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Yuan K, Zhou S, Li N, Li T, Ding B, Guo D, Ma Y. Fault-tolerant quantum chemical calculations with improved machine-learning models. J Comput Chem 2024. [PMID: 39072777 DOI: 10.1002/jcc.27459] [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: 11/30/2023] [Revised: 05/30/2024] [Accepted: 06/18/2024] [Indexed: 07/30/2024]
Abstract
Easy and effective usage of computational resources is crucial for scientific calculations. Following our recent work of machine-learning (ML) assisted scheduling optimization [J. Comput. Chem. 2023, 44, 1174], we further propose (1) the improved ML models for the better predictions of computational loads, and as such, more elaborate load-balancing calculations can be expected; (2) the idea of coded computation, that is, the integration of gradient coding, in order to introduce fault tolerance during the distributed calculations; and (3) their applications together with re-normalized exciton model with time-dependent density functional theory (REM-TDDFT) for calculating the excited states. Illustrated benchmark calculations include P38 protein, and solvent model with one or several excitable centers. The results show that the improved ML-assisted coded calculations can further improve the load-balancing and cluster utilization, owing primarily profit in fault tolerance that aims at the automated quantum chemical calculations for both ground and excited states.
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Affiliation(s)
- Kai Yuan
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Shuai Zhou
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
- School of Computer Science and Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Ning Li
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, China
| | - Tianyan Li
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Bowen Ding
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Danhuai Guo
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yingjin Ma
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
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2
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Masoumifeshani E, Korona T. Intermolecular interaction energies with AROFRAG-A systematic approach for fragmentation of aromatic molecules. J Comput Chem 2024. [PMID: 38946399 DOI: 10.1002/jcc.27429] [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: 12/30/2023] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 07/02/2024]
Abstract
Intermolecular interactions with polycyclic aromatic hydrocarbons (PAHs) represent an important area of physisorption studies. These investigations are often hampered by a size of interacting PAHs, which makes the calculation prohibitively expensive. Therefore, methods designed to deal with large molecules could be helpful to reduce the computational costs of such studies. Recently we have introduced a new systematic approach for the molecular fragmentation of PAHs, denoted as AROFRAG, which decomposes a large PAH molecule into a set of predefined small PAHs with a benzene ring being the smallest unbreakable unit, and which in conjunction with the Molecules-in-Molecules (MIM) approach provides an accurate description of total molecular energies. In this contribution we propose an extension of the AROFRAG, which provides a description of intermolecular interactions for complexes composed of PAH molecules. The examination of interaction energy partitioning for various test cases shows that the AROFRAG3 model connected with the MIM approach accurately reproduces all important components of the interaction energy. An additional important finding in our study is that the computationally expensive long-range electron-correlation part of the interaction energy, that is, the dispersion component, is well described at lower AROFRAG levels even without MIM, which makes the latter models interesting alternatives to existing methods for an accurate description of the electron-correlated part of the interaction energy.
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Affiliation(s)
| | - Tatiana Korona
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
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3
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Sandhu G, Agrawal P, Bose S, Thelma BK. Building polarization into protein-inhibitor binding dynamics in rational drug design for rheumatoid arthritis. J Biomol Struct Dyn 2024; 42:5912-5930. [PMID: 37378542 DOI: 10.1080/07391102.2023.2229449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/20/2023] [Indexed: 06/29/2023]
Abstract
Standard force field-based simulations to accomplish structure-based evaluations of lead molecules is a powerful tool. Combining protein fragmentation into tractable sub-systems with continuum solvation method is envisaged to enable quantum mechanics-based electronic structure calculations of macromolecules in their realistic environment. This along with incorporation of many-body polarization effect in molecular dynamics simulations may augment an accurate description of electrostatics of protein-inhibitor systems for effective drug design. Rheumatoid arthritis (RA) is a complex autoimmune disorder plagued by the ceiling effect of current targeted therapies, encouraging identification of new druggable targets and corresponding drug design to tackle the refractory form of disease. In this study, polarization-inclusive force field approach has been used to model protein solvation and ligand binding for 'Mitogen-activated protein kinase' (MAP3K8), a regulatory node of notable pharmacological relevance in RA synovial biology. For MAP3K8 inhibitors belonging to different scaffold series, the calculations illustrated differential electrostatic contribution to their relative binding affinities and successfully explained examples from available structure-activity relationship studies. Results from this study exemplified i) the advantage of this approach in reliably ranking inhibitors having close nanomolar range activities for the same target; and ii) its prospective application in lead molecule identification aiding drug discovery efforts in RA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gurvisha Sandhu
- Department of Genetics, University of Delhi South Campus, New Delhi, Delhi, India
| | - Praveen Agrawal
- LeadInvent Technologies Private Limited, Biotech Centre, University of Delhi South Campus, New Delhi, Delhi, India
| | - Surojit Bose
- LeadInvent Technologies Private Limited, Biotech Centre, University of Delhi South Campus, New Delhi, Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, Delhi, India
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4
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Liu J, Ma H, Shang H, Li Z, Yang J. Quantum-centric high performance computing for quantum chemistry. Phys Chem Chem Phys 2024; 26:15831-15843. [PMID: 38787657 DOI: 10.1039/d4cp00436a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
High performance computing (HPC) is renowned for its capacity to tackle complex problems. Meanwhile, quantum computing (QC) provides a potential way to accurately and efficiently solve quantum chemistry problems. The emerging field of quantum-centric high performance computing (QCHPC), which merges these two powerful technologies, is anticipated to enhance computational capabilities for solving challenging problems in quantum chemistry. The implementation of QCHPC for quantum chemistry requires interdisciplinary research and collaboration across multiple fields, including quantum chemistry, quantum physics, computer science and so on. This perspective provides an introduction to the quantum algorithms that are suitable for deployment in QCHPC, focusing on conceptual insights rather than technical details. Parallel strategies to implement these algorithms on quantum-centric supercomputers are discussed. We also summarize high performance quantum emulating simulators, which are considered a viable tool to explore QCHPC. We conclude with challenges and outlooks in this field.
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Affiliation(s)
- Jie Liu
- Hefei National Laboratory, University of Science and Technology of China, Hefei 230088, China.
| | - Huan Ma
- Hefei National Laboratory, University of Science and Technology of China, Hefei 230088, China.
| | - Honghui Shang
- Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Zhenyu Li
- Hefei National Laboratory, University of Science and Technology of China, Hefei 230088, China.
- Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Jinlong Yang
- Hefei National Laboratory, University of Science and Technology of China, Hefei 230088, China.
- Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China.
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5
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de Carvalho Matias EG, Bezerra KS, Costa AHL, Clemente Junior WS, Oliveira JIN, Ribeiro Junior LA, Galvão DS, Fulco UL. Quantum biochemical analysis of the TtgR regulator and effectors. Sci Rep 2024; 14:8519. [PMID: 38609407 PMCID: PMC11015042 DOI: 10.1038/s41598-024-58441-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
The recent expansion of multidrug-resistant (MDR) pathogens poses significant challenges in treating healthcare-associated infections. Although antibacterial resistance occurs by numerous mechanisms, active efflux of the drugs is a critical concern. A single species of efflux pump can produce a simultaneous resistance to several drugs. One of the best-studied efflux pumps is the TtgABC: a tripartite resistance-nodulation-division (RND) efflux pump implicated in the intrinsic antibiotic resistance in Pseudomonas putida DOT-T1E. The expression of the TtgABC gene is down-regulated by the HTH-type transcriptional repressor TtgR. In this context, by employing quantum chemistry methods based on the Density Functional Theory (DFT) within the Molecular Fragmentation with Conjugate Caps (MFCC) approach, we investigate the coupling profiles of the transcriptional regulator TtgR in complex with quercetin (QUE), a natural polyphenolic flavonoid, tetracycline (TAC), and chloramphenicol (CLM), two broad-spectrum antimicrobial agents. Our quantum biochemical computational results show the: [i] convergence radius, [ii] total binding energy, [iii] relevance (energetically) of the ligands regions, and [iv] most relevant amino acids residues of the TtgR-QUE/TAC/CLM complexes, pointing out distinctions and similarities among them. These findings improve the understanding of the binding mechanism of effectors and facilitate the development of new chemicals targeting TtgR, helping in the battle against the rise of resistance to antimicrobial drugs. These advances are crucial in the ongoing fight against rising antimicrobial drug resistance, providing hope for a future where healthcare-associated infections can be more beneficially treated.
