151
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Interplay of weak intermolecular interactions in two Schiff's bases with organic fluorine derived from 5-nitrothiophene-2-carboxaldehyde: Crystal structures, DFT calculation and in vitro evaluation of bioactivities. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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152
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153
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Pinto AV, Magalhães AL. Intramolecular Hydrogen Bonds in Tip-Functionalized Single-Walled Carbon Nanotubes as pH-Sensitive Gates. J Phys Chem A 2020; 124:9542-9551. [PMID: 33169998 DOI: 10.1021/acs.jpca.0c03710] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since their discovery, carbon nanotubes and other related nanomaterials are in the spotlight due to their unique molecular structures and properties, having a wide range of applications. The cage-like structure of carbon nanotubes is especially appealing as a route to confine molecules, isolating them from the solvent medium. This study aims to explore and characterize, through density functional theory (DFT) calculations, covalent tip-functionalization of single-walled carbon nanotubes (SWCNTS) with carboxymethyl moieties that establish pH sensitive molecular gates. The response of the molecular gate to pH fluctuations arises from variations in the noncovalent interactions between functionalized groups, which depend on the extent of protonation, leading to conformational changes. Overall, the hydrogen bonds present in the molecular models under study, as evaluated through topological analysis and pKa calculations, suggest that functionalized SWCNTs may be suitable for the design of drug delivery systems to enhance the efficiency of some pharmacological treatments, or even in the area of catalysis and separation processes, through their incorporation in nanocomposites.
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Affiliation(s)
- A V Pinto
- LAQV/Requimte, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - A L Magalhães
- LAQV/Requimte, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
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154
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van der Lubbe SC, Haim A, van Heesch T, Fonseca Guerra C. Tuning the Binding Strength of Even and Uneven Hydrogen-Bonded Arrays with Remote Substituents. J Phys Chem A 2020; 124:9451-9463. [PMID: 33054218 PMCID: PMC7667637 DOI: 10.1021/acs.jpca.0c07815] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/01/2020] [Indexed: 12/20/2022]
Abstract
We investigated the tunability of hydrogen bond strength by altering the charge accumulation around the frontier atoms with remote substituents. For pyridine···H2O with NH2 and CN substituted at different positions on pyridine, we find that the electron-withdrawing CN group decreases the negative charge accumulation around the frontier atom N, resulting in weakening of the hydrogen bond, whereas the electron-donating NH2 group increases the charge accumulation around N, resulting in strengthening of the hydrogen bond. By applying these design principles on DDAA-AADD, DADA-ADAD, DAA-ADD, and ADA-DAD hydrogen-bonded dimers, we find that the effect of the substituent is delocalized over the whole molecular system. As a consequence, systems with an equal number of hydrogen bond donor (D) and acceptor (A) atoms are not tunable in a predictable way because of cancellation of counteracting strengthening and weakening effects. Furthermore, we show that the position of the substituent and long-range electrostatics can play an important role as well. Overall, the design principles presented in this work are suitable for monomers with an unequal number of donor and acceptor atoms and can be exploited to tune the binding strength of supramolecular building blocks.
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Affiliation(s)
- Stephanie
C. C. van der Lubbe
- Department
of Theoretical Chemistry, Amsterdam Institute of Molecular and Life
Sciences (AIMMS), Amsterdam Center of Multiscale
Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Anissa Haim
- Department
of Theoretical Chemistry, Amsterdam Institute of Molecular and Life
Sciences (AIMMS), Amsterdam Center of Multiscale
Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Thor van Heesch
- Department
of Theoretical Chemistry, Amsterdam Institute of Molecular and Life
Sciences (AIMMS), Amsterdam Center of Multiscale
Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Célia Fonseca Guerra
- Department
of Theoretical Chemistry, Amsterdam Institute of Molecular and Life
Sciences (AIMMS), Amsterdam Center of Multiscale
Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
- Leiden
Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg
55, 2333 CD Leiden, The Netherlands
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155
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Borah S, Kumar PP. Hydration structure of As–III aqueous solutions from ab initio molecular dynamics simulations. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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156
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157
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Pal D, Agrawal SK, Chakraborty A, Chakraborty S. Competition between the hydrogen bond and the halogen bond in a [CH 3OH-CCl 4] complex: a matrix isolation IR spectroscopy and computational study. Phys Chem Chem Phys 2020; 22:22465-22476. [PMID: 32996938 DOI: 10.1039/d0cp03855e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Methanol (CH3OH) is the simplest alcohol and carbon tetrachloride (CCl4) is widely used as a solvent in the chemical industry. CH3OH and CCl4 are both important volatile substances in the atmosphere and CCl4 is an important precursor for atmospheric ozone depletion. Moreover, mixtures of CH3OH and CCl4 are an important class of non-aqueous mixtures as they exhibit a large deviation from Raoult's law. The specific interaction between CH3OH and CCl4 is not yet investigated experimentally. The interaction between CH3OH and CCl4 at the molecular level can be twofold: hydrogen bond (O-HCl) and halogen bond (C-ClO) interaction. One halogen bonded minimum and two hydrogen bonded minima are identified in the dimer potential energy surface. Herein, the 1 : 1 complex of [CH3OH-CCl4] has been characterised using matrix-isolation infrared spectroscopy and electronic structure calculations to investigate the competition between hydrogen bonded and halogen bonded complexes. Vibrational spectra have been monitored in the C-Cl, C-O, and O-H stretching regions. The exclusive formation of halogen bonded 1 : 1 complexes in argon and nitrogen matrices is confirmed by a combination of experimental and simulated vibrational frequency, stabilisation energy, energy decomposition analysis, and natural bond orbital and atoms-in-molecules analyses. This investigation helps to understand the specific interactions in the [CH3OH-CCl4] mixture and also the possibilities of formation of halogen bonded atmospheric complexes that may influence the atmospheric chemical activities, and enhance aerosol formation and deposition of CCl4.
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Affiliation(s)
- Dhritabrata Pal
- Department of Chemistry, Birla Institute of Technology and Science, Vidya Vihar, Pilani, Rajasthan - 333031, India.
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158
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Magos-Palasyuk E, Litwiniuk A, Palasyuk T. Experimental and theoretical evidence of dihydrogen bonds in lithium amidoborane. Sci Rep 2020; 10:17431. [PMID: 33060733 PMCID: PMC7567059 DOI: 10.1038/s41598-020-74654-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 09/29/2020] [Indexed: 11/20/2022] Open
Abstract
In situ high-pressure synchrotron X-ray diffraction, Raman scattering, and complementary first-principles calculations have revealed that structural and spectroscopic properties of lithium amidoborane compound are largely determined by multiple heteropolar dihydrogen bonds. The crystal structure of the compound is stabilized by dimeric complexes, wherein molecular ions bind together by intermolecular dihydrogen bonds of unconventional type. This strong intermolecular coupling determines stable character of the crystal structure in the pressure range up to ~ 30 GPa and is spectroscopically manifested by pronounced changes related to molecular vibrations of the amino group: the splitting of stretching modes, the anomalous behavior of wagging modes as well as Fermi resonance due to vibrational coupling of bending and stretching modes, significantly enhanced above 10 GPa. Unconventional nature of dihydrogen bonds is confirmed by the frequency increase, blueshift, of NH stretching modes with pressure. A role of certain hydrogen mediated interactions in the process of dehydrogenation of ammonia borane and its alkali metal derivatives is speculated. Findings presented here call for reconsideration of hydrogen release mechanism from alkali metal ammonia borane derivatives. The work makes significant contribution towards establishing the general theory of ubiquitous and versatile hydrogen mediated interactions.
