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Zhang J, Chen J, Yang B, Ma S, Yin L, Liu Z, Xiang W, Liu H, Zhao J, Sheng P. Energy Level, Crystal Morphology and Fluorescence Emission Tuning in Cocrystals via Molecular-Level Engineering. Chemistry 2023; 29:e202202915. [PMID: 36404599 DOI: 10.1002/chem.202202915] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 11/08/2022] [Accepted: 11/18/2022] [Indexed: 11/22/2022]
Abstract
Organic donor-acceptor complexes as new organic semiconductor class have attracted wide attention, due to their potential applications in functional optoelectronics. Herein, we present two new charge transfer cocrystals of di-cyanodiazafluorene -perylene (DCPE) and di-cyanodiazaflfluorene-pyrene (DCPY) through a rational cocrystal-engineering strategy. Although they are both 1 : 1 mixed stacking cocrystals with similar chemical structures, the DCPE cocrystal possesses a non-centrosymmetric space group and narrower band gap compared to DCPY cocrystal, because of the non-covalent bonding variation. The electrostatic potential accumulated in the lateral facets leads to highly twisted DCPE nanobelts, and the small band gap causes near infrared fluorescence. Meanwhile, the DCPY crystals with centrosymmetric space groups and weaker intermolecular interactions exhibited an untwisted morphology and red emission. This study will be helpful for the design and understanding of functional cocrystal materials that can be used in flexible micro/nano-mechanics, mechanical energy, and optical devices.
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Affiliation(s)
- Jing Zhang
- Key Laboratory for Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, P. R. China
| | - Jinqiu Chen
- Key Laboratory for Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, P. R. China
| | - Bo Yang
- Key Laboratory for Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, P. R. China
| | - Shuang Ma
- Key Laboratory for Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, P. R. China
| | - Lina Yin
- College of Chemistry and Materials Science, Jinan University, 601 Huang-Pu Avenue West, Guangzhou, 510632, P. R. China
| | - Zhiqi Liu
- Key Laboratory for Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, P. R. China
| | - Wenxin Xiang
- Key Laboratory for Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, P. R. China
| | - Hongguang Liu
- College of Chemistry and Materials Science, Jinan University, 601 Huang-Pu Avenue West, Guangzhou, 510632, P. R. China.,School of Applied Physics and Materials, Wuyi University, Jiangmen, 529020, P. R. China
| | - Jianfen Zhao
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM) @School of Flexible Electronics (SIFE), Jiangsu National Synergetic Innovation Center for, Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), Nanjing, 211816, P. R. China
| | - Peng Sheng
- Material Laboratory of State Grid Corporation of China, State Key Laboratory of Advanced Transmission Technology, Global Energy Interconnection Research Institute, Beijing, 102211, P. R. China
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Issa NT, Byers SW, Dakshanamurthy S. ES-Screen: A Novel Electrostatics-Driven Method for Drug Discovery Virtual Screening. Int J Mol Sci 2022; 23:ijms232314830. [PMID: 36499162 PMCID: PMC9736079 DOI: 10.3390/ijms232314830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/02/2022] Open
Abstract
Electrostatic interactions drive biomolecular interactions and associations. Computational modeling of electrostatics in biomolecular systems, such as protein-ligand, protein-protein, and protein-DNA, has provided atomistic insights into the binding process. In drug discovery, finding biologically plausible ligand-protein target interactions is challenging as current virtual screening and adjuvant techniques such as docking methods do not provide optimal treatment of electrostatic interactions. This study describes a novel electrostatics-driven virtual screening method called 'ES-Screen' that performs well across diverse protein target systems. ES-Screen provides a unique treatment of electrostatic interaction energies independent of total electrostatic free energy, typically employed by current software. Importantly, ES-Screen uses initial ligand pose input obtained from a receptor-based pharmacophore, thus independent of molecular docking. ES-Screen integrates individual polar and nonpolar replacement energies, which are the energy costs of replacing the cognate ligand for a target with a query ligand from the screening. This uniquely optimizes thermodynamic stability in electrostatic and nonpolar interactions relative to an experimentally determined stable binding state. ES-Screen also integrates chemometrics through shape and other physicochemical properties to prioritize query ligands with the greatest physicochemical similarities to the cognate ligand. The applicability of ES-Screen is demonstrated with in vitro experiments by identifying novel targets for many drugs. The present version includes a combination of many other descriptor components that, in a future version, will be purely based on electrostatics. Therefore, ES-Screen is a first-in-class unique electrostatics-driven virtual screening method with a unique implementation of replacement electrostatic interaction energies with broad applicability in drug discovery.
