1
|
Christensen EG, Steele RP. Probing the Partial Activation of Water by Open-Shell Interactions, Cl(H 2O) 1-4. J Phys Chem A 2019; 123:8657-8673. [PMID: 31513400 DOI: 10.1021/acs.jpca.9b07235] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The partial chemical activation of water by reactive radicals was examined computationally for small clusters of chlorine and water, Cl•(H2O)n=1-4. Using an automated isomer-search procedure, dozens of unique, stable structures were computed. Among the resulting structural classes were intact, hydrated-chlorine isomers, as well as hydrogen-abstracted (HCl)(OH)(H2O)n-1 configurations. The latter showed increased stability as the degree of hydration increased, until n = 4, where a new class of structures was discovered with a chloride ion bound to an oxidized water network. The electronic structure of these three structural classes was investigated, and spectral signatures of this hydration-based evolution were connected to these electronic properties. An ancillary outcome of this detailed computational analysis, including coupled-cluster benchmarks, was the calibration of cost-effective quantum chemistry methods for future studies of these radical-water complexes.
Collapse
Affiliation(s)
- Elizabeth G Christensen
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Ryan P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| |
Collapse
|
2
|
Jiang LT, Bai PK, