1
|
Bernard J, Martin S, Al-Mogeeth A, Joblin C, Ji M, Zettergren H, Cederquist H, Stockett MH, Indrajith S, Dontot L, Spiegelman F, Toublanc D, Rapacioli M. Near-infrared absorption and radiative cooling of naphthalene dimers (C 10H 8) 2. Phys Chem Chem Phys 2024; 26:18571-18583. [PMID: 38949429 DOI: 10.1039/d4cp01200c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The radiative cooling of naphthalene dimer cations, (C10H8)2+ was studied experimentally through action spectroscopy using two different electrostatic ion-beam storage rings, DESIREE in Stockholm and Mini-Ring in Lyon. The spectral characteristics of the charge resonance (CR) band were observed to vary significantly with a storage time of up to 30 seconds in DESIREE. In particular, the position of the CR band shifts to the blue, with specific times (inverse of rates) of 0.64 s and 8.0 s in the 0-5 s and 5-30 s storage time ranges, respectively. These long-time scales indicate that the internal energy distribution of the stored ions evolves by vibrational radiative cooling, which is consistent with the absence of fast radiative cooling via recurrent fluorescence for (C10H8)2+. Density functional based tight binding calculations with local excitations and configuration interactions (DFTB-EXCI) were used to simulate the absorption spectrum for ion temperatures between 10 and 500 K. The evolution of the bandwidth and position with temperature is in qualitative agreement with the experimental findings. Furthermore, these calculations yielded linear temperature dependencies for both the shift and the broadening. Combining the relationship between the CR band position and the ion temperature with the results of the statistical model, we demonstrate that the observed blue shift can be used to determine the radiative cooling rate of (C10H8)2+.
Collapse
Affiliation(s)
- Jérôme Bernard
- Institut Lumière Matière (iLM), UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne, France.
| | - Serge Martin
- Institut Lumière Matière (iLM), UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne, France.
| | - Abdulaziz Al-Mogeeth
- Institut Lumière Matière (iLM), UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne, France.
| | - Christine Joblin
- Institut de Recherche en Astrophysique et Planétologie (IRAP), UMR5277, Université Toulouse III - Paul Sabatier, CNRS, CNES, 9 Av. du Colonel Roche, 31028 Toulouse Cedex 4, France
| | - MingChao Ji
- Department of Physics, Stockholm University, Roslagstullsbacken 21, SE-106 91, Stockholm, Sweden
| | - Henning Zettergren
- Department of Physics, Stockholm University, Roslagstullsbacken 21, SE-106 91, Stockholm, Sweden
| | - Henrik Cederquist
- Department of Physics, Stockholm University, Roslagstullsbacken 21, SE-106 91, Stockholm, Sweden
| | - Mark H Stockett
- Department of Physics, Stockholm University, Roslagstullsbacken 21, SE-106 91, Stockholm, Sweden
| | - Suvasthika Indrajith
- Institut Lumière Matière (iLM), UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne, France.
- Department of Physics, Stockholm University, Roslagstullsbacken 21, SE-106 91, Stockholm, Sweden
| | - Léo Dontot
- CIMAP, Unité Mixte CEA-CNRS-ENSICAEN-UCBN 6252, BP 5133, F-14070 Caen, Cedex 05, France
| | - Fernand Spiegelman
- Laboratoire de Chimie et Physique Quantiques (LCPQ)/Institut FeRMI, UMR5626, Université Toulouse III - Paul Sabatier and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Dominique Toublanc
- Laboratoire Collisions Agrégats Réactivité (LCAR)/Institut FeRMI, UMR5589, Université Toulouse III - Paul Sabatier and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantiques (LCPQ)/Institut FeRMI, UMR5626, Université Toulouse III - Paul Sabatier and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| |
Collapse
|
2
|
Zhu Q, Wu Y, Zhao S, Cieplak P, Duan Y, Luo R. Streamlining and Optimizing Strategies of Electrostatic Parameterization. J Chem Theory Comput 2023; 19:6353-6365. [PMID: 37676646 PMCID: PMC10530599 DOI: 10.1021/acs.jctc.3c00659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Accurate characterization of electrostatic interactions is crucial in molecular simulation. Various methods and programs have been developed to obtain electrostatic parameters for additive or polarizable models to replicate electrostatic properties obtained from experimental measurements or theoretical calculations. Electrostatic potentials (ESPs), a set of physically well-defined observables from quantum mechanical (QM) calculations, are well suited for optimization efforts due to the ease of collecting a large amount of conformation-dependent data. However, a reliable set of QM ESP computed at an appropriate level of theory and atomic basis set is necessary. In addition, despite the recent development of the PyRESP program for electrostatic parameterizations of induced dipole-polarizable models, the time-consuming and error-prone input file preparation process has limited the widespread use of these protocols. This work aims to comprehensively evaluate the quality of QM ESPs derived by eight methods, including wave function methods such as Hartree-Fock (HF), second-order Møller-Plesset (MP2), and coupled cluster-singles and doubles (CCSD), as well as five hybrid density functional theory (DFT) methods, used in conjunction with 13 different basis sets. The highest theory levels CCSD/aug-cc-pV5Z (a5z) and MP2/aug-cc-pV5Z (a5z) were selected as benchmark data over two homemade data sets. The results show that the hybrid DFT method, ωB97X-D, combined with the aug-cc-pVTZ (a3z) basis set, performs well in reproducing ESPs while taking both accuracy and efficiency into consideration. Moreover, a flexible and user-friendly program called PyRESP_GEN was developed to streamline input file preparation. The restraining strengths, along with strategies for polarizable Gaussian multipole (pGM) model parameterizations, were also optimized. These findings and the program presented in this work facilitate the development and application of induced dipole-polarizable models, such as pGM models, for molecular simulations of both chemical and biological significance.
