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Ligorio RF, Grosskopf P, Dos Santos LHR, Krawczuk A. Unveiling GruPol: Predicting Electric and Electrostatic Properties of Macromolecules via the Building Block Approach. J Phys Chem B 2024. [PMID: 38976348 DOI: 10.1021/acs.jpcb.4c03062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Understanding electrostatics and electric properties of macromolecules is crucial in uncovering the intricacies of their behavior and functionality. The precise knowledge of these properties enhances our ability to manipulate and engineer macromolecules for diverse applications, spanning from drug design to materials science. Having that in mind, we present here the GruPol database approach to characterize and accurately predict dipole moments, static polarizabilities, and electrostatic potential of proteins and their subunits. The method involves partitioning of the electron density, calculated at the M06-HF/aug-cc-pVDZ level of theory, of small peptides into predefined building blocks that are averaged over the database. By manipulating and positioning these building blocks, GruPol enables the description of proteins assembled from over nearly 100 residual entries, allowing for efficient and precise computation of the above-mentioned properties across a broad range of proteins. The database enables the user to include solvent effects as well as define protonation states on the protein's backbone to account for pH variations. The precision of the proposed scheme is benchmarked against experimental data for myoglobin species.
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Affiliation(s)
- Raphael F Ligorio
- Institute of Inorganic Chemistry, University of Goettingen, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Paul Grosskopf
- Institute of Inorganic Chemistry, University of Goettingen, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Leonardo H R Dos Santos
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, 31270-901 Belo Horizonte, MG, Brazil
| | - Anna Krawczuk
- Institute of Inorganic Chemistry, University of Goettingen, Tammannstrasse 4, D-37077 Göttingen, Germany
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Ligório RF, Rodrigues JL, Krawczuk A, Dos Santos LHR. A building-block database of distributed polarizabilities and dipole moments to estimate optical properties of biomacromolecules in isolation or in an explicitly solvated medium. J Comput Chem 2023; 44:745-754. [PMID: 36433655 DOI: 10.1002/jcc.27037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/10/2022] [Accepted: 10/24/2022] [Indexed: 11/27/2022]
Abstract
Since atomic or functional-group properties in the bulk are generally not available from experimental methods, computational approaches based on partitioning schemes have emerged as a rapid yet accurate pathway to estimate the materials behavior from chemically meaningful building blocks. Among several applications, a comprehensive and systematically built database of atomic or group polarizabilities and related opto-electronic quantities would be very useful not only to envisage linear or non-linear optical properties of biomacromolecules but also to improve the accuracy of classical force fields devoted to simulate biochemical processes. In this work, we propose the first entries of such database that contains distributed polarizabilities and dipole moments extracted from fragments of peptides. Twenty three prototypical conformers of the dipeptides alanine-alanine and glycine-glycine were used to extract functional groups such as CH2 , CHCH3 , NH2 , COOH, CONH, thus allowing construction of a diversity of chemically relevant environments. To evaluate the accuracy of our database, reconstructed properties of larger peptides containing up to six residues of alanine and glycine were tested against density functional theory calculations at the M06-HF/aug-cc-pVDZ level of theory. The procedure is particularly accurate for the diagonal components of the polarizability tensor with errors up to 15%. In order to include solvent effects explicitly, the peptides were also surrounded by a box of water molecules whose distribution was optimized using the CHARMM force field. Solvent effects introduced by a classical dipole-dipole interaction model were compared to those obtained from polarizable-continuum model calculations.
