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Ashkarran AA, Hosseini A, Loloee R, Perry G, Lee KB, Lund M, Ejtehadi MR, Mahmoudi M. Conformation- and phosphorylation-dependent electron tunnelling across self-assembled monolayers of tau peptides. J Colloid Interface Sci 2022; 606:2038-2050. [PMID: 34749450 DOI: 10.1016/j.jcis.2021.09.185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/17/2021] [Accepted: 09/28/2021] [Indexed: 10/20/2022]
Abstract
We report on charge transport across self-assembled monolayers (SAMs) of short tau peptides by probing the electron tunneling rates and quantum mechanical simulation. We measured the electron tunneling rates across SAMs of carboxyl-terminated linker molecules (C6H12O2S) and short cis-tau (CT) and trans-tau (TT) peptides, supported on template-stripped gold (AuTS) bottom electrode, with Eutectic Gallium-Indium (EGaIn)(EGaIn) top electrode. Measurements of the current density across thousands of AuTS/linker/tau//Ga2O3/EGaIn single-molecule junctions show that the tunneling current across CT peptide is one order of magnitude lower than that of TT peptide. Quantum mechanical simulation demonstrated a wider energy bandgap of the CT peptide, as compared to the TT peptide, which causes a reduction in its electron tunneling current. Our findings also revealed the critical role of phosphorylation in altering the charge transport characteristics of short peptides; more specifically, we found that the presence of phosphate groups can reduce the energy band gap in tau peptides and alter their electrical properties. Our results suggest that conformational and phosphorylation of short peptides (e.g., tau) can significantly change their charge transport characteristics and energy levels.
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Affiliation(s)
- Ali Akbar Ashkarran
- Precision Health Program and Department of Radiology, Michigan State University, East Lansing, MI 48824, USA.
| | - Atiyeh Hosseini
- Division of Theoretical Chemistry, Lund University, Lund, Sweden; Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran, Iran
| | - Reza Loloee
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
| | - George Perry
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Mikael Lund
- Division of Theoretical Chemistry, Lund University, Lund, Sweden.
| | | | - Morteza Mahmoudi
- Precision Health Program and Department of Radiology, Michigan State University, East Lansing, MI 48824, USA
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2
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Hosseini N, Lund M, Ejtehadi MR. Polarization Switching Method for Effective Free Energy Calculation of Membrane Translocation on the Nano-scale. Phys Chem Chem Phys 2022; 24:12281-12292. [DOI: 10.1039/d2cp00056c] [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
Free-energy calculations are crucial for investigating biomolecular interactions on the Nano-scale level. However, in theoretical studies, the neglect of electronic polarization can jeopardize their accuracy and correct predictive capabilities, specifically...
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Xing YY, Chen SS, Chen DZ, Tantillo DJ. Effects of electrostatic drag on the velocity of hydrogen migration - pre- and post-transition state enthalpy/entropy compensation. Phys Chem Chem Phys 2020; 22:26955-26960. [PMID: 33206074 DOI: 10.1039/d0cp05000h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ab initio molecular dynamics calculations were used to explore the underlying factors that modulate the velocity of hydrogen migration for 1,2 hydrogen shifts in carbocations in which different groups interact noncovalently with the migrating hydrogen. Our results indicate that stronger electrostatic interactions between the migrating hydrogen and nearby π-systems lead to slower hydrogen migration, an effect tied to entropic contributions from the hydrogen + neighboring group substructures.
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Affiliation(s)
- Yang-Yang Xing
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan 250014, P. R. China.
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4
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de Oliveira BG, Zabardasti A, do Rego DG, Pour MM. The formation of H···X hydrogen bond, C···X carbon-halide or Si···X tetrel bonds on the silylene-halogen dimers (X = F or Cl): intermolecular strength, molecular orbital interactions and prediction of covalency. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02644-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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5
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Liao J, Zeng W, Zheng B, Cao X, Wang Z, Wang G, Yang Q. Highly efficient CO 2 capture and conversion of a microporous acylamide functionalized rht-type metal–organic framework. Inorg Chem Front 2020. [DOI: 10.1039/d0qi00231c] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A microporous acylamide functionalized rht-type MOF (HNUST-9) with Lewis acidic open copper sites and CO2-philic acylamide groups exhibits high performance for CO2 capture, separation and chemical conversion.
