1
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Li Y, Zhang Q, Zhao J, Wang Z, Zong X, Yang L, Zhang C, Zhao H. Mechanical behavior and microstructure of porcine brain tissues under pulsed electric fields. Biomech Model Mechanobiol 2024; 23:241-254. [PMID: 37861916 DOI: 10.1007/s10237-023-01771-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/29/2023] [Indexed: 10/21/2023]
Abstract
Pulsed electric fields are extensively utilized in clinical treatments, such as subthalamic deep brain stimulation, where electric field loading is in direct contact with brain tissue. However, the alterations in brain tissue's mechanical properties and microstructure due to changes in electric field parameters have not received adequate attention. In this study, the mechanical properties and microstructure of the brain tissue under pulsed electric fields were focused on. Herein, a custom indentation device was equipped with a module for electric field loading. Parameters such as pulse amplitude and frequency were adjusted. The results demonstrated that following an indentation process lasting 5 s and reaching a depth of 1000 μm, and a relaxation process of 175 s, the average shear modulus of brain tissue was reduced, and viscosity decreased. At the same amplitude, high-frequency pulsed electric fields had a smaller effect on brain tissue than low-frequency ones. Furthermore, pulsed electric fields induced cell polarization and reduced the proteoglycan concentration in brain tissue. As pulse frequency increased, cell polarization diminished, and proteoglycan concentration decreased significantly. High-frequency pulsed electric fields applied to brain tissue were found to reduce impedance fluctuation amplitude. This study revealed the effect of pulsed electric fields on the mechanical properties and microstructure of ex vivo brain tissue, providing essential information to promote the advancement of brain tissue electrotherapy in clinical settings.
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Affiliation(s)
- Yiqiang Li
- School of Mechanical & Aerospace Engineering, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
- Key Laboratory of CNC Equipment Reliability, Ministry of Education, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
| | - Qixun Zhang
- School of Mechanical & Aerospace Engineering, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
- Key Laboratory of CNC Equipment Reliability, Ministry of Education, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
- Chongqing Research Institute, Jilin University, Chongqing, 401100, People's Republic of China
| | - Jiucheng Zhao
- School of Mechanical & Aerospace Engineering, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
- Key Laboratory of CNC Equipment Reliability, Ministry of Education, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
| | - Zhaoxin Wang
- School of Mechanical & Aerospace Engineering, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
- Key Laboratory of CNC Equipment Reliability, Ministry of Education, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
| | - Xiangyu Zong
- School of Mechanical & Aerospace Engineering, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
- Key Laboratory of CNC Equipment Reliability, Ministry of Education, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
| | - Li Yang
- School of Mechanical & Aerospace Engineering, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, People's Republic of China
| | - Chi Zhang
- School of Mechanical & Aerospace Engineering, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China.
- Key Laboratory of CNC Equipment Reliability, Ministry of Education, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China.
| | - Hongwei Zhao
- School of Mechanical & Aerospace Engineering, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China.
- Key Laboratory of CNC Equipment Reliability, Ministry of Education, Jilin University, 5988 Renmin Street, Changchun, 130025, People's Republic of China.
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2
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Kumar D, Kuijken PF, van de Poel T, Neumann K, Galimberti DR. Revealing the Unique Role of Water in the Formation of Benzothiazoles: an Experimental and Computational Study. Chemistry 2024; 30:e202302596. [PMID: 37812133 DOI: 10.1002/chem.202302596] [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: 08/09/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 10/10/2023]
Abstract
We present here a joint experimental and computational study on the formation of benzothiazoles. Our investigation reveals a green protocol for accessing benzothiazoles from acyl chlorides using either water alongside a reducing agent as the reaction medium or in combination with stoichiometric amounts of a weak acid, instead of the harsh conditions and catalysts previously reported. Specifically, we show that a protic solvent, particularly water, enables the formation of 2-substituted benzothiazoles from N-acyl 1,2-aminothiophenols already at room temperature, without the need for strong acids or metal catalysts. DFT Molecular Dynamics simulations coupled with advanced enhanced sampling techniques provide a clear understanding of the catalytic role of water. We demonstrate how bulk water - due to its extended network of hydrogen bonds and an efficient Grotthuss mechanism - provides a reaction path that strongly reduces the reaction barriers compared to aprotic environments, namely more than 80 kJ/mol for the first reaction step and 250 kJ/mol for the second. Finally, we discuss the influence of different aliphatic and aromatic substituents with varying electronic properties on chemical reactivity. Besides providing in-depth mechanistic insights, we believe that our findings pave the way for a greener route toward an important class of bioactive molecules.
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Affiliation(s)
- Dipanshu Kumar
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Peter F Kuijken
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Tjerk van de Poel
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Kevin Neumann
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Daria Ruth Galimberti
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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3
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Movilla S, Roca M, Moliner V, Magistrato A. Molecular Basis of RNA-Driven ATP Hydrolysis in DExH-Box Helicases. J Am Chem Soc 2023; 145:6691-6701. [PMID: 36926902 DOI: 10.1021/jacs.2c11980] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
The spliceosome machinery catalyzes precursor messenger (pre-m)RNA splicing. In each cycle, the spliceosome experiences massive compositional and conformational remodeling fueled by the concerted action of specific RNA-dependent ATPases/helicases. Intriguingly, these enzymes are allosterically activated to perform ATP hydrolysis and trigger helicase activity only upon pre-mRNA binding. Yet, the molecular mechanism underlying the RNA-driven regulation of their ATPase function remains elusive. Here, we focus on the Prp2 ATPase/helicase which contributes to reshaping the spliceosome into its catalytic competent state. By performing classical and quantum-classical molecular dynamics simulations, we unprecedentedly unlock the molecular terms governing the Prp2 ATPase/helicase function. Namely, we dissect the molecular mechanism of ATP hydrolysis, and we disclose that RNA binding allosterically triggers the formation of a set of interactions linking the RNA binding tunnel to the catalytic site. This activates the Prp2's ATPase function by optimally placing the nucleophilic water and the general base of the enzymatic process to perform ATP hydrolysis. The key structural motifs, mechanically coupling RNA gripping and the ATPase/helicase functions, are conserved across all DExH-box helicases. This mechanism could thus be broadly applicable to all DExH-box helicase family.