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Affiliation(s)
- Ewelina Magos-Palasyuk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Aleksander Litwiniuk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Taras Palasyuk
- Faculty of Mathematics and Natural Sciences, Cardinal Stefan Wyszynski University in Warsaw, Woycickiego 1/3, 01-938, Warsaw, Poland.
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159
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Sherbow TJ, Zakharov LN, Johnson DW, Pluth MD. Hydrosulfide Oxidation at a Molybdenum Tetrasulfido Complex. Inorg Chem 2020; 59:15574-15578. [DOI: 10.1021/acs.inorgchem.0c02622] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Tobias J. Sherbow
- Department of Chemistry and Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Lev N. Zakharov
- Department of Chemistry and Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Darren W. Johnson
- Department of Chemistry and Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Michael D. Pluth
- Department of Chemistry and Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, and Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1253, United States
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160
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Jindal A, Vasudevan S. Molecular Conformation and Hydrogen Bond Formation in Liquid Ethylene Glycol. J Phys Chem B 2020; 124:9136-9143. [PMID: 32945675 DOI: 10.1021/acs.jpcb.0c06324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The ethylene glycol (EG) molecule, HOCH2CH2OH, adopts a conformation where the central OCCO dihedral is exclusively gauche in the gaseous and crystalline states, but in the liquid state, for close to 20% of the molecules, the central OCCO adopts the energetically unfavorable trans conformation. Here we report calculations, based on ab initio molecular dynamics simulations, on the thermodynamics associated with hydrogen bond formation in the liquid state of EG between donor-acceptor pairs with different molecular conformations. We establish an operational, geometric definition of hydrogen bonds in liquid EG from an analysis of the proton NMR data and show that the key feature, irrespective of the conformation, is marked directionality with almost linear ∠HO···O angles. The free energy for hydrogen bond formation estimated as the potential of mean force for the reversible work associated with the passage from a hypothetical state where hydrogen bonding is absent and donor-acceptor pairs are randomly oriented to the hydrogen-bonded state where the pairs are oriented showed comparable magnitudes irrespective of the molecular conformation of either the donor or acceptor. The results suggest that the presence of the trans conformer in liquid EG would require an understanding of its role in the extended hydrogen-bonded network of the liquid.
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Affiliation(s)
- Aman Jindal
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sukumaran Vasudevan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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161
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Sherbow TJ, Fargher HA, Haley MM, Pluth MD, Johnson DW. Solvent-Dependent Linear Free-Energy Relationship in a Flexible Host-Guest System. J Org Chem 2020; 85:12367-12373. [PMID: 32916056 PMCID: PMC10778081 DOI: 10.1021/acs.joc.0c01616] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Supramolecular chemistry provides an effective strategy for the molecular recognition of diverse molecules. Significant efforts to design synthetic hosts have enabled the successful binding of many types of guests; however, less is known about how host-guest environments influence binding. Herein, we present a comprehensive study in which we measure the host-guest binding of a bis(arylethynyl phenylurea) host with a chloride guest in eight solvents spanning ET(30) values ranging from nonpolar (40.7 kcal mol-1) to polar (47.4 kcal mol-1). Polar solvents show significantly weaker binding in comparison to nonpolar solvents, and the bulk solvent polarity parameter, ET(30), shows a linear free-energy relationship with respect to the free energy of binding in the host-guest complex. These studies provide a better understanding of how host-guest binding in flexible receptors is governed by their environments and highlight the importance of host reorganization contributions in the free energy of binding. In addition, these studies highlight that preorganization may not be as important as previously thought for weak binding in which enthalpic contributions are smaller versus in polar solvents where solvent effects are magnified.
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Affiliation(s)
- Tobias J. Sherbow
- Department of Chemistry & Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Hazel A. Fargher
- Department of Chemistry & Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Michael M. Haley
- Department of Chemistry & Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Michael D. Pluth
- Department of Chemistry & Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Darren W. Johnson
- Department of Chemistry & Biochemistry, Materials Science Institute, Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, Oregon 97403-1253, United States
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162
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Chapleski RC, Chowdhury AU, Wanhala AK, Bocharova V, Roy S, Keller PC, Everly D, Jansone-Popova S, Kisliuk A, Sacci RL, Stack AG, Anderson CG, Doughty B, Bryantsev VS. A Molecular-Scale Approach to Rare-Earth Beneficiation: Thinking Small to Avoid Large Losses. iScience 2020; 23:101435. [PMID: 32827853 PMCID: PMC7452217 DOI: 10.1016/j.isci.2020.101435] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/26/2020] [Accepted: 07/31/2020] [Indexed: 11/29/2022] Open
Abstract
Separating rare-earth-element-rich minerals from unwanted gangue in mined ores relies on selective binding of collector molecules at the interface to facilitate froth flotation. Salicylhydroxamic acid (SHA) exhibits enhanced selectivity for bastnäsite over calcite in microflotation experiments. Through a multifaceted approach, leveraging density functional theory calculations, and advanced spectroscopic methods, we provide molecular-level mechanistic insight to this selectivity. The hydroxamic acid moiety introduces strong interactions at metal-atom surface sites and hinders subsurface-cation stabilization at vacancy-defect sites, in calcite especially. Resulting from hydrogen-bond-induced interactions, SHA lies flat on the bastnäsite surface and shows a tendency for multilayer formation at high coverages. In this conformation, SHA complexation with bastnäsite metal ions is stabilized, leading to advanced flotation performance. In contrast, SHA lies perpendicular to the calcite surface due to a difference in cationic spacing. We anticipate that these insights will motivate rational design and selection of future collector molecules for enhanced ore beneficiation.