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Affiliation(s)
- Junxiong Liao
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule of Ministry of Education
- Hunan Provincial Key Laboratory of Controllable Preparation and Functional Application of Fine Polymers
- Hunan Provincial Key Laboratory of Advanced Materials for New Energy Storage and Conversion
- School of Chemistry and Chemical Engineering
- Hunan University of Science and Technology
| | - Wenjiang Zeng
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule of Ministry of Education
- Hunan Provincial Key Laboratory of Controllable Preparation and Functional Application of Fine Polymers
- Hunan Provincial Key Laboratory of Advanced Materials for New Energy Storage and Conversion
- School of Chemistry and Chemical Engineering
- Hunan University of Science and Technology
| | - Baishu Zheng
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule of Ministry of Education
- Hunan Provincial Key Laboratory of Controllable Preparation and Functional Application of Fine Polymers
- Hunan Provincial Key Laboratory of Advanced Materials for New Energy Storage and Conversion
- School of Chemistry and Chemical Engineering
- Hunan University of Science and Technology
| | - Xiyang Cao
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule of Ministry of Education
- Hunan Provincial Key Laboratory of Controllable Preparation and Functional Application of Fine Polymers
- Hunan Provincial Key Laboratory of Advanced Materials for New Energy Storage and Conversion
- School of Chemistry and Chemical Engineering
- Hunan University of Science and Technology
| | - Zhaoxu Wang
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule of Ministry of Education
- Hunan Provincial Key Laboratory of Controllable Preparation and Functional Application of Fine Polymers
- Hunan Provincial Key Laboratory of Advanced Materials for New Energy Storage and Conversion
- School of Chemistry and Chemical Engineering
- Hunan University of Science and Technology
| | - Guanyu Wang
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule of Ministry of Education
- Hunan Provincial Key Laboratory of Controllable Preparation and Functional Application of Fine Polymers
- Hunan Provincial Key Laboratory of Advanced Materials for New Energy Storage and Conversion
- School of Chemistry and Chemical Engineering
- Hunan University of Science and Technology
| | - Qingyuan Yang
- State Key Laboratory of Organic-Inorganic Composites
- Beijing University of Chemical Technology
- Beijing 100029
- China
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6
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S Pillai R, Suresh CH. Computational prediction of promising pyrazine and bipyridine analogues of a fluorinated MOF platform, MFN-Ni-L (M = SI/AL; N = SIX/FIVE; L = pyr/bipyr), for CO 2 capture under pre-humidified conditions. Phys Chem Chem Phys 2019; 21:16127-16136. [PMID: 31290872 DOI: 10.1039/c9cp00845d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The CO2 separation performance has been explored under dry and pre-humidified conditions for the fluorinated metal organic frameworks SIFSIX-Ni-pyr, ALFFIVE-Ni-pyr, SIFSIX-Ni-bipyr and ALFFIVE-Ni-bipyr, which are incorporated with/without a coordinatively unsaturated site (CUS), Al, and organic linkers 1,4-pyrazine and 4,4'-bipyridine. The ultra-small pore size (∼4 Å) of the pyrazine analogues of fluorinated-MOFs, i.e. SIFSIX-Ni-pyr and ALFFIVE-Ni-pyr, showed infinite selectivity towards CO2 with low uptake capability under dry conditions, which drastically reduced to 0 wt% under very low pre-humidification conditions (∼10-15 wt% adsorbed moisture). In marked contrast, the bipyridine analogues SIFSIX-Ni-bipyr and ALFFIVE-Ni-bipyr showed significant CO2 capture performance of up to 30-40 wt% with pre-humidification. Further, both SIFSIX-Ni-bipyr and ALFFIVE-Ni-bipyr showed high CO2 selectivity as well as good working capacity at 1-10 bar while poor selectivity is observed for the pyrazine analogues with pre-humidification. The incorporation of Al as a CUS provides stability to the ALFFIVE-Ni-bipyr fluorinated-MOF under pre-humidified conditions due to the ability of Al to co-ordinate with water molecules in hydrogen bonded networks. Therefore, to develop physisorption-based CO2 capturing processes under pre-humidified conditions, the use of Al incorporated ALFFIVE-Ni-bipyr is highly suitable, which may outperform most of the fluorinated-MOFs and other classes of porous solids reported so far.