Collapse
Affiliation(s)
- Qiang Zhu
- Department of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Yongxian Wu
- Department of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States
| | - Shiji Zhao
- Nurix Therapeutics, Inc., 1700 Owens St, Suite 205, San Francisco, California 94158, United States
| | - Piotr Cieplak
- SBP Medical Discovery Institute, La Jolla, California 92037, United States
| | - Yong Duan
- UC Davis Genome Center and Department of Biomedical Engineering, University of California, Davis, Davis, California 95616, United States
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States
| |
Collapse
|
3
|
Kirchhoff B, Jung C, Gaissmaier D, Braunwarth L, Fantauzzi D, Jacob T. In silico characterization of nanoparticles. Phys Chem Chem Phys 2023; 25:13228-13243. [PMID: 37161752 DOI: 10.1039/d3cp01073b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Nanoparticles (NPs) make for intriguing heterogeneous catalysts due to their large active surface area and excellent and often size-dependent catalytic properties that emerge from a multitude of chemically different surface reaction sites. NP catalysts are, in principle, also highly tunable: even small changes to the NP size or surface facet composition, doping with heteroatoms, or changes of the supporting material can significantly alter their physicochemical properties. Because synthesis of size- and shape-controlled NP catalysts is challenging, the ability to computationally predict the most favorable NP structures for a catalytic reaction of interest is an in-demand skill that can help accelerate and streamline the material optimization process. Fundamentally, simulations of NP model systems present unique challenges to computational scientists. Not only must considerable methodological hurdles be overcome in performing calculations with hundreds to thousands of atoms while retaining appropriate accuracy to be able to probe the desired properties. Also, the data generated by simulations of NPs are typically more complex than data from simulations of, for example, single crystal surface models, and therefore often require different data analysis strategies. To this end, the present work aims to review analytical methods and data analysis strategies that have proven useful in extracting thermodynamic trends from NP simulations.
Collapse
Affiliation(s)
- Björn Kirchhoff
- Institute of Electrochemistry, Ulm University, Albert-Einstein-Allee 47, 89081 Ulm, Germany.
| | - Christoph Jung
- Institute of Electrochemistry, Ulm University, Albert-Einstein-Allee 47, 89081 Ulm, Germany.
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, Helmholtz-Straße 16, 89081 Ulm, Germany
- Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Daniel Gaissmaier
- Institute of Electrochemistry, Ulm University, Albert-Einstein-Allee 47, 89081 Ulm, Germany.
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, Helmholtz-Straße 16, 89081 Ulm, Germany
- Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Laura Braunwarth
- Institute of Electrochemistry, Ulm University, Albert-Einstein-Allee 47, 89081 Ulm, Germany.
| | - Donato Fantauzzi
- Institute of Electrochemistry, Ulm University, Albert-Einstein-Allee 47, 89081 Ulm, Germany.
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, Albert-Einstein-Allee 47, 89081 Ulm, Germany.
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, Helmholtz-Straße 16, 89081 Ulm, Germany
- Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021 Karlsruhe, Germany
| |
Collapse
|
4
|
Guseva DV, Glagolev MK, Lazutin AA, Vasilevskaya VV. Revealing Structural and Physical Properties of Polylactide: What Simulation Can Do beyond the Experimental Methods. POLYM REV 2023. [DOI: 10.1080/15583724.2023.2174136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- D. V. Guseva
- A. N. Nesmeyanov Institute of Organoelement Compounds RAS, Moscow, Russia
| | - M. K. Glagolev
- A. N. Nesmeyanov Institute of Organoelement Compounds RAS, Moscow, Russia
| | - A. A. Lazutin
- A. N. Nesmeyanov Institute of Organoelement Compounds RAS, Moscow, Russia
| | - V. V. Vasilevskaya
- A. N. Nesmeyanov Institute of Organoelement Compounds RAS, Moscow, Russia
- Chemistry Department, M. V. Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
5
|
Janeček M, Kührová P, Mlýnský V, Otyepka M, Šponer J, Banáš P. W-RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model. J Chem Theory Comput 2021; 17:3495-3509. [PMID: 33999623 DOI: 10.1021/acs.jctc.0c00976] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Representation of electrostatic interactions by a Coulombic pairwise potential between atom-centered partial charges is a fundamental and crucial part of empirical force fields used in classical molecular dynamics simulations. The broad success of the AMBER force-field family originates mainly from the restrained electrostatic potential (RESP) charge model, which derives partial charges to reproduce the electrostatic field around the molecules. However, the description of the electrostatic potential around molecules by standard RESP may be biased for some types of molecules. In this study, we modified the RESP charge derivation model to improve its description of the electrostatic potential around molecules and thus electrostatic interactions in the force field. In particular, we reoptimized the atomic radii for definition of the grid points around the molecule, redesigned the restraining scheme, and included extra point (EP) charges. The RESP fitting was significantly improved for aromatic heterocyclic molecules. Thus, the suggested W-RESP(-EP) charge derivation model shows some potential for improving the performance of the nucleic acid force fields, for which the poor description of nonbonded interactions, such as the underestimated stability of base pairing, is well-established. We also report some preliminary simulation tests (around 1 ms of simulation data) on A-RNA duplexes, tetranucleotides, and tetraloops. The simulations reveal no adverse effects, while the description of base-pairing interactions might be improved. The new charges can thus be used in future attempts to improve the nucleic acid simulation force fields, in combination with reparametrization of the other terms.
