1
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Sahu N, Khire SS, Gadre SR. Combining fragmentation method and high-performance computing: Geometry optimization and vibrational spectra of proteins. J Chem Phys 2023; 159:044309. [PMID: 37522406 DOI: 10.1063/5.0149572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023] Open
Abstract
Exploring the structures and spectral features of proteins with advanced quantum chemical methods is an uphill task. In this work, a fragment-based molecular tailoring approach (MTA) is appraised for the CAM-B3LYP/aug-cc-pVDZ-level geometry optimization and vibrational infrared (IR) spectra calculation of ten real proteins containing up to 407 atoms and 6617 basis functions. The use of MTA and the inherently parallel nature of the fragment calculations enables a rapid and accurate calculation of the IR spectrum. The applicability of MTA to optimize the protein geometry and evaluate its IR spectrum employing a polarizable continuum model with water as a solvent is also showcased. The typical errors in the total energy and IR frequencies computed by MTA vis-à-vis their full calculation (FC) counterparts for the studied protein are 5-10 millihartrees and 5 cm-1, respectively. Moreover, due to the independent execution of the fragments, large-scale parallelization can also be achieved. With increasing size and level of theory, MTA shows an appreciable advantage in computer time as well as memory and disk space requirement over the corresponding FCs. The present study suggests that the geometry optimization and IR computations on the biomolecules containing ∼1000 atoms and/or ∼15 000 basis functions using MTA and HPC facility can be clearly envisioned in the near future.
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Affiliation(s)
- Nityananda Sahu
- Theoretische Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Subodh S Khire
- RIKEN Center for Computational Science, Kobe 650-0047, Japan
| | - Shridhar R Gadre
- Departments of Scientific Computing, Modelling & Simulation and Chemistry, Savitribai Phule Pune University, Pune 411007, India
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2
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Liu Y, Li X, Pu Q, Fu R, Wang Z, Li Y, Li X. Innovative screening for functional improved aromatic amine derivatives: Toxicokinetics, free radical oxidation pathway and carcinogenic adverse outcome pathway. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131541. [PMID: 37146326 DOI: 10.1016/j.jhazmat.2023.131541] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/08/2023] [Accepted: 04/28/2023] [Indexed: 05/07/2023]
Abstract
Aromatic amines, one of the most widely used low-cost antioxidants in rubbers, have been regarded as pollutants with human health concerns. To overcome this problem, this study developed a systematic molecular design, screening, and performance evaluation method to design functionally improved, environmentally friendly and synthesizable aromatic amine alternatives for the first time. Nine of 33 designed aromatic amine derivatives have improved antioxidant property (lower bond dissociation energy of N-H), and their environmental and bladder carcinogenicity impacts were evaluated through toxicokinetic model and molecular dynamics simulation. The environmental fate of the designed AAs-11-8, AAs-11-16, and AAs-12-2 after antioxidation (i.e., peroxyl radicals (ROO·), hydroxyl radicals (HO·), superoxide anion radicals (O2·-) and ozonation reaction) was also analyzed. Results showed that the by-products of AAs-11-8 and AAs-12-2 have less toxicity after antioxidation. In addition, human bladder carcinogenicity of the screened alternatives was also evaluated through adverse outcome pathway. The carcinogenic mechanisms were analyzed and verified through amino acid residue distribution characteristics, 3D-QSAR and 2D-QSAR models. AAs-12-2, with high antioxidation property, low environmental impacts and carcinogenicity, was screened as the optimum alternative for 3,5-Dimethylbenzenamine. This study provided theoretical support for designing environmentally friendly and functionally improved aromatic amine alternatives from toxicity evaluation and mechanism analysis.
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Affiliation(s)
- Yajing Liu
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China
| | - Xinao Li
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China
| | - Qikun Pu
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China
| | - Rui Fu
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China
| | - Zhonghe Wang
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China
| | - Yu Li
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China
| | - Xixi Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3X5, Canada.
