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Brzeski J, Wyrzykowski D, Makowska J. Application of a modern theoretical approach to the study of the interaction of KR-12 peptides derived from human cathelicidins with Cu(II) ions. Dalton Trans 2024; 53:9942-9951. [PMID: 38809157 DOI: 10.1039/d4dt01027b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
The human cationic antimicrobial protein (hCAP) corresponding to the overlapping sequences of 151-162 of hCAP named KR-12 peptide is the smallest portion of the only type of human Cathelicidin, which has been shown to be modifiable into a more effective antimicrobial. In this study, an in silico analysis, supported by potentiometric titration and isothermal titration calorimetry techniques, was performed to identify potential Cu(II) binding sites of KR-12. The analysis of the presented data at the given theoretical level (GFN2-xTB/ALPB) revealed which peptide chain fragments are involved in the most favourable KR-12-Cu(II) binding mode. Based on a quantum chemical approach, the most favourable coordination modes of Cu(II) to peptides are proposed together with the discussion of the chemical nature of the interactions. The presented results demonstrated that KR-12 interacts with metal ions mostly via the main chain's oxygen atoms; however, the two types of amino acids that are expected to be vital for the interaction of Cu(II) are D (aspartic acid) and R29 (arginine). It was demonstrated that in order to explain the complexity of the interaction process in peptide-metal ion systems, the use of theoretical methods is sometimes necessary to explain the details of the experimental results and provide an in-depth understanding of these dynamic systems.
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Affiliation(s)
- Jakub Brzeski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Dariusz Wyrzykowski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Joanna Makowska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
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2
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Tao Y, Giese TJ, York DM. Electronic and Nuclear Quantum Effects on Proton Transfer Reactions of Guanine-Thymine (G-T) Mispairs Using Combined Quantum Mechanical/Molecular Mechanical and Machine Learning Potentials. Molecules 2024; 29:2703. [PMID: 38893576 PMCID: PMC11173453 DOI: 10.3390/molecules29112703] [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: 05/01/2024] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
Rare tautomeric forms of nucleobases can lead to Watson-Crick-like (WC-like) mispairs in DNA, but the process of proton transfer is fast and difficult to detect experimentally. NMR studies show evidence for the existence of short-time WC-like guanine-thymine (G-T) mispairs; however, the mechanism of proton transfer and the degree to which nuclear quantum effects play a role are unclear. We use a B-DNA helix exhibiting a wGT mispair as a model system to study tautomerization reactions. We perform ab initio (PBE0/6-31G*) quantum mechanical/molecular mechanical (QM/MM) simulations to examine the free energy surface for tautomerization. We demonstrate that while the ab initio QM/MM simulations are accurate, considerable sampling is required to achieve high precision in the free energy barriers. To address this problem, we develop a QM/MM machine learning potential correction (QM/MM-ΔMLP) that is able to improve the computational efficiency, greatly extend the accessible time scales of the simulations, and enable practical application of path integral molecular dynamics to examine nuclear quantum effects. We find that the inclusion of nuclear quantum effects has only a modest effect on the mechanistic pathway but leads to a considerable lowering of the free energy barrier for the GT*⇌G*T equilibrium. Our results enable a rationalization of observed experimental data and the prediction of populations of rare tautomeric forms of nucleobases and rates of their interconversion in B-DNA.
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3
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Moscato D, Mandelli G, Bondanza M, Lipparini F, Conte R, Mennucci B, Ceotto M. Unraveling Water Solvation Effects with Quantum Mechanics/Molecular Mechanics Semiclassical Vibrational Spectroscopy: The Case of Thymidine. J Am Chem Soc 2024; 146:8179-8188. [PMID: 38470354 DOI: 10.1021/jacs.3c12700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
We introduce a quantum mechanics/molecular mechanics semiclassical method for studying the solvation process of molecules in water at the nuclear quantum mechanical level with atomistic detail. We employ it in vibrational spectroscopy calculations because this is a tool that is very sensitive to the molecular environment. Specifically, we look at the vibrational spectroscopy of thymidine in liquid water. We find that the C═O frequency red shift and the C═C frequency blue shift, experienced by thymidyne upon solvation, are mainly due to reciprocal polarization effects, that the molecule and the water solvent exert on each other, and nuclear zero-point energy effects. In general, this work provides an accurate and practical tool to study quantum vibrational spectroscopy in solution and condensed phase, incorporating high-level and computationally affordable descriptions of both electronic and nuclear problems.
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Affiliation(s)
- Davide Moscato
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi, 19, 20133 Milano, Italy
| | - Giacomo Mandelli
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi, 19, 20133 Milano, Italy
| | - Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, 56124 Pisa, Italy
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi, 19, 20133 Milano, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, 56124 Pisa, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi, 19, 20133 Milano, Italy
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4
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Udagawa T, Tanaka H, Kuwahata K, Tachikawa M. Location of the Shared Proton in Proton-Bound Dimer Compound of Hydrogen Sulfate and Formate: Path Integral Molecular Dynamics Study. J Phys Chem A 2024; 128:2103-2110. [PMID: 38414141 DOI: 10.1021/acs.jpca.4c00239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
The structure of the proton-bound dimer compound of hydrogen sulfate and formate has been studied by considering nuclear quantum effects (NQEs) using the path integral molecular dynamics method. This study unveiled the location of the shared proton and answered the following question: "Is the shared proton localized on either an anion or located around the center of two anions?" We have elucidated that the shared proton is distributed in the region beyond the transition state due to the NQEs, even though the shared proton did not completely overcome the transition state for the proton shuttle.
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Affiliation(s)
- Taro Udagawa
- Department of Chemistry and Biomolecular Science, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
| | - Hikaru Tanaka
- Department of Chemistry and Biomolecular Science, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
| | - Kazuaki Kuwahata
- Graduate School of NanobioScience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
| | - Masanori Tachikawa
- Graduate School of NanobioScience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
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5
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Kang XW, Wang K, Zhang X, Zhong D, Ding B. Elementary Reactions in the Functional Triads of the Blue-Light Photoreceptor BLUF Domain. J Phys Chem B 2024; 128:2065-2075. [PMID: 38391132 DOI: 10.1021/acs.jpcb.3c07988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
The blue light using the flavin (BLUF) domain is one of the smallest photoreceptors in nature, which consists of a unique bidirectional electron-coupled proton relay process in its photoactivation reaction cycle. This perspective summarizes our recent efforts in dissecting the photocycle into three elementary processes, including proton-coupled electron transfer (PCET), proton rocking, and proton relay. Using ultrafast spectroscopy, we have determined the temporal sequence, rates, kinetic isotope effects (KIEs), and concertedness of these elementary steps. Our findings provide important implications for illuminating the photoactivation mechanism of the BLUF domain and suggest an engineering platform to characterize intricate reactions involving proton motions that are ubiquitous in nonphotosensitive protein machines.
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Affiliation(s)
- Xiu-Wen Kang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kailin Wang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaofan Zhang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongping Zhong
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Programs of Chemical Physics, and Programs of Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Bei Ding
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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6
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Yusef-Buey M, Mineva T, Talbi D, Rapacioli M. Temperature driven transformations of glycine molecules embedded in interstellar ice. Phys Chem Chem Phys 2024; 26:2414-2425. [PMID: 38168973 DOI: 10.1039/d3cp03575a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The formation of glycine amino acid on ice grains in space raises fundamental questions about glycine chemistry in interstellar media. In this work, we studied glycine conformational space and the related tautomerization mechanisms in water media by means of QM/MM molecular dynamics simulations of four glycine conformational isomers (cc, ct, tc, and tt). Interstellar low density amorphous (LDA) ice and T = 20 K were considered as representative for a cold interstellar ice environment, while temperatures of 250 and 450 K were included to model rapid local heating in the ice. In addition to the LDA environment, water clusters with 4, 17, and 27 H2O molecules were subjected to QM/MM dynamics simulations that allowed glycine tautomerization behaviour to be evaluated in water surface-like environments. The tautomerization processes were found to be strongly dependent on the number of water molecules and specific isomer structure. All the glycine isomers mostly preserve their canonical "neutral" conformations under interstellar conditions.
