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Jung J, Yagi K, Tan C, Oshima H, Mori T, Yu I, Matsunaga Y, Kobayashi C, Ito S, Ugarte La Torre D, Sugita Y. GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models. J Phys Chem B 2024; 128:6028-6048. [PMID: 38876465 PMCID: PMC11215777 DOI: 10.1021/acs.jpcb.4c02096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 06/16/2024]
Abstract
GENeralized-Ensemble SImulation System (GENESIS) is a molecular dynamics (MD) software developed to simulate the conformational dynamics of a single biomolecule, as well as molecular interactions in large biomolecular assemblies and between multiple biomolecules in cellular environments. To achieve the latter purpose, the earlier versions of GENESIS emphasized high performance in atomistic MD simulations on massively parallel supercomputers, with or without graphics processing units (GPUs). Here, we implemented multiscale MD simulations that include atomistic, coarse-grained, and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. They demonstrate high performance and are integrated with enhanced conformational sampling algorithms and free-energy calculations without using external programs except for the QM programs. In this article, we review new functions, molecular models, and other essential features in GENESIS version 2.1 and discuss ongoing developments for future releases.
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Affiliation(s)
- Jaewoon Jung
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Kiyoshi Yagi
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Cheng Tan
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Hiraku Oshima
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
- Graduate
School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan
| | - Takaharu Mori
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
- Department
of Chemistry, Tokyo University of Science, Shinjuku-ku, Tokyo 162-8601, Japan
| | - Isseki Yu
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
- Department
of Bioinformatics, Maebashi Institute of
Technology, Maebashi, Gunma 371-0816, Japan
| | - Yasuhiro Matsunaga
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
- Graduate
School of Science and Engineering, Saitama
University, Saitama 338-8570, Japan
| | - Chigusa Kobayashi
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Shingo Ito
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Diego Ugarte La Torre
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Yuji Sugita
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, Kobe, Hyogo 650-0047, Japan
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
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2
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Côrtes PB, Bitencourt Leão M, Reis GLR, de Vargas DD, Murillo GF, Köhler MH, Ferreira de Matos Jauris C. Unraveling the Phosphorus Adsorption Mechanisms in Three-dimensional Reduced Graphene Oxide Materials. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:11173-11183. [PMID: 38753444 PMCID: PMC11140737 DOI: 10.1021/acs.langmuir.4c00810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024]
Abstract
To prevent eutrophication, controlling the phosphate concentration levels is one of the most important issues in surface water management. One of the most utilized methods is phosphate adsorption. However, its application faces a bottleneck due to the unclear understanding of adsorption and interaction mechanisms. The present work unlocks the phosphorus adsorption mechanisms in three-dimensional reduced graphene oxide with different reduction levels and pore sizes to remove phosphate from water using experiments and multiscale simulations. Experiments were performed to evaluate the influence of pH, ionic strength, and temperature on the adsorption. Molecular Dynamics and Ab Initio simulations evaluated the influence of the pore size and oxidation degrees of the materials. We show that the adsorption capacity of the materials increases with increasing pH and ionic strength and decreasing temperature. It is observed that the more oxidized the material and the less compact the structure, the better the adsorption. These results are theoretically explained in terms of the interaction of functional groups and the clustering of phosphate ions, which results in better adsorption in materials with larger pores. The underlying mechanisms for the 3D-reduced graphene oxide performance were confirmed by spectroscopy analysis. All the results show that 3D-reduced graphene oxide can sorb phosphate in different complex water remediation systems with characteristics that can be modulated by changing the material synthesis method.
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Affiliation(s)
- Patrick
R. B. Côrtes
- Department
of Physics, Federal University of Santa
Maria, Santa
Maria 97105-900, Brazil
| | - Mayara Bitencourt Leão
- Environmental
Science and Technology Center, Federal University
of Pampa, Caçapava do Sul 96570000, Brazil
| | - Gabriel Lopes Rezende Reis
- Environmental
Science and Technology Center, Federal University
of Pampa, Caçapava do Sul 96570000, Brazil
| | - Douglas D. de Vargas
- Department
of Physics, Federal University of Santa
Maria, Santa
Maria 97105-900, Brazil
| | | | - Mateus H. Köhler
- Department
of Physics, Federal University of Santa
Maria, Santa
Maria 97105-900, Brazil
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3
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Hill TD, Basnet S, Lepird HH, Rightnowar BW, Moran SD. Anisotropic dynamics of an interfacial enzyme active site observed using tethered substrate analogs and ultrafast 2D IR spectroscopy. J Chem Phys 2023; 159:165101. [PMID: 37870142 PMCID: PMC10597647 DOI: 10.1063/5.0167991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/29/2023] [Indexed: 10/24/2023] Open
Abstract
Enzymes accelerate the rates of biomolecular reactions by many orders of magnitude compared to bulk solution, and it is widely understood that this catalytic effect arises from a combination of polar pre-organization and electrostatic transition state stabilization. A number of recent reports have also implicated ultrafast (femtosecond-picosecond) timescale motions in enzymatic activity. However, complications arising from spatially-distributed disorder, the occurrence of multiple substrate binding modes, and the influence of hydration dynamics on solvent-exposed active sites still confound many experimental studies. Here we use ultrafast two-dimensional infrared (2D IR) spectroscopy and covalently-tethered substrate analogs to examine dynamical properties of the promiscuous Pyrococcus horikoshii ene-reductase (PhENR) active site in two binding configurations mimicking proposed "inactive" and "reactive" Michaelis complexes. Spectral diffusion measurements of aryl-nitrile substrate analogs reveal an end-to-end tradeoff between fast (sub-ps) and slow (>5 ps) motions. Fermi resonant aryl-azide analogs that sense interactions of coupled oscillators are described. Lineshape and quantum beat analyses of these probes reveal characteristics that correlate with aryl-nitrile frequency fluctuation correlation functions parameters, demonstrating that this anisotropy is an intrinsic property of the water-exposed active site, where countervailing gradients of fast dynamics and disorder in the reactant ground state are maintained near the hydration interface. Our results suggest several plausible factors leading to state-selective rate enhancement and promiscuity in PhENR. This study also highlights a strategy to detect perturbations to vibrational modes outside the transparent window of the mid-IR spectrum, which may be extended to other macromolecular systems.