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Affiliation(s)
- Santiago Movilla
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Maite Roca
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Alessandra Magistrato
- Department National Research Council of Italy (CNR), Institute of Material (IOM) c/o International School for Advanced Studies (SISSA), 34136 Trieste, Italy
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4
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Unraveling sulfur chemistry in interstellar carbon oxide ices. Nat Commun 2022; 13:7150. [DOI: 10.1038/s41467-022-34949-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 11/11/2022] [Indexed: 11/24/2022] Open
Abstract
AbstractFormyl radical (HCO•) and hydroxycarbonyl radical (HOCO•) are versatile building blocks in the formation of biorelevant complex organic molecules (COMs) in interstellar medium. Understanding the chemical pathways for the formation of HCO• and HOCO• starting with primordial substances (e.g., CO and CO2) is of vital importance in building the complex network of prebiotic chemistry. Here, we report the efficient formation of HCO• and HOCO• in the photochemistry of hydroxidooxidosulfur radical (HOSO•)–a key intermediate in SO2 photochemistry–in interstellar analogous ices of CO and CO2 at 16 K through hydrogen atom transfer (HAT) reactions. Specifically, 266 nm laser photolysis of HOSO• embedded in solid CO ice yields the elusive hydrogen‑bonded complexes HCO•···SO2 and HOCO•···SO, and the latter undergoes subsequent HAT to furnish CO2···HOS• under the irradiation conditions. Similar photo-induced HAT of HOSO• in solid CO2 ice leads to the formation of HOCO•···SO2. The HAT reactions of HOSO• in astronomical CO and CO2 ices by forming reactive acyl radicals may contribute to understanding the interplay between the sulfur and carbon ice-grain chemistry in cold molecular clouds and also in the planetary atmospheric chemistry.
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5
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Rimola A, Balucani N, Ceccarelli C, Ugliengo P. Tracing the Primordial Chemical Life of Glycine: A Review from Quantum Chemical Simulations. Int J Mol Sci 2022; 23:4252. [PMID: 35457069 PMCID: PMC9030215 DOI: 10.3390/ijms23084252] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 12/28/2022] Open
Abstract
Glycine (Gly), NH2CH2COOH, is the simplest amino acid. Although it has not been directly detected in the interstellar gas-phase medium, it has been identified in comets and meteorites, and its synthesis in these environments has been simulated in terrestrial laboratory experiments. Likewise, condensation of Gly to form peptides in scenarios resembling those present in a primordial Earth has been demonstrated experimentally. Thus, Gly is a paradigmatic system for biomolecular building blocks to investigate how they can be synthesized in astrophysical environments, transported and delivered by fragments of asteroids (meteorites, once they land on Earth) and comets (interplanetary dust particles that land on Earth) to the primitive Earth, and there react to form biopolymers as a step towards the emergence of life. Quantum chemical investigations addressing these Gly-related events have been performed, providing fundamental atomic-scale information and quantitative energetic data. However, they are spread in the literature and difficult to harmonize in a consistent way due to different computational chemistry methodologies and model systems. This review aims to collect the work done so far to characterize, at a quantum mechanical level, the chemical life of Gly, i.e., from its synthesis in the interstellar medium up to its polymerization on Earth.
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Affiliation(s)
- Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Catalonia, Spain
| | - Nadia Balucani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy;
- Osservatorio Astrosico di Arcetri, Largo E. Fermi 5, 50125 Firenze, Italy
| | - Cecilia Ceccarelli
- CNRS, Institut de Planétologie et d’Astrophysique de Grenoble (IPAG), Université Grenoble Alpes, 38000 Grenoble, France;
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Centre, Università degli Studi di Torino, Via P. Giuria 7, 10125 Torino, Italy;
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6
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Ying J, Ding R, Liu Y, Zhao Y. Prebiotic Chemistry in Aqueous Environment: A Review of Peptide Synthesis and Its Relationship with Genetic Code. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jianxi Ying
- Institute of Drug Discovery Technology Ningbo University, No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo University No.818 Fenghua Road, Ningbo Zhejiang 315211 China
| | - Ruiwen Ding
- Institute of Drug Discovery Technology Ningbo University, No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo University No.818 Fenghua Road, Ningbo Zhejiang 315211 China
| | - Yan Liu
- College of Chemistry and Chemical Engineering Xiamen University, No. 422, Siming South Road Xiamen Fujian 361005 China
| | - Yufen Zhao
- Institute of Drug Discovery Technology Ningbo University, No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo University No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- College of Chemistry and Chemical Engineering Xiamen University, No. 422, Siming South Road Xiamen Fujian 361005 China
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7
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Muñoz-Santiburcio D, Marx D. Confinement-Controlled Aqueous Chemistry within Nanometric Slit Pores. Chem Rev 2021; 121:6293-6320. [PMID: 34006106 DOI: 10.1021/acs.chemrev.0c01292] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this Focus Review, we put the spotlight on very recent insights into the fascinating world of wet chemistry in the realm offered by nanoconfinement of water in mechanically rather rigid and chemically inert planar slit pores wherein only monolayer and bilayer water lamellae can be hosted. We review the effect of confinement on different aspects such as hydrogen bonding, ion diffusion, and charge defect migration of H+(aq) and OH-(aq) in nanoconfined water depending on slit pore width. A particular focus is put on the strongly modulated local dielectric properties as quantified in terms of anisotropic polarization fluctuations across such extremely confined water films and their putative effects on chemical reactions therein. The stunning findings disclosed only recently extend wet chemistry in particular and solvation science in general toward extreme molecular confinement conditions.