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Affiliation(s)
- Robert C. Chapleski
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 27831, USA
| | - Azhad U. Chowdhury
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 27831, USA
| | - Anna K. Wanhala
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 27831, USA
| | - Vera Bocharova
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 27831, USA
| | - Santanu Roy
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 27831, USA
| | - Philip C. Keller
- Kroll Institute for Extractive Metallurgy, Colorado School of Mines, Golden, CO 80401, USA
| | - Dylan Everly
- Kroll Institute for Extractive Metallurgy, Colorado School of Mines, Golden, CO 80401, USA
| | - Santa Jansone-Popova
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 27831, USA
| | - Alexander Kisliuk
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 27831, USA
| | - Robert L. Sacci
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 27831, USA
| | - Andrew G. Stack
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 27831, USA
| | - Corby G. Anderson
- Kroll Institute for Extractive Metallurgy, Colorado School of Mines, Golden, CO 80401, USA
| | - Benjamin Doughty
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 27831, USA
| | - Vyacheslav S. Bryantsev
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 27831, USA
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163
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Hydrogen-bonded host-guest systems are stable in ionic liquids. Sci Rep 2020; 10:15414. [PMID: 32963260 PMCID: PMC7508985 DOI: 10.1038/s41598-020-71803-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/17/2020] [Indexed: 11/08/2022] Open
Abstract
We show that H-bonded host–guest systems associate in ionic liquids (ILs), pure salts with melting point below room temperature, in which dipole–dipole electrostatic interactions should be negligible in comparison with dipole-charge interactions. Binding constants (Ka) obtained from titrations of four H-bonded host–guest systems in two organic solvents and two ionic liquids yield smaller yet comparable Ka values in ionic liquids than in organic solvents. We also detect the association event using force spectroscopy, which confirms that the binding is not solely due to (de)solvation processes. Our results indicate that classic H-bonded host–guest supramolecular chemistry takes place in ILs. This implies that strong H-bonds are only moderately affected by surroundings composed entirely of charges, which can be interpreted as an indication that the balance of Coulombic to covalent forces in strong H-bonds is not tipped towards the former.
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164
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Agrawal MB, Patel MM. Optimization and in vivo evaluation of quetiapine-loaded transdermal drug delivery system for the treatment of schizophrenia. Drug Dev Ind Pharm 2020; 46:1819-1831. [PMID: 32896163 DOI: 10.1080/03639045.2020.1821051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The prevailing studies were carried out to formulate and optimize the quetiapine transdermal matrix patch by the usage of Box-Behnken design for ameliorated bioavailability when contrasted with conventional drug delivery. The Box-Behnken design with three-level and three-factor was utilized to explore the intermingle impact of critical attributes on tensile strength, in vitro drug release, and flux. Optimized formulation was characterized for Fourier transform infrared, differential scanning calorimetry, in vivo pharmacokinetics, and skin irritation along with stability studies. The inference of the finalized batch (F14) depicted the flux of 51.81 ± 0.32 µg/h/cm2, TS of 6.46 ± 0.56 MPa, and the % drug release after 20 h of 82.98 ± 1.48% with no remarkable variation even after 6 months stability studies. Correlation between predicted and the observed values of the dependent variables was very closer. Optimized quetiapine transdermal patch did not exert any symptoms of skin irritation. The bioavailability of quetiapine was enhanced almost 4.59 times after topical delivery when contrasted with the conventional dosage form. The outputs of the research work divulged that the developed matrix patch of quetiapine for transdermal drug delivery can be a propitious opportunity that affords effective treatment of schizophrenia. Novelty statement The oral route is not suitable for the drugs having extensive first-pass metabolism which leads to reduced bioavailability. For the parenteral route, invasiveness causes the patient noncompliance while sterility contributes to the cost factor. Moreover, the treatment of schizophrenic patients is a challenging task for caregivers and doctors. Hence, the transdermal patch of quetiapine was developed to bypass the biotransformation of drugs and thereby to enhance the bioavailability as well as to provide sustained drug delivery which ultimately reduces the dosage frequency.
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Affiliation(s)
- Milan B Agrawal
- Department of Pharmaceutics, Institute of Pharmacy, Nirma University, Ahmedabad, India
| | - Mayur M Patel
- Department of Pharmaceutics, Institute of Pharmacy, Nirma University, Ahmedabad, India
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165
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Theoretical analysis of the influence of C–H$$\cdots $$O bonds on the NMR constants of uracil in DMSO. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02670-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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166
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Hu J, Tao L, Deng W, Liu L. Fabrication and sustained‐release property of vinyl silica hollow spheres as a delivery system for aroma compounds. FLAVOUR FRAG J 2020. [DOI: 10.1002/ffj.3616] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Jing Hu
- School of Perfume and Aroma Technology Shanghai Institute of Technology Shanghai P. R. China
- Department of Chemical Engineering The University of Melbourne Parkville Vic. Australia
| | - Li Tao
- School of Perfume and Aroma Technology Shanghai Institute of Technology Shanghai P. R. China
| | - Weijun Deng
- School of Chemical and Environmental Engineering Shanghai Institute of Technology Shanghai P. R. China
| | - Liqin Liu
- School of Perfume and Aroma Technology Shanghai Institute of Technology Shanghai P. R. China
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167
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Jiao Y, Weinhold F. NBO/NRT Two-State Theory of Bond-Shift Spectral Excitation. Molecules 2020; 25:E4052. [PMID: 32899858 PMCID: PMC7571041 DOI: 10.3390/molecules25184052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/04/2022] Open
Abstract
We show that natural bond orbital (NBO) and natural resonance theory (NRT) analysis methods provide both optimized Lewis-structural bonding descriptors for ground-state electronic properties as well as suitable building blocks for idealized "diabatic" two-state models of the associated spectroscopic excitations. Specifically, in the framework of single-determinant Hartree-Fock or density functional methods for a resonance-stabilized molecule or supramolecular complex, we employ NBO/NRT descriptors of the ground-state determinant to develop a qualitative picture of the associated charge-transfer excitation that dominates the valence region of the electronic spectrum. We illustrate the procedure for the elementary bond shifts of SN2-type halide exchange reaction as well as the more complex bond shifts in a series of conjugated cyanine dyes. In each case, we show how NBO-based descriptors of resonance-type 3-center, 4-electron (3c/4e) interactions provide simple estimates of spectroscopic excitation energy, bond orders, and other vibronic details of the excited-state PES that anticipate important features of the full multi-configuration description. The deep 3c/4e connections to measurable spectral properties also provide evidence for NBO-based estimates of ground-state donor-acceptor stabilization energies (sometimes criticized as "too large" compared to alternative analysis methods) that are also found to be of proper magnitude to provide useful estimates of excitation energies and structure-dependent spectral shifts.
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Affiliation(s)
- Yinchun Jiao
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecules, Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China;
| | - Frank Weinhold
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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168
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Investigation the isotherm and kinetics of adsorption mechanism of herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) on corn cob biochar. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.biteb.2020.100520] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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169
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Chen X, Zhu J, Luo Y, Chen J, Ma X, Bukhvalov D, Liu H, Zhang M, Luo Z. Molecular dynamics simulation insight into the temperature dependence and healing mechanism of an intrinsic self-healing polyurethane elastomer. Phys Chem Chem Phys 2020; 22:17620-17631. [PMID: 32720967 DOI: 10.1039/d0cp03013a] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
An intrinsic self-healing polyurethane (PU) elastomer was synthesized in our previous work. In this work, three-dimensional (3D) micro-crack models based on experimental samples were further introduced to investigate their self-healing behavior, mechanism, and temperature dependence by molecular dynamics (MD) simulations. In particular, the number, type, strength, and lifetime of hydrogen bonds as well as the microscopic behavior of molecular diffusion in the self-healing process were investigated. It was found that the self-healing capacity of PU mainly results from intermolecular electrostatic interactions, and the hydrogen bond plays a key role in electrostatic interactions. There is an optimum ratio of soft and hard segments at which the number of hydrogen bonds is appropriate and the self-healing capacity is optimum. Besides, the temperature has an optimal value at which the self-healing rate of PU is the fastest. The exchanges of hydrogen bonds, which endowed PU with self-healing capacity, were further revealed intuitively. We found that the exchanges of hydrogen bonds are reversible and more likely to occur on the urethane groups. This study deepened the understanding of the self-healing character of PU at the molecular level.