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Affiliation(s)
| | - Sunil Basnet
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Hannah H. Lepird
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Blaze W. Rightnowar
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
| | - Sean D. Moran
- School of Chemical and Biomolecular Sciences, Southern Illinois University Carbondale, 1245 Lincoln Drive MC 4409, Carbondale, Illinois 62901, USA
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4
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Katsyuba SA, Burganov TI. Computational analysis of the vibrational spectra and structure of aqueous cytosine. Phys Chem Chem Phys 2023; 25:24121-24128. [PMID: 37655545 DOI: 10.1039/d3cp03059h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The recently developed efficient protocol for the explicit quantum mechanical modeling of the structure and IR spectra of liquids and solutions [Katsyuba et al., J. Phys. Chem. B, 2020, 124, 6664-6670] is used to describe aqueous solutions of cytosine. The same cluster model of a solute surrounded by the first solvation shell of solvent molecules was shown to be sufficient to reproduce experimental vibrational frequencies and relative IR and Raman intensities. An equally good quality of Raman spectra was provided by B3LYP-D3/def2-TZVP and B3LYP-D3/aug-cc-pVDZ simulations. Computations using the PBE functional were sufficient for modeling of the IR spectra but failed in the simulations of Raman scattering. It is shown that strong changes of frequencies and relative intensities of Raman and IR bands of cytosine, caused by its hydration, cannot be completely assigned to the influence of hydrogen bonds (HBs) with 7 or 8 closest water molecules. They are rather ascribed to the combined effect of solute-solute and solute-solvent HBs with the participation of at least 30 water molecules separating cytosine from the bulk solvent. This suggests that the vibrational modes and derivatives of the polarizability and dipole moment of the solute are mainly locally influenced by its first hydration shell, while the influence of bulk water is rather modest.
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Affiliation(s)
- Sergey A Katsyuba
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Centre of RAS, Arbuzov st. 8, 420088 Kazan, Russia.
| | - Timur I Burganov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Centre of RAS, Arbuzov st. 8, 420088 Kazan, Russia.
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Artiukhin DG, Godtliebsen IH, Schmitz G, Christiansen O. Gaussian process regression adaptive density-guided approach: Toward calculations of potential energy surfaces for larger molecules. J Chem Phys 2023; 159:024102. [PMID: 37428042 DOI: 10.1063/5.0152367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/15/2023] [Indexed: 07/11/2023] Open
Abstract
We present a new program implementation of the Gaussian process regression adaptive density-guided approach [Schmitz et al., J. Chem. Phys. 153, 064105 (2020)] for automatic and cost-efficient potential energy surface construction in the MidasCpp program. A number of technical and methodological improvements made allowed us to extend this approach toward calculations of larger molecular systems than those previously accessible and maintain the very high accuracy of constructed potential energy surfaces. On the methodological side, improvements were made by using a Δ-learning approach, predicting the difference against a fully harmonic potential, and employing a computationally more efficient hyperparameter optimization procedure. We demonstrate the performance of this method on a test set of molecules of growing size and show that up to 80% of single point calculations could be avoided, introducing a root mean square deviation in fundamental excitations of about 3 cm-1. A much higher accuracy with errors below 1 cm-1 could be achieved with tighter convergence thresholds still reducing the number of single point computations by up to 68%. We further support our findings with a detailed analysis of wall times measured while employing different electronic structure methods. Our results demonstrate that GPR-ADGA is an effective tool, which could be applied for cost-efficient calculations of potential energy surfaces suitable for highly accurate vibrational spectra simulations.