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Affiliation(s)
- E G de Carvalho Matias
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - K S Bezerra
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - A H Lima Costa
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - W S Clemente Junior
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - J I N Oliveira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - L A Ribeiro Junior
- Institute of Physics, University of Brasília, Brasília, 70919-970, Brazil.
| | - D S Galvão
- Applied Physics Department, University of Campinas, Campinas, São Paulo, Brazil
| | - U L Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal, RN, 59072-970, Brazil
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6
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Masoumifeshani E, Korona T. AROFRAG─A Systematic Approach for Fragmentation of Aromatic Molecules. J Chem Theory Comput 2024. [PMID: 38252847 DOI: 10.1021/acs.jctc.3c00875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
We present a new systematic fragmentation scheme of polycyclic aromatic hydrocarbons (PAHs), including fullerenes and nanotubes, based on an idea to treat a sextet ring as a single unbreakable unit so that the basic unit of aromaticity remains preserved upon fragmentation. In the approach, denoted as AROFRAG (from aromatic fragmentation), a set of predefined elementary subsystems, such as naphthalene and biphenyl in the first model and larger PAHs in the second and third models, is generated with appropriate weights with the aim of reproducing the structure of the original molecule. The energies of the molecules are approximated as weighted sums of the energies of these subsystems. For symmetric cases, e.g., fullerenes, the point-group symmetry is preserved during the decomposition. The AROFRAG is used in conjunction with the molecule-in-molecule (MIM) technique to obtain an accurate description of the electronic energies. The new approach has been applied for selected graphene structures and fullerene doped with boron and nitrogen atoms, for which isomerization energies were calculated, as well as for several nanotubes and regular fullerene molecules. The combination of the third AROFRAG model and the MIM approach leads to the reproduction of electronic energies with a few milli-hartree accuracy at a fraction of the computational cost of the original method.
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Affiliation(s)
- Emran Masoumifeshani
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
| | - Tatiana Korona
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
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Lima Costa AH, Bezerra KS, de Lima Neto JX, Oliveira JIN, Galvão DS, Fulco UL. Deciphering Interactions between Potential Inhibitors and the Plasmodium falciparum DHODH Enzyme: A Computational Perspective. J Phys Chem B 2023; 127:9461-9475. [PMID: 37897437 DOI: 10.1021/acs.jpcb.3c05738] [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: 10/30/2023]
Abstract
Malaria is a parasitic disease that, in its most severe form, can even lead to death. Insect-resistant vectors, insufficiently effective vaccines, and drugs that cannot stop parasitic infestations are making the fight against the disease increasingly difficult. It is known that the enzyme dihydroorotate dehydrogenase (DHODH) is of paramount importance for the synthesis of pyrimidine from the Plasmodium precursor, that is, for its growth and reproduction. Therefore, its blockade can lead to disruption of the parasite's life cycle in the vertebrate host. In this scenario, PfDHODH inhibitors have been considered candidates for a new therapy to stop the parasitic energy source. Given what is known, in this work, we applied molecular fractionation with conjugated caps (MFCC) in the framework of the quantum formalism of density functional theory (DFT) to evaluate the energies of the interactions between the enzyme and the different triazolopyrimidines (DSM483, DMS557, and DSM1), including a complex carrying the mutation C276F. From these results, it was possible to identify the main features of each system, focusing on the wild-type and mutant PfDHODH and examining the major amino acid residues that are part of the four complexes. Our analysis provides new information that can be used to develop new drugs that could prove to be more effective alternatives to present antimalarial drugs.
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Affiliation(s)
- Aranthya Hevelly Lima Costa
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - Katyanna Sales Bezerra
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
- Applied Physics Department, University of Campinas, 130838-59 Campinas, São Paulo, Brazil
| | - José Xavier de Lima Neto
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - Jonas Ivan Nobre Oliveira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
| | - Douglas Soares Galvão
- Applied Physics Department, University of Campinas, 130838-59 Campinas, São Paulo, Brazil
| | - Umberto Laino Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN, Brazil
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8
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Tripathy V, Raghavachari K. Fragment-based models for dissociation of strong acids in water: Electrostatic embedding minimizes the dependence on the fragmentation schemes. J Chem Phys 2023; 159:124106. [PMID: 38127382 DOI: 10.1063/5.0164089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/28/2023] [Indexed: 12/23/2023] Open
Abstract
Fragmentation methods such as MIM (Molecules-in-Molecules) provide a route to accurately model large systems and have been successful in predicting their structures, energies, and spectroscopic properties. However, their use is often limited to systems at equilibrium due to the inherent complications in the choice of fragments in systems away from equilibrium. Furthermore, the presence of charges resulting from any heterolytic bond breaking may increase the fragmentation error. We have previously suggested EE-MIM (Electrostatically Embedded Molecules-In-Molecules) as a method to mitigate the errors resulting from the missing long-range interactions in molecular clusters in equilibrium. Here, we show that the same method can be applied to improve the performance of MIM to solve the longstanding problem of dependency of the fragmentation energy error on the choice of the fragmentation scheme. We chose four widely used acid dissociation reactions (HCl, HClO4, HNO3, and H2SO4) as test cases due to their importance in chemical processes and complex reaction potential energy surfaces. Electrostatic embedding improves the performance at both one and two-layer MIM as shown by lower EE-MIM1 and EE-MIM2 errors. The EE-MIM errors are also demonstrated to be less dependent on the choice of the fragmentation scheme by analyzing the variation in fragmentation energy at the points with more than one possible fragmentation scheme (points where the fragmentation scheme changes). EE-MIM2 with M06-2X as the low-level resulted in a variation of less than 1 kcal/mol for all the cases and 1 kJ/mol for all but three cases, rendering our method fragmentation scheme-independent for acid dissociation processes.
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Affiliation(s)
- Vikrant Tripathy
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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9
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Sahu N, Khire SS, Gadre SR. Combining fragmentation method and high-performance computing: Geometry optimization and vibrational spectra of proteins. J Chem Phys 2023; 159:044309. [PMID: 37522406 DOI: 10.1063/5.0149572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023] Open
Abstract
Exploring the structures and spectral features of proteins with advanced quantum chemical methods is an uphill task. In this work, a fragment-based molecular tailoring approach (MTA) is appraised for the CAM-B3LYP/aug-cc-pVDZ-level geometry optimization and vibrational infrared (IR) spectra calculation of ten real proteins containing up to 407 atoms and 6617 basis functions. The use of MTA and the inherently parallel nature of the fragment calculations enables a rapid and accurate calculation of the IR spectrum. The applicability of MTA to optimize the protein geometry and evaluate its IR spectrum employing a polarizable continuum model with water as a solvent is also showcased. The typical errors in the total energy and IR frequencies computed by MTA vis-à-vis their full calculation (FC) counterparts for the studied protein are 5-10 millihartrees and 5 cm-1, respectively. Moreover, due to the independent execution of the fragments, large-scale parallelization can also be achieved. With increasing size and level of theory, MTA shows an appreciable advantage in computer time as well as memory and disk space requirement over the corresponding FCs. The present study suggests that the geometry optimization and IR computations on the biomolecules containing ∼1000 atoms and/or ∼15 000 basis functions using MTA and HPC facility can be clearly envisioned in the near future.
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Affiliation(s)
- Nityananda Sahu
- Theoretische Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Subodh S Khire
- RIKEN Center for Computational Science, Kobe 650-0047, Japan
| | - Shridhar R Gadre
- Departments of Scientific Computing, Modelling & Simulation and Chemistry, Savitribai Phule Pune University, Pune 411007, India
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Ma Y, Li Z, Chen X, Ding B, Li N, Lu T, Zhang B, Suo B, Jin Z. Machine-learning assisted scheduling optimization and its application in quantum chemical calculations. J Comput Chem 2023; 44:1174-1188. [PMID: 36648254 DOI: 10.1002/jcc.27075] [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: 09/29/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 01/18/2023]
Abstract
Easy and effective usage of computational resources is crucial for scientific calculations, both from the perspectives of timeliness and economic efficiency. This work proposes a bi-level optimization framework to optimize the computational sequences. Machine-learning (ML) assisted static load-balancing, and different dynamic load-balancing algorithms can be integrated. Consequently, the computational and scheduling engine of the ParaEngine is developed to invoke optimized quantum chemical (QC) calculations. Illustrated benchmark calculations include high-throughput drug suit, solvent model, P38 protein, and SARS-CoV-2 systems. The results show that the usage rate of given computational resources for high throughput and large-scale fragmentation QC calculations can primarily profit, and faster accomplishing computational tasks can be expected when employing high-performance computing (HPC) clusters.