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Affiliation(s)
- Raphael F Ligório
- Institut für Anorganische Chemie, Universität Göttingen, Göttingen, Germany
| | - José L Rodrigues
- Departamento de Química, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.,Departamento de Química, Instituto Federal de Educação, Ciência e Tecnologia do Maranhão - Campus Grajaú, Grajaú, MA, Brazil
| | - Anna Krawczuk
- Institut für Anorganische Chemie, Universität Göttingen, Göttingen, Germany
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Distributed functional-group polarizabilities in polypeptides and peptide clusters toward accurate prediction of electro-optical properties of biomacromolecules. J Mol Model 2023; 29:49. [PMID: 36662338 DOI: 10.1007/s00894-023-05451-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/10/2023] [Indexed: 01/21/2023]
Abstract
CONTEXT Aiming at accurately predicting electro-optical properties of biomolecules, this work presents distributed atomic and functional-group polarizability tensors for a series of polypeptides and peptide clusters constructed from glycine and its residuals. By partitioning the electron density using the quantum theory of atoms in molecules, we demonstrated a very good transferability of the group polarizabilities. We were able to identify and extract the most efficient functional groups capable of generating the largest electrical susceptibility in condensed phases. Both the isotropic polarizability and its anisotropy were used to understand the way functional groups act as sources of linear optical responses, how they interact with each other reinforcing the macroscopic optical behavior within the material, and how covalent bonds and non-covalent interactions, such as hydrogen bonds, determine refractive indices and birefringence. Particular attention is devoted to the peptide bonds as they provide links to build biomacromolecules or polymers. An adequate quantum-mechanical treatment of at least the first interaction sphere of a given functional group is required to properly describe the effects of mutual polarization, but we identified optimum cluster size and shape to better estimate polarizabilities and dipole moments of larger molecules or molecular aggregates from the knowledge of the electron density of a central molecule or amino acid residual that is representative of the bulk. The strategy outlined here is a fast yet effective tool for estimating the optical properties of proteins but could eventually find application in the rational design of optical organic materials as well. METHODS Electronic-structure calculations were performed on the Gaussin16 program at the DFT level using the CAMB3LYP functional and the double-ζ quality Dunning basis set aug-cc-pVDZ. Electron density partitioning followed the concepts of the Quantum Theory of Atoms and Molecules (QTAIM) and was performed using the AIMAll program. The locally developed Polaber routine was applied to calculate dipole moment vectors and polarizability tensors. It was amended to include the effects of the local field on a given central molecule by means of a modified Atom-Dipole Interaction Model (ADIM).
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Ligorio RF, Rodrigues JL, Zuev A, Dos Santos LHR, Krawczuk A. Benchmark of a functional-group database for distributed polarizability and dipole moment in biomolecules. Phys Chem Chem Phys 2022; 24:29495-29504. [PMID: 36459116 DOI: 10.1039/d2cp04052b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The extraction of functional-group properties in condensed phases is very useful for predicting material behaviors, including those of biomaterials. For this reason, computational approaches based on partitioning schemes have been developed aiming at rapidly and accurately estimating properties from chemically meaningful building blocks. A comprehensive database of group polarizabilities and dipole moments is useful not only to predict the optical properties of biomacromolecules but also to improve molecular force fields focused on simulating biochemical processes. In this work we benchmark a database of distributed polarizabilities and dipole moments for functional groups extracted from a series of polypeptides. This allows reconstruction of a variety of relevant chemical environments. The accuracy of our database was tested to predict the electro-optical properties of larger peptides and also simpler amino acids for which density functional theory calculations at the M06-HF/aug-cc-pVDZ level of theory was chosen as the reference. This approach is reasonably accurate for the diagonal components of the polarizability tensor, with errors not larger than 15-20%. The anisotropy of the polarizability is predicted with smaller efficacy though. Solvent effects were included explicitly by surrounding the database entries by a box of water molecules whose distribution was optimized using the CHARMM force field.
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Affiliation(s)
- Raphael F Ligorio
- Institut für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany.
| | - Jose L Rodrigues
- Departamento de Química, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos 6627, 31270-901 Belo Horizonte, MG, Brazil
| | - Anatoly Zuev
- Institut für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany.
| | - Leonardo H R Dos Santos
- Departamento de Química, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos 6627, 31270-901 Belo Horizonte, MG, Brazil
| | - Anna Krawczuk
- Institut für Anorganische Chemie, Universität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany.