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Affiliation(s)
- Denis G Artiukhin
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Ian H Godtliebsen
- Department of Chemistry, Aarhus Universitet, DK-8000 Aarhus, Denmark
| | - Gunnar Schmitz
- Lehrstuhl für Theoretische Chemie II, Ruhr-Universität Bochum, Universitätstraße 150, 44801 Bochum, Germany
| | - Ove Christiansen
- Department of Chemistry, Aarhus Universitet, DK-8000 Aarhus, Denmark
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6
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Quijia CR, Navegante G, Sábio RM, Valente V, Ocaña A, Alonso-Moreno C, Frem RCG, Chorilli M. Macrophage Cell Membrane Coating on Piperine-Loaded MIL-100(Fe) Nanoparticles for Breast Cancer Treatment. J Funct Biomater 2023; 14:319. [PMID: 37367283 DOI: 10.3390/jfb14060319] [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: 05/12/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/28/2023] Open
Abstract
Piperine (PIP), a compound found in Piper longum, has shown promise as a potential chemotherapeutic agent for breast cancer. However, its inherent toxicity has limited its application. To overcome this challenge, researchers have developed PIP@MIL-100(Fe), an organic metal-organic framework (MOF) that encapsulates PIP for breast cancer treatment. Nanotechnology offers further treatment options, including the modification of nanostructures with macrophage membranes (MM) to enhance the evasion of the immune system. In this study, the researchers aimed to evaluate the potential of MM-coated MOFs encapsulated with PIP for breast cancer treatment. They successfully synthesized MM@PIP@MIL-100(Fe) through impregnation synthesis. The presence of MM coating on the MOF surface was confirmed through SDS-PAGE analysis, which revealed distinct protein bands. Transmission electron microscopy (TEM) images demonstrated the existence of a PIP@MIL-100(Fe) core with a diameter of around 50 nm, surrounded by an outer lipid bilayer layer measuring approximately 10 nm in thickness. Furthermore, the researchers evaluated the cytotoxicity indices of the nanoparticles against various breast cancer cell lines, including MCF-7, BT-549, SKBR-3, and MDA. The results demonstrated that the MOFs exhibited between 4 and 17 times higher cytotoxicity (IC50) in all four cell lines compared to free PIP (IC50 = 193.67 ± 0.30 µM). These findings suggest that MM@PIP@MIL-100(Fe) holds potential as an effective treatment for breast cancer. The study's outcomes highlight the potential of utilizing MM-coated MOFs encapsulated with PIP as an innovative approach for breast cancer therapy, offering improved cytotoxicity compared to free PIP alone. Further research and development are warranted to explore the clinical translation and optimize the efficacy and safety of this treatment strategy.
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Affiliation(s)
- Christian Rafael Quijia
- Department of Drugs and Medicines, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Rodovia Araraquara Jau, Km 01-s/n-Campos Ville, Araraquara 14800-903, Brazil
| | - Geovana Navegante
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Rodovia Araraquara Jau, Km 01-s/n-Campos Ville, Araraquara 14800-903, Brazil
| | - Rafael Miguel Sábio
- Department of Drugs and Medicines, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Rodovia Araraquara Jau, Km 01-s/n-Campos Ville, Araraquara 14800-903, Brazil
| | - Valeria Valente
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Rodovia Araraquara Jau, Km 01-s/n-Campos Ville, Araraquara 14800-903, Brazil
| | - Alberto Ocaña
- Department of Medical Oncology, Hospital Clinico San Carlos and Health Research Institute of the Hospital Clinico San Carlos, 28040 Madrid, Spain
| | - Carlos Alonso-Moreno
- Unidad NanoDrug, Facultad de Farmacia, Universidad de Castilla-La Mancha, 02008 Albacete, Spain
| | - Regina Célia Galvão Frem
- Institute of Chemistry, São Paulo State University (UNESP), Prof. Francisco Degni 55, Araraquara 14800-060, Brazil
| | - Marlus Chorilli
- Department of Drugs and Medicines, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Rodovia Araraquara Jau, Km 01-s/n-Campos Ville, Araraquara 14800-903, Brazil
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7
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Ito S, Yagi K, Sugita Y. Allosteric regulation of β-reaction stage I in tryptophan synthase upon the α-ligand binding. J Chem Phys 2023; 158:115101. [PMID: 36948822 DOI: 10.1063/5.0134117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Tryptophan synthase (TRPS) is a bifunctional enzyme consisting of α- and β-subunits that catalyzes the last two steps of L-tryptophan (L-Trp) biosynthesis. The first stage of the reaction at the β-subunit is called β-reaction stage I, which converts the β-ligand from an internal aldimine [E(Ain)] to an α-aminoacrylate [E(A-A)] intermediate. The activity is known to increase 3-10-fold upon the binding of 3-indole-D-glycerol-3'-phosphate (IGP) at the α-subunit. The effect of α-ligand binding on β-reaction stage I at the distal β-active site is not well understood despite the abundant structural information available for TRPS. Here, we investigate the β-reaction stage I by carrying out minimum-energy pathway searches based on a hybrid quantum mechanics/molecular mechanics (QM/MM) model. The free-energy differences along the pathway are also examined using QM/MM umbrella sampling simulations with QM calculations at the B3LYP-D3/aug-cc-pVDZ level of theory. Our simulations suggest that the sidechain orientation of βD305 near the β-ligand likely plays an essential role in the allosteric regulation: a hydrogen bond is formed between βD305 and the β-ligand in the absence of the α-ligand, prohibiting a smooth rotation of the hydroxyl group in the quinonoid intermediate, whereas the dihedral angle rotates smoothly after the hydrogen bond is switched from βD305-β-ligand to βD305-βR141. This switch could occur upon the IGP-binding at the α-subunit, as evidenced by the existing TRPS crystal structures.