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Affiliation(s)
- Daniel Muñoz-Santiburcio
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.,CIC nanoGUNE BRTA, Tolosa Hiribidea 76, 20018 San Sebastián, Spain
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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8
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Tripathi R, Durán Caballero L, Pérez de Tudela R, Hölzl C, Marx D. Unveiling Zwitterionization of Glycine in the Microhydration Limit. ACS OMEGA 2021; 6:12676-12683. [PMID: 34056419 PMCID: PMC8154221 DOI: 10.1021/acsomega.1c00869] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/24/2021] [Indexed: 06/12/2023]
Abstract
Charge separation under solvation stress conditions is a fundamental process that comes in many forms in doped water clusters. Yet, the mechanism of intramolecular charge separation, where constraints due to the molecular structure might be intricately tied to restricted solvation structures, remains largely unexplored. Microhydrated amino acids are such paradigmatic molecules. Ab initio simulations are carried out at 300 K in the frameworks of metadynamics sampling and thermodynamic integration to map the thermal mechanisms of zwitterionization using Gly(H2O) n with n = 4 and 10. In both cases, a similar water-mediated proton transfer chain mechanism is observed; yet, detailed analyses of thermodynamics and kinetics demonstrate that the charge-separated zwitterion is the preferred species only for n = 10 mainly due to kinetic stabilization. Structural analyses disclose that bifurcated H-bonded water bridges, connecting the cationic and anionic sites in the fluctuating microhydration network at room temperature, are enhanced in the transition-state ensemble exclusively for n = 10 and become overwhelmingly abundant in the stable zwitterion. The findings offer potential insights into charge separation under solvation stress conditions beyond the present example.
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9
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Morais MAB, Coines J, Domingues MN, Pirolla RAS, Tonoli CCC, Santos CR, Correa JBL, Gozzo FC, Rovira C, Murakami MT. Two distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X-ray and QM/MM simulations. Nat Commun 2021; 12:367. [PMID: 33446650 PMCID: PMC7809346 DOI: 10.1038/s41467-020-20620-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
Xylanolytic enzymes from glycoside hydrolase family 43 (GH43) are involved in the breakdown of hemicellulose, the second most abundant carbohydrate in plants. Here, we kinetically and mechanistically describe the non-reducing-end xylose-releasing exo-oligoxylanase activity and report the crystal structure of a native GH43 Michaelis complex with its substrate prior to hydrolysis. Two distinct calcium-stabilized conformations of the active site xylosyl unit are found, suggesting two alternative catalytic routes. These results are confirmed by QM/MM simulations that unveil the complete hydrolysis mechanism and identify two possible reaction pathways, involving different transition state conformations for the cleavage of xylooligosaccharides. Such catalytic conformational promiscuity in glycosidases is related to the open architecture of the active site and thus might be extended to other exo-acting enzymes. These findings expand the current general model of catalytic mechanism of glycosidases, a main reaction in nature, and impact on our understanding about their interaction with substrates and inhibitors.
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Affiliation(s)
- Mariana A B Morais
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain
| | - Joan Coines
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain
| | - Mariane N Domingues
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Renan A S Pirolla
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Celisa C C Tonoli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Camila R Santos
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Jessica B L Correa
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil
| | - Fabio C Gozzo
- Dalton Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, Campinas, 13083-970, Brazil
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica & Institut de Química Teórica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, 08028, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010, Spain.
| | - Mario T Murakami
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, 13083-100, Brazil.
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10
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Proton transfer from water to aromatic N-heterocyclic anions from DFT-MD simulations. J Mol Graph Model 2020; 103:107818. [PMID: 33333423 DOI: 10.1016/j.jmgm.2020.107818] [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: 11/03/2020] [Revised: 11/30/2020] [Accepted: 11/30/2020] [Indexed: 11/20/2022]
Abstract
The phenomenon of proton transfer from water to six N-heterocyclic anions and free energy landscapes of this process are studied using both electronic structure calculations and first principles molecular metadynamics simulations. Our investigation involves microhydrated and aqueous phase interaction of water with six aromatic heterocyclic anions relevant to chemistry and biology: imidazolide, pyrrolide, benzimidazolide, 2-cyanopyrrolide, indolide, and indazolide. The basic structures of all these heterocyclic anions differ by substituted functional groups as well as fused rings. We study the proton transfer reaction and the minimum number of required water molecules for the reaction in hydrated microclusters. We find out that at least four water molecules are necessary for hydrated clusters to facilitate the intracluster proton transfer reaction from water to anions except for pyrrolide, for which this magic number is 3. To obtain the reaction free energy and activation barrier of the proton transfer process in an aqueous solution, the metadynamics method based first principles molecular dynamics simulations were performed. The complete proton transfer was observed in aqueous solutions for all the anions. The water molecule directly involved in proton transfer becomes acidic due to the cooperative effect of neighboring water molecules. From the metadynamics simulation, we obtain the values of activation barrier for the proton transfer processes from neutral water to anions, and the highest activation barrier is obtained for benzimidazolide, whereas the lowest activation barrier is obtained for pyrrolide. The structures and free energy profiles of the process for all the anions are discussed, and a comparative outlook of the study is presented here.