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Affiliation(s)
- Renjith S Pillai
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram-695019, India and Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603203, Chennai, India.
| | - Cherumuttathu H Suresh
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram-695019, India
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7
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Theoretical study of an anti-Markovnikov addition reaction catalyzed by β-cyclodextrin. J Mol Model 2018; 24:77. [PMID: 29500625 DOI: 10.1007/s00894-018-3595-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/25/2018] [Indexed: 10/17/2022]
Abstract
β-Cyclodextrin (β-CD) has a hydrophilic exterior and a hydrophobic internal cavity, which allows it to form host-guest complexes with a wide range of guests, such as organics, inorganics, and biomolecules. The aforementioned features lead to an extensive range of applications of β-CD, as the properties of β-CD mean that it is environmentally friendly and can be recovered and reused without mass loss. Here, the β-CD-catalyzed anti-Markovnikov addition of styrene to thiophenol in the presence of aerial oxygen and in aqueous solution to give 1-phenyl-2-(phenylsulfanyl)-1-ethanol was studied using density functional theory (DFT) and the Hartree-Fock (HF) method. The optimal configuration of the inclusion complex of styrene and thiophenol within β-CD was obtained, which indicated that styrene and thiophenol enter from the secondary and primary hydroxyl ends of β-CD, respectively. Moreover, hydrogen bonding of β-CD with styrene and thiophenol contributes to the stability of the inclusion complex. An investigation of the charges from electrostatic potentials using a grid-based method (CHELPG) highlighted the distribution of atomic charges upon complexation. The reaction sites of styrene and thiophenol were determined based on electrostatic potentials (ESPs) and condensed dual descriptors. The calculated 1H nuclear magnetic resonance (1H NMR) spectrum of β-CD implied that the chemical shifts of its protons change and H3 and H5 move to higher fields upon complexation, while the calculated 13C nuclear magnetic resonance (13C NMR) spectrum of styrene suggested that this molecule is electrophilic. Graphical abstract ᅟ.
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8
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Viana RB. On the structure of the simplest triselenide compound model and the stabilizing effect of water molecules. Polyhedron 2017. [DOI: 10.1016/j.poly.2017.03.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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9
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Correra TC, Fernandes AS, Riveros JM. Dynamic/Thermochemical Balance Drives Unusual Alkyl/F Exchange Reactions in Siloxides and Analogs. J Phys Chem A 2016; 120:1644-51. [PMID: 26911457 DOI: 10.1021/acs.jpca.6b00390] [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
A recent report has shown that siloxides can undergo an unusual Me/F exchange reaction promoted by NF3 in the gas phase ( Angew. Chem. Int. Ed. 2012, 51, 8632-8635). A more extensive study of this kind of exchange has been carried out using mass spectrometry techniques (FT-ICR), DFT calculations, natural bond orbital (NBO) analysis, and Born-Oppenheimer molecular dynamics simulations (BOMD), using NF3, SO2F2, and CF4 as fluorine donors and evaluating the effect of replacing the Si center by Ge and C. This comprehensive approach shows that NF3 is crucial for the exchange reaction, as SO2F2 forms SO3F(-) via a pentacoordinated channel whereas no reaction is observed for CF4. The uniqueness of NF3 is caused by favorable thermochemical consideration and by dynamic effects that preclude the formation of the ubiquitous Si-F pentacoordinated species. Me3GeO(-) was shown to be as reactive as siloxides toward NF3, whereas C analogs showed no reactions under our experimental conditions. The exchange reaction was also shown to take place for triethylsiloxides. These exchange reactions are examples of reaction systems that avoid the lower energy pathway and are driven by dynamic effects that cannot be explained by the potential energy surface.