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Matsuura Y, Joti Y, Bagautdinov B, Yutani K. Evaluating the strengths of salt bridges in the CutA1 protein using molecular dynamic simulations: a comparison of different force fields. FEBS Open Bio 2019; 9:1939-1956. [PMID: 31509647 PMCID: PMC6823277 DOI: 10.1002/2211-5463.12731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/01/2019] [Accepted: 09/06/2019] [Indexed: 11/15/2022] Open
Abstract
Ion–ion interactions (salt bridges) between favorable pairs of charged residues are important for the conformational stability of proteins. Molecular dynamic (MD) simulations are useful for elucidating the interactions among charged residues fluctuating in solution. However, the quality of MD results depends strongly on the force fields used. In this study, we compared the strengths of salt bridges among force fields by performing MD simulations using the CutA1 protein (trimer) from the hyperthermophile Pyrococcus horikoshii (PhCutA1), which has an unusually large proportion of charged residues. The force fields Chemistry at HARvard Macromolecular Mechanics (Charmm)27, Assisted Model Building and Energy Refinement (Amber)99sb, Amber14sb, GROningen Molecular Simulation (Gromos)43a1, and Gromos53a6 were used in combination with two different water models, tip3p (for Charmm27, Amber99sb, and Amber14sb) and simple point charge/extended (for Amber99sb, Gromos43a1, and Gromos53a6), yielding a total of six combinations. The RMSDs of all Cα atoms of PhCutA1 were similar among force fields, except for Charmm27, during 400‐ns MD simulations at 300 K; however, the radius of gyration (Rg) was greater for Amber99sb and shorter for Gromos43a1. The average strengths of salt bridges for each positively charged residue did not differ greatly among force fields, but the strengths at specific sites within the structure depended sensitively on the force field used. In the case of the Gromos group, positively charged residues could engage in favorable interactions with many more charged residues than in the other force fields, especially in loop regions; consequently, the apparent strength at each site was lower.
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Affiliation(s)
| | - Yasumasa Joti
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan.,Japan Synchrotron Radiation Research Institute, Sayo, Hyogo, Japan
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Abstract
The precise modeling of molecular interactions remains an important goal among molecular modeling techniques. Some of the challenges in the field include the precise definition of a Hamiltonian for biomolecular systems, together with precise parameters derived from Molecular Mechanics Force Fields, for example. The problem is even more challenging when interaction energies from different species are computed, such as the interaction energy involving a ligand and a protein, given that small differences must be computed from large energies. Here we evaluated the effects of the electrostatic model for ligand binding energy evaluation in the context of ligand docking. For this purpose, a classical Coulomb potential with distance-dependent dielectrics was compared with a Poisson-Boltzmann (PB) model for electrostatic potential computation, based on DelPhi calculations. We found that, although the electrostatic energies were highly correlated for the Coulomb and PB models, the ligand pose and the enrichment of actual ligands against decoy compounds, were improved when binding energies were computed using PB as compared to the Coulomb model. We observed that the electrostatic energies computed with the Coulomb model were, on average, ten times larger than the energies computed with the PB model, suggesting a strong overestimation of the polar interactions in the Coulomb model. We also found that a slightly smoothed Lennard-Jones potential combined with the PB model resulted in a good compromise between ligand sampling and energetic scoring.
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Jabłoński M. Bond paths between distant atoms do not necessarily indicate dominant interactions. J Comput Chem 2018; 39:2183-2195. [PMID: 30298926 DOI: 10.1002/jcc.25532] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 06/27/2018] [Accepted: 06/27/2018] [Indexed: 12/16/2022]
Abstract
The goal of the article is to revive discussion on the interpretation of bond paths linking distant atoms, particularly tracing weak interactions in dimers. According to the Pendás' concept of privileged exchange channel, a bond path is formed between this pair of competing atoms, which is associated with larger value of the exchange energy. We point out that, due to the short-range nature of the exchange energy, bond paths linking distant atoms clearly become doubtful indicators of dominant intermolecular interactions, particularly if some other characteristics (geometric, spectroscopic, based on electrostatic parameters, etc.) indicate other intermolecular interactions as dominant. Several such cases are thoroughly investigated. We show that electrostatic parameters are much more reliable indicators of dominant intermolecular interactions than bond paths. Then, we pay attention that the presence of ("unexpected", i.e., not necessarily indicating dominant intermolecular interactions) bond paths between pairs of atoms featuring highly expanded charge distributions can be easily explained by visual exploration of isodensity contour plots. As always pointing in the direction of the steepest increase, the gradient vector of the electron density favors areas of its high values gaining higher exchange energy, yet being blind to highly electron deficient areas nearby, which, however, can quite often be involved in dominant intermolecular interactions as strongly suggested by many other bonding analysis. We also suggest that an interatomic component of Hellmann-Feynman force would most likely be the most reliable indicator of attractive or repulsive character of individual interatomic interaction. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Mirosław Jabłoński
- Department of Quantum Chemistry, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, 7-Gagarina Street, 87-100, Toruń, Poland
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Zhang Z, Lu L, Zhang Y, Hua Li C, Wang CX, Zhang XY, Tan JJ. A combinatorial scoring function for protein-RNA docking. Proteins 2017; 85:741-752. [PMID: 28120375 DOI: 10.1002/prot.25253] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 01/16/2017] [Accepted: 01/17/2017] [Indexed: 12/13/2022]
