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Ligorio R, 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; 128:7954-7965. [PMID: 38976348 PMCID: PMC11345817 DOI: 10.1021/acs.jpcb.4c03062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/14/2024] [Accepted: 06/20/2024] [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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2
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Bhandary S, Beliš M, Shukla R, Bourda L, Kaczmarek AM, Van Hecke K. Single-Crystal-to-Single-Crystal Photosynthesis of Supramolecular Organoboron Polymers with Dynamic Effects. J Am Chem Soc 2024; 146:8659-8667. [PMID: 38407928 DOI: 10.1021/jacs.4c00978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The solid-state synthesis of single-crystalline organic polymers, having functional properties, remains an attractive and developing research area in polymer chemistry and materials science. However, light-triggered topochemical synthesis of crystalline polymers comprising an organoboron backbone has not yet been reported. Here, we describe an intriguing example of single-crystal-to-single-crystal (SCSC) rapid photosynthesis (occurs on a seconds-scale) of two structurally different linear organoboron polymers, driven by environmentally sustainable visible/sun light, obtained from the same monomer molecule. A newly designed Lewis acid-base type molecular B ← N organoboron adduct (consisting of an organoboron core and naphthylvinylpyridine ligands) crystallizes in two solid-state forms featuring the same chemical structure but different 3D structural topologies, namely, monomers 1 and 2. The solvate molecule-free crystals of 1 undergo topochemical photopolymerization via an unusual olefin-naphthyl ring [2 + 2] cyclization to yield the single crystalline [3]-ladderane polymer 1P growing along the B ← N linkages, accompanied by instantaneous and violent macroscopic mechanical motions or photosalient effects (such as bending-reshaping and jumping motions). In contrast, visible light-harvesting single crystals of 2 quantitatively polymerize to a B ← N bond-stabilized polymer 2P in a SCSC fashion owing to the rapid [2 + 2] cycloaddition reaction among olefin double bonds. Such olefin bonds in the crystals of 2 are suitably preorganized for photoreaction due to the presence of solvate molecules in the crystal packing. Single crystals of 2 also show photodynamic jumping motions - in response to visible light but in a relatively slower fashion than the crystals of 1. In addition to SCSC topochemical polymerization and dynamic motions, both monomer crystals and their single-crystalline polymers feature green emissive and short-lived room-temperature phosphorescence properties upon excitation with visible-light wavelength.
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Affiliation(s)
- Subhrajyoti Bhandary
- XStruct, Department of Chemistry, Ghent University, Krijgslaan 281-Building S3, Ghent B-9000, Belgium
| | - Marek Beliš
- XStruct, Department of Chemistry, Ghent University, Krijgslaan 281-Building S3, Ghent B-9000, Belgium
| | - Rahul Shukla
- Department of Chemistry (NCI Lab), GITAM (Deemed to be University), Visakhapatnam 530045, Andhra Pradesh, India
| | - Laurens Bourda
- XStruct, Department of Chemistry, Ghent University, Krijgslaan 281-Building S3, Ghent B-9000, Belgium
| | - Anna M Kaczmarek
- NanoSensing Group, Department of Chemistry, Ghent University, Krijgslaan 281-Building S3, Ghent B-9000, Belgium
| | - Kristof Van Hecke
- XStruct, Department of Chemistry, Ghent University, Krijgslaan 281-Building S3, Ghent B-9000, Belgium
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3
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Bhandary S, Pathigoolla A, Madhusudhanan MC, Sureshan KM. Azide–Alkyne Interactions: A Crucial Attractive Force for Their Preorganization for Topochemical Cycloaddition Reaction. Chemistry 2022; 28:e202200820. [DOI: 10.1002/chem.202200820] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Indexed: 12/17/2022]
Affiliation(s)
- Subhrajyoti Bhandary
- School of Chemistry Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
| | - Atchutarao Pathigoolla
- School of Chemistry Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
| | - Mithun C. Madhusudhanan
- School of Chemistry Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
| | - Kana M. Sureshan
- School of Chemistry Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
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4
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Omodemi O, Sprouse S, Herbert D, Kaledin M, Kaledin AL. On the Cartesian Representation of the Molecular Polarizability Tensor Surface by Polynomial Fitting to Ab Initio Data. J Chem Theory Comput 2021; 18:37-45. [PMID: 34958587 DOI: 10.1021/acs.jctc.1c01015] [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
We describe an approach to constructing an analytic Cartesian representation of the molecular dipole polarizability tensor surface in terms of polynomials in interatomic distances with a training set of ab initio data points obtained from a molecular dynamics (MD) simulation or by any other available means. The proposed formulation is based on a perturbation treatment of the unmodified point dipole polarizability model of Applequist [ J. Am. Chem. Soc. 1972, 94, 2952] and is shown here to be, by construction (i) free of short-range or other singularities or discontinuities, (ii) symmetric and translationally invariant, and (iii) nonreliant on a body-fixed coordinate system. Permutational invariance of like nuclei is demonstrated to be readily applicable, making this approach useful for highly fluxional and reactive systems. Derivation of the method is described in detail, adding brief didactic numerical examples of H2 and H2O and concluding with an MD simulation of the Raman spectrum of H5O2+ at 300 K with the polarizability tensor fitted to CCSD(T)/aug-cc-pVTZ data obtained using the HBB-4B potential [ J. Chem. Phys. 2005, 122, 044308].