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3
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Wu Y, Si H, Yu X, Fu F, Wang Z, Yao J, Liu X. Enhancing the solubility and antimicrobial activity of cellulose through esterification modification using amino acid hydrochlorides. Int J Biol Macromol 2023; 226:793-802. [PMID: 36526062 DOI: 10.1016/j.ijbiomac.2022.12.068] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/22/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
Most amino acid molecules have good water solubility and are rich in functional groups, which makes them a promising derivatizing agent for cellulose. However, self-condensation of amino acids and low reaction efficiency always happen during esterification. Here, amino acid hydrochloride ([AA]Cl) is selected as raw material to synthesize cellulose amino acid ester (CAE). Based on TG-MS coupling technology, a significantly faster reaction rate of [AA]Cl compared to raw amino acid can be observed visually. CAE with the degree of substitution 0.412-0.516 is facilely synthesized under 130-170 °C for 10-50 min. Moreover, the effects of amounts of [AA]Cl agent, temperature, and time on the esterification are studied. The CAE can be well dissolved in 7 wt% NaOH aq., resulting in a 7.5 wt% dope. The rheological test of the dope demonstrated a shear-thinning behavior for Newtonian-like fluid, and a high gel temperature (41.7 °C). Further, the synthesized products show distinct antibacterial activity and the bacteriostatic reduction rate against E. coli can reach 99.5 %.
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Affiliation(s)
- Yang Wu
- Institute of Composite Materials, School of Materials Science and Engineering, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Hongkuo Si
- Institute of Composite Materials, School of Materials Science and Engineering, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xiaodong Yu
- Institute of Composite Materials, School of Materials Science and Engineering, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Feiya Fu
- Institute of Composite Materials, School of Materials Science and Engineering, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Zongqian Wang
- School of Textile and Garment, Anhui Polytechnic University, Wuhu 241000, China.
| | - Juming Yao
- Institute of Composite Materials, School of Materials Science and Engineering, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xiangdong Liu
- Institute of Composite Materials, School of Materials Science and Engineering, Zhejiang Sci-Tech University, Hangzhou 310018, China
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4
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Gloaguen E, Mons M, Schwing K, Gerhards M. Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues. Chem Rev 2020; 120:12490-12562. [PMID: 33152238 DOI: 10.1021/acs.chemrev.0c00168] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.
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Affiliation(s)
- Eric Gloaguen
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Kirsten Schwing
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - Markus Gerhards
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
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Bakels S, Gaigeot MP, Rijs AM. Gas-Phase Infrared Spectroscopy of Neutral Peptides: Insights from the Far-IR and THz Domain. Chem Rev 2020; 120:3233-3260. [PMID: 32073261 PMCID: PMC7146864 DOI: 10.1021/acs.chemrev.9b00547] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
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Gas-phase, double
resonance IR spectroscopy has proven to be an
excellent approach to obtain structural information on peptides ranging
from single amino acids to large peptides and peptide clusters. In
this review, we discuss the state-of-the-art of infrared action spectroscopy
of peptides in the far-IR and THz regime. An introduction to the field
of far-IR spectroscopy is given, thereby highlighting the opportunities
that are provided for gas-phase research on neutral peptides. Current
experimental methods, including spectroscopic schemes, have been reviewed.
Structural information from the experimental far-IR spectra can be
obtained with the help of suitable theoretical approaches such as
dynamical DFT techniques and the recently developed Graph Theory.
The aim of this review is to underline how the synergy between far-IR
spectroscopy and theory can provide an unprecedented picture of the
structure of neutral biomolecules in the gas phase. The far-IR signatures
of the discussed studies are summarized in a far-IR map, in order
to gain insight into the origin of the far-IR localized and delocalized
motions present in peptides and where they can be found in the electromagnetic
spectrum.
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Affiliation(s)
- Sjors Bakels
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7-c, 6525 ED Nijmegen, The Netherlands
| | - Marie-Pierre Gaigeot
