751
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Encapsulation of monomers, homodimers and heterodimers of amides and carboxylic acids in three non-covalent assemblies. Struct Chem 2015. [DOI: 10.1007/s11224-015-0682-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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752
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Yoshida T, Hayashi T, Mashima A, Chuman H. A simple and efficient dispersion correction to the Hartree-Fock theory (2): Incorporation of a geometrical correction for the basis set superposition error. Bioorg Med Chem Lett 2015; 25:4179-84. [PMID: 26292629 DOI: 10.1016/j.bmcl.2015.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 07/29/2015] [Accepted: 08/04/2015] [Indexed: 02/02/2023]
Abstract
One of the most challenging problems in computer-aided drug discovery is the accurate prediction of the binding energy between a ligand and a protein. For accurate estimation of net binding energy ΔEbind in the framework of the Hartree-Fock (HF) theory, it is necessary to estimate two additional energy terms; the dispersion interaction energy (Edisp) and the basis set superposition error (BSSE). We previously reported a simple and efficient dispersion correction, Edisp, to the Hartree-Fock theory (HF-Dtq). In the present study, an approximation procedure for estimating BSSE proposed by Kruse and Grimme, a geometrical counterpoise correction (gCP), was incorporated into HF-Dtq (HF-Dtq-gCP). The relative weights of the Edisp (Dtq) and BSSE (gCP) terms were determined to reproduce ΔEbind calculated with CCSD(T)/CBS or /aug-cc-pVTZ (HF-Dtq-gCP (scaled)). The performance of HF-Dtq-gCP (scaled) was compared with that of B3LYP-D3(BJ)-bCP (dispersion corrected B3LYP with the Boys and Bernadi counterpoise correction (bCP)), by taking ΔEbind (CCSD(T)-bCP) of small non-covalent complexes as 'a golden standard'. As a critical test, HF-Dtq-gCP (scaled)/6-31G(d) and B3LYP-D3(BJ)-bCP/6-31G(d) were applied to the complex model for HIV-1 protease and its potent inhibitor, KNI-10033. The present results demonstrate that HF-Dtq-gCP (scaled) is a useful and powerful remedy for accurately and promptly predicting ΔEbind between a ligand and a protein, albeit it is a simple correction procedure.
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Affiliation(s)
- Tatsusada Yoshida
- Institute of Biomedical Sciences, Tokushima University, Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Takahisa Hayashi
- Institute of Biomedical Sciences, Tokushima University, Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Akira Mashima
- Institute of Biomedical Sciences, Tokushima University, Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Hiroshi Chuman
- Institute of Biomedical Sciences, Tokushima University, Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan.
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753
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Qiu L, Lin J, Bertaccini EJ. Insights into the Nature of Anesthetic-Protein Interactions: An ONIOM Study. J Phys Chem B 2015; 119:12771-82. [PMID: 26388288 DOI: 10.1021/acs.jpcb.5b05897] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Anesthetics have been employed widely to relieve surgical suffering, but their mechanism of action is not yet clear. For over a century, the mechanism of anesthesia was previously thought to be via lipid bilayer interactions. In the present work, a rigorous three-layer ONIOM(M06-2X/6-31+G*:PM6:AMBER) method was utilized to investigate the nature of interactions between several anesthetics and actual protein binding sites. According to the calculated structural features, interaction energies, atomic charges, and electrostatic potential surfaces, the amphiphilic nature of anesthetic-protein interactions was demonstrated for both inhalational and injectable anesthetics. The existence of hydrogen and halogen bonding interactions between anesthetics and proteins was clearly identified, and these interactions served to assist ligand recognition and binding by the protein. Within all complexes of inhalational or injectable anesthetics, the polarization effects play a dominant role over the steric effects and induce a significant asymmetry in the otherwise symmetric atomic charge distributions of the free ligands in vacuo. This study provides new insight into the mechanism of action of general anesthetics in a more rigorous way than previously described. Future rational design of safer anesthetics for an aging and more physiologically vulnerable population will be predicated on this greater understanding of such specific interactions.