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Affiliation(s)
- Oluwaseun Omodemi
- Department of Chemistry & Biochemistry, Kennesaw State University, 370 Paulding Avenue NW, Box # 1203, Kennesaw, Georgia 30144, United States
| | - Sarah Sprouse
- Department of Chemistry & Biochemistry, Kennesaw State University, 370 Paulding Avenue NW, Box # 1203, Kennesaw, Georgia 30144, United States
| | - Destyni Herbert
- Department of Chemistry & Biochemistry, Kennesaw State University, 370 Paulding Avenue NW, Box # 1203, Kennesaw, Georgia 30144, United States
| | - Martina Kaledin
- Department of Chemistry & Biochemistry, Kennesaw State University, 370 Paulding Avenue NW, Box # 1203, Kennesaw, Georgia 30144, United States
| | - Alexey L Kaledin
- Cherry L. Emerson Center for Scientific Computation, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
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5
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The response of electronic and energetic properties of conjugated vs aromatic molecules to an external uniform electric field. Struct Chem 2019. [DOI: 10.1007/s11224-019-01345-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Gryl M, Rydz A, Wojnarska J, Krawczuk A, Kozieł M, Seidler T, Ostrowska K, Marzec M, Stadnicka KM. Origin of chromic effects and crystal-to-crystal phase transition in the polymorphs of tyraminium violurate. IUCRJ 2019; 6:226-237. [PMID: 30867920 PMCID: PMC6400187 DOI: 10.1107/s2052252518017037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/30/2018] [Indexed: 06/09/2023]
Abstract
Chromic materials are nowadays widely used in various technological applications, however understanding the effect and the possibility of tuning the obtained colour of a material are still challenging. Here a combined experimental and theoretical study is presented on the solvatochromic and crystallochromic effects in the (pseudo)polymorphs of tyraminium violurate. This organic material exhibits a large solvatochromic shift (ca 192 nm) associated with broad colour change (from yellow to dark violet). Tyraminum violurate crystallizes as red crystals of form (I) from water as a solvate, and as an unsolvated form [violet crystals of (II)] from methanol solution. Form (I), when heated, undergoes two crystal-to-crystal phase transformations associated with colour change of the crystals. Crystals of (II) show extreme birefringence (ca 0.46) and high refractive index (n γ above 1.90), which can be correlated with preferential orientation of the resultant dipole moments of the ions. Examination of optical effects (UV-Vis spectra) along with theoretical calculations (QTAIM, atomic and bond polarizabilities) enabled the description of the origin of colour in the studied materials.
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Affiliation(s)
- Marlena Gryl
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Agnieszka Rydz
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Joanna Wojnarska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Anna Krawczuk
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Marcin Kozieł
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Tomasz Seidler
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Katarzyna Ostrowska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Monika Marzec
- Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
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7
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Sitkiewicz SP, Rodríguez-Mayorga M, Luis JM, Matito E. Partition of optical properties into orbital contributions. Phys Chem Chem Phys 2019; 21:15380-15391. [DOI: 10.1039/c9cp02662b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A new tool to analyze the response property through the partition of nonlinear optical properties in terms of orbital contributions (PNOC), valuable in the assessment of the electronic structure methods in the NLOPs computations, is presented.