Collapse
Affiliation(s)
- Michal Janeček
- Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic
| | - Vojtěch Mlýnský
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| |
Collapse
|
6
|
Ghafari H, Mohammadi-Manesh H. How Does the Guest—Host Hydrogen Bonding Affect the Thermal Properties of Clathrate Hydrates? J STRUCT CHEM+ 2020. [DOI: 10.1134/s0022476620030038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
7
|
Marenich AV, Olson RM, Chamberlin AC, Cramer CJ, Truhlar DG. Polarization Effects in Aqueous and Nonaqueous Solutions. J Chem Theory Comput 2015; 3:2055-67. [PMID: 26636201 DOI: 10.1021/ct7001539] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Polarization effects in aqueous and nonaqueous solutions were analyzed for nine neutral and three charged organic solutes by the SM8 universal implicit solvation model and class IV partial atomic charges based on Charge Model 4M (CM4M) with the M06-2X density functional. The CM4M partial atomic charges in neutral and ionic solutes and in the corresponding clustered solutes (supersolutes), which included one solute molecule and one or two solvent molecules, were modeled in three solvents (benzene, methylene chloride, and water) and compared to those in the gas phase. The use of the supersolute approach (microsolvation) allows one to account for charge transfer from the solute to the solvent, and we find charge transfers as large as 0.06 atomic units for neutral solutes (pyridine in water) and 0.32 atomic units for ions (methoxide anion in water). Relaxation of the electronic structure of the solute in the presence of solvent increases the polarization free energy of the neutral solutes studied here, on average, by 16% in benzene, 30% in methylene chloride, and 43% in water. The increase for the ions in water averaged 43%.
Collapse
Affiliation(s)
- Aleksandr V Marenich
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Ryan M Olson
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Adam C Chamberlin
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Christopher J Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| |
Collapse
|
8
|
Marenich AV, Olson RM, Kelly CP, Cramer CJ, Truhlar DG. Self-Consistent Reaction Field Model for Aqueous and Nonaqueous Solutions Based on Accurate Polarized Partial Charges. J Chem Theory Comput 2015; 3:2011-33. [PMID: 26636198 DOI: 10.1021/ct7001418] [Citation(s) in RCA: 360] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new universal continuum solvation model (where "universal" denotes applicable to all solvents), called SM8, is presented. It is an implicit solvation model, also called a continuum solvation model, and it improves on earlier SMx universal solvation models by including free energies of solvation of ions in nonaqueous media in the parametrization. SM8 is applicable to any charged or uncharged solute composed of H, C, N, O, F, Si, P, S, Cl, and/or Br in any solvent or liquid medium for which a few key descriptors are known, in particular dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters. It does not require the user to assign molecular-mechanics types to an atom or group; all parameters are unique and continuous functions of geometry. It may be used with any level of electronic structure theory as long as accurate partial charges can be computed for that level of theory; we recommend using it with self-consistently polarized Charge Model 4 or other self-consistently polarized class IV charges, in which case analytic gradients are available. The model separates the observable solvation free energy into two components: the long-range bulk electrostatic contribution arising from a self-consistent reaction field treatment using the generalized Born approximation for electrostatics is augmented by the non-bulk-electrostatic contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell. The cavities for the bulk electrostatics calculation are defined by superpositions of nuclear-centered spheres whose sizes are determined by intrinsic atomic Coulomb radii. The radii used for aqueous solution are the same as parametrized previously for the SM6 aqueous solvation model, and the radii for nonaqueous solution are parametrized by a training set of 220 bare ions and 21 clustered ions in acetonitrile, methanol, and dimethyl sulfoxide. The non-bulk-electrostatic terms are proportional to the solvent-accessible surface areas of the atoms of the solute and have been parametrized using solvation free energies for a training set of 2346 solvation free energies for 318 neutral solutes in 90 nonaqueous solvents and water and 143 transfer free energies for 93 neutral solutes between water and 15 organic solvents. The model is tested with three density functionals and with four basis sets: 6-31+G(d,p), 6-31+G(d), 6-31G(d), and MIDI!6D. The SM8 model achieves mean unsigned errors of 0.5-0.8 kcal/mol in the solvation free energies of tested neutrals and mean unsigned errors of 2.2-7.0 kcal/mol for ions. The model outperforms the earlier SM5.43R and SM7 universal solvation models as well as the default Polarizable Continuum Model (PCM) implemented in Gaussian 98/03, the Conductor-like PCM as implemented in GAMESS, Jaguar's continuum model based on numerical solution of the Poisson equation, and the GCOSMO model implemented in NWChem.