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11
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Prebiotic chemistry and origins of life research with atomistic computer simulations. Phys Life Rev 2020; 34-35:105-135. [DOI: 10.1016/j.plrev.2018.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/10/2018] [Indexed: 02/02/2023]
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12
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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13
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Biswas S, Kwon H, Barsanti KC, Myllys N, Smith JN, Wong BM. Ab initio metadynamics calculations of dimethylamine for probing pKb variations in bulk vs. surface environments. Phys Chem Chem Phys 2020; 22:26265-26277. [DOI: 10.1039/d0cp03832f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Free energy landscape obtained from ab initio metadynamics calculations for dimethylamine protonation at the air–water interface.
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Affiliation(s)
- Sohag Biswas
- Department of Chemical & Environmental Engineering
- University of California-Riverside
- Riverside
- USA
| | - Hyuna Kwon
- Department of Chemical & Environmental Engineering
- University of California-Riverside
- Riverside
- USA
| | - Kelley C. Barsanti
- Department of Chemical & Environmental Engineering
- University of California-Riverside
- Riverside
- USA
| | - Nanna Myllys
- Department of Chemistry
- University of California-Irvine
- Irvine
- USA
| | - James N. Smith
- Department of Chemistry
- University of California-Irvine
- Irvine
- USA
| | - Bryan M. Wong
- Department of Chemical & Environmental Engineering
- University of California-Riverside
- Riverside
- USA
- Materials Science & Engineering Program
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14
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Galvez-Martinez S, Escamilla-Roa E, Zorzano MP, Mateo-Marti E. Defects on a pyrite(100) surface produce chemical evolution of glycine under inert conditions: experimental and theoretical approaches. Phys Chem Chem Phys 2019; 21:24535-24542. [PMID: 31663552 DOI: 10.1039/c9cp03577j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The presence of non-stoichiometric sites on the pyrite(100) surface makes it a suitable substrate for driving the chemical evolution of the amino acid glycine over time, even under inert conditions. Spectroscopic molecular fingerprints prove a transition process from a zwitterionic species to an anionic species over time on the monosulfide enriched surface. By combining experimental and theoretical approaches, we propose a surface mechanism where the interaction between the amino acid species and the surface will be driven by the quenching of the surface states at Fe sites and favoured by sulfur vacancies. This study demonstrates the potential capability of pyrite to act as a surface catalyst.
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Affiliation(s)
- Santos Galvez-Martinez
- Centro de Astrobiología (CSIC-INTA), Ctra. Ajalvir, Km. 4, 28850 Torrejón de Ardoz, Madrid, Spain.
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15
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Tripathi R, Forbert H, Marx D. Settling the Long-Standing Debate on the Proton Storage Site of the Prototype Light-Driven Proton Pump Bacteriorhodopsin. J Phys Chem B 2019; 123:9598-9608. [DOI: 10.1021/acs.jpcb.9b09608] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Gupta PK, Esser A, Forbert H, Marx D. Toward theoretical terahertz spectroscopy of glassy aqueous solutions: partially frozen solute-solvent couplings of glycine in water. Phys Chem Chem Phys 2019; 21:4975-4987. [PMID: 30758388 DOI: 10.1039/c8cp07489e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular-level understanding of THz spectra of aqueous solutions under ambient conditions has been greatly advanced in recent years. Here, we go beyond previous analyses by performing ab initio molecular dynamics simulations of glycine in water with artificially frozen solute or solvent molecules, respectively, while computing the total THz response as well as its decomposition into mode-specific resonances based on the "supermolecular solvation complex" technique. Clamping the water molecules and keeping glycine moving breaks the coupling of glycine to the structural dynamics of the solvent, however, the polarization and dielectric solvation effects in the static solvation cage are still at work since the full electronic structure of the quenched solvent is taken into account. The complementary approach of fixing glycine reveals both the dynamical and electronic response of the solvation cage at the level of its THz response. Moreover, to quantitatively account for the electronic contribution solely due to solvent embedding, the solute species is "vertically desolvated", thus preserving the fully coupled solute-solvent motion in terms of the solute's structural dynamics in solution, while its electronic structure is no longer subject to solute-solvent polarization and charge transfer effects. When referenced to the free simulation of Gly(aq), this three-fold approach allows us to decompose the THz spectral contributions due to the correlated solute-solvent dynamics into entirely structural and purely electronic effects. Beyond providing hitherto unknown insights, the observed systematic changes of THz spectra in terms of peak shifts and lineshape modulations due to conformational freezing and frozen solvation cages might be useful to investigate the solvation of molecules in highly viscous H-bonding solvents such as ionic liquids and even in cryogenic ices as relevant to polar stratospheric and dark interstellar clouds.