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Affiliation(s)
- Maysa Yusef-Buey
- Laboratoire de Chimie et Physique Quantique (LCPQ/FERMI), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Tzonka Mineva
- ICGM, Univ. Montpellier, CNRS, ENSCM, Montpellier, France.
| | - Dahbia Talbi
- LUPM, Univ. Montpellier, CNRS, Montpellier, France.
| | - Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantique (LCPQ/FERMI), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
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7
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Nesterov SV, Yaguzhinsky LS. Directed proton transfer from F o to F 1 extends the multifaceted proton functions in ATP synthase. Biophys Rev 2023; 15:859-873. [PMID: 37975013 PMCID: PMC10643803 DOI: 10.1007/s12551-023-01132-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/30/2023] [Indexed: 11/19/2023] Open
Abstract
The role of protons in ATP synthase is typically considered to be energy storage in the form of an electrochemical potential, as well as an operating element proving rotation. However, this review emphasizes that protons also act as activators of conformational changes in F1 and as direct participants in phosphorylation reaction. The protons transferred through Fo do not immediately leave to the bulk aqueous phase, but instead provide for the formation of a pH gradient between acidifying Fo and alkalizing F1. It facilitates a directed inter-subunit proton transfer to F1, where they are used in the ATP synthesis reaction. This ensures that the enzyme activity is not limited by a lack of protons in the alkaline mitochondrial matrix or chloroplast stroma. Up to one hundred protons bind to the carboxyl groups of the F1 subunit, altering the electrical interactions between the amino acids of the enzyme. This removes the inhibition of ATP synthase caused by the electrostatic attraction of charged amino acids of the stator and rotor and also makes the enzyme more prone to conformational changes. Protonation occurs during ATP synthesis initiation and during phosphorylation, while deprotonation blocks the rotation inhibiting both synthesis and hydrolysis. Thus, protons participate in the functioning of all main components of ATP synthase molecular machine making it effectively a proton-driven electric machine. The review highlights the key role of protons as a coupling factor in ATP synthase with multifaceted functions, including charge and energy transport, torque generation, facilitation of conformational changes, and participation in the ATP synthesis reaction.
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Affiliation(s)
- Semen V. Nesterov
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, 123182 Moscow, Russia
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Lev S. Yaguzhinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Belozersky Research Institute for Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
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8
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Min Y, Mei SC, Pan XQ, Chen JJ, Yu HQ, Xiong Y. Mimicking reductive dehalogenases for efficient electrocatalytic water dechlorination. Nat Commun 2023; 14:5134. [PMID: 37612275 PMCID: PMC10447495 DOI: 10.1038/s41467-023-40906-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/16/2023] [Indexed: 08/25/2023] Open
Abstract
Electrochemical technology is a robust approach to removing toxic and persistent chlorinated organic pollutants from water; however, it remains a challenge to design electrocatalysts with high activity and selectivity as elaborately as natural reductive dehalogenases. Here we report the design of high-performance electrocatalysts toward water dechlorination by mimicking the binding pocket configuration and catalytic center of reductive dehalogenases. Specifically, our designed electrocatalyst is an assembled heterostructure by sandwiching a molecular catalyst into the interlayers of two-dimensional graphene oxide. The electrocatalyst exhibits excellent dechlorination performance, which enhances reduction of intermediate dichloroacetic acid by 7.8 folds against that without sandwich configuration and can selectively generate monochloro-groups from trichloro-groups. Molecular simulations suggest that the sandwiched inner space plays an essential role in tuning solvation shell, altering protonation state and facilitating carbon-chlorine bond cleavage. This work demonstrates the concept of mimicking natural reductive dehalogenases toward the sustainable treatment of organohalogen-contaminated water and wastewater.
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Affiliation(s)
- Yuan Min
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Shu-Chuan Mei
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Xiao-Qiang Pan
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Jie-Jie Chen
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China.
| | - Han-Qing Yu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China.
| | - Yujie Xiong
- Hefei National Research Center for Physical Sciences at the Microscale, Collaborative Innovative Center of Chemistry for Energy Materials (iChEM), School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, China.
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9
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Chow M, Lambros E, Li X, Hammes-Schiffer S. Nuclear-Electronic Orbital QM/MM Approach: Geometry Optimizations and Molecular Dynamics. J Chem Theory Comput 2023. [PMID: 37329317 DOI: 10.1021/acs.jctc.3c00361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods allow simulations of chemical reactions in atomistic solvent and heterogeneous environments such as proteins. Herein, the nuclear-electronic orbital (NEO) QM/MM approach is introduced to enable the quantization of specified nuclei, typically protons, in the QM region using a method such as NEO-density functional theory (NEO-DFT). This approach includes proton delocalization, polarization, anharmonicity, and zero-point energy in geometry optimizations and dynamics. Expressions for the energies and analytical gradients associated with the NEO-QM/MM method, as well as the previously developed polarizable continuum model (NEO-PCM), are provided. Geometry optimizations of small organic molecules hydrogen bonded to water in either dielectric continuum solvent or explicit atomistic solvent illustrate that aqueous solvation can strengthen hydrogen-bonding interactions for the systems studied, as indicated by shorter intermolecular distances at the hydrogen-bond interface. We then performed a real-time direct dynamics simulation of a phenol molecule in explicit water using the NEO-QM/MM method. These developments and initial examples provide the foundation for future studies of nuclear-electronic quantum dynamics in complex chemical and biological environments.
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Affiliation(s)
- Mathew Chow
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Eleftherios Lambros
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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10
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Huang H, Xue L, Lu G, Cheng S, Bu Y. Hydrated electrons as nodes in porous clathrate hydrates. J Chem Phys 2023; 158:114504. [PMID: 36948798 DOI: 10.1063/5.0135335] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
We investigate the structures of hydrated electrons (e- aq) in one of water's solid phases, namely, clathrate hydrates (CHs). Using density functional theory (DFT) calculations, DFT-based ab initio molecular dynamics (AIMD), and path-integral AIMD simulations with periodic boundary conditions, we find that the structure of the e- aq@node model is in good agreement with the experiment, suggesting that an e- aq could form a node in CHs. The node is a H2O defect in CHs that is supposed to be composed of four unsaturated hydrogen bonds. Since CHs are porous crystals that possess cavities that can accommodate small guest molecules, we expect that these guest molecules can be used to tailor the electronic structure of the e- aq@node, and it leads to experimentally observed optical absorption spectra of CHs. Our findings have a general interest and extend the knowledge of e- aq into porous aqueous systems.