Collapse
Affiliation(s)
- Aleksandr V Marenich
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Ryan M Olson
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Casey P Kelly
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Christopher J Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| |
Collapse
|
9
|
Kelly CP, Cramer CJ, Truhlar DG. SM6: A Density Functional Theory Continuum Solvation Model for Calculating Aqueous Solvation Free Energies of Neutrals, Ions, and Solute-Water Clusters. J Chem Theory Comput 2015; 1:1133-52. [PMID: 26631657 DOI: 10.1021/ct050164b] [Citation(s) in RCA: 356] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new charge model, called Charge Model 4 (CM4), and a new continuum solvent model, called Solvation Model 6 (SM6), are presented. Using a database of aqueous solvation free energies for 273 neutrals, 112 ions, and 31 ion-water clusters, parameter sets for the mPW0 hybrid density functional of Adamo and Barone (Adamo, C.; Barone, V. J. Chem. Phys. 1998, 108, 664-675) were optimized for use with the following four basis sets: MIDI!6D, 6-31G(d), 6-31+G(d), and 6-31+G(d,p). SM6 separates the observable aqueous solvation free energy into two different components: one arising from long-range bulk electrostatic effects and a second from short-range interactions between the solute and solvent molecules in the first solvation shell. This partition of the observable solvation free energy allows SM6 to effectively model a wide range of solutes. For the 273 neutral solutes in the test set, SM6 achieves an average error of ∼0.50 kcal/mol in the aqueous solvation free energies. For solutes, especially ions, that have highly concentrated regions of charge density, adding an explicit water molecule to the calculation significantly improves the performance of SM6 for predicting solvation free energies. The performance of SM6 was tested against several other continuum models, including SM5.43R and several different implementations of the Polarizable Continuum Model (PCM). For both neutral and ionic solutes, SM6 outperforms all of the models against which it was tested. Also, SM6 is the only model (except for one with an average error 3.4 times larger) that improves when an explicit solvent molecule is added to solutes with concentrated charge densities. Thus, in SM6, unlike the other continuum models tested here, adding one or more explicit solvent molecules to the calculation is an effective strategy for improving the prediction of the aqueous solvation free energies of solutes with strong local solute-solvent interactions. This is important, because local solute-solvent interactions are not specifically accounted for by bulk electrostatics, but modeling these interactions correctly is important for predicting the aqueous solvation free energies of certain solutes. Finally, SM6 retains its accuracy when used in conjunction with the B3LYP and B3PW91 functionals, and in fact the solvation parameters obtained with a given basis set may be used with any good density functional or fraction of Hartree-Fock exchange.
Collapse
Affiliation(s)
- Casey P Kelly
- Department of Chemistry and Supercomputing Institute, 207 Pleasant St. SE, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Christopher J Cramer
- Department of Chemistry and Supercomputing Institute, 207 Pleasant St. SE, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, 207 Pleasant St. SE, University of Minnesota, Minneapolis, Minnesota 55455-0431
| |
Collapse
|
10
|
Geidl S, Bouchal T, Raček T, Svobodová Vařeková R, Hejret V, Křenek A, Abagyan R, Koča J. High-quality and universal empirical atomic charges for chemoinformatics applications. J Cheminform 2015; 7:59. [PMID: 26633997 PMCID: PMC4667495 DOI: 10.1186/s13321-015-0107-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/16/2015] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Partial atomic charges describe the distribution of electron density in a molecule and therefore provide clues to the chemical behaviour of molecules. Recently, these charges have become popular in chemoinformatics, as they are informative descriptors that can be utilised in pharmacophore design, virtual screening, similarity searches etc. Especially conformationally-dependent charges perform very successfully. In particular, their fast and accurate calculation via the Electronegativity Equalization Method (EEM) seems very promising for chemoinformatics applications. Unfortunately, published EEM parameter sets include only parameters for basic atom types and they often miss parameters for halogens, phosphorus, sulphur, triple bonded carbon etc. Therefore their applicability for drug-like molecules is limited. RESULTS We have prepared six EEM parameter sets which enable the user to calculate EEM charges in a quality comparable to quantum mechanics (QM) charges based on the most common charge calculation schemes (i.e., MPA, NPA and AIM) and a robust QM approach (HF/6-311G, B3LYP/6-311G). The calculated EEM parameters exhibited very good quality on a training set ([Formula: see text]) and also on a test set ([Formula: see text]). They are applicable for at least 95 % of molecules in key drug databases (DrugBank, ChEMBL, Pubchem and ZINC) compared to less than 60 % of the molecules from these databases for which currently used EEM parameters are applicable. CONCLUSIONS We developed EEM parameters enabling the fast calculation of high-quality partial atomic charges for almost all drug-like molecules. In parallel, we provide a software solution for their easy computation (http://ncbr.muni.cz/eem_parameters). It enables the direct application of EEM in chemoinformatics.
Collapse
Affiliation(s)
- Stanislav Geidl
- />National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Tomáš Bouchal
- />National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Tomáš Raček
- />National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
- />Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic
| | - Radka Svobodová Vařeková
- />National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Václav Hejret
- />National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Aleš Křenek
- />Institute of Computer Science, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic
| | - Ruben Abagyan
- />Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, 9500 Gilman Drive, San Diego, MC 0657 USA
| | - Jaroslav Koča
- />National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| |
Collapse
|
11
|
AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules. J Cheminform 2015; 7:50. [PMID: 26500704 PMCID: PMC4613891 DOI: 10.1186/s13321-015-0099-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 10/08/2015] [Indexed: 01/24/2023] Open
Abstract
Background Partial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites. Results This paper introduces AtomicChargeCalculator (ACC), a web-based application for the calculation and analysis of atomic charges which respond to changes in molecular conformation and chemical environment. ACC relies on an empirical
method to rapidly compute atomic charges with accuracy comparable to quantum mechanical approaches. Due to its efficient implementation, ACC can handle any type of molecular system, regardless of size and chemical complexity, from drug-like molecules to biomacromolecular complexes with hundreds of thousands of atoms. ACC writes out atomic charges into common molecular structure files, and offers interactive facilities for statistical analysis and comparison of the results, in both tabular and graphical form. Conclusions Due to high customizability and speed, easy streamlining and the unified platform for calculation and analysis, ACC caters to all fields of life sciences, from drug design to nanocarriers. ACC is freely available via the Internet at http://ncbr.muni.cz/ACC. Electronic supplementary material The online version of this article (doi:10.1186/s13321-015-0099-x) contains supplementary material, which is available to authorized users.