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Affiliation(s)
- Prashant Kumar Gupta
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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17
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Chang YL, Sasaki T, Ribas-Ariño J, Machida M, Shiga M. Understanding Competition of Polyalcohol Dehydration Reactions in Hot Water. J Phys Chem B 2019; 123:1662-1671. [DOI: 10.1021/acs.jpcb.8b11615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yong Lik Chang
- Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa 277-8561, Japan
| | - Takehiko Sasaki
- Department of Complexity Science and Engineering, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa 277-8561, Japan
| | - Jordi Ribas-Ariño
- Departament de Química-Física i CERQT, Universitat de Barcelona, Diagonal, 645, 08028 Barcelona, Spain
| | - Masahiko Machida
- Center for Computational Science and e-Systems, Japan Atomic Energy Agency, 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
| | - Motoyuki Shiga
- Center for Computational Science and e-Systems, Japan Atomic Energy Agency, 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
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18
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Rimola A, Sodupe M, Ugliengo P. Role of Mineral Surfaces in Prebiotic Chemical Evolution. In Silico Quantum Mechanical Studies. Life (Basel) 2019; 9:E10. [PMID: 30658501 PMCID: PMC6463156 DOI: 10.3390/life9010010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/10/2019] [Accepted: 01/12/2019] [Indexed: 01/07/2023] Open
Abstract
There is a consensus that the interaction of organic molecules with the surfaces of naturally-occurring minerals might have played a crucial role in chemical evolution and complexification in a prebiotic era. The hurdle of an overly diluted primordial soup occurring in the free ocean may have been overcome by the adsorption and concentration of relevant molecules on the surface of abundant minerals at the sea shore. Specific organic⁻mineral interactions could, at the same time, organize adsorbed molecules in well-defined orientations and activate them toward chemical reactions, bringing to an increase in chemical complexity. As experimental approaches cannot easily provide details at atomic resolution, the role of in silico computer simulations may fill that gap by providing structures and reactive energy profiles at the organic⁻mineral interface regions. Accordingly, numerous computational studies devoted to prebiotic chemical evolution induced by organic⁻mineral interactions have been proposed. The present article aims at reviewing recent in silico works, mainly focusing on prebiotic processes occurring on the mineral surfaces of clays, iron sulfides, titanium dioxide, and silica and silicates simulated through quantum mechanical methods based on the density functional theory (DFT). The DFT is the most accurate way in which chemists may address the behavior of the molecular world through large models mimicking chemical complexity. A perspective on possible future scenarios of research using in silico techniques is finally proposed.
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Affiliation(s)
- Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS), Università degli Studi di Torino, Via P. Giuria 7, 10125 Torino, Italy.
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19
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Kroonblawd MP, Pietrucci F, Saitta AM, Goldman N. Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model. J Chem Theory Comput 2018. [PMID: 29543444 DOI: 10.1021/acs.jctc.7b01266] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTB model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol-1.
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Affiliation(s)
- Matthew P Kroonblawd
- Physical and Life Sciences Directorate , Lawrence Livermore National Laboratory , Livermore , California 94550 , United States
| | - Fabio Pietrucci
- Sorbonne Université, Muséum National d'Histoire Naturelle , UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC , F-75005 Paris , France
| | - Antonino Marco Saitta
- Sorbonne Université, Muséum National d'Histoire Naturelle , UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC , F-75005 Paris , France
| | - Nir Goldman
- Physical and Life Sciences Directorate , Lawrence Livermore National Laboratory , Livermore , California 94550 , United States.,Department of Chemical Engineering , University of California , Davis , California 95616 , United States
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20
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Dalai P, Pleyer HL, Strasdeit H, Fox S. The Influence of Mineral Matrices on the Thermal Behavior of Glycine. ORIGINS LIFE EVOL B 2017; 47:427-452. [PMID: 27757771 DOI: 10.1007/s11084-016-9523-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 08/27/2016] [Indexed: 10/20/2022]
Abstract
On the Hadean-Early Archean Earth, the first islands must have provided hot and dry environments for abiotically formed organic molecules. The heat sources, mainly volcanism and meteorite impacts, were also available on Mars during the Noachian period. In recent work simulating this scenario, we have shown that neat glycine forms a black, sparingly water-soluble polymer ("thermomelanoid") when dry-heated at 200 °C under pure nitrogen. The present study explores whether relevant minerals and mineral mixtures can change this thermal behavior. Most experiments were conducted at 200 or 250 °C for 2 or 7 days. The mineral matrices used were phyllosilicates (Ca-montmorillonites SAz-1 and STx-1, Na-montmorillonite SAz-1-Na, nontronite NAu-1, kaolinite KGa-1), salts (NaCl, NaCl-KCl, CaCl2, artificial sea salt, gypsum, magnesite), picritic basalt, and three Martian regolith simulants (P-MRS, S-MRS, JSC Mars-1A). The main analytical method employed was high-performance liquid chromatography (HPLC). Glycine intercalated in SAz-1 and SAz-1-Na was well protected against thermomelanoid formation and sublimation at 200 °C: after 2 days, 95 and 79 %, respectively, had either survived unaltered or been transformed into the cyclic dipeptide (DKP) and linear peptides up to Gly6. The glycine survival rate followed the order SAz-1 > SAz-1-Na > STx-1 ≈ NAu-1 > KGa-1. Very good protection was also provided by artificial sea salt (84 % unaltered glycine after 200 °C for 7 days). P-MRS promoted the condensation up to Gly6, consistent with its high phyllosilicate content. The remaining matrices were less effective in preserving glycine as such or as peptides.
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Affiliation(s)
- Punam Dalai
- Department of Bioinorganic Chemistry, Institute of Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Hannes Lukas Pleyer
- Department of Bioinorganic Chemistry, Institute of Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Henry Strasdeit
- Department of Bioinorganic Chemistry, Institute of Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany.
| | - Stefan Fox
- Department of Bioinorganic Chemistry, Institute of Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
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21
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Muñoz-Santiburcio D, Marx D. Chemistry in nanoconfined water. Chem Sci 2017; 8:3444-3452. [PMID: 28507716 PMCID: PMC5418629 DOI: 10.1039/c6sc04989c] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/16/2017] [Indexed: 01/06/2023] Open
Abstract
Nanoconfined liquids have extremely different properties from the bulk, which profoundly affects chemical reactions taking place in nanosolvation.