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Affiliation(s)
- Shingo Ito
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kiyoshi Yagi
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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8
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Sun MZ, Lyu LS, Zheng QC. How does multiple substrate binding lead to substrate inhibition of CYP2D6 metabolizing dextromethorphan? A theoretical study. Phys Chem Chem Phys 2023; 25:5164-5173. [PMID: 36723118 DOI: 10.1039/d2cp05634h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
CYP2D6 is one of the most important metalloenzymes involved in the biodegradation of many drug molecules in the human body. It has been found that multiple substrate binding can lead to substrate inhibition of CYP2D6 metabolizing dextromethorphan (DM), but the corresponding theoretical mechanism is rarely reported. Therefore, we chose DM as the probe and performed molecular dynamics simulations and quantum mechanical calculations on CYP2D6-DM systems to investigate the mechanism of how the multiple substrate binding leads to the substrate inhibition of CYP2D6 metabolizing substrates. According to our results, three gate residues (Arg221, Val374, and Phe483) for the catalytic pocket are determined. We also found that the multiple substrate binding can lead to substrate inhibition by reducing the stability of CYP2D6 binding DM and increasing the reactive activation energy of the rate-determining step. Our findings would help to understand the substrate inhibition of CYP2D6 metabolizing the DM and enrich the knowledge of the drug-drug interactions for the cytochrome P450 superfamily.
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Affiliation(s)
- Min-Zhang Sun
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
| | - Ling-Shan Lyu
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
| | - Qing-Chuan Zheng
- School of Pharmaceutical Sciences, Jilin University, Changchun, 130023, China. .,Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
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9
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Hanaoka K, Iwaki S, Yagi K, Myochin T, Ikeno T, Ohno H, Sasaki E, Komatsu T, Ueno T, Uchigashima M, Mikuni T, Tainaka K, Tahara S, Takeuchi S, Tahara T, Uchiyama M, Nagano T, Urano Y. General Design Strategy to Precisely Control the Emission of Fluorophores via a Twisted Intramolecular Charge Transfer (TICT) Process. J Am Chem Soc 2022; 144:19778-19790. [PMID: 36191139 DOI: 10.1021/jacs.2c06397] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorogenic probes for bioimaging have become essential tools for life science and medicine, and the key to their development is a precise understanding of the mechanisms available for fluorescence off/on control, such as photoinduced electron transfer (PeT) and Förster resonance energy transfer (FRET). Here we establish a new molecular design strategy to rationally develop activatable fluorescent probes, which exhibit a fluorescence off/on change in response to target biomolecules, by controlling the twisted intramolecular charge transfer (TICT) process. This approach was developed on the basis of a thorough investigation of the fluorescence quenching mechanism of N-phenyl rhodamine dyes (commercially available as the QSY series) by means of time-dependent density functional theory (TD-DFT) calculations and photophysical evaluation of their derivatives. To illustrate and validate this TICT-based design strategy, we employed it to develop practical fluorogenic probes for HaloTag and SNAP-tag. We further show that the TICT-controlled fluorescence off/on mechanism is generalizable by synthesizing a Si-rhodamine-based fluorogenic probe for HaloTag, thus providing a palette of chemical dyes that spans the visible and near-infrared range.
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Affiliation(s)
- Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30 Shibakoen, Minoto-ku, Tokyo105-8512, Japan
| | | | - Kiyoshi Yagi
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama351-0198, Japan
| | | | | | - Hisashi Ohno
- Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30 Shibakoen, Minoto-ku, Tokyo105-8512, Japan
| | - Eita Sasaki
- Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30 Shibakoen, Minoto-ku, Tokyo105-8512, Japan
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10
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Sato K, Sasaki R, Matsuda R, Nakagawa M, Ekimoto T, Yamane T, Ikeguchi M, Tabata KV, Noji H, Kinbara K. Correction to "Supramolecular Mechanosensitive Potassium Channel Formed by Fluorinated Amphiphilic Cyclophane". J Am Chem Soc 2022; 144:13983-13984. [PMID: 35861320 DOI: 10.1021/jacs.2c07339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Suzuki K, Maeda S. Multistructural microiteration combined with QM/MM-ONIOM electrostatic embedding. Phys Chem Chem Phys 2022; 24:16762-16773. [PMID: 35775395 DOI: 10.1039/d2cp02270b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multistructural microiteration (MSM) is a method to take account of contributions of multiple surrounding structures in a geometrical optimization or reaction path calculation using the quantum mechanics/molecular mechanics (QM/MM) ONIOM method. In this study, we combined MSM with the electrostatic embedding (EE) scheme of the QM/MM-ONIOM method by extending its original formulation for mechanical embedding (ME). MSM-EE takes account of the polarization in the QM region induced by point charges assigned to atoms in the multiple surrounding structures, where the point charges are scaled by the weight factor of each surrounding structure determined through MSM. The performance of MSM-EE was compared with that of the other methods, i.e., ONIOM-ME, ONIOM-EE, and MSM-ME, by applying them to three chemical processes: (1) chorismate-to-prephenate transformation in aqueous solution, (2) the same transformation as (1) in an enzyme, and (3) hydroxylation in p-hydroxybenzoate hydroxylase. These numerical tests of MSM-EE yielded barriers and reaction energies close to experimental values with computational costs comparable to those of the other three methods.