Collapse
|
12
|
A new equation based on ionization energies and electron affinities of atoms for calculating of group electronegativity. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.11.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
13
|
Rosli AN, Abu Bakar MA, Lee VS, Zain SM, Ahmad MR, Abdul Manan NS, Alias Y, Woi PM. Rational design of carbonitrile-carboxaldehyde cation receptor models: probing the nature of the heteroatom-metal interaction. J Mol Model 2014; 20:2428. [PMID: 25149440 DOI: 10.1007/s00894-014-2428-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/07/2014] [Indexed: 11/30/2022]
Abstract
In this work, hybrid functional and G4 methods were employed in the rational design of carbonitrile-carboxaldehyde receptor models for cation recognition. Electron-sharing and ionic interactions between the models and the cations were analyzed utilizing the concepts of overlap population, atomic valence, electrostatic potential, and CHELPG charge in order to elucidate the nature of the heteroatom-metal interaction, the N versus O disparity, and the effect of pH. Receptor fragment models from ionomycin were employed to rationalize the selection of receptor models for discriminating group I cations and enhancing the selectivity for Mg(II) rather than Ca(II), and to examine the effects of keto-enol forms and negatively charged sites. The changes in geometries, overlap population, metal valence, and CHELPG charge upon solvation in heptane medium as compared to the gas phase were negligible. The optimized geometries reveal that the interaction between group II cations and the keto, enol, and enolate forms of 2-cyanoethanal causes 12 % bending of the C-C-N angle from linearity. Overlap populations show that the electron-sharing interaction favors group II cations but that the same mechanism allows Li(I) to compete. The total spin of Li(I) is 17 % greater than that of Ca(II), but the G4 binding energies of the two are separated by more than 50 kcal/mol, favoring group II cations, which may eliminate interference from Li(I). 1,2-Dicyanoethylene, which has only one form, shows similar characteristics. CHELPG analysis shows that Mg(II) transfers 25 and 18 % of its positive charge to 2-cyanoethanal enolate and 1,2-dicyanoethylene, respectively. Hydrogen atoms receive most of the positive charge in both receptors, but the N-termini exhibit strikingly different characteristics. Electrostatic potential contour profiles were found to be in good agreement with the atomic charge distributions. The application of uncharged 1,3-dicarbonyl and 2-cyanocarbonyl receptors and a judicious choice of polymeric membrane that suppresses the Hofmeister effect should lead to high selectivity for magnesium, whereas the utilization of multiple negatively charged ionophores should result in selectivity for calcium.
Collapse
|
14
|
Yang ZZ, Wang JJ, Zhao DX. Valence state parameters of all transition metal atoms in metalloproteins-development of ABEEMσπ fluctuating charge force field. J Comput Chem 2014; 35:1690-706. [DOI: 10.1002/jcc.23676] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 06/01/2014] [Accepted: 06/18/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering; Department of Chemistry, Liaoning Normal University; Dalian China 116029
| | - Jian-Jiang Wang
- School of Chemistry and Chemical Engineering; Department of Chemistry, Liaoning Normal University; Dalian China 116029
| | - Dong-Xia Zhao
- School of Chemistry and Chemical Engineering; Department of Chemistry, Liaoning Normal University; Dalian China 116029
| |
Collapse
|
15
|
Ionescu CM, Geidl S, Svobodová Vařeková R, Koča J. Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method. J Chem Inf Model 2013; 53:2548-58. [DOI: 10.1021/ci400448n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Crina-Maria Ionescu
- CEITEC—Central European
Institute of Technology, and National Centre for Biomolecular Research,
Faculty of Science, Masaryk University Brno, Kamenice 5, 625 00, Brno-Bohunice, Czech Republic
| | - Stanislav Geidl
- CEITEC—Central European
Institute of Technology, and National Centre for Biomolecular Research,
Faculty of Science, Masaryk University Brno, Kamenice 5, 625 00, Brno-Bohunice, Czech Republic
| | - Radka Svobodová Vařeková
- CEITEC—Central European
Institute of Technology, and National Centre for Biomolecular Research,
Faculty of Science, Masaryk University Brno, Kamenice 5, 625 00, Brno-Bohunice, Czech Republic
| | - Jaroslav Koča
- CEITEC—Central European
Institute of Technology, and National Centre for Biomolecular Research,
Faculty of Science, Masaryk University Brno, Kamenice 5, 625 00, Brno-Bohunice, Czech Republic
| |
Collapse
|
16
|
Ahmed A, Sandler SI. Hydration Free Energies of Multifunctional Nitroaromatic Compounds. J Chem Theory Comput 2013; 9:2774-85. [DOI: 10.1021/ct3011002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Alauddin Ahmed
- Department
of Chemical and Biomolecular Engineering,
University of Delaware, Newark, Delaware 19716, United States
| | - Stanley I. Sandler
- Department
of Chemical and Biomolecular Engineering,
University of Delaware, Newark, Delaware 19716, United States
| |
Collapse
|
17
|
Vařeková RS, Geidl S, Ionescu CM, Skřehota O, Bouchal T, Sehnal D, Abagyan R, Koča J. Predicting p Ka values from EEM atomic charges. J Cheminform 2013; 5:18. [PMID: 23574978 PMCID: PMC3663834 DOI: 10.1186/1758-2946-5-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 03/27/2013] [Indexed: 11/19/2022] Open
Abstract