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Affiliation(s)
- Yingjin Ma
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - ZhiYing Li
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Xin Chen
- ShenZhen Bay Laboratory, Shenzhen, China
| | - Bowen Ding
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Ning Li
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
- College of Chemistry and Materials Engineering, Wenzhou University, Wen Zhou, China
| | - Teng Lu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Baohua Zhang
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - BingBing Suo
- Department of Physics, Northwest University, Xi'an, China
| | - Zhong Jin
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
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11
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Sun Z, He Q, Gong Z, Kalhor P, Huai Z, Liu Z. A General Picture of Cucurbit[8]uril Host–Guest Binding: Recalibrating Bonded Interactions. Molecules 2023; 28:molecules28073124. [PMID: 37049887 PMCID: PMC10095826 DOI: 10.3390/molecules28073124] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/15/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Atomic-level understanding of the dynamic feature of host–guest interactions remains a central challenge in supramolecular chemistry. The remarkable guest binding behavior of the Cucurbiturils family of supramolecular containers makes them promising drug carriers. Among Cucurbit[n]urils, Cucurbit[8]uril (CB8) has an intermediate portal size and cavity volume. It can exploit almost all host–guest recognition motifs formed by this host family. In our previous work, an extensive computational investigation of the binding of seven commonly abused and structurally diverse drugs to the CB8 host was performed, and a general dynamic binding picture of CB8-guest interactions was obtained. Further, two widely used fixed-charge models for drug-like molecules were investigated and compared in great detail, aiming at providing guidelines in choosing an appropriate charge scheme in host-guest modelling. Iterative refitting of atomic charges leads to improved binding thermodynamics and the best root-mean-squared deviation from the experimental reference is 2.6 kcal/mol. In this work, we focus on a thorough evaluation of the remaining parts of classical force fields, i.e., the bonded interactions. The widely used general Amber force fields are assessed and refitted with generalized force-matching to improve the intra-molecular conformational preference, and thus the description of inter-molecular host–guest interactions. The interaction pattern and binding thermodynamics show a significant dependence on the modelling parameters. The refitted system-specific parameter set improves the consistency of the modelling results and the experimental reference significantly. Finally, combining the previous charge-scheme comparison and the current force-field refitting, we provide general guidelines for the theoretical modelling of host–guest binding.
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12
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Liu J, He X. Recent advances in quantum fragmentation approaches to complex molecular and condensed‐phase systems. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy China Pharmaceutical University Nanjing China
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering East China Normal University Shanghai China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering East China Normal University Shanghai China
- New York University‐East China Normal University Center for Computational Chemistry New York University Shanghai Shanghai China
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13
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de Paula Junior VF, van Tilburg MF, Morais PA, Júnior FFM, Lima EG, Oliveira VTDS, Guedes MIF, Caetano EWS, Freire VN. Quantum Biochemistry and MM-PBSA Description of the ZIKV NS2B-NS3 Protease: Insights into the Binding Interactions beyond the Catalytic Triad Pocket. Int J Mol Sci 2022; 23:ijms231710088. [PMID: 36077486 PMCID: PMC9456192 DOI: 10.3390/ijms231710088] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
The Zika virus protease NS2B-NS3 has a binding site formed with the participation of a H51-D75-S135 triad presenting two forms, active and inactive. Studies suggest that the inactive conformation is a good target for the design of inhibitors. In this paper, we evaluated the co-crystallized structures of the protease with the inhibitors benzoic acid (5YOD) and benzimidazole-1-ylmethanol (5H4I). We applied a protocol consisting of two steps: first, classical molecular mechanics energy minimization followed by classical molecular dynamics were performed, obtaining stabilized molecular geometries; second, the optimized/relaxed geometries were used in quantum biochemistry and molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) calculations to estimate the ligand interactions with each amino acid residue of the binding pocket. We show that the quantum-level results identified essential residues for the stabilization of the 5YOD and 5H4I complexes after classical energy minimization, matching previously published experimental data. The same success, however, was not observed for the MM-PBSA simulations. The application of quantum biochemistry methods seems to be more promising for the design of novel inhibitors acting on NS2B-NS3.
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Affiliation(s)
- Valdir Ferreira de Paula Junior
- Biotechnology & Molecular Biology Laboratory, State University of Ceará, Fortaleza 60714-903, Brazil
- Correspondence: ; Tel.: +55-859-8541-8255
| | | | - Pablo Abreu Morais
- Federal Institute of Education, Science and Technology of Ceará, Campus Horizonte, Horizonte 62884-105, Brazil
| | - Francisco Franciné Maia Júnior
- Departamento de Ciências Naturais, Matemática e Estatística, Universidade Federal Rural do Semi-Árido, Mossoró 59625-900, Brazil
| | - Elza Gadelha Lima
- Laboratório Central de Saúde Pública do Ceará (LACEN), Fortaleza 60120-002, Brazil
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França VLB, Amaral JL, Martins YA, Caetano EWS, Brunaldi K, Freire VN. Characterization of the binding interaction between atrazine and human serum albumin: Fluorescence spectroscopy, molecular dynamics and quantum biochemistry. Chem Biol Interact 2022; 366:110130. [PMID: 36037875 DOI: 10.1016/j.cbi.2022.110130] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/18/2022] [Accepted: 08/20/2022] [Indexed: 11/03/2022]
Abstract
Atrazine (ATR), one of the most used herbicides worldwide, causes persistent contamination of water and soil due to its high resistance to degradation. ATR is associated with low fertility and increased risk of prostate cancer in humans, as well as birth defects, low birth weight and premature delivery. Describing ATR binding to human serum albumin (HSA) is clinically relevant to future studies about pharmacokinetics, pharmacodynamics and toxicity of ATR, as albumin is the most abundant carrier protein in plasma and binds important small biological molecules. In this work we characterize, for the first time, the binding of ATR to HSA by using fluorescence spectroscopy and performing simulations using molecular docking, classical molecular dynamics and quantum biochemistry based on density functional theory (DFT). We determine the most likely binding sites of ATR to HSA, highlighting the fatty acid binding site FA8 (located between subdomains IA-IB-IIA and IIB-IIIA-IIIB) as the most important one, and evaluate each nearby amino acid residue contribution to the binding interactions explaining the fluorescence quenching due to ATR complexation with HSA. The stabilization of the ATR/FA8 complex was also aided by the interaction between the atrazine ring and SER454 (hydrogen bond) and LEU481(alkyl interaction).
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Affiliation(s)
- Victor L B França
- Departament of Physics, Federal University of Ceará, Fortaleza, 60440-900, Brazil
| | - Jackson L Amaral
- Departament of Physics, Federal University of Ceará, Fortaleza, 60440-900, Brazil
| | - Yandara A Martins
- Departament of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Ewerton W S Caetano
- Federal Institute of Education, Science and Technology of Ceará, Fortaleza, 60040-531, Brazil
| | - Kellen Brunaldi
- Departament of Physiological Sciences, State University of Maringá, Maringá, 87020-900, Brazil.
| | - Valder N Freire
- Departament of Physics, Federal University of Ceará, Fortaleza, 60440-900, Brazil.
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15
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Liu J, Lan J, He X. Toward High-level Machine Learning Potential for Water Based on Quantum Fragmentation and Neural Networks. J Phys Chem A 2022; 126:3926-3936. [PMID: 35679610 DOI: 10.1021/acs.jpca.2c00601] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Accurate and efficient simulation of liquids, such as water and salt solutions, using high-level wave function theories is still a formidable task for computational chemists owing to the high computational costs. In this study, we develop a deep machine learning potential based on fragment-based second-order Møller-Plesset perturbation theory (DP-MP2) for water through neural networks. We show that the DP-MP2 potential predicts the structural, dynamical, and thermodynamic properties of liquid water in better agreement with the experimental data than previous studies based on density functional theory (DFT). The nuclear quantum effects (NQEs) on the properties of liquid water are also examined, which are noticeable in affecting the structural and dynamical properties of liquid water under ambient conditions. This work provides a general framework for quantitative predictions of the properties of condensed-phase systems with the accuracy of high-level wave function theory while achieving significant computational savings compared to ab initio simulations.
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Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China.,Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Jinggang Lan
- Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,New York University-East China Normal University Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, China
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16
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Masoumifeshani E, Chojecki M, Korona T. Electronic Correlation Contribution to the Intermolecular Interaction Energy from Symmetrized Systematic Molecular Fragmentation Model. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Shen C, Wang X, He X. Fragment-Based Quantum Mechanical Calculation of Excited-State Properties of Fluorescent RNAs. Front Chem 2022; 9:801062. [PMID: 35004616 PMCID: PMC8727457 DOI: 10.3389/fchem.2021.801062] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Fluorescent RNA aptamers have been successfully applied to track and tag RNA in a biological system. However, it is still challenging to predict the excited-state properties of the RNA aptamer–fluorophore complex with the traditional electronic structure methods due to expensive computational costs. In this study, an accurate and efficient fragmentation quantum mechanical (QM) approach of the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) scheme was applied for calculations of excited-state properties of the RNA aptamer–fluorophore complex. In this method, the excited-state properties were first calculated with one-body fragment quantum mechanics/molecular mechanics (QM/MM) calculation (the excited-state properties of the fluorophore) and then corrected with a series of two-body fragment QM calculations for accounting for the QM effects from the RNA on the excited-state properties of the fluorophore. The performance of the EE-GMFCC on prediction of the absolute excitation energies, the corresponding transition electric dipole moment (TEDM), and atomic forces at both the TD-HF and TD-DFT levels was tested using the Mango-II RNA aptamer system as a model system. The results demonstrate that the calculated excited-state properties by EE-GMFCC are in excellent agreement with the traditional full-system time-dependent ab initio calculations. Moreover, the EE-GMFCC method is capable of providing an accurate prediction of the relative conformational excited-state energies for different configurations of the Mango-II RNA aptamer system extracted from the molecular dynamics (MD) simulations. The fragmentation method further provides a straightforward approach to decompose the excitation energy contribution per ribonucleotide around the fluorophore and then reveals the influence of the local chemical environment on the fluorophore. The applications of EE-GMFCC in calculations of excitation energies for other RNA aptamer–fluorophore complexes demonstrate that the EE-GMFCC method is a general approach for accurate and efficient calculations of excited-state properties of fluorescent RNAs.