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Affiliation(s)
- Thiago C Correra
- Departamento de Quı́mica Fundamental, Instituto de Quı́mica, Universidade de São Paulo , São Paulo, Brazil - CEP 05508-000
| | - André S Fernandes
- Departamento de Quı́mica Fundamental, Instituto de Quı́mica, Universidade de São Paulo , São Paulo, Brazil - CEP 05508-000
| | - José M Riveros
- Departamento de Quı́mica Fundamental, Instituto de Quı́mica, Universidade de São Paulo , São Paulo, Brazil - CEP 05508-000
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10
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Hori Y, Ida T, Mizuno M. A comparative theoretical study of the hydride transfer mechanisms during LiAlH 4 and LiBH 4 reductions. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2015.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Gardarsson H, Schweizer WB, Trapp N, Diederich F. Structures and Properties of Molecular Torsion Balances to Decipher the Nature of Substituent Effects on the Aromatic Edge-to-Face Interaction. Chemistry 2014; 20:4608-16. [DOI: 10.1002/chem.201304810] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Indexed: 11/10/2022]
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12
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Viana RB, Guimarães AR, de Souza AR, da Silva ABF. Molecular properties of the PCO radical: heat of formation and the isomerization pathways. J Mol Model 2014; 20:2074. [PMID: 24504453 DOI: 10.1007/s00894-014-2074-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 11/12/2013] [Indexed: 11/29/2022]
Abstract
The potential energy surface of [P,C,O] system in the ground state was investigated by quantum chemical methods. Four different isomers were characterized at the B3LYP/aug-cc-pVTZ: COP (i1), cPCO (i2), PCO (i3), and CPO (i4). The linear species i3 is the global minimum in the ground state surface, while i4 is a bent structure, and i2 is a cyclic isomer. In view to evaluate the bond nature of each isomer, a QTAIM and a NBO analyses were applied. The triangular species presents a ring critical point which confirms its cyclic structure instead of a T-shape one. The stability increases in the following order: i3 > i2 > i1 > i4. The energy gap between i3 and i2 ranges from 49.20 to 51.15 kcal mol(-1). The reaction barrier energies that converge into the direction of i3 showed values around 10 kcal mol(-1), while the reverse barriers are considerably large (62.85 kcal mol(-1)). The i3 heat of formation at 298 K ranges from 11.83 to 19.41 kcal mol(-1).
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Affiliation(s)
- Rommel B Viana
- Instituto de Química de São Carlos, Universidade de São Paulo, USP, São Carlos, SP, Brasil,
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13
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Megow J, Plehn T, Steffen R, Röder B, May V. Photoinduced excitation energy transfer in hexapyropheophorbide a. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.08.076] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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14
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Yang Q, Liu D, Zhong C, Li JR. Development of computational methodologies for metal-organic frameworks and their application in gas separations. Chem Rev 2013; 113:8261-323. [PMID: 23826973 DOI: 10.1021/cr400005f] [Citation(s) in RCA: 284] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Qingyuan Yang
- Laboratory of Computational Chemistry and State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology , Beijing 100029, China
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15
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Monajjemi M, Boggs JE. A new generation of B(n)N(n) rings as a supplement to boron nitride tubes and cages. J Phys Chem A 2013; 117:1670-84. [PMID: 23347207 DOI: 10.1021/jp312073q] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In B(n)N(n) cages or tubes, when the quasi-borazine rings are attached to each other through a pair of common atoms of B and N, the bonding structure is named class A. On the other hand, there are some B(n)N(n) rings including a covalent bond between two atoms of B and N, which are named class B. In all previous studies, both reports of synthesis and theoretical calculation of boron nitride tubes and cages, the quasi-borazine units are attached together like class A. There are no theoretical or experimental reports from class B compounds except for a brief study in our previous works (Struct. Chem. 2012, 23, 551-580; J. Phys. Chem. C 2010, 114, 15315.). In this study, we have used two kinds of boron nitride rings from a twisted BN sheet in the same chirality created by different mechanisms. For (4, 4) chirality, the molecules B(16)N(16) and B(15)N(15) are found to respectively represent class A and B, and for (5, 5) chirality the molecules B(20)N(20) and B(18)N(18) are respectively again of class A and B. The structure of class A rings is similar to boron nitride tubes, but we have shown that it is impossible to produce a macromolecule of class B form as tubes or cages, because there is much more instability and intermolecular tension in macro forms of class B. This is the main reason that the class B molecules are rare and, because of their small size, have not yet been synthesized, although we have some suggestions for the synthesis of these kinds of molecules. The stability and electromagnetic properties with hybrid density functional theory using the EPR-III and EPR-II basis sets for explanation of hyperfine parameters and spin densities, electrical potential, and isotropic Fermi coupling constant of these rings have been studied by the nonbonded interaction models. Normal mode analyses including aromaticity have been investigated by using the nucleus independent chemical shift values at the ring center. Interaction energy and gain in energy aid in describing the stability that is promoted upon gradual binding with molecular hydrogen, and a linear relationship occurred between them.