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Affiliation(s)
- Haibei Huang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, People's Republic of China
| | - Lijuan Xue
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, People's Republic of China
| | - Gang Lu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, People's Republic of China
| | - Shibo Cheng
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, People's Republic of China
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, People's Republic of China
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11
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Lai Z, Shen M, Shen Y, Ye YX, Zhu F, Xu J, Ouyang G. Hydrogen bond networks in gas-phase complex anions. RSC Adv 2022; 12:29137-29142. [PMID: 36320744 PMCID: PMC9558071 DOI: 10.1039/d2ra05029c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/02/2022] [Indexed: 11/05/2022] Open
Abstract
Hydrogen bond networks (HBNs) have piqued the interest of the scientific community due to their crucial roles in nature. However, HBNs that are isolated from complicated backgrounds for unraveling their characteristics are still scarce. Herein, we propose that HBNs exist in complex anions formed between α-cyclodextrin (α-CD) and four benzoic acids (RBAs) in the gas phase. The complex anions are facilely extracted from solutions via the electrospray ionization technique, and subsequently activated through collision for the investigation of their transition dynamics. It is revealed that the generation of deprotonated α-CD and neutral RBAs is the unexpected dominant dissociation pathway for all the four complex anions, and the complex anions formed from more acidic RBAs exhibit higher stabilities. These dissociation results are successfully explained by the cooperative stretching dynamics of the proposed HBNs that are formed involving the intramolecular HBN of α-CD and the intermolecular hydrogen bonds (HBs) between α-CD and RBAs. Furthermore, the rarely observed low barrier HBs (LBHBs) are suggested to be present in the HBNs. It is believed that the present complex anions can serve as a facilely accessible and informative model for studying HBNs in the future. Hydrogen bond networks and low barrier hydrogen bonds are demonstrated in the complex anions formed between α-cyclodextrin and benzoic acids.![]()
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Affiliation(s)
- Zhisheng Lai
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Minhui Shen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Yong Shen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Yu-Xin Ye
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Fang Zhu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Jianqiao Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Gangfeng Ouyang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China,College of Chemistry, Center of Advanced Analysis and Gene Sequencing, Zhengzhou UniversityZhengzhou450001China,Guangdong Provincial Key Laboratory of Emergency Testing for Dangerous Chemicals, Guangdong Institute of Analysis (China National Analytical Center Guangzhou), Guangdong Academy of SciencesGuangzhou510070China
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12
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Tu Y, Chu W, Shi Y, Zhu W, Zheng Q, Zhao J. High Photoreactivity on a Reconstructed Anatase TiO 2(001) Surface Predicted by Ab Initio Nonadiabatic Molecular Dynamics. J Phys Chem Lett 2022; 13:5766-5775. [PMID: 35723976 DOI: 10.1021/acs.jpclett.2c01417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Anatase TiO2(001) surface with (4 × 1) reconstruction is proposed to be a highly active catalytic surface. In this work, using time-domain ab initio nonadiabatic molecular dynamics, we reveal that the ridge structure formed by anatase(001) surface reconstruction is the photoreactive site for hole migration and trapping. Moreover, the ridge structure is destroyed by low-coverage CH3OH adsorption, leading to the suppression of its high photoreactivity. However, when the CH3OH coverage is increased and intermolecular hydrogen bonds (H-bonds) form, the ridge structure and its high photoreactivity are restored. Furthermore, the hole trapping dynamics is strongly coherent with intermolecular proton transfer in structures with intermolecular H-bonds. Our study proves that anatase TiO2(001)-(4 × 1) is a highly photoreactive surface where the ridge is the photoreactive site for hole trapping, which is coherent with the proton transfer process.
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Affiliation(s)
- Youyou Tu
- Department of Physics and ICQD/Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Weibin Chu
- Key Laboratory of Computational Physical Sciences (Ministry of Education), Institute of Computational Physical Sciences, Fudan University, Shanghai 200433, People's Republic of China
| | - Yongliang Shi
- Center for Spintronics and Quantum Systems, State Key Laboratory for Mechanical Behavior of Materials, School of Materials Science and Engineering, Xi'an Jiaotong University, Xi'an, Shanxi 710049, China
| | - Wenguang Zhu
- Department of Physics and ICQD/Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Qijing Zheng
- Department of Physics and ICQD/Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jin Zhao
- Department of Physics and ICQD/Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
- Department of Physics and ICQD/Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
- Synergetic Innovation Center of Quantum Information & Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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13
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Chu W, Tan S, Zheng Q, Fang W, Feng Y, Prezhdo OV, Wang B, Li XZ, Zhao J. Ultrafast charge transfer coupled to quantum proton motion at molecule/metal oxide interface. SCIENCE ADVANCES 2022; 8:eabo2675. [PMID: 35714193 DOI: 10.1126/sciadv.abo2675] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Understanding how the nuclear quantum effects (NQEs) in the hydrogen bond (H-bond) network influence the photoexcited charge transfer at semiconductor/molecule interface is a challenging problem. By combining two kinds of emerging molecular dynamics methods at the ab initio level, the path integral-based molecular dynamics and time-dependent nonadiabatic molecular dynamics, and choosing CH3OH/TiO2 as a prototypical system to study, we find that the quantum proton motion in the H-bond network is strongly coupled with the ultrafast photoexcited charge dynamics at the interface. The hole trapping ability of the adsorbed methanol molecule is notably enhanced by the NQEs, and thus, it behaves as a hole scavenger on titanium dioxide. The critical role of the H-bond network is confirmed by in situ scanning tunneling microscope measurements with ultraviolet light illumination. It is concluded the quantum proton motion in the H-bond network plays a critical role in influencing the energy conversion efficiency based on photoexcitation.
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Affiliation(s)
- Weibin Chu
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
- Departments of Chemistry, and Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
- Key Laboratory of Computational Physical Sciences (Ministry of Education), Institute of Computational Physical Sciences, Fudan University, Shanghai 200433, People's Republic of China
| | - Shijing Tan
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Qijing Zheng
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Wei Fang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China
- Department of Chemistry, Fudan University, Shanghai 200438, People's Republic of China
- Laboratory of Physical Chemistry, ETH Zurich, CH-8093 Zürich, Switzerland
| | - Yexin Feng
- School of Physics and Electronics, Hunan University, Changsha 410082, People's Republic of China
| | - Oleg V Prezhdo
- Departments of Chemistry, and Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
| | - Bing Wang
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Xin-Zheng Li
- Interdisciplinary Institute of Light-Element Quantum Materials, Research Center for Light-Element Advanced Materials, State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Frontier Science Center for Nano-optoelectronics and School of Physics, Peking University, Beijing 100871, People's Republic of China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu 226010, People's Republic of China
| | - Jin Zhao
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
- Hefei National Laboratory, Hefei 230088, People's Republic of China
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14
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Wu C, Li R, Yu K. Learning the Quantum Centroid Force Correction in Molecular Systems: A Localized Approach. Front Mol Biosci 2022; 9:851311. [PMID: 35664679 PMCID: PMC9161153 DOI: 10.3389/fmolb.2022.851311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Molecular mechanics (MM) is a powerful tool to study the properties of molecular systems in the fields of biology and materials science. With the development of ab initio force field and the application of ab initio potential energy surface, the nuclear quantum effect (NQE) is becoming increasingly important for the robustness of the simulation. However, the state-of-the-art path-integral molecular dynamics simulation, which incorporates NQE in MM, is still too expensive to conduct for most biological and material systems. In this work, we analyze the locality of NQE, using both analytical and numerical approaches, and conclude that NQE is an extremely localized phenomenon in nonreactive molecular systems. Therefore, we can use localized machine learning (ML) models to predict quantum force corrections both accurately and efficiently. Using liquid water as example, we show that the ML facilitated centroid MD can reproduce the NQEs in both the thermodynamical and the dynamical properties, with a minimal increase in computational time compared to classical molecular dynamics. This simple approach thus largely decreases the computational cost of quantum simulations, making it really accessible to the studies of large-scale molecular systems.
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Affiliation(s)
| | | | - Kuang Yu
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
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15
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Yang Z, Hajlasz N, Kulik HJ. Computational Modeling of Conformer Stability in Benenodin-1, a Thermally Actuated Lasso Peptide Switch. J Phys Chem B 2022; 126:3398-3406. [PMID: 35481742 DOI: 10.1021/acs.jpcb.2c00762] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Benenodin-1 is a thermally actuated lasso peptide rotaxane switch with two primary translational isomers that differ in the relative position of the residue Gln15. The conversion from one conformer to the other involves substantial enthalpy-entropy compensation: one conformer is energetically favored and the other is entropically favored. Here, we take a multi-scale quantum mechanical (QM) and classical molecular dynamic (MD) approach to reveal residue-specific sources of these differences in stability. QM reveals that the two benenodin-1 conformers involve distinct hydrogen bonding networks, with the enthalpically favored conformer having more intra-peptide hydrogen bonds between the Gln15 side chain and nearby residues. The evaluation of configurational entropy over the MD-sampled geometries reveals that the entropically favored conformer has enhanced conformational flexibility. By computing the by-residue-sum entropies, we identify the role of Gln15 and neighboring Glu14 in mediating the entropic variation during the switching process. These computational insights help explain the effects of Glu14Ala and Gln15Ala mutations on the conformational population of benenodin-1 observed experimentally.