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Affiliation(s)
- Kimichi Suzuki
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan. .,Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.,JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Sapporo 060-0810, Japan
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan. .,Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.,JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Sapporo 060-0810, Japan.,Research and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science (NIMS), Tsukuba 305-0044, Japan
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12
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Lorenz-Fonfria VA, Yagi K, Ito S, Kandori H. Retinal Vibrations in Bacteriorhodopsin are Mechanically Harmonic but Electrically Anharmonic: Evidence From Overtone and Combination Bands. Front Mol Biosci 2022; 8:749261. [PMID: 34977154 PMCID: PMC8718751 DOI: 10.3389/fmolb.2021.749261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/18/2021] [Indexed: 11/28/2022] Open
Abstract
Fundamental vibrations of the chromophore in the membrane protein bacteriorhodopsin (BR), a protonated Schiff base retinal, have been studied for decades, both by resonance Raman and by infrared (IR) difference spectroscopy. Such studies started comparing vibrational changes between the initial BR state (all-trans retinal) and the K intermediate (13-cis retinal), being later extended to the rest of intermediates. They contributed to our understanding of the proton-pumping mechanism of BR by exploiting the sensitivity of fundamental vibrational transitions of the retinal to its conformation. Here, we report on new bands in the 2,500 to 1,800 cm−1 region of the K-BR difference FT-IR spectrum. We show that the bands between 2,500 and 2,300 cm−1 originate from overtone and combination transitions from C-C stretches of the retinal. We assigned bands below 2,300 cm−1 to the combination of retinal C-C stretches with methyl rocks and with hydrogen-out-of-plane vibrations. Remarkably, experimental C-C overtone bands appeared at roughly twice the wavenumber of their fundamentals, with anharmonic mechanical constants ≤3.5 cm−1, and in some cases of ∼1 cm−1. Comparison of combination and fundamental bands indicates that most of the mechanical coupling constants are also very small. Despite the mechanical quasi-harmonicity of the C-C stretches, the area of their overtone bands was only ∼50 to ∼100 times smaller than of their fundamental bands. We concluded that electrical anharmonicity, the second mechanism giving intensity to overtone bands, must be particularly high for the retinal C-C stretches. We corroborated the assignments of negative bands in the K-BR difference FT-IR spectrum by ab initio anharmonic vibrational calculations of all-trans retinal in BR using a quantum-mechanics/molecular mechanics approach, reproducing reasonably well the small experimental anharmonic and coupling mechanical constants. Yet, and in spite accounting for both mechanical and electrical anharmonicities, the intensity of overtone C-C transitions was underestimated by a factor of 4–20, indicating room for improvement in state-of-the-art anharmonic vibrational calculations. The relatively intense overtone and combination bands of the retinal might open the possibility to detect retinal conformational changes too subtle to significantly affect fundamental transitions but leaving a footprint in overtone and combination transitions.
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Affiliation(s)
| | - Kiyoshi Yagi
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Shota Ito
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan
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13
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Yagi K, Re S, Mori T, Sugita Y. Weight average approaches for predicting dynamical properties of biomolecules. Curr Opin Struct Biol 2021; 72:88-94. [PMID: 34592697 DOI: 10.1016/j.sbi.2021.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 11/16/2022]
Abstract
Recent advances in atomistic molecular dynamics (MD) simulations of biomolecules allow us to explore their conformational spaces widely, observing large-scale conformational fluctuations or transitions between distinct structures. To reproduce or refine experimental data using MD simulations, structure ensembles, which are characterized by multiple structures and their statistical weights on the rugged free-energy landscapes, are often used. Here, we summarize weight average approaches for various experimental measurements. Weight average approaches are now applied to hybrid quantum mechanics/molecular mechanics MD simulations to predict fast vibrational motions in a protein with a high accuracy for better understanding of molecular functions from atomic structures.
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Affiliation(s)
- Kiyoshi Yagi
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Suyong Re
- RIKEN Center for Biosystems Dynamics Research, 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health, and Nutrition 7-6-8, Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
| | - Takaharu Mori
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuji Sugita
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; RIKEN Center for Biosystems Dynamics Research, 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
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14
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Zanetti-Polzi L, Amadei A, Daidone I. Segregation on the nanoscale coupled to liquid water polyamorphism in supercooled aqueous ionic-liquid solution. J Chem Phys 2021; 155:104502. [PMID: 34525825 DOI: 10.1063/5.0061659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The most intriguing hypothesis explaining many water anomalies is a metastable liquid-liquid phase transition (LLPT) at high pressure and low temperatures, experimentally hidden by homogeneous nucleation. Recent infrared spectroscopic experiments showed that upon addition of hydrazinium trifluoroacetate to water, the supercooled ionic solution undergoes a sharp, reversible LLPT at ambient pressure, possible offspring of that in pure water. Here, we calculate the temperature-dependent signature of the OH-stretching band, reporting on the low/high density phase of water, in neat water and in the same experimentally investigated ionic solution. The comparison between the infrared signature of the pure liquid and that of the ionic solution can be achieved only computationally, providing insight into the nature of the experimentally observed phase transition and allowing us to investigate the effects of ionic compounds on the high to low density supercooled liquid water transition. We show that the experimentally observed crossover behavior in the ionic solution can be reproduced only if the phase transition between the low- and high-density liquid states of water is coupled to a mixing-unmixing transition between the water component and the ions: at low temperatures, water and ions are separated and the water component is a low density liquid. At high temperatures, water and ions get mixed and the water component is a high-density liquid. The separation at low temperatures into ion-rich and ion-poor regions allows unveiling the polyamorphic nature of liquid water, leading to a crossover behavior resembling that observed in supercooled neat water under high pressure.