The acid dissociation constant p Kais a very important molecular property, and there is a strong interest in the development of reliable and fast methods for p Kaprediction. We have evaluated the p Kaprediction capabilities of QSPR models based on empirical atomic charges calculated by the Electronegativity Equalization Method (EEM). Specifically, we collected 18 EEM parameter sets created for 8 different quantum mechanical (QM) charge calculation schemes. Afterwards, we prepared a training set of 74 substituted phenols. Additionally, for each molecule we generated its dissociated form by removing the phenolic hydrogen. For all the molecules in the training set, we then calculated EEM charges using the 18 parameter sets, and the QM charges using the 8 above mentioned charge calculation schemes. For each type of QM and EEM charges, we created one QSPR model employing charges from the non-dissociated molecules (three descriptor QSPR models), and one QSPR model based on charges from both dissociated and non-dissociated molecules (QSPR models with five descriptors). Afterwards, we calculated the quality criteria and evaluated all the QSPR models obtained. We found that QSPR models employing the EEM charges proved as a good approach for the prediction of p Ka(63% of these models had R2 > 0.9, while the best had R2 = 0.924). As expected, QM QSPR models provided more accurate p Kapredictions than the EEM QSPR models but the differences were not significant. Furthermore, a big advantage of the EEM QSPR models is that their descriptors (i.e., EEM atomic charges) can be calculated markedly faster than the QM charge descriptors. Moreover, we found that the EEM QSPR models are not so strongly influenced by the selection of the charge calculation approach as the QM QSPR models. The robustness of the EEM QSPR models was subsequently confirmed by cross-validation. The applicability of EEM QSPR models for other chemical classes was illustrated by a case study focused on carboxylic acids. In summary, EEM QSPR models constitute a fast and accurate p Kaprediction approach that can be used in virtual screening.
Collapse
Affiliation(s)
- Radka Svobodová Vařeková
- National Centre for Biomolecular Research, Faculty of Science and CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic.
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Andino JG, Mazumder S, Pal K, Caulton KG. Neue Ansätze zur Funktionalisierung von metallkoordiniertem N2. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209168] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
19
|
Andino JG, Mazumder S, Pal K, Caulton KG. New Approaches to Functionalizing Metal-Coordinated N2. Angew Chem Int Ed Engl 2013; 52:4726-32. [DOI: 10.1002/anie.201209168] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Indexed: 11/08/2022]
|
20
|
Wang B, Truhlar DG. Partial Atomic Charges and Screened Charge Models of the Electrostatic Potential. J Chem Theory Comput 2012; 8:1989-98. [PMID: 26593833 DOI: 10.1021/ct2009285] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We propose a new screened charge method for calculating partial atomic charges in molecules by electrostatic potential (ESP) fitting. The model, called full density screening (FDS), is used to approximate the screening effect of full charge densities of atoms in molecules. The results are compared to the conventional ESP fitting method based on point charges and to our previously proposed outer density screening (ODS) method, in which the parameters are reoptimized for the present purpose. In ODS, the charge density of an atom is represented by the sum of a point charge and a smeared negative charge distributed in a Slater-type orbital (STO). In FDS, the charge density of an atom is taken to be the sum of the charge density of the neutral atom and a partial atomic charge (of either sign) distributed in an STO. The ζ values of the STOs used in these two models are optimized in the present study to best reproduce the electrostatic potentials. The quality of the fit to the electrostatics is improved in the screened charge methods, especially for the regions that are within one van der Waals radius of the centers of atoms. It is also found that the charges derived by fitting electrostatic potentials with screened charges are less sensitive to the positions of the fitting points than are those derived with conventional electrostatic fitting. Moreover, we found that the electrostatic-potential-fitted (ESP) charges from the screened charge methods are similar to those from the point-charge method except for molecules containing the methyl group, where we have explored the use of restraints on nonpolar H atoms. We recommend the FDS model if the only goal is ESP fitting to obtain partial atomic charges or a fit to the ESP field. However, the ODS model is more accurate for electronic embedding in combined quantum mechanical and molecular mechanical (QM/MM) modeling and is more accurate than point-charge models for ESP fitting, and it is recommended for applications involving QM/MM methods. Since the screened charges describe the electrostatic potentials more accurately than point charges, since they asymptotically act as point charges at long distances, and since the electrostatic potential in terms of the screened charges is still a sum of functions centered at the atoms, the screened-charge representation of the electrostatic potential can be used in the same way as the conventional point-charge representation to model the electrostatic interactions, but it is more realistic. For the H atom and p block elements, the error in the fit to the electrostatic potential is reduced by about a factor of 3, and the sensitivity of the derived partial atomic charges to the choice of fitting points is reduced by about a factor of 2. For s and d block elements, there are also improvements in the inner regions but not necessarily in the outer regions.