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Affiliation(s)
- Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Natalia Hajlasz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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16
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True-atomic-resolution insights into the structure and functional role of linear chains and low-barrier hydrogen bonds in proteins. Nat Struct Mol Biol 2022; 29:440-450. [PMID: 35484235 DOI: 10.1038/s41594-022-00762-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/14/2022] [Indexed: 12/21/2022]
Abstract
Hydrogen bonds are fundamental to the structure and function of biological macromolecules and have been explored in detail. The chains of hydrogen bonds (CHBs) and low-barrier hydrogen bonds (LBHBs) were proposed to play essential roles in enzyme catalysis and proton transport. However, high-resolution structural data from CHBs and LBHBs is limited. The challenge is that their 'visualization' requires ultrahigh-resolution structures of the ground and functionally important intermediate states to identify proton translocation events and perform their structural assignment. Our true-atomic-resolution structures of the light-driven proton pump bacteriorhodopsin, a model in studies of proton transport, show that CHBs and LBHBs not only serve as proton pathways, but also are indispensable for long-range communications, signaling and proton storage in proteins. The complete picture of CHBs and LBHBs discloses their multifunctional roles in providing protein functions and presents a consistent picture of proton transport and storage resolving long-standing debates and controversies.
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17
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Kurzydłowski D. Potential energy barrier for proton transfer in compressed benzoic acid. RSC Adv 2022; 12:11436-11441. [PMID: 35425083 PMCID: PMC9004587 DOI: 10.1039/d2ra01736a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/06/2022] [Indexed: 11/21/2022] Open
Abstract
Benzoic acid (BA) is a model system for studying proton transfer (PT) reactions. The properties of solid BA subject to high pressure (exceeding 1 kbar = 0.1 GPa) are of particular interest due to the possibility of compression-tuning of the PT barrier. Here we present simulations aimed at evaluating the value of this barrier in solid BA in the 1 atm – 15 GPa pressure range. We find that pressure-induced shortening of O⋯O contacts within the BA dimers leads to a decrease in the PT barrier, and subsequent symmetrization of the hydrogen bond. However, this effect is obtained only after taking into account zero-point energy (ZPE) differences between BA tautomers and the transition state. The obtained results shed light on previous experiments on compressed benzoic acid, and indicate that a common scaling behavior with respect to the O⋯O distance might be applicable for hydrogen-bond symmetrization in both organic and inorganic systems. Pressure-induced shortening of O⋯O contacts within the dimers of solid benzoic acid leads to a decrease in the PT barrier and subsequent symmetrization of the hydrogen bond (an effect obtained only after taking into account the ZPE correction).![]()
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Affiliation(s)
- Dominik Kurzydłowski
- Faculty of Mathematics and Natural Sciences, Cardinal Stefan Wyszyński University in Warsaw 01-038 Warsaw Poland
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18
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Kang X, Chen Z, Zhou Z, Zhou Y, Tang S, Zhang Y, Zhang T, Ding B, Zhong D. Direct Observation of Ultrafast Proton Rocking in the BLUF Domain. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Xiu‐Wen Kang
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Zijing Chen
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Zhongneng Zhou
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yalin Zhou
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Siwei Tang
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yifei Zhang
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Tianyi Zhang
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Bei Ding
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Dongping Zhong
- Center for Ultrafast Science and Technology School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
- Department of Physics Department of Chemistry and Biochemistry and Programs of Biophysics Chemical Physics, and Biochemistry The Ohio State University Columbus OH 43210 USA
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19
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Zhang X, Zhou S, Leonik FM, Wang L, Kuroda DG. Quantum mechanical effects in acid–base chemistry. Chem Sci 2022; 13:6998-7006. [PMID: 35774178 PMCID: PMC9200130 DOI: 10.1039/d2sc01784a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/17/2022] [Indexed: 01/04/2023] Open
Abstract
Acid–base chemistry has immense importance for explaining and predicting the chemical products formed by an acid and a base when mixed together. However, the traditional chemistry theories used to describe acid–base reactions do not take into account the effect arising from the quantum mechanical nature of the acidic hydrogen shuttling potential and its dependence on the acid base distance. Here, infrared and NMR spectroscopies, in combination with first principles simulations, are performed to demonstrate that quantum mechanical effects, including electronic and nuclear quantum effects, play an essential role in defining the acid–base chemistry when 1-methylimidazole and acetic acid are mixed together. In particular, it is observed that the acid and the base interact to form a complex containing a strong hydrogen bond, in which the acidic hydrogen atom is neither close to the acid nor to the base, but delocalized between them. In addition, the delocalization of the acidic hydrogen atom in the complex leads to characteristic IR and NMR signatures. The presence of a hydrogen delocalized state in this simple system challenges the conventional knowledge of acid–base chemistry and opens up new avenues for designing materials in which specific properties produced by the hydrogen delocalized state can be harvested. Acid-based theories do not consider the quantum mechanical nature of the acidic hydrogen shuttling potential. Here, it is demonstrated that this particularity is needed to explain the formation acid-base complex with a delocalized acidic hydrogen.![]()
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Affiliation(s)
- Xiaoliu Zhang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Shengmin Zhou
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Fedra M. Leonik
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Daniel G. Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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20
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Atomic mass dependence of the nuclear quantum effect in NH4+(H2O). Chem Phys 2022. [DOI: 10.1016/j.chemphys.2021.111381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Chen K, Li WL, Head-Gordon T. Linear Combination of Atomic Dipoles to Calculate the Bond and Molecular Dipole Moments of Molecules and Molecular Liquids. J Phys Chem Lett 2021; 12:12360-12369. [PMID: 34936765 DOI: 10.1021/acs.jpclett.1c03476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We report a linear combination of atomic dipole (LCAD) method for calculating the bond dipole moments of molecules. We show that the LCAD method reproduces the known molecular dipole moments of small to large molecules with a small error with respect to experimental and benchmark ab initio calculations, and molecular dipole distributions of bulk water that agree with maximally localized Wannier functions. The bond dipole moments derived from LCAD are also chemically interpretable in terms of the trend in bond ionicity in going from neutral to charged molecules. Moreover, the LCAD method accurately captures the influence of electric fields, supported by the correct trend in the change of the dipole moment under a uniform external electric field. The better grounding of bond dipole calculations indicates that it should also serve as a useful approach to bond dipole-field models used in catalysis or to reconstruct the small dipole of a H-terminated graphene flake.
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Affiliation(s)
- Kaixuan Chen
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, California 94720, United States
- Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Wan-Lu Li
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, California 94720, United States
- Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, California 94720, United States
- Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
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22
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Ding B, Kang XW, Chen Z, Zhou Z, Zhou Y, Tang S, Zhang Y, Zhang T, Zhong D. Direct Observation of Ultrafast Proton Rocking in the BLUF Domain. Angew Chem Int Ed Engl 2021; 61:e202114423. [PMID: 34927328 DOI: 10.1002/anie.202114423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Indexed: 11/10/2022]
Abstract
We present direct observation of ultrafast proton rocking in the central motif of a BLUF domain protein scaffold. The mutant design has taken considerations of modulating the proton-coupled electron transfer (PCET) driving forces by replacing Tyr in the original motif with Trp, as well as of removing the interference of a competing electron transfer pathway. Using femtosecond pump-probe spectroscopy and detailed kinetics analysis, we resolved an electron-transfer-coupled Grotthuss-type forward and reversed proton rocking along the FMN-Gln-Trp proton relay chain. The rates of forward and reversed proton transfer are determined to be very close, namely 51 ps vs 52 ps. The kinetic isotope effect (KIE) constants associated with the forward and reversed proton transfer are 3.9 and 5.3, respectively. The observation of ultrafast proton rocking is not only a crucial step towards revealing the nature of proton relay in BLUF domain, but also provides a new paradigm of proton transfer in proteins for theoretical investigations.