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Affiliation(s)
- Ling Qiu
- Key Laboratory of Nuclear Medicine, Ministry of Health & Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine , Wuxi 214063, P. R. China.,Department of Anesthesia, Stanford University School of Medicine, Palo Alto VA Health Care System , 112A, PAVAHCS, 3801 Miranda Avenue, Palo Alto, California 94304, United States
| | - Jianguo Lin
- Key Laboratory of Nuclear Medicine, Ministry of Health & Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine , Wuxi 214063, P. R. China
| | - Edward J Bertaccini
- Department of Anesthesia, Stanford University School of Medicine, Palo Alto VA Health Care System , 112A, PAVAHCS, 3801 Miranda Avenue, Palo Alto, California 94304, United States
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754
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Li Y, Li X, Liu J, Duan F, Yu J. In silico prediction and screening of modular crystal structures via a high-throughput genomic approach. Nat Commun 2015; 6:8328. [PMID: 26395233 PMCID: PMC4667440 DOI: 10.1038/ncomms9328] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 08/11/2015] [Indexed: 12/28/2022] Open
Abstract
High-throughput computational methods capable of predicting, evaluating and identifying promising synthetic candidates with desired properties are highly appealing to today's scientists. Despite some successes, in silico design of crystalline materials with complex three-dimensionally extended structures remains challenging. Here we demonstrate the application of a new genomic approach to ABC-6 zeolites, a family of industrially important catalysts whose structures are built from the stacking of modular six-ring layers. The sequences of layer stacking, which we deem the genes of this family, determine the structures and the properties of ABC-6 zeolites. By enumerating these gene-like stacking sequences, we have identified 1,127 most realizable new ABC-6 structures out of 78 groups of 84,292 theoretical ones, and experimentally realized 2 of them. Our genomic approach can extract crucial structural information directly from these gene-like stacking sequences, enabling high-throughput identification of synthetic targets with desired properties among a large number of candidate structures. High-throughput computation aids design of new functional materials. Here, Yu et al. develop a high-throughput screening method for a group of zeolites with crystalline modular structures which are viewed as having gene-like stacking codes, and identify the most promising structures with desired properties.
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Affiliation(s)
- Yi Li
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Xu Li
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Jiancong Liu
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Fangzheng Duan
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Jilin University, Qianjin Street 2699, Changchun 130012, China
| | - Jihong Yu
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Jilin University, Qianjin Street 2699, Changchun 130012, China
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755
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Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse. Proc Natl Acad Sci U S A 2015; 112:E5228-36. [PMID: 26351676 DOI: 10.1073/pnas.1511207112] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DNA polymerases facilitate faithful insertion of nucleotides, a central reaction occurring during DNA replication and repair. DNA synthesis (forward reaction) is "balanced," as dictated by the chemical equilibrium by the reverse reaction of pyrophosphorolysis. Two closely spaced divalent metal ions (catalytic and nucleotide-binding metals) provide the scaffold for these reactions. The catalytic metal lowers the pKa of O3' of the growing primer terminus, and the nucleotide-binding metal facilitates substrate binding. Recent time-lapse crystallographic studies of DNA polymerases have identified an additional metal ion (product metal) associated with pyrophosphate formation, leading to the suggestion of its possible involvement in the reverse reaction. Here, we establish a rationale for a role of the product metal using quantum mechanical/molecular mechanical calculations of the reverse reaction in the confines of the DNA polymerase β active site. Additionally, site-directed mutagenesis identifies essential residues and metal-binding sites necessary for pyrophosphorolysis. The results indicate that the catalytic metal site must be occupied by a magnesium ion for pyrophosphorolysis to occur. Critically, the product metal site is occupied by a magnesium ion early in the pyrophosphorolysis reaction path but must be removed later. The proposed dynamic nature of the active site metal ions is consistent with crystallographic structures. The transition barrier for pyrophosphorolysis was estimated to be significantly higher than that for the forward reaction, consistent with kinetic activity measurements of the respective reactions. These observations provide a framework to understand how ions and active site changes could modulate the internal chemical equilibrium of a reaction that is central to genome stability.
