. The development and evaluation of new energy functions is critical to accurately modeling the properties of biological macromolecules. Knowledge-based mean force potentials are derived from statistical analysis of proteins of known structures. Current knowledge-based potentials are almost in the form of weighted linear sum of interaction pairs. In this study, a class of novel nonlinear knowledge-based mean force potentials is presented. The potential parameters are obtained by nonlinear classifiers, instead of relative frequencies of interaction pairs against a reference state or linear classifiers. The support vector machine is used to derive the potential parameters on data sets that contain both native structures and decoy structures. Five knowledge-based mean force Boltzmann-based or linear potentials are introduced and their corresponding nonlinear potentials are implemented. They are the DIH potential (single-body residue-level Boltzmann-based potential), the DFIRE-SCM potential (two-body residue-level Boltzmann-based potential), the FS potential (two-body atom-level Boltzmann-based potential), the HR potential (two-body residue-level linear potential), and the T32S3 potential (two-body atom-level linear potential). Experiments are performed on well-established decoy sets, including the LKF data set, the CASP7 data set, and the Decoys “R”Us data set. The evaluation metrics include the energy Z score and the ability of each potential to discriminate native structures from a set of decoy structures. Experimental results show that all nonlinear potentials significantly outperform the corresponding Boltzmann-based or linear potentials, and the proposed discriminative framework is effective in developing knowledge-based mean force potentials. The nonlinear potentials can be widely used for ab initio protein structure prediction, model quality assessment, protein docking, and other challenging problems in computational biology.
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Affiliation(s)
- Qiwen Dong
- Shanghai Key Lab of Intelligent Information Processing and the School of Computer Science, Fudan University, Old Yifu Building, Room 202-5, 220 Handan Road, Shanhai 200433, China.
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35
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Aumanen J, Teobaldi G, Zerbetto F, Korppi-Tommola J. The effect of temperature on the internal dynamics of dansylated POPAM dendrimers. RSC Adv 2011. [DOI: 10.1039/c1ra00625h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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36
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Fortuna S, Troisi A. Agent-based modeling for the 2D molecular self-organization of realistic molecules. J Phys Chem B 2010; 114:10151-9. [PMID: 20684638 DOI: 10.1021/jp103950m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We extend our previously developed agent-based (AB) algorithm to the study of the self-assembly of a fully atomistic model of experimental interest. We study the 2D self-assembly of a rigid organic molecule (1,4-benzene-dicarboxylic acid or TPA), comparing the AB results with Monte Carlo (MC) and MC simulated annealing, a technique traditionally used to solve the global minimization problem. The AB algorithm gives a lower energy configuration in the same simulation time than both of the MC simulation techniques. We also show how the AB algorithm can be used as a part of the protocol to calculate the phase diagram with less computational effort than standard techniques.
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Affiliation(s)
- Sara Fortuna
- Department of Chemistry and Centre for Scientific Computing, Warwick University, Coventry, United Kingdom.
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37
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Freddolino PL, Harrison CB, Liu Y, Schulten K. Challenges in protein folding simulations: Timescale, representation, and analysis. NATURE PHYSICS 2010; 6:751-758. [PMID: 21297873 PMCID: PMC3032381 DOI: 10.1038/nphys1713] [Citation(s) in RCA: 232] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Experimental studies of protein folding processes are frequently hampered by the fact that only low resolution structural data can be obtained with sufficient temporal resolution. Molecular dynamics simulations offer a complementary approach, providing extremely high resolution spatial and temporal data on folding processes. The effectiveness of such simulations is currently hampered by continuing questions regarding the ability of molecular dynamics force fields to reproduce the true potential energy surfaces of proteins, and ongoing difficulties with obtaining sufficient sampling to meaningfully comment on folding mechanisms. We review recent progress in the simulation of three common model systems for protein folding, and discuss how recent advances in technology and theory are allowing protein folding simulations to address their current shortcomings.
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Affiliation(s)
- Peter L. Freddolino
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | | | - Yanxin Liu
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Klaus Schulten
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Corresponding author.
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38
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Biomolecular Structure and Modeling: Historical Perspective. INTERDISCIPLINARY APPLIED MATHEMATICS 2010. [PMCID: PMC7124002 DOI: 10.1007/978-1-4419-6351-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
physics, chemistry, and biology have been connected by a web of causal explanation organized by induction-based theories that telescope into one another. … Thus, quantum theory underlies atomic physics, which is the foundation of reagent chemistry and its specialized offshoot biochemistry, which interlock with molecular biology — essentially, the chemistry of organic macromolecules — and hence, through successively higher levels of organization, cellular, organismic, and evolutionary biology. … Such is the unifying and highly productive understanding of the world that has evolved in the natural sciences.