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Affiliation(s)
- Bei Ding
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, 800 Dongchuan Road, 200240, Shanghai, CHINA
| | - Xiu-Wen Kang
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Zijing Chen
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Zhongneng Zhou
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Yalin Zhou
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Siwei Tang
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Yifei Zhang
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Tianyi Zhang
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Dongping Zhong
- The Ohio State University, Department of Chemical and Biomolecular Engineering, CHINA
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23
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Kędzierski P, Moskal M, Sokalski WA. Catalytic Fields as a Tool to Analyze Enzyme Reaction Mechanism Variants and Reaction Steps. J Phys Chem B 2021; 125:11606-11616. [PMID: 34648705 PMCID: PMC8558854 DOI: 10.1021/acs.jpcb.1c05256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/19/2021] [Indexed: 11/29/2022]
Abstract
Catalytic fields representing the topology of the optimal molecular environment charge distribution that reduces the activation barrier have been used to examine alternative reaction variants and to determine the role of conserved catalytic residues for two consecutive reactions catalyzed by the same enzyme. Until now, most experimental and conventional top-down theoretical studies employing QM/MM or ONIOM methods have focused on the role of enzyme electric fields acting on broken bonds of reactants. In contrast, our bottom-up approach dealing with a small reactant and transition-state model allows the analysis of the opposite effects: how the catalytic field resulting from the charge redistribution during the enzyme reaction acts on conserved amino acid residues and contributes to the reduction of the activation barrier. This approach has been applied to the family of histidyl tRNA synthetases involved in the translation of the genetic code into the protein amino acid sequence. Activation energy changes related to conserved charged amino acid residues for 12 histidyl tRNA synthetases from different biological species allowed to compare on equal footing the catalytic residues involved in ATP aminoacylation and tRNA charging reactions and to analyze different reaction mechanisms proposed in the literature. A scan of the library of atomic multipoles for amino acid side-chain rotamers within the catalytic field pointed out the change in the Glu83 conformation as the critical catalytic effect, providing, at low computational cost, insight into the electrostatic preorganization of the enzyme catalytic site at a level of detail that has not yet been accessible in conventional experimental or theoretical methods. This opens the way for rational reverse biocatalyst design at a very limited computational cost without resorting to empirical methods.
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Affiliation(s)
- Paweł Kędzierski
- Department of Chemistry, Wrocław
University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Martyna Moskal
- Department of Chemistry, Wrocław
University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - W. Andrzej Sokalski
- Department of Chemistry, Wrocław
University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
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24
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Mauger N, Plé T, Lagardère L, Bonella S, Mangaud É, Piquemal JP, Huppert S. Nuclear Quantum Effects in Liquid Water at Near Classical Computational Cost Using the Adaptive Quantum Thermal Bath. J Phys Chem Lett 2021; 12:8285-8291. [PMID: 34427440 DOI: 10.1021/acs.jpclett.1c01722] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We demonstrate the accuracy and efficiency of a recently introduced approach to account for nuclear quantum effects (NQEs) in molecular simulations: the adaptive quantum thermal bath (adQTB). In this method, zero-point energy is introduced through a generalized Langevin thermostat designed to precisely enforce the quantum fluctuation-dissipation theorem. We propose a refined adQTB algorithm with improved accuracy and report adQTB simulations of liquid water. Through extensive comparison with reference path integral calculations, we demonstrate that it provides excellent accuracy for a broad range of structural and thermodynamic observables as well as infrared vibrational spectra. The adQTB has a computational cost comparable to that of classical molecular dynamics, enabling simulations of up to millions of degrees of freedom.
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Affiliation(s)
- Nastasia Mauger
- Sorbonne Université, LCT, UMR 7616 CNRS, F-75005 Paris, France
| | - Thomas Plé
- CNRS, Sorbonne Université, Institut des NanoSciences de Paris, UMR 7588, 4 Place Jussieu, F-75005 Paris, France
| | - Louis Lagardère
- Sorbonne Université, LCT, UMR 7616 CNRS, F-75005 Paris, France
| | - Sara Bonella
- CECAM Centre Européen de Calcul Atomique et Moléculaire, École Polytechnique Fédérale de Lausanne, Batochimie, Avenue Forel 2, 1015 Lausanne, Switzerland
| | - Étienne Mangaud
- CNRS, Sorbonne Université, Institut des NanoSciences de Paris, UMR 7588, 4 Place Jussieu, F-75005 Paris, France
| | - Jean-Philip Piquemal
- Sorbonne Université, LCT, UMR 7616 CNRS, F-75005 Paris, France
- Institut Universitaire de France, 75005 Paris, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Simon Huppert
- CNRS, Sorbonne Université, Institut des NanoSciences de Paris, UMR 7588, 4 Place Jussieu, F-75005 Paris, France
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25
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Yang Z, Kulik HJ. Protein Dynamics and Substrate Protonation States Mediate the Catalytic Action of trans-4-Hydroxy-l-Proline Dehydratase. J Phys Chem B 2021; 125:7774-7784. [PMID: 34236200 DOI: 10.1021/acs.jpcb.1c05320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enzyme trans-4-hydroxy-l-proline (Hyp) dehydratase (HypD) is among the most abundant glycyl radical enzymes (GREs) in the healthy human gut microbiome and is considered a promising antibiotic target for the prominent antibiotic-resistant pathogen Clostridium difficile. Although an enzymatic mechanism has been proposed, the role of the greater HypD protein environment in mediating radical reactivity is not well understood. To fill this gap in understanding, we investigate HypD across multiple time- and length-scales using electronic structure modeling and classical molecular dynamics. We observe that the Hyp substrate protonation state significantly alters both its enzyme-free reactivity and its dynamics within the enzyme active site. Accurate coupled-cluster modeling suggests the deprotonated form of Hyp to be the most reactive protonation state for C5-Hpro-S activation. In the protein environment, hydrophobic interactions modulate the positioning of the Cys434 radical to enhance the reactivity of C5-Hpro-S abstraction. Long-time dynamics reveal that changing Hyp protonation states triggers the switching of a Leu643-gated water tunnel, a functional feature that has not yet been observed for members of the GRE superfamily.
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Affiliation(s)
- Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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26
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Cahlík A, Hellerstedt J, Mendieta-Moreno JI, Švec M, Santhini VM, Pascal S, Soler-Polo D, Erlingsson SI, Výborný K, Mutombo P, Marsalek O, Siri O, Jelínek P. Significance Of Nuclear Quantum Effects In Hydrogen Bonded Molecular Chains. ACS NANO 2021; 15:10357-10365. [PMID: 34033457 DOI: 10.1021/acsnano.1c02572] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In hydrogen-bonded systems, nuclear quantum effects such as zero-point motion and tunneling can significantly affect their material properties through underlying physical and chemical processes. Presently, direct observation of the influence of nuclear quantum effects on the strength of hydrogen bonds with resulting structural and electronic implications remains elusive, leaving opportunities for deeper understanding to harness their fascinating properties. We studied hydrogen-bonded one-dimensional quinonediimine molecular networks which may adopt two isomeric electronic configurations via proton transfer. Herein, we demonstrate that concerted proton transfer promotes a delocalization of π-electrons along the molecular chain, which enhances the cohesive energy between molecular units, increasing the mechanical stability of the chain and giving rise to distinctive electronic in-gap states localized at the ends. These findings demonstrate the identification of a class of isomeric hydrogen-bonded molecular systems where nuclear quantum effects play a dominant role in establishing their chemical and physical properties. This identification is a step toward the control of mechanical and electronic properties of low-dimensional molecular materials via concerted proton tunneling.