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Affiliation(s)
- Xianling Chen
- College of Science, Nanjing Forestry University, Nanjing 210037, P. R. China.
| | - Jing Zhu
- Tsinghua Univ, Dept Elect Engn, State Key Lab Power Syst, Beijing 100084, P. R. China
| | - Yanlong Luo
- College of Science, Nanjing Forestry University, Nanjing 210037, P. R. China. and Institute of Polymer Materials, Nanjing Forestry University, Nanjing 210037, P. R. China.
| | - Jun Chen
- College of Science, Nanjing Forestry University, Nanjing 210037, P. R. China.
| | - Xiaofeng Ma
- College of Science, Nanjing Forestry University, Nanjing 210037, P. R. China. and Institute of Polymer Materials, Nanjing Forestry University, Nanjing 210037, P. R. China.
| | - Danil Bukhvalov
- College of Science, Nanjing Forestry University, Nanjing 210037, P. R. China. and Institute of Polymer Materials, Nanjing Forestry University, Nanjing 210037, P. R. China.
| | - Haobei Liu
- China Building Material Federation, Beijing 100037, P. R. China
| | - Meng Zhang
- Institute of Chemical Industry of Forestry Products, CAF, Nanjing, 210042, P. R. China.
| | - Zhenyang Luo
- College of Science, Nanjing Forestry University, Nanjing 210037, P. R. China. and Institute of Polymer Materials, Nanjing Forestry University, Nanjing 210037, P. R. China.
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170
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Chand A, Sahoo DK, Rana A, Jena S, Biswal HS. The Prodigious Hydrogen Bonds with Sulfur and Selenium in Molecular Assemblies, Structural Biology, and Functional Materials. Acc Chem Res 2020; 53:1580-1592. [PMID: 32677432 DOI: 10.1021/acs.accounts.0c00289] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Hydrogen bonds (H-bonds) play important roles in imparting functionality to the basic molecules of life by stabilizing their structures and directing their interactions. Numerous studies have been devoted to understanding H-bonds involving highly electronegative atoms like nitrogen, oxygen, and halogens and consequences of those H-bonds in chemical reactions, catalysis, and structure and function of biomolecules; but the involvement of less electronegative atoms like sulfur and selenium in H-bond formation establishes the concept of noncanonical H-bonds. Initially belittled for the "weak" nature of their interactions, these perceptions have gradually evolved over time through dedicated efforts by several research groups. This has been facilitated by advancements in experimental methods for their detection through gas-phase laser spectroscopy and solution NMR spectroscopy, as well as through theoretical predictions from high level quantum chemical calculations.In this Account, we present insights into the versatility of the sulfur and selenium centered H-bonds (S/SeCHBs) by highlighting their multifarious applications in various fields from chemical reactions to optoelectronic properties to structural biology. Our group has highlighted the significance and strength of such H-bonds in natural and modified biomolecules. Here, we have reviewed several molecular assemblies, biomolecules, and functional materials, where the role of these H-bonds is pivotal in influencing biological functions. It is worth mentioning here that the precise experimental data obtained from gas-phase laser spectroscopy have contributed considerably to changing the existing perceptions toward S/SeCHBs. Thus, molecular beam experiments, though difficult to perform on smaller model thio- or seleno-substituted Molecules, etc. (amides, nucleobases, drug molecules), are inevitable to gather elementary knowledge and convincing concepts on S/SeCHBs that can be extended from a small four-atom sulfanyl dimer to a large 14 kDa iron-sulfur protein, ferredoxin. These H-bonds can also tailor a fascinating array of molecular frameworks and design supramolecular assemblies by inter- and intralinking of individual "molecular Lego-like" units.The discussion is indeed intriguing when it turns to the usage of S/SeCHBs in facile synthetic strategies like tuning regioselectivity in reactions, as well as invoking phenomena like dual phosphorescence and chemiluminescence. This is in addition to our investigations of the dispersive nature of the hydrogen bond between metal hydrides and sulfur or selenium as acceptor, which we anticipate would lead to progress in the areas of proton and hydride transfer, as well as force-field design. This Account demonstrates how ease of fabrication, enhanced efficiency, and alteration of physicochemical properties of several functional materials is facilitated owing to the presence of S/SeCHBs. Our efforts have been instrumental in the evaluation of various S/SeCHBs in flue gas capture, as well as design of organic energy harvesting materials, where dipole moment and polarizability have important roles to play. We hope this Account invokes newer perspectives with regard to how H-bonds with sulfur and selenium can be adequately adopted for crystal engineering, for more photo- and biophysical studies with different spectroscopic methods, and for developing next-generation field-effect transistors, batteries, superconductors, and organic thin-film transistors, among many other multifunctional materials for the future.
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Affiliation(s)
- Apramita Chand
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Abhijit Rana
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Himansu S. Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
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171
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Kjaersgaard A, Vogt E, Hansen AS, Kjaergaard HG. Room Temperature Gas-Phase Detection and Gibbs Energies of Water Amine Bimolecular Complex Formation. J Phys Chem A 2020; 124:7113-7122. [DOI: 10.1021/acs.jpca.0c07399] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander Kjaersgaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100Copenhagen, Denmark
| | - Emil Vogt
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100Copenhagen, Denmark
| | - Anne S. Hansen
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Henrik G. Kjaergaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100Copenhagen, Denmark
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172
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Ahirwar MB, Gadre SR, Deshmukh MM. Direct and Reliable Method for Estimating the Hydrogen Bond Energies and Cooperativity in Water Clusters, W n, n = 3 to 8. J Phys Chem A 2020; 124:6699-6706. [PMID: 32786666 DOI: 10.1021/acs.jpca.0c05631] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
No direct method for estimating the individual O-H···O hydrogen bond (H-bond) energies in water clusters (Wn) exists in the literature. In this work, we propose such a direct method based on the molecular tailoring approach, which also enables the estimation of the cooperativity contributions. The calculated H-bond energies at MP2(full)/aug-cc-pVTZ and CCSD(T)/aug-cc-pVDZ levels for Wn, n = 3 to 8, agree well with one another and fall between 0.3 and 11.6 kcal mol-1 with the cooperativity contributions in the range of -1.2 and 7.0 kcal mol-1. For gauging the accuracy of our H-bond energies for a cluster, the H-bond energy sum is added to the sum of monomer energies, and the results are compared with the respective total energy. These two values agree with each other to within 8.3 mH (∼5 kcal mol-1), testifying the accuracy of our estimated H-bond energies. Further, these H-bond strengths show a good correlation with the respective O-H stretching frequencies and the molecular electron density values at the (3, -1) O-H···O H-bond critical point.