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Affiliation(s)
- Laura Zanetti-Polzi
- Center S3, CNR-Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy
| | - Andrea Amadei
- Department of Chemical and Technological Sciences, University of Rome "Tor Vergata", Via della Ricerca Scientifica, I-00185 Rome, Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), 67010 L'Aquila, Italy
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15
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Ozaki Y, Beć KB, Morisawa Y, Yamamoto S, Tanabe I, Huck CW, Hofer TS. Advances, challenges and perspectives of quantum chemical approaches in molecular spectroscopy of the condensed phase. Chem Soc Rev 2021; 50:10917-10954. [PMID: 34382961 DOI: 10.1039/d0cs01602k] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The purpose of this review is to demonstrate advances, challenges and perspectives of quantum chemical approaches in molecular spectroscopy of the condensed phase. Molecular spectroscopy, particularly vibrational spectroscopy and electronic spectroscopy, has been used extensively for a wide range of areas of chemical sciences and materials science as well as nano- and biosciences because it provides valuable information about structure, functions, and reactions of molecules. In the meantime, quantum chemical approaches play crucial roles in the spectral analysis. They also yield important knowledge about molecular and electronic structures as well as electronic transitions. The combination of spectroscopic approaches and quantum chemical calculations is a powerful tool for science, in general. Thus, our article, which treats various spectroscopy and quantum chemical approaches, should have strong implications in the wider scientific community. This review covers a wide area of molecular spectroscopy from far-ultraviolet (FUV, 120-200 nm) to far-infrared (FIR, 400-10 cm-1)/terahertz and Raman spectroscopy. As quantum chemical approaches, we introduce several anharmonic approaches such as vibrational self-consistent field (VSCF) and the combination of periodic harmonic calculations with anharmonic corrections based on finite models, grid-based techniques like the Numerov approach, the Cartesian coordinate tensor transfer (CCT) method, Symmetry-Adapted Cluster Configuration-Interaction (SAC-CI), and the ZINDO (Semi-empirical calculations at Zerner's Intermediate Neglect of Differential Overlap). One can use anharmonic approaches and grid-based approaches for both infrared (IR) and near-infrared (NIR) spectroscopy, while CCT methods are employed for Raman, Raman optical activity (ROA), FIR/terahertz and low-frequency Raman spectroscopy. Therefore, this review overviews cross relations between molecular spectroscopy and quantum chemical approaches, and provides various kinds of close-reality advanced spectral simulation for condensed phases.
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Affiliation(s)
- Yukihiro Ozaki
- School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan. and Toyota Physical and Chemical Research Institute, Yokomichi, Nagakute, Aichi 480-1192, Japan
| | - Krzysztof B Beć
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Yusuke Morisawa
- Department of Chemistry, School of Science and Engineering, Kindai University, Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Shigeki Yamamoto
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ichiro Tanabe
- Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Christian W Huck
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Thomas S Hofer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A6020 Innsbruck, Austria
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Yagi K, Sugita Y. Anharmonic Vibrational Calculations Based on Group-Localized Coordinates: Applications to Internal Water Molecules in Bacteriorhodopsin. J Chem Theory Comput 2021; 17:5007-5020. [PMID: 34296615 PMCID: PMC10986902 DOI: 10.1021/acs.jctc.1c00060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
An efficient anharmonic vibrational method is developed exploiting the locality of molecular vibration. Vibrational coordinates localized to a group of atoms are employed to divide the potential energy surface (PES) of a system into intra- and inter-group contributions. Then, the vibrational Schrödinger equation is solved based on a PES, in which the inter-group coupling is truncated at the harmonic level while accounting for the intra-group anharmonicity. The method is applied to a pentagonal hydrogen bond network (HBN) composed of internal water molecules and charged residues in a membrane protein, bacteriorhodopsin. The PES is calculated by the quantum mechanics/molecular mechanics (QM/MM) calculation at the level of B3LYP-D3/aug-cc-pVDZ. The infrared (IR) spectrum is computed using a set of coordinates localized to each water molecule and amino acid residue by second-order vibrational quasi-degenerate perturbation theory (VQDPT2). Benchmark calculations show that the proposed method yields the N-D/O-D stretching frequencies with an error of 7 cm-1 at the cost reduced by more than five times. In contrast, the harmonic approximation results in a severe error of 150 cm-1. Furthermore, the size of QM regions is carefully assessed to find that the QM regions should include not only the pentagonal HBN itself but also its HB partners. VQDPT2 calculations starting from transient structures obtained by molecular dynamics simulations have shown that the structural sampling has a significant impact on the calculated IR spectrum. The incorporation of anharmonicity, sufficiently large QM regions, and structural samplings are of essential importance to reproduce the experimental IR spectrum. The computational spectrum paves the way for decoding the IR signal of strong HBNs and helps elucidate their functional roles in biomolecules.