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Affiliation(s)
- Chenfei Shen
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Xianwei Wang
- College of Science, Zhejiang University of Technology, Hangzhou, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.,New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Shanghai, China
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18
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Santos JLS, Bezerra KS, Barbosa ED, Pereira ACL, Meurer YSR, Oliveira JIN, Gavioli EC, Fulco UL. In silico analysis of energy interactions between nociceptin/orfanin FQ receptor and two antagonists with potential antidepressive action. NEW J CHEM 2022. [DOI: 10.1039/d2nj00916a] [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
This study addresses the binding energies of NOPR-ligand complexes and presents the main amino acid residues involved in the interaction between these complexes.
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Affiliation(s)
- J. L. S. Santos
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil
| | - K. S. Bezerra
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil
| | - E. D. Barbosa
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil
| | - A. C. L. Pereira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil
| | - Y. S. R. Meurer
- Departamento de Psicologia, Universidade Federal da Paraíba, 58051-900, João Pessoa-PB, Brazil
| | - J. I. N. Oliveira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil
| | - E. C. Gavioli
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil
| | - U. L. Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal-RN, Brazil
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19
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Sun Z, Huai Z, He Q, Liu Z. A General Picture of Cucurbit[8]uril Host-Guest Binding. J Chem Inf Model 2021; 61:6107-6134. [PMID: 34818004 DOI: 10.1021/acs.jcim.1c01208] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Describing, understanding, and designing complex interaction networks within macromolecular systems remain challenging in modern chemical research. Host-guest systems, despite their relative simplicity in both the structural feature and interaction patterns, still pose problems in theoretical modeling. The barrel-shaped supramolecular container cucurbit[8]uril (CB8) shows promising functionalities in various areas, e.g., catalysis and molecular recognition. It can stably coordinate a series of structurally diverse guests with high affinities. In this work, we examine the binding of seven commonly abused drugs to the CB8 host, aiming at providing a general picture of CB8-guest binding. Extensive sampling of the configurational space of these host-guest systems is performed, and the binding pathway and interaction patterns of CB8-guest complexes are investigated. A thorough comparison of widely used fixed-charge models for drug-like molecules is presented. Iterative refitting of the atomic charges suggests significant conformation dependence of charge generation. The initial model generated at the original conformation could be inaccurate for new conformations explored during conformational search, and the newly fitted charge set improves the prediction-experiment correlation significantly. Our investigations of the configurational space of CB8-drug complexes suggest that the host-guest interactions are more complex than expected. Despite the structural simplicities of these molecules, the conformational fluctuations of the host and the guest molecules and orientations of functional groups lead to the existence of an ensemble of binding modes. The insights of the binding thermodynamics, performance of fixed-charge models, and binding patterns of the CB8-guest systems are useful for studying and elucidating the binding mechanism of other host-guest complexes.
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Affiliation(s)
- Zhaoxi Sun
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhe Huai
- XtalPi-AI Research Center (XARC), 9F, Tower A, Dongsheng Building, No. 8, Zhongguancun East Road, Haidian District, Beijing 100083, P.R. China
| | - Qiaole He
- AI Department of Enzymaster (Ningbo) Bio-Engineering Co., Ltd., North Century Avenue 333, Ningbo 315100, China
| | - Zhirong Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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20
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Barbosa ED, Lima Neto JX, Bezerra KS, Oliveira JIN, Machado LD, Fulco UL. Quantum Biochemical Investigation of Lys49-PLA 2 from Bothrops moojeni. J Phys Chem B 2021; 125:12972-12980. [PMID: 34793159 DOI: 10.1021/acs.jpcb.1c07298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Envenomation via snakebites occurs largely in areas where it is harder to access the hospital. Its mortality rate and sequelae acquired by the survivors symbolize a big challenge for antivenom therapy. In particular, the homologous phospholipase A2 (Lys49-PLA2) proteins can induce myonecrosis and are not effectively neutralized by current treatments. Thus, by taking advantage of crystallographic structures of Bothrops moojeni Lys49-PLA2 complexed with VRD (varespladib) and AIN (aspirin), a quantum biochemistry study based on the molecular fractionation with conjugate cap scheme within the density functional theory formalism is performed to unveil these complexes' detailed interaction energies. The calculations revealed that important interactions between ligands and the Lys49-PLA2 pocket could occur up to a pocket radius of r = 6.5 (5.0 Å) for VRD (AIN), with the total interaction energy of the VRD ligand being higher than that of the AIN ligand, which is well-correlated with the experimental binding affinity. Furthermore, we have identified the role played by the amino acids LYS0069, LYS0049, LEU0005, ILE0009, CYS0029, GLY0030, HIS0048, PRO0018, ALA0019, CYS0045, TYR0052, TYR0022, PRO0125*, and PHE0126* (LYS0069, LYS0049, GLY0032, LEU0002, and LEU0005) in the VRD↔Lys49-PLA2 (AIN↔Lys49-PLA2) complex. Our simulations are a valuable tool to support the big challenge for neutralizing the damages in victims of snakebites.
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Affiliation(s)
- E D Barbosa
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal 59072-970, Rio Grande do Norte, Brazil
| | - J X Lima Neto
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal 59072-970, Rio Grande do Norte, Brazil
| | - K S Bezerra
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal 59072-970, Rio Grande do Norte, Brazil
| | - J I N Oliveira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal 59072-970, Rio Grande do Norte, Brazil
| | - L D Machado
- Departamento de Física Teórica e Experimental, Universidade Federal do Rio Grande do Norte, Natal 59072-970, Rio Grande do Norte, Brazil
| | - U L Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal 59072-970, Rio Grande do Norte, Brazil
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21
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Liu J, He X. Ab initio molecular dynamics simulation of liquid water with fragment-based quantum mechanical approach under periodic boundary conditions. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2110183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Shanghai 200062, China
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22
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Heindel JP, Xantheas SS. Molecular Dynamics Driven by the Many-Body Expansion (MBE-MD). J Chem Theory Comput 2021; 17:7341-7352. [PMID: 34723531 DOI: 10.1021/acs.jctc.1c00780] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a protocol for classical and nuclear quantum dynamics, in which the energies and forces are generated by the many-body expansion (MBE), and apply it to water clusters using the TTM2.1-F and MB-Pol interaction potentials at various temperatures. We carry out MBE-molecular dynamics (MD) classical and nuclear quantum dynamical simulations, in which the energies and forces of the full system are approximated by the two-, three-, and four-body terms of the MBE, and compare the average potential and the vibrational density of states with the full simulation, i.e., the one for which no MBE is used. Our results indicate that the thermally averaged potential energy from the MBE up to the four-body term converges with near-identical behavior to the one from the full simulation. The three-body makes a substantial contribution (∼20%) to the energy, whereas the four-body is necessary for obtaining quantitatively accurate energetics and forces, albeit making a small contribution to each (∼2%). We further show that the harmonic frequencies are reproduced to within a few wavenumbers (cm-1) at the four-body level and that the slowest modes to converge with the MBE rank are those involving the strongest hydrogen bonds. Anharmonicity exacerbates this effect, so that a four-body description of the energies and forces is needed to achieve accurate anharmonic vibrational frequencies in the hydrogen-bonded OH-stretching region. We also discuss the asymptotic scaling of the MBE-MD protocol with respect to the cost of the underlying potential energy evaluation, suggesting that electronic structure methods that scale at least as N4, N being the size of the system, are needed to result in savings over the traditional full MD simulation. We anticipate that the MBE-MD protocol can evolve into a powerful and practical method, which will allow for highly accurate ab initio MD simulations on a much broader range of molecular systems than can be currently handled.