Collapse
Affiliation(s)
- Bo Wang
- Department of Chemistry and Supercomputing Institute, University of Minnesota , 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431, United States
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota , 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431, United States
| |
Collapse
|
21
|
Marenich AV, Jerome SV, Cramer CJ, Truhlar DG. Charge Model 5: An Extension of Hirshfeld Population Analysis for the Accurate Description of Molecular Interactions in Gaseous and Condensed Phases. J Chem Theory Comput 2012; 8:527-41. [DOI: 10.1021/ct200866d] [Citation(s) in RCA: 520] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Aleksandr V. Marenich
- Department of Chemistry
and Supercomputing Institute,
University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota
55455-0431, United States
| | - Steven V. Jerome
- Department of Chemistry
and Supercomputing Institute,
University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota
55455-0431, United States
| | - Christopher J. Cramer
- Department of Chemistry
and Supercomputing Institute,
University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota
55455-0431, United States
| | - Donald G. Truhlar
- Department of Chemistry
and Supercomputing Institute,
University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota
55455-0431, United States
| |
Collapse
|
22
|
Pascal TA, Karasawa N, Goddard WA. Quantum mechanics based force field for carbon (QMFF-Cx) validated to reproduce the mechanical and thermodynamics properties of graphite. J Chem Phys 2010; 133:134114. [DOI: 10.1063/1.3456543] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
23
|
Rapacioli M, Spiegelman F, Talbi D, Mineva T, Goursot A, Heine T, Seifert G. Correction for dispersion and Coulombic interactions in molecular clusters with density functional derived methods: application to polycyclic aromatic hydrocarbon clusters. J Chem Phys 2009; 130:244304. [PMID: 19566150 DOI: 10.1063/1.3152882] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The density functional based tight binding (DFTB) is a semiempirical method derived from the density functional theory (DFT). It inherits therefore its problems in treating van der Waals clusters. A major error comes from dispersion forces, which are poorly described by commonly used DFT functionals, but which can be accounted for by an a posteriori treatment DFT-D. This correction is used for DFTB. The self-consistent charge (SCC) DFTB is built on Mulliken charges which are known to give a poor representation of Coulombic intermolecular potential. We propose to calculate this potential using the class IV/charge model 3 definition of atomic charges. The self-consistent calculation of these charges is introduced in the SCC procedure and corresponding nuclear forces are derived. Benzene dimer is then studied as a benchmark system with this corrected DFTB (c-DFTB-D) method, but also, for comparison, with the DFT-D. Both methods give similar results and are in agreement with references calculations (CCSD(T) and symmetry adapted perturbation theory) calculations. As a first application, pyrene dimer is studied with the c-DFTB-D and DFT-D methods. For coronene clusters, only the c-DFTB-D approach is used, which finds the sandwich configurations to be more stable than the T-shaped ones.
Collapse
Affiliation(s)
- Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantiques, IRSAMC, Université de Toulouse, UPS and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
| | | | | | | | | | | | | |
Collapse
|
24
|
Leverentz HR, Truhlar DG. Electrostatically Embedded Many-Body Approximation for Systems of Water, Ammonia, and Sulfuric Acid and the Dependence of Its Performance on Embedding Charges. J Chem Theory Comput 2009; 5:1573-84. [DOI: 10.1021/ct900095d] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hannah R. Leverentz
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| |
Collapse
|
25
|
White BR, Wagner CR, Truhlar DG, Amin EA. Molecular Modeling of Geometries, Charge Distributions, and Binding Energies of Small, Drug-Like Molecules Containing Nitrogen Heterocycles and Exocyclic Amino Groups in the Gas Phase and Aqueous Solution. J Chem Theory Comput 2008; 4:1718-1732. [PMID: 23700392 PMCID: PMC3658833 DOI: 10.1021/ct8000766] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have tested a variety of approximate methods for modeling 30 systems containing mixtures of nitrogen heterocycles and exocyclic amines, each of which is studied with up to 31 methods in one or two phases (gaseous and aqueous). Fifteen of the systems are protonated, and 15 are not. We consider a data set consisting of geometric parameters, partial atomic charges, and water binding energies for the methotrexate fragments 2-(aminomethyl)pyrazine and 2,4-diaminopyrimidine, as well as their cationic forms 1H-2-(aminomethyl)pyrazine and 1H-2,4-diaminopyrimidine. We first evaluated the suitability of several density functionals with the 6-31+G(d,p) basis set to serve as a benchmark by comparing calculated molecular geometries to results obtained from coupled-cluster [CCSD/6-31+G(d,p)] wave function theory (WFT). We found that the M05-2X density functional can be used to obtain reliable geometries for our data set. To accurately model partial charges in our molecules, we elected to utilize the well-validated Charge Model 4 (CM4). In the process of establishing benchmark values, we consider gas-phase coupled cluster and density functional theory (DFT) calculations followed by aqueous-phase DFT calculations, where the effect of solvent is treated by the SM6 quantum mechanical implicit solvation model. The resulting benchmarks were used to test several widely available and economical semiempirical molecular orbital (SE-MO) methods and molecular mechanical (MM) force fields for their ability to accurately predict the partial charges, binding energies to a water molecule, and molecular geometries of representative fragments of methotrexate in the gaseous and aqueous phases, where effects of water were simulated by the SM5.4 and SM5.42 quantum mechanical implicit solvation models for SE-MO and explicit solvation used for MM. In addition, we substituted CM4 charges into the MM force fields tested to observe the effect of improved charge assignment on geometric and energetic modeling. The most accurate MM force fields (with or without CM4 charges substituted) were validated against gas-phase and aqueous-phase geometries and charge distributions of a larger set of 16 drug-like ligands, both neutral and cationic. This process showed that the Merck Molecular Force Field (MMFF94) with or without CM4 charges substituted, is, on average, the most accurate force field for geometries of molecules containing nitrogen heterocycles and exocyclic amino groups, both protonated and unprotonated. This force field was then applied to the complete methotrexate molecule, in an effort to systematically explore its accuracy for trends in geometries and charge distributions. The most accurate force fields for the binding energies of nitrogen heterocycles to a water molecule are OPLS2005 and AMBER.