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Affiliation(s)
- Kiyoshi Yagi
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuji Sugita
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, 1-6-5 Minatojima-Minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
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17
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Pinto SMV, Tasinato N, Barone V, Zanetti-Polzi L, Daidone I. A computational insight into the relationship between side chain IR line shapes and local environment in fibril-like structures. J Chem Phys 2021; 154:084105. [PMID: 33639764 DOI: 10.1063/5.0038913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Infrared spectroscopy is a widely used technique to characterize protein structures and protein mediated processes. While the amide I band provides information on proteins' secondary structure, amino acid side chains are used as infrared probes for the investigation of protein reactions and local properties. In this paper, we use a hybrid quantum mechanical/classical molecular dynamical approach based on the perturbed matrix method to compute the infrared band due to the C=O stretching mode of amide-containing side chains. We calculate, at first, the infrared band of zwitterionic glutamine in water and obtain results in very good agreement with the experimental data. Then, we compute the signal arising from glutamine side chains in a microcrystal of the yeast prion Sup35-derived peptide, GNNQQNY, with a fibrillar structure. The infrared bands obtained by selective isotopic labeling of the two glutamine residues, Q4 and Q5, of each peptide were experimentally used to investigate the local hydration in the fibrillar microcrystal. The experimental spectra of the two glutamine residues, which experience different hydration environments, feature different spectral signals that are well reproduced by the corresponding calculated spectra. In addition, the analysis of the simulated spectra clarifies the molecular origin of the experimentally observed spectroscopic differences that arise from the different local electric field experienced by the two glutamine residues, which is, in turn, determined by a different hydrogen bonding pattern.
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Affiliation(s)
- Sandra M V Pinto
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | | | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, I-67100 L'Aquila, Italy
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18
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Beć KB, Grabska J, Huck CW. Current and future research directions in computer-aided near-infrared spectroscopy: A perspective. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 254:119625. [PMID: 33706116 DOI: 10.1016/j.saa.2021.119625] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
The present review aims to draw a perspective on the vibrational spectroscopy combined with the tools of computational chemistry. This includes an overview of the accomplishments made so far, the assessment of the present development trends and the prospects for continuing these advances. State-of-the-art methods, current challenges and the expected future advances are evaluated from the point-of-view of the practical application in vibrational spectroscopy. A special attention is given to near-infrared (NIR) spectroscopy, which occupies a distinct position among the techniques of vibrational spectroscopy. As the result of intrinsically complex spectra, reliance on the anharmonicity as well as keen interest given to complex materials, NIR spectroscopy may particularly benefit from computational chemistry. The present key limitations hindering development of NIR spectroscopy are identified; these constitute primarily the limit in the treatable system size and the inability to effectively include chemical matrix effects. Given the expanding role of NIR spectroscopy in science and industry, lifting these limitations would directly enhance the general potential of this technique.
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Affiliation(s)
- Krzysztof B Beć
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, CCB-Center for Chemistry and Biomedicine, Innrain 80/82, 6020 Innsbruck, Austria
| | - Justyna Grabska
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, CCB-Center for Chemistry and Biomedicine, Innrain 80/82, 6020 Innsbruck, Austria.
| | - Christian W Huck
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, CCB-Center for Chemistry and Biomedicine, Innrain 80/82, 6020 Innsbruck, Austria
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19
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Yagi K, Ito S, Sugita Y. Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations. J Phys Chem B 2021; 125:4701-4713. [PMID: 33914537 PMCID: PMC10986901 DOI: 10.1021/acs.jpcb.1c01862] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding molecular mechanisms of enzymatic reactions is of vital importance in biochemistry and biophysics. Here, we introduce new functions of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations in the GENESIS program to compute the minimum-energy pathways (MEPs) and free-energy profiles of enzymatic reactions. For this purpose, an interface in GENESIS is developed to utilize a highly parallel electronic structure program, QSimulate-QM (https://qsimulate.com), calling it as a shared library from GENESIS. Second, algorithms to search the MEP are implemented, combining the string method (E et al. J. Chem. Phys. 2007, 126, 164103) with the energy minimization of the buffer MM region. The method implemented in GENESIS is applied to an enzyme, triosephosphate isomerase, which converts dihyroxyacetone phosphate to glyceraldehyde 3-phosphate in four proton-transfer processes. QM/MM-molecular dynamics simulations show performances of greater than 1 ns/day with the density functional tight binding (DFTB), and 10-30 ps/day with the hybrid density functional theory, B3LYP-D3. These performances allow us to compute not only MEP but also the potential of mean force (PMF) of the enzymatic reactions using the QM/MM calculations. The barrier height obtained as 13 kcal mol-1 with B3LYP-D3 in the QM/MM calculation is in agreement with the experimental results. The impact of conformational sampling in PMF calculations and the level of electronic structure calculations (DFTB vs B3LYP-D3) suggests reliable computational protocols for enzymatic reactions without high computational costs.
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Affiliation(s)
- Kiyoshi Yagi
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shingo Ito
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuji Sugita
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, 7-1-26 minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, 1-6-5 minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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20
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Supunyabut C, Paiboonvorachat N, Vchirawongkwin V. Non-Hessian method for normal coordinate calculations: Application to evaluate vibrational spectra. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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21
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Artiukhin DG, Klinting EL, König C, Christiansen O. Adaptive density-guided approach to double incremental potential energy surface construction. J Chem Phys 2020; 152:194105. [PMID: 33687258 DOI: 10.1063/5.0004686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We present a combination of the recently developed double incremental expansion of potential energy surfaces with the well-established adaptive density-guided approach to grid construction. This unique methodology is based on the use of an incremental expansion for potential energy surfaces, known as n-mode expansion; an incremental many-body representation of the electronic energy; and an efficient vibrational density-guided approach to automated determination of grid dimensions and granularity. The reliability of the method is validated calculating potential energy surfaces and obtaining fundamental excitation energies for three moderate-size chain-like molecular systems. The use of our methodology leads to considerable computational savings for potential energy surface construction compared to standard approaches while maintaining a high level of accuracy in the resulting potential energy surfaces. Additional investigations indicate that our method can be applied to covalently bound and strongly interacting molecular systems, even though these cases are known to be very unfavorable for fragmentation schemes. We therefore conclude that the presented methodology is a robust and flexible approach to potential energy surface construction, which introduces considerable computational savings without compromising the accuracy of vibrational spectra calculations.