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Affiliation(s)
- Joseph P Heindel
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Sotiris S Xantheas
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States.,Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States
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23
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Cheng Z, Du J, Zhang L, Ma J, Li W, Li S. Building quantum mechanics quality force fields of proteins with the generalized energy-based fragmentation approach and machine learning. Phys Chem Chem Phys 2021; 24:1326-1337. [PMID: 34718360 DOI: 10.1039/d1cp03934b] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We combined our generalized energy-based fragmentation (GEBF) approach and machine learning (ML) technique to construct quantum mechanics (QM) quality force fields for proteins. In our scheme, the training sets for a protein are only constructed from its small subsystems, which capture all short-range interactions in the target system. The energy of a given protein is expressed as the summation of atomic contributions from QM calculations of various subsystems, corrected by long-range Coulomb and van der Waals interactions. With the Gaussian approximation potential (GAP) method, our protocol can automatically generate training sets with high efficiency. To facilitate the construction of training sets for proteins, we store all trained subsystem data in a library. If subsystems in the library are detected in a new protein, corresponding datasets can be directly reused as a part of the training set on this new protein. With two polypeptides, 4ZNN and 1XQ8 segment, as examples, the energies and forces predicted by GEBF-GAP are in good agreement with those from conventional QM calculations, and dihedral angle distributions from GEBF-GAP molecular dynamics (MD) simulations can also well reproduce those from ab initio MD simulations. In addition, with the training set generated from GEBF-GAP, we also demonstrate that GEBF-ML force fields constructed by neural network (NN) methods can also show QM quality. Therefore, the present work provides an efficient and systematic way to build QM quality force fields for biological systems.
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Affiliation(s)
- Zheng Cheng
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China.
| | - Jiahui Du
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China.
| | - Lei Zhang
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China.
| | - Jing Ma
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China.
| | - Wei Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China.
| | - Shuhua Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China.
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24
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Hellmers J, König C. A unified and flexible formulation of molecular fragmentation schemes. J Chem Phys 2021; 155:164105. [PMID: 34717347 DOI: 10.1063/5.0059598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We present a flexible formulation for energy-based molecular fragmentation schemes. This framework does not only incorporate the majority of existing fragmentation expansions but also allows for flexible formulation of novel schemes. We further illustrate its application in multi-level approaches and for electronic interaction energies. For the examples of small water clusters, a small protein, and protein-protein interaction energies, we show how this flexible setup can be exploited to generate a well-suited multi-level fragmentation expansion for the given case. With such a setup, we reproduce the electronic protein-protein interaction energy of ten different structures of a neurotensin and an extracellular loop of its receptor with a mean absolute deviation to the respective super-system calculations below 1 kJ/mol.
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Affiliation(s)
- Janine Hellmers
- Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, Hannover, Germany
| | - Carolin König
- Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, Hannover, Germany
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25
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Vianna JF, Bezerra KS, Lima Costa AH, Barbosa ED, Lima Neto JX, Oliveira JIN, Freire VN, Fulco UL. New ethionamide boosters and EthR2: structural and energetic analysis. Phys Chem Chem Phys 2021; 23:23233-23241. [PMID: 34623361 DOI: 10.1039/d1cp02853g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ethionamide (ETH) is a high-profile drug for the treatment of patients with multidrug-resistant Mycobacterium tuberculosis and, in order to produce its inhibitory effects, it needs to be bioactivated by monooxygenase EthA. This process is under the control of the transcriptional repressors EthR and EthR2, so that their inhibition results in the boosting of ethionamide activation. Herein, through crystallographic data and computer simulations, we calculated the interaction binding energies of four inhibitors with improved in vitro potency, namely BDM76060 (PDB ID: 6HS1), BDM72201 (PDB ID: 6HRX), BDM76150 (PDB ID: 6HS2) and BDM72719 (PDB ID: 6HRY), in complexes with the transcriptional repressor EthR2, using density functional theory (DFT) within the molecular fractionation with conjugated caps (MFCC) approach. It was observed that these ligands share the same binding site within a 10.0 Å radius of the EthR2 protein; however, their structural particularities have a significant impact on the global energies of systems. The BDM72201 and BDM72719 components are weakly attached to the binding site, while BDM76060 and BDM76150 components produce stronger bonds, corroborating with experimental studies demonstrating that BDM76060 and BDM76150 are more successful in producing inhibitory effects. BDM76060 and BDM76150 have many functional groups that increase the contact surface with the protein and attract a more significant number of amino acid residues, being able to produce polarities that generate stronger interactions. In the current scenario of a growing number of cases of bacterial resistance, the obtained data can be used to guide clinical trials of these inhibitors and other inhibitors that act on the alternative EthR2 pathway, focusing on improving the activity of ethionamide, its effectiveness, a reduction in the treatment time and exposure to cytotoxic effects.
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Affiliation(s)
- J F Vianna
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil.
| | - K S Bezerra
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil.
| | - A H Lima Costa
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil.
| | - E D Barbosa
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil.
| | - J X Lima Neto
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil.
| | - J I N Oliveira
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil.
| | - V N Freire
- Departamento de Física, Universidade Federal do Ceará, 60455-760, Fortaleza, CE, Brazil
| | - U L Fulco
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970, Natal, RN, Brazil.
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26
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Symmetrized systematic molecular fragmentation model and its application for molecular properties. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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27
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Shen C, Jin X, Glover WJ, He X. Accurate Prediction of Absorption Spectral Shifts of Proteorhodopsin Using a Fragment-Based Quantum Mechanical Method. Molecules 2021; 26:4486. [PMID: 34361639 PMCID: PMC8347797 DOI: 10.3390/molecules26154486] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/17/2022] Open
Abstract
Many experiments have been carried out to display different colors of Proteorhodopsin (PR) and its mutants, but the mechanism of color tuning of PR was not fully elucidated. In this study, we applied the Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps (EE-GMFCC) method to the prediction of excitation energies of PRs. Excitation energies of 10 variants of Blue Proteorhodopsin (BPR-PR105Q) in residue 105GLN were calculated with the EE-GMFCC method at the TD-B3LYP/6-31G* level. The calculated results show good correlation with the experimental values of absorption wavelengths, although the experimental wavelength range among these systems is less than 50 nm. The ensemble-averaged electric fields along the polyene chain of retinal correlated well with EE-GMFCC calculated excitation energies for these 10 PRs, suggesting that electrostatic interactions from nearby residues are responsible for the color tuning. We also utilized the GMFCC method to decompose the excitation energy contribution per residue surrounding the chromophore. Our results show that residues ASP97 and ASP227 have the largest contribution to the absorption spectral shift of PR among the nearby residues of retinal. This work demonstrates that the EE-GMFCC method can be applied to accurately predict the absorption spectral shifts for biomacromolecules.
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Affiliation(s)
- Chenfei Shen
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; (C.S.); (X.J.)
| | - Xinsheng Jin
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; (C.S.); (X.J.)
| | - William J. Glover
- NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China;
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; (C.S.); (X.J.)
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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28
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Fragment-Based Ab Initio Molecular Dynamics Simulation for Combustion. Molecules 2021; 26:molecules26113120. [PMID: 34071128 PMCID: PMC8197069 DOI: 10.3390/molecules26113120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/21/2021] [Accepted: 05/21/2021] [Indexed: 11/17/2022] Open
Abstract
We develop a fragment-based ab initio molecular dynamics (FB-AIMD) method for efficient dynamics simulation of the combustion process. In this method, the intermolecular interactions are treated by a fragment-based many-body expansion in which three- or higher body interactions are neglected, while two-body interactions are computed if the distance between the two fragments is smaller than a cutoff value. The accuracy of the method was verified by comparing FB-AIMD calculated energies and atomic forces of several different systems with those obtained by standard full system quantum calculations. The computational cost of the FB-AIMD method scales linearly with the size of the system, and the calculation is easily parallelizable. The method is applied to methane combustion as a benchmark. Detailed reaction network of methane reaction is analyzed, and important reaction species are tracked in real time. The current result of methane simulation is in excellent agreement with known experimental findings and with prior theoretical studies.
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29
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Wolter M, von Looz M, Meyerhenke H, Jacob CR. Systematic Partitioning of Proteins for Quantum-Chemical Fragmentation Methods Using Graph Algorithms. J Chem Theory Comput 2021; 17:1355-1367. [PMID: 33591754 DOI: 10.1021/acs.jctc.0c01054] [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
Quantum-chemical fragmentation methods offer an efficient approach for the treatment of large proteins, in particular if local target quantities such as protein-ligand interaction energies, enzymatic reaction energies, or spectroscopic properties of embedded chromophores are sought. However, the accuracy that is achievable for such local target quantities intricately depends on how the protein is partitioned into smaller fragments. While the commonly employed naı̈ve approach of using fragments with a fixed size is widely used, it can result in large and unpredictable errors when varying the fragment size. Here, we present a systematic partitioning scheme that aims at minimizing the fragmentation error of a local target quantity for a given maximum fragment size. To this end, we construct a weighted graph representation of the protein, in which the amino acids constitute the nodes. These nodes are connected by edges weighted with an estimate for the fragmentation error that is expected when cutting this edge. This allows us to employ graph partitioning algorithms provided by computer science to determine near-optimal partitions of the protein. We apply this scheme to a test set of six proteins representing various prototypical applications of quantum-chemical fragmentation methods using a simplified molecular fractionation with conjugate caps (MFCC) approach with hydrogen caps. We show that our graph-based scheme consistently improves upon the naı̈ve approach.