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756
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Li J, Iyengar SS. Ab Initio Molecular Dynamics Using Recursive, Spatially Separated, Overlapping Model Subsystems Mixed within an ONIOM-Based Fragmentation Energy Extrapolation Technique. J Chem Theory Comput 2015; 11:3978-91. [DOI: 10.1021/acs.jctc.5b00433] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Junjie Li
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Ave, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and
Department of Physics, Indiana University, 800 E. Kirkwood Ave, Bloomington, Indiana 47405, United States
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757
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Sengupta A, Ramabhadran RO, Raghavachari K. Breaking a bottleneck: Accurate extrapolation to “gold standard” CCSD(T) energies for large open shell organic radicals at reduced computational cost. J Comput Chem 2015; 37:286-95. [DOI: 10.1002/jcc.24050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/14/2015] [Accepted: 07/20/2015] [Indexed: 11/11/2022]
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758
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Kellie JL, Wilson KA, Wetmore SD. An ONIOM and MD Investigation of Possible Monofunctional Activity of Human 8-Oxoguanine–DNA Glycosylase (hOgg1). J Phys Chem B 2015; 119:8013-23. [PMID: 26018802 DOI: 10.1021/acs.jpcb.5b04051] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jennifer L. Kellie
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada, T1K 3M4
| | - Katie A. Wilson
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada, T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada, T1K 3M4
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759
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Hirao H, Ng WKH, Moeljadi AMP, Bureekaew S. Multiscale Model for a Metal–Organic Framework: High-Spin Rebound Mechanism in the Reaction of the Oxoiron(IV) Species of Fe-MOF-74. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00475] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hajime Hirao
- Division of Chemistry and
Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Wilson Kwok Hung Ng
- Division of Chemistry and
Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Adhitya Mangala Putra Moeljadi
- Division of Chemistry and
Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
| | - Sareeya Bureekaew
- Division of Chemistry and
Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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760
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Gomez-Gualdron DA, Dix ST, Getman RB, Snurr RQ. A modelling approach for MOF-encapsulated metal catalysts and application to n-butane oxidation. Phys Chem Chem Phys 2015; 17:27596-608. [DOI: 10.1039/c5cp04705f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A surrogate pore mimics the steric constraints provided by a MOF on n-butane in a MOF-encapsulated metal catalyst.
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Affiliation(s)
| | - Sean T. Dix
- Department of Chemical and Biomolecular Engineering
- Clemson University
- Clemson
- USA
| | - Rachel B. Getman
- Department of Chemical and Biomolecular Engineering
- Clemson University
- Clemson
- USA
| | - Randall Q. Snurr
- Department of Chemical and Biological Engineering
- Northwestern University
- Evanston
- USA
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761
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Wang W, Wang GC. Computational study on the mechanism and enantioselectivity of Rh2(S-PTAD)4 catalyzed asymmetric [4+3] cycloaddition between vinylcarbenoids and dienes. RSC Adv 2015. [DOI: 10.1039/c5ra14815d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In this paper, the mechanism of asymmetric [4+3] cycloaddition between a vinylcarbenoid and a diene to form cycloheptadiene has been studied using a two-layer ONIOM methodology consisting of density functional theory and semiempirical PM6.
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Affiliation(s)
- Wan Wang
- Department of Chemistry
- Tianjin Key Lab of Metal and Molecule-based Material Chemistry and Synergetic Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- P. R. China
| | - Gui-Chang Wang
- Department of Chemistry
- Tianjin Key Lab of Metal and Molecule-based Material Chemistry and Synergetic Innovation Center of Chemical Science and Engineering (Tianjin)
- Nankai University
- Tianjin 300071
- P. R. China
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762
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Zeifman AA, Novikov FN, Stroylov VS, Stroganov OV, Svitanko IV, Chilov GG. An explicit account of solvation is essential for modeling Suzuki–Miyaura coupling in protic solvents. Dalton Trans 2015; 44:17795-9. [DOI: 10.1039/c5dt03126e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We compared explicit and implicit solvation approaches in modeling the free energy profile of the final step of Suzuki–Miyaura coupling.
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Affiliation(s)
- Alexey A. Zeifman
- N. D. Zelinsky Institute Of Organic Chemistry (ZIOC RAS)
- 119991 Moscow
- Russian Federation
| | - Fedor N. Novikov
- N. D. Zelinsky Institute Of Organic Chemistry (ZIOC RAS)
- 119991 Moscow
- Russian Federation
| | - Victor S. Stroylov
- N. D. Zelinsky Institute Of Organic Chemistry (ZIOC RAS)
- 119991 Moscow
- Russian Federation
| | - Oleg V. Stroganov
- N. D. Zelinsky Institute Of Organic Chemistry (ZIOC RAS)
- 119991 Moscow
- Russian Federation
| | - Igor V. Svitanko
- N. D. Zelinsky Institute Of Organic Chemistry (ZIOC RAS)
- 119991 Moscow
- Russian Federation
| | - Ghermes G. Chilov
- N. D. Zelinsky Institute Of Organic Chemistry (ZIOC RAS)
- 119991 Moscow
- Russian Federation
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763
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Jover J, Maseras F. QM/MM Calculations on Selectivity in Homogeneous Catalysis. STRUCTURE AND BONDING 2015. [DOI: 10.1007/430_2015_188] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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