Collapse
Affiliation(s)
- Brian R. White
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
| | - Carston R. Wagner
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
- Department of Chemistry and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455
| | - Donald G. Truhlar
- Department of Chemistry and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455
| | - Elizabeth A. Amin
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455
| |
Collapse
|
26
|
Studies on free energy and its components of 2-Phenylindole and its derivatives. J Mol Liq 2008. [DOI: 10.1016/j.molliq.2007.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
27
|
Chamberlin AC, Cramer CJ, Truhlar DG. Extension of a Temperature-Dependent Aqueous Solvation Model to Compounds Containing Nitrogen, Fluorine, Chlorine, Bromine, and Sulfur. J Phys Chem B 2008; 112:3024-39. [DOI: 10.1021/jp076682v] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adam C. Chamberlin
- Department of Chemistry and Supercomputing Institute, 207 Pleasant Street SE, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Christopher J. Cramer
- Department of Chemistry and Supercomputing Institute, 207 Pleasant Street SE, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, 207 Pleasant Street SE, University of Minnesota, Minneapolis, Minnesota 55455-0431
| |
Collapse
|
28
|
Nicholls A, Mobley DL, Guthrie JP, Chodera JD, Bayly CI, Cooper MD, Pande VS. Predicting small-molecule solvation free energies: an informal blind test for computational chemistry. J Med Chem 2008; 51:769-79. [PMID: 18215013 DOI: 10.1021/jm070549+] [Citation(s) in RCA: 215] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Experimental data on the transfer of small molecules between vacuum and water are relatively sparse. This makes it difficult to assess whether computational methods are truly predictive of this important quantity or merely good at explaining what has been seen. To explore this, a prospective test was performed of two different methods for estimating solvation free energies: an implicit solvent approach based on the Poisson-Boltzmann equation and an explicit solvent approach using alchemical free energy calculations. For a set of 17 small molecules, root mean square errors from experiment were between 1.3 and 2.6 kcal/mol, with the explicit solvent free energy approach yielding somewhat greater accuracy but at greater computational expense. Insights from outliers and suggestions for future prospective challenges of this kind are presented.
Collapse
Affiliation(s)
- Anthony Nicholls
- OpenEye Scientific Software, Inc., Santa Fe, New Mexico 87508,USA.
| | | | | | | | | | | | | |
Collapse
|
29
|
Rai N, Siepmann JI. Transferable Potentials for Phase Equilibria. 9. Explicit Hydrogen Description of Benzene and Five-Membered and Six-Membered Heterocyclic Aromatic Compounds. J Phys Chem B 2007; 111:10790-9. [PMID: 17713943 DOI: 10.1021/jp073586l] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The explicit hydrogen version of the transferable potentials for phase equilibria (TraPPE-EH) force field is extended to benzene, pyridine, pyrimidine, pyrazine, pyridazine, thiophene, furan, pyrrole, thiazole, oxazole, isoxazole, imidazole, and pyrazole. While the Lennard-Jones parameters for carbon, hydrogen (two types), nitrogen (two types), oxygen, and sulfur are transferable for all 13 compounds, the partial charges are specific for each compound. The benzene dimer energies for sandwich, T-shape, and parallel-displaced configurations obtained for the TraPPE-EH force field compare favorably with high-level electronic structure calculations. Gibbs ensemble Monte Carlo simulations were carried out to compute the single-component vapor-liquid equilibria for benzene, pyridine, three diazenes, and eight five-membered heterocycles. The agreement with experimental data is excellent with the liquid densities and vapor pressures reproduced within 1 and 5%, respectively. The critical temperatures and normal boiling points are predicted with mean deviations of 0.8 and 1.6%, respectively.
Collapse
Affiliation(s)
- Neeraj Rai
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, USA.
| | | |
Collapse
|
30
|
Dahlke EE, Truhlar DG. Electrostatically Embedded Many-Body Expansion for Large Systems, with Applications to Water Clusters. J Chem Theory Comput 2006; 3:46-53. [DOI: 10.1021/ct600253j] [Citation(s) in RCA: 231] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Erin E. Dahlke
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| |
Collapse
|
31
|
Chamberlin AC, Cramer CJ, Truhlar DG. Predicting Aqueous Free Energies of Solvation as Functions of Temperature. J Phys Chem B 2006; 110:5665-75. [PMID: 16539512 DOI: 10.1021/jp057264y] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work introduces a model, solvation model 6 with temperature dependence (SM6T), to predict the temperature dependence of aqueous free energies of solvation for compounds containing H, C, and O in the range 273-373 K. In particular, we extend solvation model 6 (SM6), which was previously developed (Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. J. Chem. Theory Comput. 2005, 1, 1133) for predicting aqueous free energies of solvation at 298 K, to predict the variation of the free energy of solvation relative to 298 K. Also, we describe the database of experimental aqueous free energies of solvation for compounds containing H, C, and O that was used to parametrize and test the new model. SM6T partitions the temperature dependence of the free energy of solvation into two components: the temperature dependence of the bulk electrostatic contribution to the free energy of solvation, which is computed using the generalized Born equation, and the temperature dependence of first-solvation-shell effects which is modeled using a parametrized solvent-exposed surface-area-dependent term. We found that SM6T predicts the temperature dependence of aqueous free energies of solvation with a mean unsigned error of 0.08 kcal/mol over our entire database, whereas using the experimental value at 298 K produces a mean unsigned error of 0.53 kcal/mol.
Collapse
Affiliation(s)
- Adam C Chamberlin
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA
| | | | | |
Collapse
|