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Affiliation(s)
- Aleš Cahlík
- Institute of Physics of the Czech Academy of Sciences, v.v.i., Cukrovarnicka 10, CZ-16200 Prague 6, Czech Republic
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 78/7, CZ-11519 Prague 1, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Jack Hellerstedt
- Institute of Physics of the Czech Academy of Sciences, v.v.i., Cukrovarnicka 10, CZ-16200 Prague 6, Czech Republic
| | - Jesús I Mendieta-Moreno
- Institute of Physics of the Czech Academy of Sciences, v.v.i., Cukrovarnicka 10, CZ-16200 Prague 6, Czech Republic
| | - Martin Švec
- Institute of Physics of the Czech Academy of Sciences, v.v.i., Cukrovarnicka 10, CZ-16200 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Vijai M Santhini
- Institute of Physics of the Czech Academy of Sciences, v.v.i., Cukrovarnicka 10, CZ-16200 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Simon Pascal
- Aix Marseille Univ, CNRS, CINaM, UMR 7325, Campus de Luminy, F-13288 Marseille Cedex 09 France
| | - Diego Soler-Polo
- Universidad Autónoma de Madrid, Campus Cantoblanco, ES-28049, Madrid, Spain
| | - Sigurdur I Erlingsson
- School of Science and Engineering, Reykjavik University, Menntavegi 1, IS-101 Reykjavik, Iceland
| | - Karel Výborný
- Institute of Physics of the Czech Academy of Sciences, v.v.i., Cukrovarnicka 10, CZ-16200 Prague 6, Czech Republic
| | - Pingo Mutombo
- Institute of Physics of the Czech Academy of Sciences, v.v.i., Cukrovarnicka 10, CZ-16200 Prague 6, Czech Republic
- Department of Petrochemistry and Refining, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Ondrej Marsalek
- Charles University, Faculty of Mathematics and Physics, Ke Karlovu 3, CZ-12116 Prague 2, Czech Republic
| | - Olivier Siri
- Aix Marseille Univ, CNRS, CINaM, UMR 7325, Campus de Luminy, F-13288 Marseille Cedex 09 France
| | - Pavel Jelínek
- Institute of Physics of the Czech Academy of Sciences, v.v.i., Cukrovarnicka 10, CZ-16200 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
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27
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28
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Yang KR, Lakshmi KV, Brudvig GW, Batista VS. Is Deprotonation of the Oxygen-Evolving Complex of Photosystem II during the S1 → S2 Transition Suppressed by Proton Quantum Delocalization? J Am Chem Soc 2021; 143:8324-8332. [DOI: 10.1021/jacs.1c00633] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Ke R. Yang
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - K. V. Lakshmi
- Department of Chemistry and Chemical Biology and The Baruch ’60 Center for Biochemical Solar Energy, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Gary W. Brudvig
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Victor S. Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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29
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Hydrogen Bonds: Raman Spectroscopic Study. Int J Mol Sci 2021; 22:ijms22105380. [PMID: 34065358 PMCID: PMC8161095 DOI: 10.3390/ijms22105380] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 11/26/2022] Open
Abstract
The work outlines general ideas on how the frequency and the intensity of proton vibrations of X–H···Y hydrogen bonding are formed as the bond evolves from weak to maximally strong bonding. For this purpose, the Raman spectra of different chemical compounds with moderate, strong, and extremely strong hydrogen bonds were obtained in the temperature region of 5 K–300 K. The dependence of the proton vibrational frequency is schematically presented as a function of the rigidity of O-H···O bonding. The problems of proton dynamics on tautomeric O–H···O bonds are considered. A brief description of the N–H···O and C–H···Y hydrogen bonds is given.
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Reinhardt CR, Sayfutyarova ER, Zhong J, Hammes-Schiffer S. Glutamate Mediates Proton-Coupled Electron Transfer Between Tyrosines 730 and 731 in Escherichia coli Ribonucleotide Reductase. J Am Chem Soc 2021; 143:6054-6059. [DOI: 10.1021/jacs.1c02152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Clorice R. Reinhardt
- Department of Molecular Biophysics & Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520, United States
| | - Elvira R. Sayfutyarova
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Jiayun Zhong
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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31
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Chowdhury SN, Huo P. Non-adiabatic Matsubara dynamics and non-adiabatic ring-polymer molecular dynamics. J Chem Phys 2021; 154:124124. [PMID: 33810665 DOI: 10.1063/5.0042136] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We present the non-adiabatic Matsubara dynamics, a general framework for computing the time-correlation function (TCF) of electronically non-adiabatic systems. This new formalism is derived based on the generalized Kubo-transformed TCF using the Wigner representation for both the nuclear degrees of freedom and the electronic mapping variables. By dropping the non-Matsubara nuclear normal modes in the quantum Liouvillian and explicitly integrating these modes out from the expression of the TCF, we derived the non-adiabatic Matsubara dynamics approach. Further making the approximation to drop the imaginary part of the Matsubara Liouvillian and enforce the nuclear momentum integral to be real, we arrived at the non-adiabatic ring-polymer molecular dynamics (NRPMD) approach. We have further justified the capability of NRPMD for simulating the non-equilibrium TCF. This work provides the rigorous theoretical foundation for several recently proposed state-dependent RPMD approaches and offers a general framework for developing new non-adiabatic quantum dynamics methods in the future.
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Affiliation(s)
- Sutirtha N Chowdhury
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, USA
| | - Pengfei Huo
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, USA
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32
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Wang Z, Zhang H, Li S, Lei D, Tang BZ, Ye R. Recent Advances in Clusteroluminescence. Top Curr Chem (Cham) 2021; 379:14. [PMID: 33655404 DOI: 10.1007/s41061-021-00326-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/08/2021] [Indexed: 01/04/2023]
Abstract
Clusteroluminescence is a phenomenon whereby the aggregation or clustering of non-conjugated electron-rich units leads to the emission of light at long wavelengths. This phenomenon was first discovered in poly(amido amine) (PAMAM) dendrimers. In recent years, clusteroluminescence has attracted growing research interest and its photophysical properties and mechanism have been thoroughly studied. In this review, we first briefly introduce the development of different types of clusteroluminogens. Then we highlight recent developments in clusteroluminescence, including mechanistic studies, the disclosure of room-temperature phosphorescence, and the extension of emission to the longer-wavelength region. Lastly, we demonstrate a few applications in various fields. With advantages such as being earth-abundant, biocompatible and biodegradable, clusteroluminogens are envisioned to be commonplace in the future.
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Affiliation(s)
- Zhaoyu Wang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Haoke Zhang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Siqi Li
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
| | - Dangyuan Lei
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
| | - Ben Zhong Tang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Center for Aggregation-Induced Emission, State Key Laboratory of Luminescent Materials and Devices, SCUT-HKUST Joint Research Institute, South China University of Technology, Guangzhou, 510640, China
- AIE Institute, Guangzhou Development District, Guangzhou, 510530, China
| | - Ruquan Ye
- Department of Chemistry, City University of Hong Kong, Hong Kong, China.
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Sauceda HE, Vassilev-Galindo V, Chmiela S, Müller KR, Tkatchenko A. Dynamical strengthening of covalent and non-covalent molecular interactions by nuclear quantum effects at finite temperature. Nat Commun 2021; 12:442. [PMID: 33469007 PMCID: PMC7815839 DOI: 10.1038/s41467-020-20212-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/12/2020] [Indexed: 11/08/2022] Open
Abstract
Nuclear quantum effects (NQE) tend to generate delocalized molecular dynamics due to the inclusion of the zero point energy and its coupling with the anharmonicities in interatomic interactions. Here, we present evidence that NQE often enhance electronic interactions and, in turn, can result in dynamical molecular stabilization at finite temperature. The underlying physical mechanism promoted by NQE depends on the particular interaction under consideration. First, the effective reduction of interatomic distances between functional groups within a molecule can enhance the n → π* interaction by increasing the overlap between molecular orbitals or by strengthening electrostatic interactions between neighboring charge densities. Second, NQE can localize methyl rotors by temporarily changing molecular bond orders and leading to the emergence of localized transient rotor states. Third, for noncovalent van der Waals interactions the strengthening comes from the increase of the polarizability given the expanded average interatomic distances induced by NQE. The implications of these boosted interactions include counterintuitive hydroxyl-hydroxyl bonding, hindered methyl rotor dynamics, and molecular stiffening which generates smoother free-energy surfaces. Our findings yield new insights into the versatile role of nuclear quantum fluctuations in molecules and materials.
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Affiliation(s)
- Huziel E Sauceda
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg.
- Machine Learning Group, Technische Universität Berlin, 10587, Berlin, Germany.
- BASLEARN, BASF-TU joint Lab, Technische Universität Berlin, 10587, Berlin, Germany.
| | - Valentin Vassilev-Galindo
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg
| | - Stefan Chmiela
- Machine Learning Group, Technische Universität Berlin, 10587, Berlin, Germany
| | - Klaus-Robert Müller
- Machine Learning Group, Technische Universität Berlin, 10587, Berlin, Germany.
- Department of Artificial Intelligence, Korea University, Anam-dong, Seongbuk-gu, Seoul, 02841, Korea.
- Max Planck Institute for Informatics, Stuhlsatzenhausweg, 66123, Saarbrücken, Germany.
- Google Research, Brain team, Berlin, Germany.
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg.