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Affiliation(s)
- Mini Bharati Ahirwar
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, India
| | - Shridhar R Gadre
- Interdisciplinary School of Scientific Computing and Department of Chemistry, Savitribai Phule Pune University, Pune 411 007, India
| | - Milind M Deshmukh
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, India
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173
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Clabaut P, Staub R, Galiana J, Antonetti E, Steinmann SN. Water adlayers on noble metal surfaces: Insights from energy decomposition analysis. J Chem Phys 2020; 153:054703. [DOI: 10.1063/5.0013040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Paul Clabaut
- Univ Lyon, Ecole Normale Supérieure de Lyon, CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182, 46 allée d’Italie, F-69364 Lyon, France
| | - Ruben Staub
- Univ Lyon, Ecole Normale Supérieure de Lyon, CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182, 46 allée d’Italie, F-69364 Lyon, France
| | - Joachim Galiana
- Univ Lyon, Ecole Normale Supérieure de Lyon, CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182, 46 allée d’Italie, F-69364 Lyon, France
| | - Elise Antonetti
- Univ Lyon, Ecole Normale Supérieure de Lyon, CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182, 46 allée d’Italie, F-69364 Lyon, France
| | - Stephan N. Steinmann
- Univ Lyon, Ecole Normale Supérieure de Lyon, CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182, 46 allée d’Italie, F-69364 Lyon, France
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174
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Østrøm I, Ortolan AO, Caramori GF, Mascal M, Muñoz‐Castro A, Parreira RLT. In Silico
Design of Cylindrophanes: The Role of Functional Groups in a Fluoride Selective Host. Chemphyschem 2020; 21:1989-2005. [DOI: 10.1002/cphc.202000321] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/23/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Ina Østrøm
- Departamento de Química Universidade Federal de Santa Catarina Campus Universitário Trindade, CP 476 Florianópolis SC, 88040-900 Brazil
| | - Alexandre O. Ortolan
- Departamento de Química Universidade Federal de Santa Catarina Campus Universitário Trindade, CP 476 Florianópolis SC, 88040-900 Brazil
| | - Giovanni F. Caramori
- Departamento de Química Universidade Federal de Santa Catarina Campus Universitário Trindade, CP 476 Florianópolis SC, 88040-900 Brazil
| | - Mark Mascal
- Department of Chemistry University of California Davis 1 Shields Avenue Davis CA 95616 USA
| | - Alvaro Muñoz‐Castro
- Laboratorio de Química Inorgánica y Materiales Moleculares, Facultad de Ingeniería Universidad Autonoma de Chile Llano Subercaseaux 2801 San Miguel, Santiago Chile
| | - Renato L. T. Parreira
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas Universidade de Franca 14404-600 Franca, SP Brazil
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175
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Abbott S. Solubility, similarity, and compatibility: A general-purpose theory for the formulator. Curr Opin Colloid Interface Sci 2020. [DOI: 10.1016/j.cocis.2020.03.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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176
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Yang Z, Wang Y, Liu X, Vanderlinden RT, Ni R, Li X, Stang PJ. Hierarchical Self-Assembly of a Pyrene-Based Discrete Organoplatinum(II) Double-Metallacycle with Triflate Anions via Hydrogen Bonding and Its Tunable Fluorescence Emission. J Am Chem Soc 2020; 142:13689-13694. [DOI: 10.1021/jacs.0c06666] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Zaiwen Yang
- College of Chemistry and Chemical Engineering, Xi’an University of Science and Technology, Xi’an 710054, P. R. China
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Yiliang Wang
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Xiangrong Liu
- College of Chemistry and Chemical Engineering, Xi’an University of Science and Technology, Xi’an 710054, P. R. China
| | - Ryan T. Vanderlinden
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Ruidong Ni
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Xiaopeng Li
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Peter J. Stang
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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177
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Mirzadeh N, Privér SH, Blake AJ, Schmidbaur H, Bhargava SK. Innovative Molecular Design Strategies in Materials Science Following the Aurophilicity Concept. Chem Rev 2020; 120:7551-7591. [DOI: 10.1021/acs.chemrev.9b00816] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Nedaossadat Mirzadeh
- Centre for Advanced Materials and Industrial Chemistry (CAMIC), School of Science, RMIT University, GPO BOX 2476, Melbourne 3001, Australia
| | - Steven H. Privér
- Centre for Advanced Materials and Industrial Chemistry (CAMIC), School of Science, RMIT University, GPO BOX 2476, Melbourne 3001, Australia
| | - Alexander J. Blake
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Hubert Schmidbaur
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, D-85747 Garching, Germany
| | - Suresh K. Bhargava
- Centre for Advanced Materials and Industrial Chemistry (CAMIC), School of Science, RMIT University, GPO BOX 2476, Melbourne 3001, Australia
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178
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Noncovalent interactions in high-performance liquid chromatography enantioseparations on polysaccharide-based chiral selectors. J Chromatogr A 2020; 1623:461202. [DOI: 10.1016/j.chroma.2020.461202] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/13/2022]
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179
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Pantatosaki E, Papadopoulos GK. Binding Dynamics of siRNA with Selected Lipopeptides: A Computer-Aided Study of the Effect of Lipopeptides' Functional Groups and Stereoisomerism. J Chem Theory Comput 2020; 16:3842-3855. [PMID: 32324997 DOI: 10.1021/acs.jctc.9b01261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The engineering issues pertaining to nanoparticle systems toward targeted gene therapies have not been fully probed. Recent experiments have identified specific structural characteristics of a novel class of lipopeptides (LP) that may lead to potent nanocarriers intended as RNAi therapeutics, albeit the molecular mechanism that underlies their performance remains unexplored. We conducted molecular dynamics simulations in atomistic detail coupled with free energy computations to study the dynamics and thermodynamics of an acrylate- and an epoxide-derived LP, members of the aforesaid class, upon their binding to siRNA in aqueous solution aiming at examining structure-potency relations. We found that the entropic part of the free energy of binding predominates; moreover, the first LP class tends to disrupt the Watson-Crick base pairing of siRNA, whereas the latter leaves the double helix intact. Moreover, the identified tug-of-war effect between LP-water and LP-siRNA hydrogen bonding in the supramolecular complex can underpin synthesis routes toward tuning the association dynamics. Our simulations on two diastereomers of the epoxide-derived LP showed significant structural and energetics differences upon binding, as a result of steric effects imposed by the different absolute configurations at their chiral centers. These findings may serve as crucial design parameters toward modulating the interplay between complex stability and ease of releasing the nucleic acid drug into the cell.