- LAMBE CNRS UMR8587, Université d'Evry val d'Essonne, Blvd F. Mitterrand, Bât Maupertuis, 91025 Evry, France
| | - Anouk M Rijs
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7-c, 6525 ED Nijmegen, The Netherlands
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Dietrich F, Bernhard D, Fatima M, Pérez C, Schnell M, Gerhards M. The Effect of Dispersion on the Structure of Diphenyl Ether Aggregates. Angew Chem Int Ed Engl 2018; 57:9534-9537. [DOI: 10.1002/anie.201801842] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 03/30/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Fabian Dietrich
- Fachbereich Chemie and Research Center Optimas; TU Kaiserslautern; Erwin-Schrödinger-Str. 52 67663 Kaiserslautern Germany
| | - Dominic Bernhard
- Fachbereich Chemie and Research Center Optimas; TU Kaiserslautern; Erwin-Schrödinger-Str. 52 67663 Kaiserslautern Germany
| | - Mariyam Fatima
- Deutsches Elektronen-Synchrotron (DESY); Max-Planck-Institut für Struktur und Dynamik der Materie; Notkestrasse 85 22607 Hamburg Germany
| | - Cristóbal Pérez
- Deutsches Elektronen-Synchrotron (DESY); Max-Planck-Institut für Struktur und Dynamik der Materie; Notkestrasse 85 22607 Hamburg Germany
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron (DESY); Max-Planck-Institut für Struktur und Dynamik der Materie; Notkestrasse 85 22607 Hamburg Germany
- Christian-Albrechts-Universität zu Kiel; Institut für Physikalische Chemie; Max-Eyth-Strasse 1 24118 Kiel Germany
| | - Markus Gerhards
- Fachbereich Chemie and Research Center Optimas; TU Kaiserslautern; Erwin-Schrödinger-Str. 52 67663 Kaiserslautern Germany
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7
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Dietrich F, Bernhard D, Fatima M, Pérez C, Schnell M, Gerhards M. Der Effekt von Dispersionswechselwirkungen auf die Struktur von Diphenylether-Aggregaten. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801842] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Fabian Dietrich
- Fachbereich Chemie und Forschungszentrum Optimas; TU Kaiserslautern; Erwin-Schrödinger-Straße 52 67663 Kaiserslautern Deutschland
| | - Dominic Bernhard
- Fachbereich Chemie und Forschungszentrum Optimas; TU Kaiserslautern; Erwin-Schrödinger-Straße 52 67663 Kaiserslautern Deutschland
| | - Mariyam Fatima
- Deutsches Elektronen-Synchrotron (DESY); Max-Planck-Institut für Struktur und Dynamik der Materie; Notkestraße 85 22607 Hamburg Deutschland
| | - Cristóbal Pérez
- Deutsches Elektronen-Synchrotron (DESY); Max-Planck-Institut für Struktur und Dynamik der Materie; Notkestraße 85 22607 Hamburg Deutschland
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron (DESY); Max-Planck-Institut für Struktur und Dynamik der Materie; Notkestraße 85 22607 Hamburg Deutschland
- Christian-Albrechts-Universität zu Kiel; Institut für Physikalische Chemie; Max-Eyth-Straße 1 24118 Kiel Deutschland
| | - Markus Gerhards
- Fachbereich Chemie und Forschungszentrum Optimas; TU Kaiserslautern; Erwin-Schrödinger-Straße 52 67663 Kaiserslautern Deutschland
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8
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Rank CK, Wall T, Dietrich F, Vidovic M, Klein MP, Sun Y, Niedner‐Schatteburg G, Gerhards M, Patureau FW. A Phosphino‐Carboxylic Acid‐Based Ru Dimeric Complex. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201701382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Christian K. Rank
- FB Chemie & Research Center Optimas TU Kaiserslautern Erwin‐Schrödinger Str. 52 67663 Kaiserslautern Germany
| | - Tatjana Wall
- FB Chemie & Research Center Optimas TU Kaiserslautern Erwin‐Schrödinger Str. 52 67663 Kaiserslautern Germany
- Forschungszentrum Optimas TU Kaiserslautern Kaiserslautern Germany
| | - Fabian Dietrich
- FB Chemie & Research Center Optimas TU Kaiserslautern Erwin‐Schrödinger Str. 52 67663 Kaiserslautern Germany
- Forschungszentrum Optimas TU Kaiserslautern Kaiserslautern Germany
| | - Marko Vidovic
- FB Chemie & Research Center Optimas TU Kaiserslautern Erwin‐Schrödinger Str. 52 67663 Kaiserslautern Germany
- Forschungszentrum Optimas TU Kaiserslautern Kaiserslautern Germany
| | - Matthias P. Klein
- FB Chemie & Research Center Optimas TU Kaiserslautern Erwin‐Schrödinger Str. 52 67663 Kaiserslautern Germany
- Forschungszentrum Optimas TU Kaiserslautern Kaiserslautern Germany
| | - Yu Sun
- FB Chemie & Research Center Optimas TU Kaiserslautern Erwin‐Schrödinger Str. 52 67663 Kaiserslautern Germany
| | - Gereon Niedner‐Schatteburg
- FB Chemie & Research Center Optimas TU Kaiserslautern Erwin‐Schrödinger Str. 52 67663 Kaiserslautern Germany
- Forschungszentrum Optimas TU Kaiserslautern Kaiserslautern Germany
| | - Markus Gerhards
- FB Chemie & Research Center Optimas TU Kaiserslautern Erwin‐Schrödinger Str. 52 67663 Kaiserslautern Germany
- Forschungszentrum Optimas TU Kaiserslautern Kaiserslautern Germany
| | - Frederic W. Patureau
- FB Chemie & Research Center Optimas TU Kaiserslautern Erwin‐Schrödinger Str. 52 67663 Kaiserslautern Germany
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