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39
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Qian P, Lu LN, Yang ZZ. Molecular dynamics simulations of N-methylacetamide (NMA) in water by the ABEEM/MM model. CAN J CHEM 2009. [DOI: 10.1139/v09-134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The N-methylacetamide (NMA) is a very interesting kind of compound and often serves as a model of the peptide bond. The interaction between NMA and water provides a convenient prototype for the solvation of peptides in aqueous solutions. We have carried out molecular dynamics (MD) simulations of a NMA molecule in water under 1 atm and 298 K. The simulations make use of the newly developed NMA–water fluctuating charge ABEEM/MM potential model ( Yang, Z. Z.; Qian, P. J. Chem. Phys. 2006, 125, 064311 ), which is based on the combination of the atom-bond electronegativity equalization method (ABEEM) and molecular mechanics (MM). This model has been successfully applied to NMA–water gas clusters, NMA(H2O)n (n = 1–6), and accurately reproduced many static properties. For the NMA–water ABEEM/MM potential model, two characters must be emphasized in the simulations. Firstly, the model allows the charges in system to fluctuate, responding to the ambient environment. Secondly, for two major types of intermolecular hydrogen bonds, which are the hydrogen bond forming between the lone-pair electron on amide oxygen and the water hydrogen, and the one forming between the lone-pair electron on water oxygen and the amide hydrogen, we take special treatments in describing the electrostatic interaction by the use of the parameters klpO=,H and klpO–,HN–, respectively, which explicitly describe the short-range interaction of hydrogen bonds in the hydrogen bond interaction region. All sorts of properties have been studied in detail, such as, radial distribution function, energy distribution, ABEEM charge distribution and dipole moment, and so on. These simulation results show that the ABEEM/MM-based NMA–water potential model appears to be robust, giving the solution properties in excellent agreement with other dynamics simulations on similar systems.
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Affiliation(s)
- Ping Qian
- College of Chemistry and Material Science, Shandong Agricultural University, Tai’an 271018, P.R.China
- Chemistry and Chemical Engineering Falculty, Liaoning Normal University, Dalian 116029, P.R.China
| | - Li-Nan Lu
- College of Chemistry and Material Science, Shandong Agricultural University, Tai’an 271018, P.R.China
- Chemistry and Chemical Engineering Falculty, Liaoning Normal University, Dalian 116029, P.R.China
| | - Zhong-Zhi Yang
- College of Chemistry and Material Science, Shandong Agricultural University, Tai’an 271018, P.R.China
- Chemistry and Chemical Engineering Falculty, Liaoning Normal University, Dalian 116029, P.R.China
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40
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Dračínský M, Bouř P. Computational Analysis of Solvent Effects in NMR Spectroscopy. J Chem Theory Comput 2009; 6:288-99. [DOI: 10.1021/ct900498b] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
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41
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Wu Q, Ayers PW, Zhang Y. Density-based energy decomposition analysis for intermolecular interactions with variationally determined intermediate state energies. J Chem Phys 2009; 131:164112. [DOI: 10.1063/1.3253797] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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42
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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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43
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Rapallo A. VARICELLA: a variable-cell direct space method for structure determination from powder diffraction data. J Chem Phys 2009; 131:044113. [PMID: 19655843 DOI: 10.1063/1.3189290] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A direct space method for structure determination from powder diffraction data is proposed. Employing a hybrid Monte Carlo algorithm for generating the random conformations of a flexible molecular model, and sampling in a modified multicanonical statistical ensemble, it allows for variable cell parameters during an iterative search process. The acceptance-rejection criterion involves both a disagreement factor between the calculated and the experimental diffraction profiles and a modified crystal energy so that the space of tentative solutions can be widely explored while maintaining some physical meaningfulness of the proposals. Allowing the cell to be variable requires the zero shift to be treated as an optimizing parameter; this, in turn, requiring the disagreement factor to be based on the Fourier transform of the spectrum. The algorithm is presented in both a serial and a parallel version, the latter presenting several advantages, such as the possibility to probe different structures at a time while keeping them far from each other in the space defined by suitable order parameters. The method is built up and carefully tested by using, as a case study, a crystal of 3-ethyl 2,3-exo-disyndiotactic norbornene heptamer recently determined by single crystal x-ray diffraction techniques.
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Affiliation(s)
- Arnaldo Rapallo
- Istituto per lo Studio delle Macromolecole del CNR, Via E. Bassini 15, 20133 Milano, Italy.