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Affiliation(s)
- Evangelia Pantatosaki
- School of Chemical Engineering, National Technical University of Athens, 15780 Athens, Greece
| | - George K Papadopoulos
- School of Chemical Engineering, National Technical University of Athens, 15780 Athens, Greece.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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180
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Mazmanian K, Sargsyan K, Lim C. How the Local Environment of Functional Sites Regulates Protein Function. J Am Chem Soc 2020; 142:9861-9871. [PMID: 32407086 DOI: 10.1021/jacs.0c02430] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteins form complex biological machineries whose functions in the cell are highly regulated at both the cellular and molecular levels. Cellular regulation of protein functions involves differential gene expressions, post-translation modifications, and signaling cascades. Molecular regulation, on the other hand, involves tuning an optimal local protein environment for the functional site. Precisely how a protein achieves such an optimal environment around a given functional site is not well understood. Herein, by surveying the literature, we first summarize the various reported strategies used by certain proteins to ensure their correct functioning. We then formulate three key physicochemical factors for regulating a protein's functional site, namely, (i) its immediate interactions, (ii) its solvent accessibility, and (iii) its conformational flexibility. We illustrate how these factors are applied to regulate the functions of free/metal-bound Cys and Zn sites in proteins.
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Affiliation(s)
- Karine Mazmanian
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Karen Sargsyan
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
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181
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Azofra LM, Elguero J, Alkorta I. Stabilisation of dianion dimers trapped inside cyanostar macrocycles. Phys Chem Chem Phys 2020; 22:11348-11353. [PMID: 32373849 DOI: 10.1039/d0cp01321h] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Interanionic H-bonds (IAHBs) are unfavourable interactions in the gas phase becoming favoured when anions are in solution. Dianion dimers are also susceptible to being trapped inside the cavities of cyanostar (CS) macrocycles, and thus, the formation of 2 : 2 anion : cyanostar aggregates is mainly supported by three kinds of interactions: IAHBs between the dianions, π-π stacking between the confronted cyanostars, and the presence of an intricate network of multiple C(sp2)HO H-bonds between cyanostar ligands and the anionic moieties. An analysis of the interaction energies supported by NBO reveals a slight cooperative effect of the CSs on the IAHB stabilisation.
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Affiliation(s)
- Luis Miguel Azofra
- CIDIA-FEAM (Unidad Asociada al Consejo Superior de Investigaciones Científicas, CSIC, avalada por el Instituto de Ciencia de Materiales de Sevilla, Universidad de Sevilla), Instituto de Estudios Ambientales y Recursos Naturales (i-UNAT), Universidad de Las Palmas de Gran Canaria (ULPGC), Campus de Tafira, 35017, Las Palmas de Gran Canaria, Spain.
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182
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Kravchenko EA, Gippius AA, Kuznetsov NT. Noncovalent Interactions in Compounds Based on Perchlorinated Boron Cluster as Monitored by 35Cl NQR (Review). RUSS J INORG CHEM+ 2020. [DOI: 10.1134/s0036023620040105] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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183
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Jindal A, Vasudevan S. Hydrogen Bonding in the Liquid State of Linear Alcohols: Molecular Dynamics and Thermodynamics. J Phys Chem B 2020; 124:3548-3555. [PMID: 32242419 DOI: 10.1021/acs.jpcb.0c01199] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Linear monohydroxy alcohols are strongly hydrogen-bonded liquids that are considered to be homologues of water. Here, we report ab initio molecular dynamics simulations of the liquid alcohols, methanol to pentanol, and from the combined radial-angular probability distribution of the intermolecular O···O distances and HO···O angles determine the geometrical parameters that define the hydrogen bonds in these systems. The key feature of hydrogen bonds in the liquid alcohols, irrespective of the size of the alkyl group, is the strong orientation dependence with the donor-acceptor HO···O angle being close to zero, similar to that observed in liquid water. Hydrogen bond formation is consequently considered to be the passage from a state where donor-acceptor pairs show no preferred orientation to one where they are almost linear. The potential of mean force, the reversible work associated with this process, is computed from the pair probability density distributions obtained from the simulations and that for a hypothetical state where donor-acceptor pairs are randomly oriented. We find that the magnitude of the free energy for hydrogen bond formation is maximum for ethanol and show that this arises from a larger electrostatic contribution to hydrogen bond formation in ethanol as compared to the other alcohols.
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Affiliation(s)
- Aman Jindal
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sukumaran Vasudevan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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184
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del Prado A, González‐Rodríguez D, Wu Y. Functional Systems Derived from Nucleobase Self-assembly. ChemistryOpen 2020; 9:409-430. [PMID: 32257750 PMCID: PMC7110180 DOI: 10.1002/open.201900363] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/05/2020] [Indexed: 12/12/2022] Open
Abstract
Dynamic and reversible non-covalent interactions endow synthetic systems and materials with smart adaptive functions that allow them to response to diverse stimuli, interact with external agents, or repair structural defects. Inspired by the outstanding performance and selectivity of DNA in living systems, scientists are increasingly employing Watson-Crick nucleobase pairing to control the structure and properties of self-assembled materials. Two sets of complementary purine-pyrimidine pairs (guanine:cytosine and adenine:thymine(uracil)) are available that provide selective and directional H-bonding interactions, present multiple metal-coordination sites, and exhibit rich redox chemistry. In this review, we highlight several recent examples that profit from these features and employ nucleobase interactions in functional systems and materials, covering the fields of energy/electron transfer, charge transport, adaptive nanoparticles, porous materials, macromolecule self-assembly, or polymeric materials with adhesive or self-healing ability.
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Affiliation(s)
- Anselmo del Prado
- Departamento de Química OrgánicaFacultad de CienciasUniversidad Autónoma de Madrid28049MadridSpain
| | - David González‐Rodríguez
- Departamento de Química OrgánicaFacultad de CienciasUniversidad Autónoma de Madrid28049MadridSpain
- Institute for Advanced Research in Chemical Sciences (IAdChem)Universidad Autónoma de Madrid28049MadridSpain
| | - Yi‐Lin Wu
- School of ChemistryCardiff UniversityPark PlaceCardiffCF10 3ATUK
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185
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Mo L, Jin S, Zhang W, Guo J, Liu H, Wang D. The crystal structures of ten supramolecular adducts of benzylamine and organic acids. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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186
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Abstract
A hydrogen bond (HB) is an essential interaction in countless phenomena, regulating the chemistry of life. HBs are characterized by two features, strength and directionality, with a high degree of heterogeneity across different chemical groups. These characteristics are dependent on the electronic configuration of the atoms involved in the interaction, which, in turn, is influenced strongly by the local molecular environment. Studies based on the analysis of HB in the solid phase, such as X-ray crystallography, suffer from significant biases due to packing forces. These will tend to better describe strong HBs at the expenses of weak ones, which will be either distorted or under-represented. Using quantum mechanics (QM), we calculated interaction energies for about a hundred acceptors and donors in a rigorously defined set of geometries. We performed 180,000 independent QM calculations, covering all relevant angular components, mapping strength and directionality in a context free from external biases, with both single-site and cooperative HBs. By quantifying directionality, we show that there is no correlation with strength; therefore, these two components need to be addressed separately. Results demonstrate that there are very strong HB acceptors (e.g., dimethyl sulfoxide) with nearly isotropic interactions and weak ones (e.g., thioacetone) with a sharp directional profile. Similarly, groups can have comparable directional propensity but be very distant in the strength spectrum (e.g., thioacetone and pyridine). Results provide a new perspective on the way HB directionality is described, with implications for biophysics and molecular recognition that ultimately can influence chemical biology, protein engineering, and drug design.