Nanoconfined liquids have extremely different properties from the bulk, which profoundly affects chemical reactions taking place in nanosolvation. Here, we present extensive ab initio simulations of a vast set of chemical reactions within a water lamella that is nanoconfined by mineral surfaces, which might be relevant to prebiotic peptide formation in aqueous environments. Our results disclose a rich interplay of distinct effects, from steric factors typical of reactions occurring in small spaces to a charge-stabilization effect in nanoconfined water at extreme conditions similar to that observed in bulk water when changing from extreme to ambient conditions. These effects are found to modify significantly not only the energetics but also the mechanisms of reactions happening in nanoconfined water in comparison to the corresponding bulk regime.
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Affiliation(s)
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie , Ruhr - Universität Bochum , 44780 Bochum , Germany .
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22
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Biswas S, Dasgupta T, Mallik BS. Proton transfer from water to ketyl radical anion: Assessment of critical size of hydrated cluster and free energy barrier in solution from first principles simulations. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.08.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Proton transfer from water to anion: Free energy profile from first principles metadynamics simulations. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.04.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Biswas S, Mallik BS. A delicate case of unidirectional proton transfer from water to an aromatic heterocyclic anion. Phys Chem Chem Phys 2016; 18:29979-29986. [DOI: 10.1039/c6cp05953h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One of the hydroxyl modes of the surrounding water molecules with the lowest stretching frequency facilitates the proton transfer from water to an anion.
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Affiliation(s)
- Sohag Biswas
- Department of Chemistry
- Indian Institute of Technology Hyderabad
- Sangareddy-502285
- India
| | - Bhabani S. Mallik
- Department of Chemistry
- Indian Institute of Technology Hyderabad
- Sangareddy-502285
- India
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25
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Ruiz-Barragan S, Ribas Ariño J, Shiga M. The reaction mechanism of polyalcohol dehydration in hot pressurized water. Phys Chem Chem Phys 2016; 18:32438-32447. [DOI: 10.1039/c6cp05695d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The use of high-temperature liquid water (HTW) as a reaction medium is a very promising technology in the field of green chemistry.
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Affiliation(s)
- Sergi Ruiz-Barragan
- CCSE
- Japan Atomic Energy Agency
- Kashiwa
- Japan
- Department of Theoretical and Computational Molecular Science
| | - Jordi Ribas Ariño
- Departament de Química-Física i CERQT
- Universitat de Barcelona
- 08028-Barcelona
- Spain
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26
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Campomanes P, Rothlisberger U, Alfonso-Prieto M, Rovira C. The Molecular Mechanism of the Catalase-like Activity in Horseradish Peroxidase. J Am Chem Soc 2015; 137:11170-8. [DOI: 10.1021/jacs.5b06796] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Pablo Campomanes
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Mercedes Alfonso-Prieto
- Departament de Química Orgànica & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08208 Barcelona, Spain
| | - Carme Rovira
- Departament de Química Orgànica & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08208 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
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27
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Martínez-Suárez L, Siemer N, Frenzel J, Marx D. Reaction Network of Methanol Synthesis over Cu/ZnO Nanocatalysts. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00442] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luis Martínez-Suárez
- Lehrstuhl für Theoretische Chemie, Ruhr−Universität Bochum, 44780 Bochum, Germany
| | - Niklas Siemer
- Lehrstuhl für Theoretische Chemie, Ruhr−Universität Bochum, 44780 Bochum, Germany
| | - Johannes Frenzel
- Lehrstuhl für Theoretische Chemie, Ruhr−Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr−Universität Bochum, 44780 Bochum, Germany
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28
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Ardèvol A, Rovira C. Reaction Mechanisms in Carbohydrate-Active Enzymes: Glycoside Hydrolases and Glycosyltransferases. Insights from ab Initio Quantum Mechanics/Molecular Mechanics Dynamic Simulations. J Am Chem Soc 2015; 137:7528-47. [DOI: 10.1021/jacs.5b01156] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Albert Ardèvol
- Departament
de Química Orgànica and Institut de Química Teòrica
i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
| | - Carme Rovira
- Departament
de Química Orgànica and Institut de Química Teòrica
i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
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29
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Farrell WS, Zavalij PY, Sita LR. Metal-Catalyzed “On-Demand” Production of Carbonyl Sulfide from Carbon Monoxide and Elemental Sulfur. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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30
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Farrell WS, Zavalij PY, Sita LR. Metal-catalyzed "on-demand" production of carbonyl sulfide from carbon monoxide and elemental sulfur. Angew Chem Int Ed Engl 2015; 54:4269-73. [PMID: 25737195 DOI: 10.1002/anie.201410353] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 12/12/2014] [Indexed: 11/07/2022]
Abstract
The group 6 molybdenum(II) cyclopentadienyl amidinate (CPAM) bis(carbonyl) complex [Cp*Mo{N(iPr)C(Ph)N(iPr)}(CO)2] (Cp*=η(5)-C5Me5) serves as a precatalyst for the high-yielding photocatalytic production of COS from CO and S8 under near-ambient conditions (e.g., 10 psi, 25 °C). Further documented is the isolation and structural characterization of several key transition-metal intermediates which collectively support a novel molybdenum(IV)-based catalytic cycle as being operative. Finally, in the presence of an excess amount of a primary amine, it is demonstrated that this catalytic system can be successfully used for the "on-demand" generation and utilization of COS as a chemical reagent for the synthesis of ureas.