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34
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Vennelakanti V, Qi HW, Mehmood R, Kulik HJ. When are two hydrogen bonds better than one? Accurate first-principles models explain the balance of hydrogen bond donors and acceptors found in proteins. Chem Sci 2021; 12:1147-1162. [PMID: 35382134 PMCID: PMC8908278 DOI: 10.1039/d0sc05084a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/18/2020] [Indexed: 01/02/2023] Open
Abstract
Hydrogen bonds (HBs) play an essential role in the structure and catalytic action of enzymes, but a complete understanding of HBs in proteins challenges the resolution of modern structural (i.e., X-ray diffraction) techniques and mandates computationally demanding electronic structure methods from correlated wavefunction theory for predictive accuracy. Numerous amino acid sidechains contain functional groups (e.g., hydroxyls in Ser/Thr or Tyr and amides in Asn/Gln) that can act as either HB acceptors or donors (HBA/HBD) and even form simultaneous, ambifunctional HB interactions. To understand the relative energetic benefit of each interaction, we characterize the potential energy surfaces of representative model systems with accurate coupled cluster theory calculations. To reveal the relationship of these energetics to the balance of these interactions in proteins, we curate a set of 4000 HBs, of which >500 are ambifunctional HBs, in high-resolution protein structures. We show that our model systems accurately predict the favored HB structural properties. Differences are apparent in HBA/HBD preference for aromatic Tyr versus aliphatic Ser/Thr hydroxyls because Tyr forms significantly stronger O–H⋯O HBs than N–H⋯O HBs in contrast to comparable strengths of the two for Ser/Thr. Despite this residue-specific distinction, all models of residue pairs indicate an energetic benefit for simultaneous HBA and HBD interactions in an ambifunctional HB. Although the stabilization is less than the additive maximum due both to geometric constraints and many-body electronic effects, a wide range of ambifunctional HB geometries are more favorable than any single HB interaction. Correlated wavefunction theory predicts and high-resolution crystal structure analysis confirms the important, stabilizing effect of simultaneous hydrogen bond donor and acceptor interactions in proteins.![]()
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Affiliation(s)
- Vyshnavi Vennelakanti
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
- Department of Chemistry
| | - Helena W. Qi
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
- Department of Chemistry
| | - Rimsha Mehmood
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
- Department of Chemistry
| | - Heather J. Kulik
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
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35
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Lin CY, Boxer SG. Unusual Spectroscopic and Electric Field Sensitivity of Chromophores with Short Hydrogen Bonds: GFP and PYP as Model Systems. J Phys Chem B 2020; 124:9513-9525. [DOI: 10.1021/acs.jpcb.0c07730] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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36
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Li J, Chen J, An L, Yuan X, Yao L. Polyol and sugar osmolytes can shorten protein hydrogen bonds to modulate function. Commun Biol 2020; 3:528. [PMID: 32968183 PMCID: PMC7511342 DOI: 10.1038/s42003-020-01260-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/28/2020] [Indexed: 12/19/2022] Open
Abstract
Polyol and sugar osmolytes are commonly used in therapeutic protein formulations. How they may affect protein structure and function is an important question. In this work, through NMR measurements, we show that glycerol and sorbitol (polyols), as well as glucose (sugar), can shorten protein backbone hydrogen bonds. The hydrogen bond shortening is also captured by molecular dynamics simulations, which suggest a hydrogen bond competition mechanism. Specifically, osmolytes weaken hydrogen bonds between the protein and solvent to strengthen those within the protein. Although the hydrogen bond change is small, with the average experimental cross hydrogen bond 3hJNC' coupling of two proteins GB3 and TTHA increased by ~ 0.01 Hz by the three osmolytes (160 g/L), its effect on protein function should not be overlooked. This is exemplified by the PDZ3-peptide binding where several intermolecular hydrogen bonds are formed and osmolytes shift the equilibrium towards the bound state.
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Affiliation(s)
- Jingwen Li
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Jingfei Chen
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Liaoyuan An
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiang Yuan
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lishan Yao
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
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37
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Zhou S, Wang L. Quantum effects and 1H NMR chemical shifts of a bifurcated short hydrogen bond. J Chem Phys 2020; 153:114301. [PMID: 32962368 DOI: 10.1063/5.0024734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The monoprotonated compound N,N',N''-tris(p-tolyl)azacalix[3](2,6)pyridine (TAPH) contains an intramolecular hydrogen bond that is formed from three N atoms in its cavity. Constrained by the macrocyclic molecular structure, the separations between the N atoms in this bifurcated hydrogen bond are about 2.6 Å, considerably shorter than those typically observed for hydrogen bonded systems in the condensed phases. As such, TAPH exhibits significantly elongated N-H lengths in its hydrogen bond and a downfield 1H NMR chemical shift of 22.1 ppm. In this work, we carry out ab initio molecular dynamics and ab initio path integral molecular dynamics simulations of TAPH in the acetonitrile solution to reveal the geometry and proton sharing conditions of the bifurcated short hydrogen bond and uncover how the interplay of electronic and nuclear quantum effects gives rise to its far downfield 1H chemical shift. Taking a linear short hydrogen bond as a reference, we demonstrate the distinct features of competing quantum effects and electronic shielding effects in the bifurcated hydrogen bond of TAPH. We further use the degree of deshielding on the proton as a measure of the hydrogen bonding interactions and evaluate the strength of the bifurcated short hydrogen bond as compared to its linear counterpart.
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Affiliation(s)
- Shengmin Zhou
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, USA
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38
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39
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Wang L, Ceriotti M, Markland TE. Quantum kinetic energy and isotope fractionation in aqueous ionic solutions. Phys Chem Chem Phys 2020; 22:10490-10499. [PMID: 31942581 DOI: 10.1039/c9cp06483d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
At room temperature, the quantum contribution to the kinetic energy of a water molecule exceeds the classical contribution by an order of magnitude. The quantum kinetic energy (QKE) of a water molecule is modulated by its local chemical environment and leads to uneven partitioning of isotopes between different phases in thermal equilibrium, which would not occur if the nuclei behaved classically. In this work, we use ab initio path integral simulations to show that QKEs of the water molecules and the equilibrium isotope fractionation ratios of the oxygen and hydrogen isotopes are sensitive probes of the hydrogen bonding structures in aqueous ionic solutions. In particular, we demonstrate how the QKE of water molecules in path integral simulations can be decomposed into translational, rotational and vibrational degrees of freedom, and use them to determine the impact of solvation on different molecular motions. By analyzing the QKEs and isotope fractionation ratios, we show how the addition of the Na+, Cl- and HPO42- ions perturbs the competition between quantum effects in liquid water and impacts their local solvation structures.
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Affiliation(s)
- Lu Wang
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.
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40
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Lan J, Rybkin VV, Iannuzzi M. Ionization of Water as an Effect of Quantum Delocalization at Aqueous Electrode Interfaces. J Phys Chem Lett 2020; 11:3724-3730. [PMID: 32315196 DOI: 10.1021/acs.jpclett.0c01025] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The enhanced probability of water dissociation at the aqueous electrode interfaces is predicted by path-integral ab initio molecular dynamics. The ionization process is observed at the aqueous platinum interface when nuclear quantum effects are introduced in the statistical sampling, while minor effects have been observed at the gold interface. We characterize the dissociation mechanism of the formed water ions. In spite of the fact that the concentration and lifetime of the ions might be challenging to experimentally detect, they may serve as a guide to future experiments. Our observation might have a significant impact on the understanding of electrochemical processes occurring at the metal electrode surface.
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Affiliation(s)
- Jinggang Lan
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Vladimir V Rybkin
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Marcella Iannuzzi
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
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41
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Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharing. Proc Natl Acad Sci U S A 2020; 117:10818-10824. [PMID: 32371483 DOI: 10.1073/pnas.1922538117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent advances in neutron crystallographic studies have provided structural bases for quantum behaviors of protons observed in enzymatic reactions. Thus, we resolved the neutron crystal structure of a bacterial copper (Cu) amine oxidase (CAO), which contains a prosthetic Cu ion and a protein-derived redox cofactor, topa quinone (TPQ). We solved hitherto unknown structures of the active site, including a keto/enolate equilibrium of the cofactor with a nonplanar quinone ring, unusual proton sharing between the cofactor and the catalytic base, and metal-induced deprotonation of a histidine residue that coordinates to the Cu. Our findings show a refined active-site structure that gives detailed information on the protonation state of dissociable groups, such as the quinone cofactor, which are critical for catalytic reactions.