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44
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Freddolino PL, Park S, Roux B, Schulten K. Force field bias in protein folding simulations. Biophys J 2009; 96:3772-80. [PMID: 19413983 DOI: 10.1016/j.bpj.2009.02.033] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Revised: 02/12/2009] [Accepted: 02/19/2009] [Indexed: 10/20/2022] Open
Abstract
Long timescale (>1 micros) molecular dynamics simulations of protein folding offer a powerful tool for understanding the atomic-scale interactions that determine a protein's folding pathway and stabilize its native state. Unfortunately, when the simulated protein fails to fold, it is often unclear whether the failure is due to a deficiency in the underlying force fields or simply a lack of sufficient simulation time. We examine one such case, the human Pin1 WW domain, using the recently developed deactivated morphing method to calculate free energy differences between misfolded and folded states. We find that the force field we used favors the misfolded states, explaining the failure of the folding simulations. Possible further applications of deactivated morphing and implications for force field development are discussed.
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Affiliation(s)
- Peter L Freddolino
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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45
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Best RB, Hummer G. Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. J Phys Chem B 2009; 113:9004-15. [PMID: 19514729 PMCID: PMC3115786 DOI: 10.1021/jp901540t] [Citation(s) in RCA: 649] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Obtaining the correct balance of secondary structure propensities is a central priority in protein force-field development. Given that current force fields differ significantly in their alpha-helical propensities, a correction to match experimental results would be highly desirable. We have determined simple backbone energy corrections for two force fields to reproduce the fraction of helix measured in short peptides at 300 K. As validation, we show that the optimized force fields produce results in excellent agreement with nuclear magnetic resonance experiments for folded proteins and short peptides not used in the optimization. However, despite the agreement at ambient conditions, the dependence of the helix content on temperature is too weak, a problem shared with other force fields. A fit of the Lifson-Roig helix-coil theory shows that both the enthalpy and entropy of helix formation are too small: the helix extension parameter w agrees well with experiment, but its entropic and enthalpic components are both only about half the respective experimental estimates. Our structural and thermodynamic analyses point toward the physical origins of these shortcomings in current force fields, and suggest ways to address them in future force-field development.
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Affiliation(s)
- Robert B Best
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
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46
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Zhao YL, Meot-Ner (Mautner) M, Gonzalez C. Ionic Hydrogen-Bond Networks and Ion Solvation. 1. An Efficient Monte Carlo/Quantum Mechanical Method for Structural Search and Energy Computations: Ammonium/Water. J Phys Chem A 2009; 113:2967-74. [DOI: 10.1021/jp808486k] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yi-Lei Zhao
- Chemical and Biochemical Reference Data Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China, Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, and Department of Chemistry, University of Canterbury, Christchurch 8001, New Zealand
| | - Michael Meot-Ner (Mautner)
- Chemical and Biochemical Reference Data Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China, Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, and Department of Chemistry, University of Canterbury, Christchurch 8001, New Zealand
| | - Carlos Gonzalez
- Chemical and Biochemical Reference Data Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China, Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, and Department of Chemistry, University of Canterbury, Christchurch 8001, New Zealand
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47
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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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48
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Houjou H, Koga R. Explicit Representation of Anisotropic Force Constants for Simulating Intermolecular Vibrations of Multiply Hydrogen-Bonded Systems. J Phys Chem A 2008; 112:11256-62. [DOI: 10.1021/jp8057614] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hirohiko Houjou
- Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Ryota Koga
- Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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49
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Molecular dynamics study on BPTI aqueous solution by ABEEM/MM fluctuating charge model. Sci Bull (Beijing) 2008. [DOI: 10.1007/s11434-007-0493-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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50
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Rao PN, Cessac JW, Boyd JW, Hanson AD, Shah J. Synthesis and antimitotic activity of novel 2-methoxyestradiol analogs--Part II. Steroids 2008; 73:158-70. [PMID: 18155740 DOI: 10.1016/j.steroids.2007.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Revised: 10/05/2007] [Accepted: 11/12/2007] [Indexed: 11/25/2022]
Abstract
The syntheses and antimitotic activity of several novel 18a-homo-analogs of 2-methoxyestradiol are described. Structural modifications of the parent 2-methoxy-18a-homoestradiol include introduction of unsaturation in the D-ring and methylation of the 17-OH. Of seven analogs synthesized, one has demonstrated superior biological activities compared to 2-methoxyestradiol. The relationship between biological activity and the conformational preference of the 13-ethyl group as determined by computational analysis is discussed.
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Affiliation(s)
- Pemmaraju N Rao
- Department of Organic Chemistry, Southwest Foundation for Biomedical Research, P.O. Box 760549, San Antonio, TX 78245-0549, USA.
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