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Affiliation(s)
- Wesley S Farrell
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742 (USA)
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31
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Computational Vibrational Spectroscopy of glycine in aqueous solution – Fundamental considerations towards feasible methodologies. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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32
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Recent Progress in Density Functional Methodology for Biomolecular Modeling. STRUCTURE AND BONDING 2013. [DOI: 10.1007/978-3-642-32750-6_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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33
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Rojas-Cervellera V, Giralt E, Rovira C. Staple Motifs, Initial Steps in the Formation of Thiolate-Protected Gold Nanoparticles: How Do They Form? Inorg Chem 2012; 51:11422-9. [DOI: 10.1021/ic301079k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Víctor Rojas-Cervellera
- Computer Simulation and Modeling
Laboratory, Parc Científic de Barcelona, Baldiri Reixac 10−12, 08028 Barcelona, Spain
- Institut de Química Teòrica i Computacional, Diagonal 647, 08028
Barcelona, Spain
- Departament de Química
Orgànica, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain
| | - Ernest Giralt
- Institut
de Recerca Biomèdica
de Barcelona, Parc Científic de Barcelona, Baldiri Reixac 10−12, 08028 Barcelona, Spain
- Departament de Química
Orgànica, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain
| | - Carme Rovira
- Computer Simulation and Modeling
Laboratory, Parc Científic de Barcelona, Baldiri Reixac 10−12, 08028 Barcelona, Spain
- Institut de Química Teòrica i Computacional, Diagonal 647, 08028
Barcelona, Spain
- Departament de Química
Orgànica, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Passeig
Lluís Companys 23, 08018 Barcelona, Spain
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34
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Wittekindt C, Marx D. Water confined between sheets of mackinawite FeS minerals. J Chem Phys 2012; 137:054710. [DOI: 10.1063/1.4739538] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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35
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Sharia O, Kuklja MM. Rapid Materials Degradation Induced by Surfaces and Voids: Ab Initio Modeling of β-Octatetramethylene Tetranitramine. J Am Chem Soc 2012; 134:11815-20. [PMID: 22703290 DOI: 10.1021/ja3044695] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Onise Sharia
- Department of Materials Science and Engineering, University of Maryland College Park, College Park,
Maryland 20742, United States
| | - Maija M. Kuklja
- Department of Materials Science and Engineering, University of Maryland College Park, College Park,
Maryland 20742, United States
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36
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Danger G, Plasson R, Pascal R. Pathways for the formation and evolution of peptides in prebiotic environments. Chem Soc Rev 2012; 41:5416-29. [PMID: 22688720 DOI: 10.1039/c2cs35064e] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
α-Amino acids are easily accessible through abiotic processes and were likely present before the emergence of life. However, the role they could have played in the process remains uncertain. Chemical pathways that could have brought about features of self-organization in a peptide world are considered in this review and discussed in relation with their possible contribution to the origin of life. An overall scheme is proposed with an emphasis on possibilities that may have led to dynamically stable far from equilibrium states. This analysis defines new lines of investigation towards a better understanding of the contribution of the systems chemistry of amino acids and peptides to the emergence of life.
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Affiliation(s)
- Grégoire Danger
- Spectrométries et Dynamique Moléculaire, Physique des Interactions Ioniques et Moléculaires (UMR CNRS 7345, Université de Provence) - Centre de St Jérôme - case 252, Avenue Escadrille Normandie-Niémen, 13397 Marseille Cedex 20, France.
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37
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Fu CW, Lin TH. Theoretical Study on the Alkaline Hydrolysis of Methyl Thioacetate in Aqueous Solution. J Phys Chem A 2011; 115:13523-33. [DOI: 10.1021/jp204658w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chein-Wei Fu
- Institute of Molecular Medicine & Department of Life Science, National Tsing Hua University, Hsinchu, 30013 Taiwan, ROC
| | - Thy-Hou Lin
- Institute of Molecular Medicine & Department of Life Science, National Tsing Hua University, Hsinchu, 30013 Taiwan, ROC
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38
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Schreiner E, Nair NN, Wittekindt C, Marx D. Peptide Synthesis in Aqueous Environments: The Role of Extreme Conditions and Pyrite Mineral Surfaces on Formation and Hydrolysis of Peptides. J Am Chem Soc 2011; 133:8216-26. [DOI: 10.1021/ja111503z] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eduard Schreiner
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Nisanth N. Nair
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Carsten Wittekindt
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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39
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Pollet R, Nair NN, Marx D. Water exchange of a ProHance MRI contrast agent: isomer-dependent free-energy landscapes and mechanisms. Inorg Chem 2011; 50:4791-7. [PMID: 21520891 DOI: 10.1021/ic102403r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The water-exchange reaction in two diastereoisomers of the clinical magnetic resonance imaging contrast agent [Gd(HP-DO3A)(H(2)O)] (also known as ProHance) has been studied using ab initio simulations. On the basis of the molecular-level details of the mechanism derived from these simulations in aqueous solution, we unravel the underlying difference in the free energies and mechanisms of water exchange in the two diastereoisomers. These findings reveal the crucial role played by hydrogen-bonding dynamics and thus suggest their appropriate control in tailoring improved gadolinium-based constrast agents.
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Affiliation(s)
- Rodolphe Pollet
- DSM/IRAMIS/SIS2M (CEA-CNRS UMR3299), Commissariat à l'Énergie Atomique, 91191 Gif-sur-Yvette, France.