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Affiliation(s)
- Diogo Santos-Martins
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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187
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von der Heiden D, Vanderkooy A, Erdélyi M. Halogen bonding in solution: NMR spectroscopic approaches. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2019.213147] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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188
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Fang W, Chen B, Chen D, Wang S, Yan Y, Jin S, Xu W, Wang D. Seven supramolecular adducts of 4-dimethylaminopyridine and carboxylic acids constructed by classical H-Bonds and some noncovalent interactions. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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189
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Chen J, Li J, Fu X, Xie Q, Zeng T, Jin S, Xu W, Wang D. Structures of ten organic salts from 2-aminothiazole/2-aminobenzothiazole and acidic compounds. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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190
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Shchur Y, Pavlyuk O, Andrushchak A, Vitusevich S, Kityk A. Porous Si Partially Filled with Water Molecules-Crystal Structure, Energy Bands and Optical Properties from First Principles. NANOMATERIALS 2020; 10:nano10020396. [PMID: 32102303 PMCID: PMC7075300 DOI: 10.3390/nano10020396] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/16/2020] [Accepted: 02/18/2020] [Indexed: 11/16/2022]
Abstract
The paper reports the results on first-principles investigation of energy band spectrum and optical properties of bulk and nanoporous silicon. We present the evolution of energy band-gap, refractive indices and extinction coefficients going from the bulk Si of cubic symmetry to porous Si with periodically ordered square-shaped pores of 7.34, 11.26 and 15.40 Å width. We consider two natural processes observed in practice, the hydroxylation of Si pores (introduction of OH groups into pores) and the penetration of water molecules into Si pores, as well as their impact on the electronic spectrum and optical properties of Si superstructures. The penetration of OH groups into the pores of the smallest 7.34 Å width causes a disintegration of hydroxyl groups and forms non-bonded protons which might be a reason for proton conductivity of porous Si. The porosity of silicon increases the extinction coefficient, k, in the visible range of the spectrum. The water structuring in pores of various diameters is analysed in detail. By using the bond valence sum approach we demonstrate that the types and geometry of most of hydrogen bonds created within the pores manifest a structural evolution from distorted hydrogen bonds inherent to small pores (∼7 Å) to typical hydrogen bonds observed by us in larger pores (∼15 Å) which are consistent with those observed in a wide database of inorganic crystals.
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Affiliation(s)
- Ya. Shchur
- Institute for Condensed Matter Physics, 1 Svientsitskii str., 79011 Lviv, Ukraine
- Correspondence:
| | - O. Pavlyuk
- Department of Inorganic Chemistry, Faculty of Chemistry, Ivan Franko National University of Lviv, 6 Kyryla and Mefodia str., 79005 Lviv, Ukraine;
| | - A.S. Andrushchak
- Department of Applied Physics and Nanomaterials Science, Lviv Polytechnic National University, 12 S. Bandery str., 79013 Lviv, Ukraine;
| | - S. Vitusevich
- Institute of Bioelectronics (IBI-3), Forschungszentrum Juelich, D-52425 Juelich, Germany;
| | - A.V. Kityk
- Faculty of the Electrical Engineering, Czestochowa University of Technology, Al. Armii Krajowej 17, 42-200 Czestochowa, Poland;
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191
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Pandey MK, Kunchur HS, Mondal D, Radhakrishna L, Kote BS, Balakrishna MS. Rare Au···H Interactions in Gold(I) Complexes of Bulky Phosphines Derived from 2,6-Dibenzhydryl-4-methylphenyl Core. Inorg Chem 2020; 59:3642-3658. [DOI: 10.1021/acs.inorgchem.9b03207] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Madhusudan K. Pandey
- Phosphorus Laboratory, Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Harish S. Kunchur
- Phosphorus Laboratory, Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Dipanjan Mondal
- Phosphorus Laboratory, Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Latchupatula Radhakrishna
- Phosphorus Laboratory, Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Basvaraj S. Kote
- Phosphorus Laboratory, Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Maravanji S. Balakrishna
- Phosphorus Laboratory, Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
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192
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Azofra LM, Elguero J, Alkorta I. A Conceptual DFT Study of Phosphonate Dimers: Dianions Supported by H-Bonds. J Phys Chem A 2020; 124:2207-2214. [DOI: 10.1021/acs.jpca.9b10681] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Luis Miguel Azofra
- CIDIA-FEAM (Unidad Asociada al Consejo Superior de Investigaciones Científicas, CSIC, avalada por el Instituto de Ciencia de Materiales de Sevilla, Universidad de Sevilla), Instituto de Estudios Ambientales y Recursos Naturales (i-UNAT), Universidad de Las Palmas de Gran Canaria (ULPGC), Campus de Tafira, 35017, Las Palmas de Gran Canaria, Spain
- Departamento de Química, Universidad de Las Palmas de Gran Canaria (ULPGC), Campus de Tafira, 35017, Las Palmas de Gran Canaria, Spain
| | - José Elguero
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva, 3, E-28006 Madrid, Spain
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193
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Afonin AV, Vashchenko AV. Quantitative decomposition of resonance-assisted hydrogen bond energy in β-diketones into resonance and hydrogen bonding (π- and σ-) components using molecular tailoring and function-based approaches. J Comput Chem 2020; 41:1285-1298. [PMID: 32061114 DOI: 10.1002/jcc.26175] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/03/2020] [Indexed: 01/07/2023]
Abstract
Using the molecular tailoring and function-based approaches allows one to divide the energy of the O─H⋯O═C resonance-assisted hydrogen bond in a series of the β-diketones into resonance and hydrogen bonding components. The magnitude of the resonance component is assessed as about 6 kcal mol-1 . This value increases by ca. 1 kcal mol-1 on going from the weak to strong resonance-assisted hydrogen bonding. The magnitude of the hydrogen bonding component varies in the wide range from 2 to 20 kcal mol-1 depending on the structure of the β-diketone in question.