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Affiliation(s)
- Majid Monajjemi
- Institute for Theoretical Chemistry, Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas, USA.
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Jämbeck JPM, Mocci F, Lyubartsev AP, Laaksonen A. Partial atomic charges and their impact on the free energy of solvation. J Comput Chem 2012; 34:187-97. [DOI: 10.1002/jcc.23117] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 08/23/2012] [Accepted: 08/24/2012] [Indexed: 11/10/2022]
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17
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Monajjemi M. Quantum investigation of non-bonded interaction between the B15N15 ring and BH2NBH2 (radical, cation, anion) systems: a nano molecularmotor. Struct Chem 2011. [DOI: 10.1007/s11224-011-9895-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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18
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Kulkarni C, Reddy SK, George SJ, Balasubramanian S. Cooperativity in the stacking of benzene-1,3,5-tricarboxamide: The role of dispersion. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.09.028] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Monajjemi M, Khaleghian M. EPR Study of Electronic Structure of [CoF6]3−and B18N18 Nano Ring Field Effects on Octahedral Complex. J CLUST SCI 2011. [DOI: 10.1007/s10876-011-0414-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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20
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Rana MK, Pazzona FG, Suffritti GB, Demontis P, Masia M. Estimation of Partial Charges in Small Zeolite Imidazolate Frameworks from Density Functional Theory Calculations. J Chem Theory Comput 2011; 7:1575-82. [DOI: 10.1021/ct100685p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Malay Kumar Rana
- Dipartimento di Chimica, Università degli Studi di Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - Federico Giovanni Pazzona
- Dipartimento di Chimica, Università degli Studi di Sassari, and Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di Ricerca di Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - Giuseppe Baldovino Suffritti
- Dipartimento di Chimica, Università degli Studi di Sassari, and Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di Ricerca di Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - Pierfranco Demontis
- Dipartimento di Chimica, Università degli Studi di Sassari, and Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di Ricerca di Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - Marco Masia
- Dipartimento di Chimica, Università degli Studi di Sassari, Istituto Officina dei Materiali del CNR, UOS SLACS, Via Vienna 2, 07100 Sassari, Italy
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21
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Świderek K, Paneth P. Differences and similarities in binding of pyruvate and l-lactate in the active site of M4 and H4 isoforms of human lactate dehydrogenase. Arch Biochem Biophys 2011; 505:33-41. [DOI: 10.1016/j.abb.2010.10.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Revised: 09/27/2010] [Accepted: 10/08/2010] [Indexed: 11/28/2022]
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22
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Zhao Z, Rogers DM, Beck TL. Polarization and charge transfer in the hydration of chloride ions. J Chem Phys 2010; 132:014502. [DOI: 10.1063/1.3283900] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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Kantardjiev AA, Atanasov BP. PHEMTO: protein pH-dependent electric moment tools. Nucleic Acids Res 2009; 37:W422-7. [PMID: 19420068 PMCID: PMC2703894 DOI: 10.1093/nar/gkp336] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Revised: 04/17/2009] [Accepted: 04/21/2009] [Indexed: 11/13/2022] Open
Abstract
PHEMTO (protein pH-dependent electric moment tools) is released in response to the high demand in protein science community for evaluation of electrostatic characteristics in relations to molecular recognition. PHEMTO will serve protein scientists with new advanced features for analysis of protein molecular interactions: Electric/dipole moments, their pH-dependence and in silico charge mutagenesis effects on these properties as well as alternative algorithms for electric/dipole moment computation--Singular value decomposition of electrostatic potential (EP) to account for reaction field. The implementation is based on long-term experience--PHEI mean field electrostatics and PHEPS server for evaluation of global and local pH-dependent properties. However, PHEMTO is not just an update of our PHEPS server. Besides standard electrostatics, we offer new, advanced and useful features for analysis of protein molecular interactions. In addition our algorithms are very fast. Special emphasis is given to the interface--intuitive and user-friendly. The input is comprised of the atomic coordinate file in Protein Data Bank format. The advanced user is provided with a special input section for addition of non-polypeptide charges. The output covers actually full electrostatic characteristics but special emphasis is given to electric/dipole moments and their interactive visualization. PHEMTO server can be accessed at http://phemto.orgchm.bas.bg/.