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Barducci A, Bonomi M, Parrinello M. Metadynamics. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.31] [Citation(s) in RCA: 712] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Alessandro Barducci
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Lugano, Switzerland
| | - Massimiliano Bonomi
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Lugano, Switzerland
| | - Michele Parrinello
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Lugano, Switzerland
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Sun J, Bousquet D, Forbert H, Marx D. Glycine in aqueous solution: solvation shells, interfacial water, and vibrational spectroscopy from ab initio molecular dynamics. J Chem Phys 2010; 133:114508. [DOI: 10.1063/1.3481576] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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42
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Leung K, Budzien JL. Ab initio molecular dynamics simulations of the initial stages of solid–electrolyte interphase formation on lithium ion battery graphitic anodes. Phys Chem Chem Phys 2010; 12:6583-6. [DOI: 10.1039/b925853a] [Citation(s) in RCA: 192] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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43
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Dong H, Nimlos MR, Himmel ME, Johnson DK, Qian X. The effects of water on beta-D-xylose condensation reactions. J Phys Chem A 2009; 113:8577-85. [PMID: 19572686 DOI: 10.1021/jp9025442] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Car-Parrinello-based ab initio molecular dynamics simulations (CPMD) combined with metadynamics (MTD) simulations were used to determine the reaction energetics for the beta-D-xylose condensation reaction to form beta-1,4-linked xylobiose in a dilute acid solution. Protonation of the hydroxyl group on the xylose molecule and the subsequent breaking of the C-O bond were found to be the rate-limiting step during the xylose condensation reaction. Water and water structure was found to play a critical role in these reactions due to the proton's high affinity for water molecules. The reaction free energy and reaction barrier were determined using CPMD-MTD. We found that solvent reorganization due to proton partial desolvation must be taken into account in order to obtain the correct reaction activation energy. Our calculated reaction free energy and reaction activation energy compare well with available experimental results.
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Affiliation(s)
- Haitao Dong
- Department of Mechanical Engineering, Colorado State University, Fort Collins, Colorado 80523, USA
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44
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Schreiner E, Nair NN, Marx D. Peptide synthesis in aqueous environments: the role of extreme conditions on peptide bond formation and peptide hydrolysis. J Am Chem Soc 2009; 131:13668-75. [PMID: 19725519 DOI: 10.1021/ja9032742] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanisms and free energetics underlying the formation of peptides from alpha-amino acids and alpha-amino acid N-carboxyanhydrides (NCAs) in bulk water at both ambient and extreme temperature and pressure conditions were investigated using accelerated ab initio molecular dynamics. In particular, peptide bond formation using an activated amino acid in form of its NCA, subsequent decarboxylation, as well as hydrolysis of the formed peptide were studied using glycine. It is shown to what extent thermodynamic conditions affect the reaction mechanisms qualitatively and the energetics quantitatively in solution. In particular, the zwitterionic intermediate in the peptidization step found in ambient water degenerates into a transient species in hot-pressurized water, whereas the hydrolysis reaction is found to follow qualitatively different pathways at ambient and extreme conditions. The work also quantifies the impact of extreme solvent conditions on both peptide bond formation and peptide hydrolysis in aqueous media. Beyond the specific case, the results provide important insights into how elevated temperatures and increased pressures affect organic reactions in aqueous solutions.
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Affiliation(s)
- Eduard Schreiner
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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Leung K, Nielsen IMB, Criscenti LJ. Elucidating the Bimodal Acid−Base Behavior of the Water−Silica Interface from First Principles. J Am Chem Soc 2009; 131:18358-65. [DOI: 10.1021/ja906190t] [Citation(s) in RCA: 191] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Kevin Leung
- Sandia National Laboratories, MS 1415 and 1322, Albuquerque, New Mexico 87185 and Sandia National Laboratories, MS 9158, Livermore, California 94551
| | - Ida M. B. Nielsen
- Sandia National Laboratories, MS 1415 and 1322, Albuquerque, New Mexico 87185 and Sandia National Laboratories, MS 9158, Livermore, California 94551
| | - Louise J. Criscenti
- Sandia National Laboratories, MS 1415 and 1322, Albuquerque, New Mexico 87185 and Sandia National Laboratories, MS 9158, Livermore, California 94551
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46
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Rimola A, Ugliengo P, Sodupe M. Formation versus hydrolysis of the peptide bond from a quantum-mechanical viewpoint: The role of mineral surfaces and implications for the origin of life. Int J Mol Sci 2009; 10:746-60. [PMID: 19399219 PMCID: PMC2672000 DOI: 10.3390/ijms10030746] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 02/16/2009] [Accepted: 02/23/2009] [Indexed: 11/16/2022] Open
Abstract
The condensation (polymerization by water elimination) of molecular building blocks to yield the first active biopolymers (e.g. of amino acids to form peptides) during primitive Earth is an intriguing question that nowadays still remains open since these processes are thermodynamically disfavoured in highly dilute water solutions. In the present contribution, formation and hydrolysis of glycine oligopeptides occurring on a cluster model of sanidine feldspar (001) surface have been simulated by quantum mechanical methods. Results indicate that the catalytic interplay between Lewis and Brønsted sites both present at the sanidine surface, in cooperation with the London forces acting between the biomolecules and the inorganic surface, plays a crucial role to: i) favour the condensation of glycine to yield oligopeptides as reaction products; ii) inhibit the hydrolysis of the newly formed oligopeptides. Both facts suggest that mineral surfaces may have helped in catalyzing, stabilizing and protecting from hydration the oligopeptides formed in the prebiotic era.
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Affiliation(s)
- Albert Rimola
- Dipartimento di Chimica IFM, NIS Centre of Excellence and INSTM (Materials Science and Technology) National Consortium, University of Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Piero Ugliengo
- Dipartimento di Chimica IFM, NIS Centre of Excellence and INSTM (Materials Science and Technology) National Consortium, University of Torino, Via P. Giuria 7, 10125, Torino, Italy
- Authors to whom correspondence should be addressed; E-Mails:
(P.U.);
(M.S.); Tel. +39-011-670-4596; Fax: +39-011-236-4596 (P.U.); Tel. +34-93-581-3031; Fax: +34-93-581-2920 (M.S.)
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
- Authors to whom correspondence should be addressed; E-Mails:
(P.U.);
(M.S.); Tel. +39-011-670-4596; Fax: +39-011-236-4596 (P.U.); Tel. +34-93-581-3031; Fax: +34-93-581-2920 (M.S.)
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