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Affiliation(s)
- Andrei V Afonin
- Institute of Chemistry, Siberian Division of Russian Academy of Sciences, Irkutsk, Russia
| | - Alexander V Vashchenko
- Institute of Chemistry, Siberian Division of Russian Academy of Sciences, Irkutsk, Russia
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194
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Kjaersgaard A, Vogt E, Christensen NF, Kjaergaard HG. Attenuated Deuterium Stabilization of Hydrogen-Bound Complexes at Room Temperature. J Phys Chem A 2020; 124:1763-1774. [DOI: 10.1021/acs.jpca.9b11762] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander Kjaersgaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Emil Vogt
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Nanna Falk Christensen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Henrik G. Kjaergaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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195
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Chayavanich K, Thiraphibundet P, Imyim A. Biocompatible film sensors containing red radish extract for meat spoilage observation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 226:117601. [PMID: 31622828 DOI: 10.1016/j.saa.2019.117601] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 07/22/2019] [Accepted: 10/06/2019] [Indexed: 06/10/2023]
Abstract
pH-sensitive films were developed based on biocompatible materials and natural pH sensitive dye. The films were successfully fabricated using starch/gelatin and red radish anthocyanin. The colors of films could be differentiated by naked eye within 5 min changing from orange to grey-purple at pH 2-12 and captured by a smartphone. The color parameters were evaluated by the Image J software. In addition, the color change of films was observed in ammonia gas atmosphere. The color stability of sensing films was evaluated and the results indicated that the films had great stability and were able to store more than two weeks. The results from intra-day and inter-day color response study showed good precision. Finally, the pH-sensitive films could be applied to real samples for real-time meat spoilage observation.
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Affiliation(s)
- Kasitnun Chayavanich
- Center of Excellence on Petrochemical and Materials Technology, Chulalongkorn University, Bangkok, 10330, Thailand; Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Pattara Thiraphibundet
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand; Nanotec-CU Center of Excellence on Food and Agriculture, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Apichat Imyim
- Center of Excellence on Petrochemical and Materials Technology, Chulalongkorn University, Bangkok, 10330, Thailand; Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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196
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Elias RS, Saeed BA, Kamounah FS, Duus F, Hansen PE. Strong intramolecular hydrogen bonds and steric effects involving C═S groups: An NMR and computational study. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:154-162. [PMID: 31705583 DOI: 10.1002/mrc.4959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 06/10/2023]
Abstract
A number of 5-acyl rhodanines and thiorhodanines with bulky acyl groups (pivaloyl and adamantoyl), not previously available, have been synthesized. The compounds are shown to exist in the enol form. Structures have been calculated using both the MP2 approach and the B3LYP-GD3BJ functional and the 6-311++G(d,p) basis set. Hydrogen bond energies are estimated by subtracting energies of a structure with the OH group turned 180° from those of the intramolecularly hydrogen-bonded one. Properties such as OH chemical shifts, two-bond isotope effects on 13 C chemical shifts, electron densities at the bond critical point from atoms in molecules analysis, and the hydrogen bond energies show that the sterically hindered compounds have stronger hydrogen bonds than methyl or isopropyl derivatives. The combination of oxygen and sulfur derivatives enables a detailed analysis of hydrogen bond energies.
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Affiliation(s)
- Rita S Elias
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Basrah, Basrah, Iraq
| | - Bahjat A Saeed
- Department of Chemistry, College of Education for Pure Sciences, University of Basrah, Basrah, Iraq
| | - Fadhil S Kamounah
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100, Copenhagen, Denmark
| | - Fritz Duus
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000, Roskilde, Denmark
| | - Poul Erik Hansen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000, Roskilde, Denmark
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197
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Construction of stable hydrogen bonds at high temperature for preparation of polyimide films with ultralow coefficient of thermal expansion and high Tg. POLYMER 2020. [DOI: 10.1016/j.polymer.2019.122100] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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198
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Fang W, Ye X, Zhang Y, Zhang Y, Jin S, Xu W, Wang D. Nine supramolecular adducts of 4-dimethylaminopyridine and organic acids constructed by classical H-Bonds and some noncovalent interactions. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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199
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Blair SL, Reed Harris AE, Frandsen BN, Kjaergaard HG, Pangui E, Cazaunau M, Doussin JF, Vaida V. Conformer-Specific Photolysis of Pyruvic Acid and the Effect of Water. J Phys Chem A 2020; 124:1240-1252. [DOI: 10.1021/acs.jpca.9b10613] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sandra L. Blair
- Department of Chemistry, University of Colorado Boulder, UCB 215, Boulder, Colorado 80309, United States
| | - Allison E. Reed Harris
- Department of Chemistry, University of Colorado Boulder, UCB 215, Boulder, Colorado 80309, United States
| | - Benjamin N. Frandsen
- Department of Chemistry, University of Colorado Boulder, UCB 215, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Henrik G. Kjaergaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Edouard Pangui
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Institut Pierre Simon Laplace (IPSL), Université Paris-Est Créteil (UPEC) et Université de Paris (UP), 94010 Créteil, France
| | - Mathieu Cazaunau
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Institut Pierre Simon Laplace (IPSL), Université Paris-Est Créteil (UPEC) et Université de Paris (UP), 94010 Créteil, France
| | - Jean-Francois Doussin
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR CNRS 7583, Institut Pierre Simon Laplace (IPSL), Université Paris-Est Créteil (UPEC) et Université de Paris (UP), 94010 Créteil, France
| | - Veronica Vaida
- Department of Chemistry, University of Colorado Boulder, UCB 215, Boulder, Colorado 80309, United States
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, UCB 216, Boulder, Colorado 80309, United States
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200
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Ahsan SAMS, Durani S, Reddy G, Subramanian Y. Shared hydrogen bonds: water in aluminated faujasite. Phys Chem Chem Phys 2020; 22:1632-1639. [PMID: 31894781 DOI: 10.1039/c9cp04972j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water confined in faujasite, a zeolite, with aluminium content, exhibits properties different from those of bulk water as well as water confined in siliceous faujasite. The RDF between oxygen of water (OW) and oxygen of aluminium (OAl) shows a prominent first peak near to 2.9 Å similar to any oxygen-oxygen RDF seen in bulk water and unlike water confined in siliceous faujasite. Further, HW-OAl shows a peak near 1.9 Å suggesting hydrogen bonding between hydrogen of water and OAl. The water satisfies the hydrogen bond criteria with both O1Al and O2Al indicating that it is participating in a shared hydrogen bond. The hydrogen bond exchange between such a water forming a shared hydrogen bond to OAl and another water molecule H2Ob is investigated through the changes in the distances and appropriate angles. The O-Al-O angle of the zeolite increases by about 7 degrees on the formation of the shared hydrogen bond. The jump dynamics of the shared hydrogen bond when the two bonds break simultaneously has been obtained and this is reported. This jump reorientation dynamics is different compared to normal hydrogen bonding reported by Laage and Hynes: it has a short lifetime, around 50-100 fs computed from SHB(t). The intermittent and continuous hydrogen bond correlation functions are also reported.
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Affiliation(s)
- S A M Shamimul Ahsan
- Atomic Mineral Directorate For Exploration & Research, Nagarbhavi, Bangalore-560072, India
| | - Smeer Durani
- Atomic Mineral Directorate For Exploration & Research, R. K. Puram, New Delhi-110066, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore-560012, India.
| | - Yashonath Subramanian
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore-560012, India.
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