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Affiliation(s)
| | - Boris P. Atanasov
- Biophysical Chemistry Group, Institute of Organic Chemistry, Bulgarian Academy of Sciences, Sofia-1113, Bulgaria
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24
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Aquilanti V, Ragni M, Bitencourt ACP, Maciel GS, Prudente FV. Intramolecular Dynamics of RS−SR′ Systems (R, R′ = H, F, Cl, CH3, C2 H5): Torsional Potentials, Energy Levels, Partition Functions. J Phys Chem A 2009; 113:3804-13. [DOI: 10.1021/jp8094215] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vincenzo Aquilanti
- Dipartimento di Chimica, Università di Perugia, 06123 Perugia, Italy, and Instituto de Física, Universidade Federal da Bahia, 40210-340 Salvador, Bahia, Brazil
| | - Mirco Ragni
- Dipartimento di Chimica, Università di Perugia, 06123 Perugia, Italy, and Instituto de Física, Universidade Federal da Bahia, 40210-340 Salvador, Bahia, Brazil
| | - Ana C. P. Bitencourt
- Dipartimento di Chimica, Università di Perugia, 06123 Perugia, Italy, and Instituto de Física, Universidade Federal da Bahia, 40210-340 Salvador, Bahia, Brazil
| | - Glauciete S. Maciel
- Dipartimento di Chimica, Università di Perugia, 06123 Perugia, Italy, and Instituto de Física, Universidade Federal da Bahia, 40210-340 Salvador, Bahia, Brazil
| | - Frederico V. Prudente
- Dipartimento di Chimica, Università di Perugia, 06123 Perugia, Italy, and Instituto de Física, Universidade Federal da Bahia, 40210-340 Salvador, Bahia, Brazil
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Yang Q, Zhong C. Molecular simulation of carbon dioxide/methane/hydrogen mixture adsorption in metal-organic frameworks. J Phys Chem B 2007; 110:17776-83. [PMID: 16956262 DOI: 10.1021/jp062723w] [Citation(s) in RCA: 470] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This work performs a systematic computational study toward a molecular understanding of the separation characteristics of metal-organic frameworks (MOFs), for which the purification of synthetic gas by two representative MOFs, MOF-5 and Cu-BTC, is adopted as an example. The simulations show that both geometry and pore size affect largely the separation efficiency, complex selectivity behaviors with different steps can occur in MOFs, and the electrostatic interactions that exist can enhance greatly the separation efficiency of gas mixtures composed of components with different chemistries. Furthermore, the macroscopic separation behaviors of the MOF materials are elucidated at a molecular level to give insight into the underlying mechanisms. The findings as well as the molecular-level elucidations provide useful microscopic information toward a complete understanding of the separation characteristics of MOFs that may lead to general design strategies for synthesizing new MOFs with tailored properties, as well as guiding their practical applications.
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Affiliation(s)
- Qingyuan Yang
- Department of Chemical Engineering, Key Laboratory of Bioprocess of Beijing, Beijing University of Chemical Technology, Beijing 100029, China
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Maciel GS, Bitencourt ACP, Ragni M, Aquilanti V. Studies of the dynamics around the O–O bond: Orthogonal local modes of hydrogen peroxide. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.10.073] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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