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Affiliation(s)
- Sebastian P. Sitkiewicz
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea (UPV/EHU)
- 20080 Donostia
- Spain
- Donostia International Physics Center (DIPC)
| | - Mauricio Rodríguez-Mayorga
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea (UPV/EHU)
- 20080 Donostia
- Spain
- Donostia International Physics Center (DIPC)
| | - Josep M. Luis
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química
- Universitat de Girona
- C/Maria Aurèlia Capmany, 69
- 17003 Girona
- Spain
| | - Eduard Matito
- Donostia International Physics Center (DIPC)
- Donostia
- Spain
- Ikerbasque Foundation for Science
- 48011 Bilbao
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8
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Sirohiwal A, Hathwar VR, Dey D, Chopra D. Investigation of Chemical Bonding in In Situ Cryocrystallized Organometallic Liquids. Chemphyschem 2017; 18:2859-2863. [DOI: 10.1002/cphc.201700585] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/14/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Abhishek Sirohiwal
- Crystallography and Crystal Chemistry Laboratory; Department of Chemistry; Indian Institute of Science Education and Research Bhopal; Bhopal- 462066 Madhya Pradesh India
- Current address: Max Planck Institute for Chemical Energy Conversion; Stiftstrasse 34-36 45470 Mülheim an der Ruhr Germany
| | - Venkatesha R. Hathwar
- Division of Physics; Faculty of Pure and Applied Sciences; University of Tsukuba; 1-1-1, Tennodai Tsukuba Ibaraki 305-8571 Japan
| | - Dhananjay Dey
- Crystallography and Crystal Chemistry Laboratory; Department of Chemistry; Indian Institute of Science Education and Research Bhopal; Bhopal- 462066 Madhya Pradesh India
| | - Deepak Chopra
- Crystallography and Crystal Chemistry Laboratory; Department of Chemistry; Indian Institute of Science Education and Research Bhopal; Bhopal- 462066 Madhya Pradesh India
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9
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A topological analysis of the bonding in [M2(CO)10] and [M3(μ-H)3(CO)12] complexes (M = Mn, Tc, Re). Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1821-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Otero N, Van Alsenoy C, Pouchan C, Karamanis P. Hirshfeld-based intrinsic polarizability density representations as a tool to analyze molecular polarizability. J Comput Chem 2015; 36:1831-43. [DOI: 10.1002/jcc.24003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 06/16/2015] [Indexed: 01/23/2023]
Affiliation(s)
- Nicolás Otero
- Équipe Chimie-Physique (ECP), Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Materiaux (IPREM) UMR 5254; Technopole Hélioparc, 2 avenue du Président Pierre Angot 64053 Pau Cedex 09 France
- Departamento de Química Física; Universidade de Vigo; 36310 Vigo Galicia Spain
| | - Christian Van Alsenoy
- Department of Chemistry; Structural Chemistry Group, University of Antwerp; Groenenborgerlaan 171 B-2020 Antwerp Belgium
| | - Claude Pouchan
- Équipe Chimie-Physique (ECP), Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Materiaux (IPREM) UMR 5254; Technopole Hélioparc, 2 avenue du Président Pierre Angot 64053 Pau Cedex 09 France
| | - Panaghiotis Karamanis
- Équipe Chimie-Physique (ECP), Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Materiaux (IPREM) UMR 5254; Technopole Hélioparc, 2 avenue du Président Pierre Angot 64053 Pau Cedex 09 France
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11
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Dos Santos LHR, Krawczuk A, Macchi P. Distributed Atomic Polarizabilities of Amino Acids and their Hydrogen-Bonded Aggregates. J Phys Chem A 2015; 119:3285-98. [DOI: 10.1021/acs.jpca.5b00069] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Leonardo H. R. Dos Santos
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, 3012 Bern, Switzerland
| | - Anna Krawczuk
- Faculty
of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland
| | - Piero Macchi
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, 3012 Bern, Switzerland
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