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Affiliation(s)
- Denis G Artiukhin
- Department of Chemistry, Aarhus Universitet, DK-8000 Aarhus, Denmark
| | | | - Carolin König
- Institute of Physical Chemistry, Christian-Albrechts-University Kiel, Max-Eyth-Straße 1, D-24118 Kiel, Germany
| | - Ove Christiansen
- Department of Chemistry, Aarhus Universitet, DK-8000 Aarhus, Denmark
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22
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Kraka E, Zou W, Tao Y. Decoding chemical information from vibrational spectroscopy data: Local vibrational mode theory. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1480] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Elfi Kraka
- Department of Chemistry Southern Methodist University Dallas Texas USA
| | - Wenli Zou
- Institute of Modern Physics Northwest University and Shaanxi Key Laboratory for Theoretical Physics Frontiers, Xi'an Shaanxi PR China
| | - Yunwen Tao
- Department of Chemistry Southern Methodist University Dallas Texas USA
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23
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24
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Lam J, Abdul-Al S, Allouche AR. Combining Quantum Mechanics and Machine-Learning Calculations for Anharmonic Corrections to Vibrational Frequencies. J Chem Theory Comput 2020; 16:1681-1689. [DOI: 10.1021/acs.jctc.9b00964] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Julien Lam
- Center for Nonlinear Phenomena and Complex Systems, Code Postal 231, Université Libre de Bruxelles, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Saleh Abdul-Al
- Lebanese International University, Bekaa, Lebanon and International University of Beirut, Beirut, Lebanon
| | - Abdul-Rahman Allouche
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne Cedex, France
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25
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Vieira Pinto SM, Tasinato N, Barone V, Amadei A, Zanetti-Polzi L, Daidone I. Modeling amino-acid side chain infrared spectra: the case of carboxylic residues. Phys Chem Chem Phys 2020; 22:3008-3016. [DOI: 10.1039/c9cp04774c] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Infrared (IR) spectroscopy is commonly utilized for the investigation of protein structures and protein-mediated processes.
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Affiliation(s)
- Sandra Mónica Vieira Pinto
- Scuola Normale Superiore
- I-56126 Pisa
- Italy
- Department of Physical and Chemical Sciences
- University of L'Aquila
| | | | | | - Andrea Amadei
- Department of Chemical and Technological Sciences
- University of Rome “Tor Vergata
- I-00185 Rome
- Italy
| | - Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences
- University of L'Aquila
- I-67010 L'Aquila
- Italy
- CNR Institute of Nanoscience
| | - Isabella Daidone
- Department of Physical and Chemical Sciences
- University of L'Aquila
- I-67010 L'Aquila
- Italy
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26
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Paneth A, Paneth P. Quantum approach to the mechanism of monothiopyrophosphate isomerization. J Mol Model 2019; 25:286. [DOI: 10.1007/s00894-019-4152-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/08/2019] [Indexed: 01/28/2023]
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27
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Giovannini T, Grazioli L, Ambrosetti M, Cappelli C. Calculation of IR Spectra with a Fully Polarizable QM/MM Approach Based on Fluctuating Charges and Fluctuating Dipoles. J Chem Theory Comput 2019; 15:5495-5507. [DOI: 10.1021/acs.jctc.9b00574] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tommaso Giovannini
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Laura Grazioli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
| | | | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
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28
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Spectra-Structure Correlations in Isotopomers of Ethanol (CX 3CX 2OX; X = H, D): Combined Near-Infrared and Anharmonic Computational Study. Molecules 2019; 24:molecules24112189. [PMID: 31212669 PMCID: PMC6600318 DOI: 10.3390/molecules24112189] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/03/2019] [Accepted: 06/08/2019] [Indexed: 11/21/2022] Open
Abstract
The effect of isotopic substitution on near-infrared (NIR) spectra has not been studied in detail. With an exception of few major bands, it is difficult to follow the spectral changes due to complexity of NIR spectra. Recent progress in anharmonic quantum mechanical calculations allows for accurate reconstruction of NIR spectra. Taking this opportunity, we carried out a systematic study of NIR spectra of six isotopomers of ethanol (CX3CX2OX; X = H, D). Besides, we calculated the theoretical spectra of two other isotopomers (CH3CD2OD and CD3CH2OD) for which the experimental spectra are not available. The anharmonic calculations were based on generalized vibrational second-order perturbation theory (GVPT2) at DFT and MP2 levels with several basis sets. We compared the accuracy and efficiency of various computational methods. It appears that the best results were obtained with B2PLYP-GD3BJ/def2-TZVP//CPCM approach. Our simulations included the first and second overtones, as well as binary and ternary combinations bands. This way, we reliably reproduced even minor bands in the spectra of diluted samples (0.1 M in CCl4). On this basis, the effect of isotopic substitution on NIR spectra of ethanol was accurately reproduced and comprehensively explained.
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