Abstract
Protein-RNA docking is still an open question. One of the main challenges is to develop an effective scoring function that can discriminate near-native structures from the incorrect ones. To solve the problem, we have constructed a knowledge-based residue-nucleotide pairwise potential with secondary structure information considered for nonribosomal protein-RNA docking. Here we developed a weighted combined scoring function RpveScore that consists of the pairwise potential and six physics-based energy terms. The weights were optimized using the multiple linear regression method by fitting the scoring function to L_rmsd for the bound docking decoys from Benchmark II. The scoring functions were tested on 35 unbound docking cases. The results show that the scoring function RpveScore including all terms performs best. Also RpveScore was compared with the statistical mechanics-based method derived potential ITScore-PR, and the united atom-based statistical potentials QUASI-RNP and DARS-RNP. The success rate of RpveScore is 71.6% for the top 1000 structures and the number of cases where a near-native structure is ranked in top 30 is 25 out of 35 cases. For 32 systems (91.4%), RpveScore can find the binding mode in top 5 that has no lower than 50% native interface residues on protein and nucleotides on RNA. Additionally, it was found that the long-range electrostatic attractive energy plays an important role in distinguishing near-native structures from the incorrect ones. This work can be helpful for the development of protein-RNA docking methods and for the understanding of protein-RNA interactions. RpveScore program is available to the public at http://life.bjut.edu.cn/kxyj/kycg/2017116/14845362285362368_1.html Proteins 2017; 85:741-752. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Zhao Zhang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Lin Lu
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Yue Zhang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Chun Hua Li
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Cun Xin Wang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Xiao Yi Zhang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Jian Jun Tan
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
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Goda T, Singi AB, Maeda Y, Matsumoto A, Torimura M, Aoki H, Miyahara Y. Label-free potentiometry for detecting DNA hybridization using peptide nucleic acid and DNA probes. Sensors (Basel) 2013; 13:2267-78. [PMID: 23435052 PMCID: PMC3649381 DOI: 10.3390/s130202267] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 01/15/2013] [Accepted: 02/04/2013] [Indexed: 02/02/2023]
Abstract
Peptide nucleic acid (PNA) has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM)-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry.
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Affiliation(s)
- Tatsuro Goda
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo 101-0062, Japan; E-Mails: (T.G.); (A.B.S.); (Y.M.); (A.M.)
| | - Ankit Balram Singi
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo 101-0062, Japan; E-Mails: (T.G.); (A.B.S.); (Y.M.); (A.M.)
| | - Yasuhiro Maeda
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo 101-0062, Japan; E-Mails: (T.G.); (A.B.S.); (Y.M.); (A.M.)
| | - Akira Matsumoto
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo 101-0062, Japan; E-Mails: (T.G.); (A.B.S.); (Y.M.); (A.M.)
| | - Masaki Torimura
- National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan; E-Mail:
| | - Hiroshi Aoki
- National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan; E-Mail:
| | - Yuji Miyahara
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda, Tokyo 101-0062, Japan; E-Mails: (T.G.); (A.B.S.); (Y.M.); (A.M.)
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Abstract
The interplay between geometry and electrostatics contributes significantly to hydrophobic interactions of biomolecules in an aqueous solution. With an implicit solvent, such a system can be described macroscopically by the dielectric boundary that separates the high-dielectric solvent from low-dielectric solutes. This work concerns the motion of a model cylindrical dielectric boundary as the steepest descent of a free-energy functional that consists of both the surface and electrostatic energies. The effective dielectric boundary force is defined and an explicit formula of the force is obtained. It is found that such a force always points from the solvent region to solute region. In the case that the interior of a cylinder is of a lower dielectric, the motion of the dielectric boundary is initially driven dominantly by the surface force but is then driven inward quickly to the cylindrical axis by both the surface and electrostatic forces. In the case that the interior of a cylinder is of a higher dielectric, the competition between the geometrical and electrostatic contributions leads to the existence of equilibrium boundaries that are circular cylinders. Linear stability analysis is presented to show that such an equilibrium is only stable for a perturbation with a wavenumber larger than a critical value. Numerical simulations are reported for both of the cases, confirming the analysis on the role of each component of the driving force. Implications of the mathematical findings to the understanding of charged molecular systems are discussed.
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Affiliation(s)
- Li-Tien Cheng
- Department of Mathematics, University of California, San Diego, 9500 Gilman Drive, Mail code: 0112, La Jolla, CA 92093-0112, U.S.A
| | - Bo Li
- Department of Mathematics and the NSF Center for Theoretical Biological Physics, University of California, San Diego, 9500 Gilman Drive, Mail code: 0112, La Jolla, CA 92093-0112, U.S.A
| | - Michael White
- Department of Mathematics and the NSF Center for Theoretical Biological Physics, University of California, San Diego, 9500 Gilman Drive, Mail code: 0112, La Jolla, CA 92093-0112, U.S.A
| | - Shenggao Zhou
- Department of Mathematics, Zhejiang University, No. 38 Zheda Road, Hangzhou, 310027, P. R. China, and Department of Mathematics and the NSF Center for Theoretical Biological Physics, University of California, San Diego, 9500 Gilman Drive, Mail code: 0112, La Jolla, CA 92093-0112, USA
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