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Affiliation(s)
- Mario Wolter
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstrasse 17, 38106 Braunschweig, Germany
| | - Moritz von Looz
- Department of Computer Science, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Henning Meyerhenke
- Department of Computer Science, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstrasse 17, 38106 Braunschweig, Germany
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30
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Shi M, Jin X, Wan Z, He X. Automated fragmentation quantum mechanical calculation of 13C and 1H chemical shifts in molecular crystals. J Chem Phys 2021; 154:064502. [PMID: 33588539 DOI: 10.1063/5.0039115] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach was applied to calculate the 13C and 1H nuclear magnetic resonance (NMR) chemical shifts in molecular crystals. Two benchmark sets of molecular crystals were selected to calculate the NMR chemical shifts. Systematic investigation was conducted to examine the convergence of AF-QM/MM calculations and the impact of various density functionals with different basis sets on the NMR chemical shift prediction. The result demonstrates that the calculated NMR chemical shifts are close to convergence when the distance threshold for the QM region is larger than 3.5 Å. For 13C chemical shift calculations, the mPW1PW91 functional is the best density functional among the functionals chosen in this study (namely, B3LYP, B3PW91, M06-2X, M06-L, mPW1PW91, OB98, and OPBE), while the OB98 functional is more suitable for the 1H NMR chemical shift prediction of molecular crystals. Moreover, with the B3LYP functional, at least a triple-ζ basis set should be utilized to accurately reproduce the experimental 13C and 1H chemical shifts. The employment of diffuse basis functions will further improve the accuracy for 13C chemical shift calculations, but not for the 1H chemical shift prediction. We further proposed a fragmentation scheme of dividing the central molecule into smaller fragments. By comparing with the results of the fragmentation scheme using the entire central molecule as the core region, the AF-QM/MM calculations with the fragmented central molecule can not only achieve accurate results but also reduce the computational cost. Therefore, the AF-QM/MM approach is capable of predicting the 13C and 1H NMR chemical shifts for molecular crystals accurately and effectively, and could be utilized for dealing with more complex periodic systems such as macromolecular polymers and biomacromolecules. The AF-QM/MM program for molecular crystals is available at https://github.com/shiman1995/NMR.
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Affiliation(s)
- Man Shi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xinsheng Jin
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Zheng Wan
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
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31
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Paz ASP, Glover WJ. Diabatic Many-Body Expansion: Development and Application to Charge-Transfer Reactions. J Chem Theory Comput 2021; 17:1497-1511. [DOI: 10.1021/acs.jctc.0c01231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amiel S. P. Paz
- NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshang Road North, Shanghai 200062, China
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - William J. Glover
- NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshang Road North, Shanghai 200062, China
- Department of Chemistry, New York University, New York, New York 10003, United States
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32
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Silva SRB, de Lima Neto JX, Fuzo CA, Fulco UL, Vieira DS. A quantum biochemistry investigation of the protein-protein interactions for the description of allosteric modulation on biomass-degrading chimera. Phys Chem Chem Phys 2020; 22:25936-25948. [PMID: 33164009 DOI: 10.1039/d0cp04415f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The worldwide dependence of population on fossil fuels continues to have several harmful implications for the environment. Bioethanol is an excellent option for renewable fuel to replace the current greenhouse gas emitters. In addition, its production by enzymatic route has gained space among the industrial processes because it replaces the traditional acid treatment. Due to its high versatility, the xylanase family is used in this process as an accessory enzyme for degrading the lignocellulosic substrate of biomass. A chimera built by a xylanolytic domain (Xyl) and a xylose-binding protein (XBP) showed an experimentally improved catalytic efficiency and interdomain allosteric modulation after xylose binding. In this context, we performed a quantum biochemistry characterization of the interactions between these domains and dynamic cross-correlation (DCC) analysis after performing molecular dynamics (DM) simulations of the systems in the presence and absence of xylose in the XBP active site. We used the density functional theory (DFT) within the molecular fractionation with the conjugated caps (MFCC) approach to describe the pair energies, and the corresponding energy difference between the chimera domains responsible for the allosteric effect and amino acid DCC to evaluate the interdomain coupling differences between the energy states. The detailed energetic investigation together with the related structural and dynamics counterparts revealed the molecular mechanisms of chimeric improvement of the xylanase activity observed experimentally. This mechanism was correlated with greater stability and high connectivity at the interdomain interface in the xylose bound relative to the free chimera. We identify the contributions of hydrogen bonds, hydrophobic interactions and water-mediated interactions in the interdomain region responsible for stability together with the structural and dynamical elements related to the allosteric effect. Taken together, these observations led to a comprehensive understanding of the chimera's modulatory action that occurs through the formation of a highly connected interface that makes the essential movements related to xylanolytic activity in xylanase correlated to those of the xylose-binding protein.
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33
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Reinholdt P, Jørgensen FK, Kongsted J, Olsen JMH. Polarizable Density Embedding for Large Biomolecular Systems. J Chem Theory Comput 2020; 16:5999-6006. [PMID: 32991163 DOI: 10.1021/acs.jctc.0c00763] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We present an efficient and robust fragment-based quantum-classical embedding model capable of accurately capturing effects from complex environments such as proteins and nucleic acids. This is realized by combining the molecular fractionation with conjugate caps (MFCC) procedure with the polarizable density embedding (PDE) model at the level of Fock matrix construction. The PDE contributions to the Fock matrix of the core region are constructed using the local molecular basis of the individual fragments rather than the supermolecular basis of the entire system. Thereby, we avoid complications associated with the application of the MFCC procedure on environment quantities such as electronic densities and molecular-orbital energies. Moreover, the computational cost associated with solving self-consistent field (SCF) equations of the core region remains unchanged from that of purely classical polarized embedding models. We analyze the performance of the resulting model in terms of the reproduction of the electrostatic potential of an insulin monomer protein and further in the context of solving problems related to electron spill-out. Finally, we showcase the model for the calculation of one- and two-photon properties of the Nile red molecule in a protein environment. Based on our analyses, we find that the combination of the MFCC approach with the PDE model is an efficient, yet accurate approach for calculating molecular properties of molecules embedded in structured biomolecular environments.
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Affiliation(s)
- Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Frederik Kamper Jørgensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway.,Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
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34
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Jin X, Glover WJ, He X. Fragment Quantum Mechanical Method for Excited States of Proteins: Development and Application to the Green Fluorescent Protein. J Chem Theory Comput 2020; 16:5174-5188. [PMID: 32551640 DOI: 10.1021/acs.jctc.9b00980] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Understanding the excited-state properties of luminescent biomolecules is of central importance to their biophysical applications. In this study, we develop the Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps (EE-GMFCC) method for quantitatively characterizing properties of covalently bonded systems with localized excitations (i.e., involving a single chromophore), such as fluorescent proteins. The excitation energy, transition dipole moment, and oscillator strength of wild-type Green Fluorescent Protein (wt-GFP) calculated by EE-GMFCC are found to be in excellent agreement with full system time-dependent density functional theory results. We also applied the Polarized Protein-Specific Charge model to wt-GFP, and found that electronic polarization of the protein is critical in stabilizing hydrogen bonding interactions in wt-GFP, which influences its absorption spectrum. The predicted absorption spectra of wt-GFP in the A and B states qualitatively agree with experiment. The fragmentation approach further allows a straightforward per residue decomposition of the excitation which reveals the influence of the protein environment on the absorption spectra of wt-GFP A and B states. Our results demonstrate that the EE-GMFCC method is both accurate and efficient for excited-state property calculations on proteins.
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Affiliation(s)
- Xinsheng Jin
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - William J Glover
- NYU Shanghai, 1555 Century Avenue, Shanghai 200122, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.,Department of Chemistry, New York University, New York, New York 10003, United States
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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35
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Liu J, He X. Fragment-based quantum mechanical approach to biomolecules, molecular clusters, molecular crystals and liquids. Phys Chem Chem Phys 2020; 22:12341-12367. [PMID: 32459230 DOI: 10.1039/d0cp01095b] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To study large molecular systems beyond the system size that the current state-of-the-art ab initio electronic structure methods could handle, fragment-based quantum mechanical (QM) approaches have been developed over the past years, and proved to be efficient in dealing with large molecular systems at various ab initio levels. According to the fragmentation approach, a large molecular system can be divided into subsystems (fragments), and subsequently the property of the whole system can be approximately obtained by taking a proper combination of the corresponding terms of individual fragments. Therefore, the standard QM calculation of a large system could be circumvented by carrying out a series of calculations on small fragments, which significantly promotes computational efficiency. The electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method is one of the fragment-based QM approaches which has been developed by our research group in recent years. This Perspective presents the theoretical framework of this fragmentation method and its applications in biomolecules, molecular clusters, molecular crystals and liquids, including total energy calculation, protein-ligand/protein binding affinity prediction, geometry optimization, vibrational spectrum simulation, ab initio molecular dynamics simulation, and prediction of excited-state properties.