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42
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Kędzierski P, Zaczkowska M, Sokalski WA. Extreme Catalytic Power of Ketosteroid Isomerase Related to the Reversal of Proton Dislocations in Hydrogen-Bond Network. J Phys Chem B 2020; 124:3661-3666. [PMID: 32293890 PMCID: PMC7467711 DOI: 10.1021/acs.jpcb.0c01489] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Dynamic
electrostatic catalytic field (DECF) vectors derived from
transition state and reactant wavefunctions for the two-step reaction
occurring within ketosteroid isomerase (KSI) have been calculated
using MP2/aug-cc-pVTZ and lower theory levels to determine the magnitude
of the catalytic effect and the optimal directions of proton transfers
in the KSI hydrogen-bond network. The most surprising and meaningful
finding is that the KSI catalytic activity is enhanced by proton dislocations
proceeding in opposite directions for each of the two consecutive
reaction steps in the same hydrogen network. Such a mechanism allows
an ultrafast switching of the catalytic proton wire environment, possibly
related to the exceptionally high KSI catalytic power.
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Affiliation(s)
- Paweł Kędzierski
- Department of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Maria Zaczkowska
- Department of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - W Andrzej Sokalski
- Department of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
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43
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Alburquerque PR, Ramachandran BR, Junk T, Karsili TNV. Hydrogen-Deuterium Exchange in Basic Near-Critical and Supercritical Media: An Experimental and Theoretical Study. J Phys Chem A 2020; 124:2530-2536. [PMID: 32149509 DOI: 10.1021/acs.jpca.9b10892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Treatment of homo- and heterocyclic aromatic substrates with basic deuterium oxide under near- or supercritical conditions results in rapid base-catalyzed hydrogen-deuterium exchange (HDE) in aromatic and benzylic positions. It has been postulated that HDE follows a simple deprotonation-reprotonation mechanism, but little evidence has been provided to date. This study correlates experimentally observed proton exchanges in n-butylbenzene with ab initio calculations of the acidities and potential energy (PE) profiles. In addition to providing further support for carbanion intermediacy in HDE, these results offer new insights into substrate acidities in near- and supercritical aqueous media and the optimal conditions required for their isotope exchange.
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Affiliation(s)
- Pia R Alburquerque
- Department of Chemistry, Grambling State University, Grambling, Louisiana 71245, United States
| | - B Ramu Ramachandran
- Institute for Micromanufacturing, Louisiana Tech University, Ruston, Louisiana 71272, United States
| | - Thomas Junk
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, United States
| | - Tolga N V Karsili
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, United States
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44
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Kumar A, Ahari D, Priyadarshi A, Ziauddin Ansari M, Swaminathan R. Weak Intrinsic Luminescence in Monomeric Proteins Arising from Charge Recombination. J Phys Chem B 2020; 124:2731-2746. [PMID: 32155070 DOI: 10.1021/acs.jpcb.9b10071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We had earlier reported on the presence of broad UV-vis electronic absorption (250-800 nm) in a monomeric protein rich in charged but lacking aromatic amino acids, referred to as Protein Charge Transfer Spectra (ProCharTS). Specifically, it was shown that the cationic amino/anionic carboxylate head groups of Lys/Glu side chains act as electronic charge acceptors/donors for photoinduced electron transfer either from/to the polypeptide backbone or to each other. In this work, we show that such excitations produce weak intrinsic luminescence in proteins originating from charge recombination. We investigated aqueous solutions of proteins with varying abundance of charged amino acids, like human serum albumin (HuSA) and hen lysozyme, and intrinsically disordered proteins, like PEST fragment of human c-Myc protein, α-synuclein, and dehydrin. The absorbance and luminescence in all protein samples were a linear function of the concentration (0-50 μM) employed, confirming their origin from a monomeric species. The slope of the luminescence/[protein] plot directly correlated with the fraction of charged amino acids present in protein. Specifically, the higher slope in proteins like HuSA was chiefly accounted by a large molar extinction coefficient rather than quantum yield. This coefficient directly correlates with the population of charged side-chain head groups lying in close spatial proximity in the protein, contributed by the three-dimensional (3D) fold of the polypeptide. ProCharTS luminescence parameters appear conserved across proteins. These include overlapping excitation/emission spectra, large Stokes shifts (14 000-3000 cm-1) that decrease with increasing excitation wavelength, low quantum yields (0.002-0.026) indicating poor radiative recombination efficiency, and multiexponential decays (mean lifetimes = 0.4-2.9 ns).
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Affiliation(s)
- Amrendra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Dileep Ahari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Anurag Priyadarshi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Mohd Ziauddin Ansari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Rajaram Swaminathan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
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45
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Zhou S, Wang L. Symmetry and 1H NMR chemical shifts of short hydrogen bonds: impact of electronic and nuclear quantum effects. Phys Chem Chem Phys 2020; 22:4884-4895. [DOI: 10.1039/c9cp06840f] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Electronic and nuclear quantum effects determine the symmetry and highly downfield 1H NMR chemical shifts of short hydrogen bonds.
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Affiliation(s)
- Shengmin Zhou
- Department of Chemistry and Chemical Biology
- Institute for Quantitative Biomedicine
- Rutgers University
- Piscataway
- USA
| | - Lu Wang
- Department of Chemistry and Chemical Biology
- Institute for Quantitative Biomedicine
- Rutgers University
- Piscataway
- USA
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46
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Protein polarization effects in the thermodynamic computation of vibrational Stark shifts. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2522-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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47
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Welborn VV, Head-Gordon T. Fluctuations of Electric Fields in the Active Site of the Enzyme Ketosteroid Isomerase. J Am Chem Soc 2019; 141:12487-12492. [DOI: 10.1021/jacs.9b05323] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Valerie Vaissier Welborn
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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Farrell KM, Zanni MT. Observing Aqueous Proton Transfer Dynamics. ACS CENTRAL SCIENCE 2019; 5:1114-1116. [PMID: 31403065 PMCID: PMC6661868 DOI: 10.1021/acscentsci.9b00603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
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Zhou S, Wang L. Unraveling the structural and chemical features of biological short hydrogen bonds. Chem Sci 2019; 10:7734-7745. [PMID: 31588321 PMCID: PMC6764281 DOI: 10.1039/c9sc01496a] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/30/2019] [Indexed: 02/06/2023] Open
Abstract
Short hydrogen bonds are ubiquitous in biological macromolecules and exhibit distinctive proton potential energy surfaces and proton sharing properties.
The three-dimensional architecture of biomolecules often creates specialized structural elements, notably short hydrogen bonds that have donor–acceptor separations below 2.7 Å. In this work, we statistically analyze 1663 high-resolution biomolecular structures from the Protein Data Bank and demonstrate that short hydrogen bonds are prevalent in proteins, protein–ligand complexes and nucleic acids. From these biological macromolecules, we characterize the preferred location, connectivity and amino acid composition in short hydrogen bonds and hydrogen bond networks, and assess their possible functional importance. Using electronic structure calculations, we further uncover how the interplay of the structural and chemical features determines the proton potential energy surfaces and proton sharing conditions in biological short hydrogen bonds.
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Affiliation(s)
- Shengmin Zhou
- Department of Chemistry and Chemical Biology , Institute for Quantitative Biomedicine , Rutgers University , Piscataway , NJ 08854 , USA .
| | - Lu Wang
- Department of Chemistry and Chemical Biology , Institute for Quantitative Biomedicine , Rutgers University , Piscataway , NJ 08854 , USA .
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Chowdhury SN, Huo P. State dependent ring polymer molecular dynamics for investigating excited nonadiabatic dynamics. J Chem Phys 2019; 150:244102. [DOI: 10.1063/1.5096276] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sutirtha N. Chowdhury
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, USA
| | - Pengfei Huo
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, USA
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