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Dagdag O, Haldhar R, Kim SC, Safi ZS, Wazzan N, Mkadmh AM, Berisha A, Berdimurodov E, Jodeh S, Nwanna EE, Akpan ED, Ebenso EE. Synthesis, physicochemical properties, theoretical and electrochemical studies of tetraglycidyl methylenedianiline. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Ligorio RF, Krawczuk A, Dos Santos LHR. Accurate Atom-Dipole Interaction Model for Prediction of Electro-optical Properties: From van der Waals Aggregates to Covalently Bonded Clusters. J Phys Chem A 2021; 125:4152-4159. [PMID: 33970633 DOI: 10.1021/acs.jpca.1c02475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This work aims at the accurate estimation of the electro-optical properties of atoms and functional groups in organic crystals. A better understanding of the nature of building blocks and the way they interact with each other enables more efficient prediction of self-assembly, and thus physical properties in condensed matter. We propose a modified version of an atom-dipole interaction model that is based on atomic dipole moments calculated from the quantum theory of atoms in molecules. The method is very reliable for the prediction of various optical and electric properties in diverse chemical environments, ranging from hydrocarbon molecules bonded by dispersive interactions to polar rings connected by hydrogen bonds, or even polymeric structures whose monomers are covalently linked. Distributed polarizabilities and electrostatic potentials are compared to those obtained using a complete quantum-mechanical approach on finite-size aggregates. Our electrostatic approximation recovers isotropic polarizabilities with an accuracy of ca. 5 au and electrostatic potentials of ca. 0.05 au, even in the worst-case scenario in which polarization and charge-transfer effects are large. Functional groups are highly exportable, estimating the properties of small peptides and polyaromatics with a maximum deviation as low as ca. 15%.
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Affiliation(s)
- Raphael F Ligorio
- Departamento de Química, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos 6627, 31270-901 Belo Horizonte, MG, Brazil
| | - Anna Krawczuk
- Institut für Anorganische Chemie, Unisersität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany.,Faculty of Chemistry, Jagiellonian University in Krakow, Gronostajowa 2, 30-387 Krakow, Poland
| | - Leonardo H R Dos Santos
- Departamento de Química, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos 6627, 31270-901 Belo Horizonte, MG, Brazil
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Ligorio RF, Krawczuk A, Dos Santos LHR. Crystal Field Effects on Atomic and Functional-Group Distributed Polarizabilities of Molecular Materials. J Phys Chem A 2020; 124:10008-10018. [DOI: 10.1021/acs.jpca.0c09293] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Raphael F. Ligorio
- Departamento de Química, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos 6627, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | - Anna Krawczuk
- Institut für Anorganische Chemie, Unisersität Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany
| | - Leonardo H. R. Dos Santos
- Departamento de Química, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos 6627, Belo Horizonte 31270-901, Minas Gerais, Brazil
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Synthesis, structural characterization, and computational study of (E)-N′-(3,4-dimethoxybenzylidene)furan-2-carbohydrazide. ARAB J CHEM 2020. [DOI: 10.1016/j.arabjc.2018.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Polok K. Simulations of the OKE Response in Simple Liquids Using a Polarizable and a Nonpolarizable Force Field. J Phys Chem B 2018; 122:1638-1654. [DOI: 10.1021/acs.jpcb.7b08724] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kamil Polok
- Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
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Pike DH, Nanda V. Empirical estimation of local dielectric constants: Toward atomistic design of collagen mimetic peptides. Biopolymers 2016; 104:360-70. [PMID: 25784456 DOI: 10.1002/bip.22644] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/06/2015] [Accepted: 03/08/2015] [Indexed: 12/21/2022]
Abstract
One of the key challenges in modeling protein energetics is the treatment of solvent interactions. This is particularly important in the case of peptides, where much of the molecule is highly exposed to solvent due to its small size. In this study, we develop an empirical method for estimating the local dielectric constant based on an additive model of atomic polarizabilities. Calculated values match reported apparent dielectric constants for a series of Staphylococcus aureus nuclease mutants. Calculated constants are used to determine screening effects on Coulombic interactions and to determine solvation contributions based on a modified Generalized Born model. These terms are incorporated into the protein modeling platform protCAD, and benchmarked on a data set of collagen mimetic peptides for which experimentally determined stabilities are available. Computing local dielectric constants using atomistic protein models and the assumption of additive atomic polarizabilities is a rapid and potentially useful method for improving electrostatics and solvation calculations that can be applied in the computational design of peptides.
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Affiliation(s)
- Douglas H Pike
- Department of Biochemistry and Molecular Biology, Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, 08854
| | - Vikas Nanda
- Department of Biochemistry and Molecular Biology, Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, 08854
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Croccolo F, Arnaud MA, Bégué D, Bataller H. Concentration dependent refractive index of a binary mixture at high pressure. J Chem Phys 2011; 135:034901. [DOI: 10.1063/1.3610368] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Tafipolsky M, Engels B. Accurate Intermolecular Potentials with Physically Grounded Electrostatics. J Chem Theory Comput 2011; 7:1791-803. [DOI: 10.1021/ct200185h] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maxim Tafipolsky
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Bernd Engels
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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