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Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
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36
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Chen X, Qu Z, Suo B, Gao J. A self-consistent coulomb bath model using density fitting. J Comput Chem 2020; 41:1698-1708. [PMID: 32369627 DOI: 10.1002/jcc.26211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 03/02/2020] [Accepted: 04/05/2020] [Indexed: 12/24/2022]
Abstract
A self-consistent Coulomb bath model is presented to provide an accurate and efficient way of performing calculations for interfragment electrostatic and polarization interactions. In this method, a condensed-phase system is partitioned into molecular fragment blocks. Each fragment is embedded in the Coulomb bath due to other fragments. Importantly, the present Coulomb bath is represented using a density fitting method in which the electron densities of molecular fragments are fitted using an atom-centered auxiliary basis set of Gaussian type. The Coulomb bath is incorporated into an effective Hamiltonian for each fragment, with which the electron density is optimized through an iterative double self-consistent field (DSCF) procedure to realize the mutual many-body polarization effects. In this work, the accuracy of interfragment interaction energies enumerated using the Coulomb bath is tested, showing a good agreement with the exact results from an energy decomposition analysis. The qualitative features of many-body polarization effects are visualized by electron density difference plots. It is also shown that the present DSCF method can yield fast and robust convergence with near-linear scaling in performance with increase in system size.
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Affiliation(s)
- Xin Chen
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China.,Shenzhen Bay Laboratory, Shenzhen, China
| | - Zexing Qu
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Bingbing Suo
- Shaanxi Key Laboratory for Theoretical Physics Frontiers, Institute of Modern Physics, Northwest University, Xi'an, Shaanxi, China
| | - Jiali Gao
- Shenzhen Bay Laboratory, Shenzhen, China.,Laboratory of Computational Chemistry and Drug Design, Peking University Shenzhen Graduate School, Shenzhen, China.,Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, USA
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37
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Zhang W, Liu J, Jin X, Gu X, Zeng XC, He X, Li H. Quantitative Prediction of Aggregation‐Induced Emission: A Full Quantum Mechanical Approach to the Optical Spectra. Angew Chem Int Ed Engl 2020; 59:11550-11555. [DOI: 10.1002/anie.202003326] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Wei Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering Beijing University of Chemical Technology Beijing 100029 China
- Department of Chemistry University of Nebraska Lincoln NE 68588 USA
| | - Jinfeng Liu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development School of Chemistry and Molecular Engineering East China Normal University Shanghai 200062 China
- Department of Basic Medicine and Clinical Pharmacy China Pharmaceutical University Nanjing 210009 China
| | - Xinsheng Jin
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development School of Chemistry and Molecular Engineering East China Normal University Shanghai 200062 China
| | - Xinggui Gu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering Beijing University of Chemical Technology Beijing 100029 China
| | - Xiao Cheng Zeng
- Department of Chemistry University of Nebraska Lincoln NE 68588 USA
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development School of Chemistry and Molecular Engineering East China Normal University Shanghai 200062 China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
| | - Hui Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering Beijing University of Chemical Technology Beijing 100029 China
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38
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Zhang W, Liu J, Jin X, Gu X, Zeng XC, He X, Li H. Quantitative Prediction of Aggregation‐Induced Emission: A Full Quantum Mechanical Approach to the Optical Spectra. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Wei Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering Beijing University of Chemical Technology Beijing 100029 China
- Department of Chemistry University of Nebraska Lincoln NE 68588 USA
| | - Jinfeng Liu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development School of Chemistry and Molecular Engineering East China Normal University Shanghai 200062 China
- Department of Basic Medicine and Clinical Pharmacy China Pharmaceutical University Nanjing 210009 China
| | - Xinsheng Jin
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development School of Chemistry and Molecular Engineering East China Normal University Shanghai 200062 China
| | - Xinggui Gu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering Beijing University of Chemical Technology Beijing 100029 China
| | - Xiao Cheng Zeng
- Department of Chemistry University of Nebraska Lincoln NE 68588 USA
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development School of Chemistry and Molecular Engineering East China Normal University Shanghai 200062 China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
| | - Hui Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering Beijing University of Chemical Technology Beijing 100029 China
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39
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Dawson W, Mohr S, Ratcliff LE, Nakajima T, Genovese L. Complexity Reduction in Density Functional Theory Calculations of Large Systems: System Partitioning and Fragment Embedding. J Chem Theory Comput 2020; 16:2952-2964. [PMID: 32216343 DOI: 10.1021/acs.jctc.9b01152] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
With the development of low order scaling methods for performing Kohn-Sham density functional theory, it is now possible to perform fully quantum mechanical calculations of systems containing tens of thousands of atoms. However, with an increase in the size of the system treated comes an increase in complexity, making it challenging to analyze such large systems and determine the cause of emergent properties. To address this issue, in this paper, we present a systematic complexity reduction methodology which can break down large systems into their constituent fragments and quantify interfragment interactions. The methodology proposed here requires no a priori information or user interaction, allowing a single workflow to be automatically applied to any system of interest. We apply this approach to a variety of different systems and show how it allows for the derivation of new system descriptors, the design of QM/MM partitioning schemes, and the novel application of graph metrics to molecules and materials.
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Affiliation(s)
- William Dawson
- RIKEN Center for Computational Science, Kobe 650-0047, Japan
| | - Stephan Mohr
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Laura E Ratcliff
- Department of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Luigi Genovese
- Université Grenoble Alpes, INAC-MEM, L_Sim, Grenoble F-38000, France.,CEA, INAC-MEM, L_Sim, Grenoble F-38000, France
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40
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Wang Z, Han Y, Li J, He X. Combining the Fragmentation Approach and Neural Network Potential Energy Surfaces of Fragments for Accurate Calculation of Protein Energy. J Phys Chem B 2020; 124:3027-3035. [PMID: 32208716 DOI: 10.1021/acs.jpcb.0c01370] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Accurate and efficient all-atom quantum mechanical (QM) calculations for biomolecules still present a challenge to computational physicists and chemists. In this study, an extensible generalized molecular fractionation with a conjugate caps method combined with neural networks (NN-GMFCC) is developed for efficient QM calculation of protein energy. In the NN-GMFCC scheme, the total energy of a given protein is calculated by taking a proper combination of the high-precision neural network potential energies of all capped residues and overlapping conjugate caps. In addition, the two-body interaction energies of residue pairs are calculated by molecular mechanics (MM). With reference to the GMFCC/MM calculation at the ωB97XD/6-31G* level, the overall mean unsigned errors of the energy deviations and atomic force root-mean-squared errors calculated by NN-GMFCC are only 2.01 kcal/mol and 0.68 kcal/mol/Å, respectively, for 14 proteins (containing up to 13,728 atoms). Meanwhile, the NN-GMFCC approach is about 4 orders of magnitude faster than the GMFCC/MM method. The NN-GMFCC method could be systematically improved by inclusion of two-body QM interaction and multibody electronic polarization effect. Moreover, the NN-GMFCC approach can also be applied to other macromolecular systems such as DNA/RNA, and it is capable of providing a powerful and efficient approach for exploration of structures and functions of proteins with QM accuracy.
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Affiliation(s)
- Zhilong Wang
- Key Laboratory of Thin Film and Micro Fabrication, Ministry of Education, Department of Micro/Nano-electronics, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanqiang Han
- Key Laboratory of Thin Film and Micro Fabrication, Ministry of Education, Department of Micro/Nano-electronics, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinjin Li
- Key Laboratory of Thin Film and Micro Fabrication, Ministry of Education, Department of Micro/Nano-electronics, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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41
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QM Implementation in Drug Design: Does It Really Help? Methods Mol Biol 2020. [PMID: 32016884 DOI: 10.1007/978-1-0716-0282-9_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
Computational chemistry allows one to characterize the structure, dynamics, and energetics of protein-ligand interactions, which makes it a valuable tool in drug discovery in both academic research and pharmaceutical industry. Molecular mechanics (MM)-based approaches are widely utilized to assist the discovery of new drug candidates. However, the complexity of protein-ligand interactions challenges the accuracy and efficiency of the commonly used empirical methods. Aiming to provide better accuracy in the description of protein-ligand interactions, quantum mechanics (QM)-based approaches are becoming increasingly explored. In principle, QM calculation includes all contributions to the energy, accounting for terms usually missing in empirical force fields, and provides a greater degree of transferability. The usefulness of QM in drug design cannot be overemphasized. In this chapter, we present recent developments and applications of fragment-based QM method in studying the protein-ligand and protein-protein interactions. We critically discuss the performance of the fragment-based QM method at different ab initio levels while trying to answer a critical question: do QM-based methods really help in drug design?
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42
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Xu J, Liu J, Liu J, Hu W, He X, Li J. Phase Transition of Ice at High Pressures and Low Temperatures. Molecules 2020; 25:molecules25030486. [PMID: 31979295 PMCID: PMC7037513 DOI: 10.3390/molecules25030486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/08/2020] [Accepted: 01/21/2020] [Indexed: 11/21/2022] Open
Abstract
The behavior of ice under extreme conditions undergoes the change of intermolecular binding patterns and leads to the structural phase transitions, which are needed for modeling the convection and internal structure of the giant planets and moons of the solar system as well as H2O-rich exoplanets. Such extreme conditions limit the structural explorations in laboratory but open a door for the theoretical study. The ice phases IX and XIII are located in the high pressure and low temperature region of the phase diagram. However, to the best of our knowledge, the phase transition boundary between these two phases is still not clear. In this work, based on the second-order Møller–Plesset perturbation (MP2) theory, we theoretically investigate the ice phases IX and XIII and predict their structures, vibrational spectra and Gibbs free energies at various extreme conditions, and for the first time confirm that the phase transition from ice IX to XIII can occur around 0.30 GPa and 154 K. The proposed work, taking into account the many-body electrostatic effect and the dispersion interactions from the first principles, opens up the possibility of completing the ice phase diagram and provides an efficient method to explore new phases of molecular crystals.
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Affiliation(s)
- Jinjin Xu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China;
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication, Key laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Micro/Nano-electronics, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinfeng Liu
- State Key Laboratory of Natural Medicines, Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China;
| | - Jinyun Liu
- Key Laboratory of Functional Molecular Solids of the Ministry of Education, Anhui Laboratory of Molecule-Based Materials, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China
- Correspondence: (J.L.); (X.H.); (J.L.)
| | - Wenxin Hu
- The Computer Center, School of Computer Science and Software Engineering, East China Normal University, Shanghai 200062, China;
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China;
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Correspondence: (J.L.); (X.H.); (J.L.)
| | - Jinjin Li
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication, Key laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Micro/Nano-electronics, Shanghai Jiao Tong University, Shanghai 200240, China
- Key Laboratory of Functional Molecular Solids of the Ministry of Education, Anhui Laboratory of Molecule-Based Materials, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China
- Correspondence: (J.L.); (X.H.); (J.L.)
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43
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Brunken C, Reiher M. Self-Parametrizing System-Focused Atomistic Models. J Chem Theory Comput 2020; 16:1646-1665. [DOI: 10.1021/acs.jctc.9b00855] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Christoph Brunken
- Laboratory for Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Markus Reiher
- Laboratory for Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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44
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Campos DMO, Bezerra KS, Esmaile SC, Fulco UL, Albuquerque EL, Oliveira JIN. Intermolecular interactions of cn-716 and acyl-KR-aldehyde dipeptide inhibitors against Zika virus. Phys Chem Chem Phys 2020; 22:15683-15695. [DOI: 10.1039/d0cp02254c] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Structural representation and graphic panel showing the most relevant residues that contribute to the ZIKV NS2B–NS3–ligand complexes.
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Affiliation(s)
- Daniel M. O. Campos
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - Katyanna S. Bezerra
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - Stephany C. Esmaile
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - Umberto L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | | | - Jonas I. N. Oliveira
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
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45
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Oliveira CX, Mocellin A, Menezes de Souza Lima F, Jesus Chaves Neto AM, Lima Azevedo D. DFT Study of L‐Cysteine Fragmentation Route using a Novel Protocol. ChemistrySelect 2019. [DOI: 10.1002/slct.201903453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Carlos Xavier Oliveira
- Institute of Physics University of Brasília Campus Darcy Ribeiro, Asa Norte Brasília-DF Brazil 70919-970
| | - Alexandra Mocellin
- Institute of Physics University of Brasília Campus Darcy Ribeiro, Asa Norte Brasília-DF Brazil 70919-970
| | | | | | - David Lima Azevedo
- Institute of Physics University of Brasília Campus Darcy Ribeiro, Asa Norte Brasília-DF Brazil 70919-970
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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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Abstract
Since the introduction of the fragment molecular orbital method 20 years ago, fragment-based approaches have occupied a small but growing niche in quantum chemistry. These methods decompose a large molecular system into subsystems small enough to be amenable to electronic structure calculations, following which the subsystem information is reassembled in order to approximate an otherwise intractable supersystem calculation. Fragmentation sidesteps the steep rise (with respect to system size) in the cost of ab initio calculations, replacing it with a distributed cost across numerous computer processors. Such methods are attractive, in part, because they are easily parallelizable and therefore readily amenable to exascale computing. As such, there has been hope that distributed computing might offer the proverbial "free lunch" in quantum chemistry, with the entrée being high-level calculations on very large systems. While fragment-based quantum chemistry can count many success stories, there also exists a seedy underbelly of rarely acknowledged problems. As these methods begin to mature, it is time to have a serious conversation about what they can and cannot be expected to accomplish in the near future. Both successes and challenges are highlighted in this Perspective.
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Affiliation(s)
- John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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48
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Liu J, Rana B, Liu KY, Herbert JM. Variational Formulation of the Generalized Many-Body Expansion with Self-Consistent Charge Embedding: Simple and Correct Analytic Energy Gradient for Fragment-Based ab Initio Molecular Dynamics. J Phys Chem Lett 2019; 10:3877-3886. [PMID: 31251619 DOI: 10.1021/acs.jpclett.9b01214] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The many-body expansion (MBE) and its extension to overlapping fragments, the generalized (G)MBE, constitute the theoretical basis for most fragment-based approaches for large-scale quantum chemistry. We reformulate the GMBE for use with embedding charges determined self-consistently from the fragment wave functions, in a manner that preserves the variational nature of the underlying self-consistent field method. As a result, the analytic gradient retains the simple "sum of fragment gradients" form that is often assumed in practice, sometimes incorrectly. This obviates (without approximation) the need to solve coupled-perturbed equations, and we demonstrate stable, fragment-based ab initio molecular dynamics simulations using this technique. Energy conservation fails when charge-response contributions to the Fock matrix are neglected, even while geometry optimizations and vibrational frequency calculations may yet be accurate. Stable simulations can be recovered by means of straightforward modifications introduced here, providing a general paradigm for fragment-based ab initio molecular dynamics.
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Affiliation(s)
- Jie Liu
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Bhaskar Rana
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Kuan-Yu Liu
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - John M Herbert
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
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49
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Liu J, Sun H, Glover WJ, He X. Prediction of Excited-State Properties of Oligoacene Crystals Using Fragment-Based Quantum Mechanical Method. J Phys Chem A 2019; 123:5407-5417. [PMID: 31187994 DOI: 10.1021/acs.jpca.8b12552] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A fundamental understanding of the excited-state properties of molecular crystals is of central importance for their optoelectronics applications. In this study, we developed the electrostatically embedded generalized molecular fractionation (EE-GMF) method for the quantitative characterization of the excited-state properties of locally excited molecular clusters. The accuracy of the EE-GMF method is systematically assessed for oligoacene crystals. Our result demonstrates that the EE-GMF method is capable of providing the lowest vertical singlet (S1) and triplet excitation energies (T1), in excellent agreement with the full-system quantum mechanical calculations. Using this method, we also investigated the performance of different density functionals in predicting the excited-state properties of the oligoacene crystals. Among the 13 tested functionals, B3LYP and MN15 give the two lowest overall mean unsigned errors with reference to the experimental S1 and T1 excitation energies. The EE-GMF approach can be readily utilized for studying the excited-state properties of large-scale organic solids at diverse ab initio levels.
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Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy , China Pharmaceutical University , Nanjing 210009 , China
| | | | - William J Glover
- NYU Shanghai , Shanghai 200122 , China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062 , China.,Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Xiao He
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062 , China
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50
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Xu M, He X, Zhu T, Zhang JZH. A Fragment Quantum Mechanical Method for Metalloproteins. J Chem Theory Comput 2019; 15:1430-1439. [PMID: 30620584 DOI: 10.1021/acs.jctc.8b00966] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An accurate energy calculation of metalloprotein is of crucial importance and also a theoretical challenge. In this work, a metal molecular fractionation with conjugate caps (metal-MFCC) approach is developed for efficient linear-scaling quantum calculation of potential energy and atomic forces of metalloprotein. In this approach, the potential energy of a given protein is calculated by a linear combination of potential energies of the neighboring residues, two-body interaction energy between non-neighboring residues that are spatially in close contact and the potential energy of the metal binding group. The calculation of each fragment is embedded in a field of point charges representing the remaining protein environment. Numerical studies were carried out to check the performance of this method, and the calculated potential energies and atomic forces all show excellent agreement with the full system calculations at the M06-2X/6-31G(d) level. By combining the energy calculation with molecular dynamic simulation, we performed an ab initio structural optimization for a zinc finger protein with high efficiency. The present metal-MFCC approach is linear-scaling with a low prefactor and trivially parallelizable. The individual fragment typically contains about 50 atoms, and it is thus possible to be calculated at higher levels of the quantum chemistry method. This fragment method can be routinely applied to perform structural optimization and ab initio molecular dynamic simulation for metalloproteins of any size.
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Affiliation(s)
- Mingyuan Xu
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai , 200062 , China
| | - Tong Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai , 200062 , China
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai , 200062 , China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai , 200062 , China.,Department of Chemistry , New York University , New York 10003 , United States
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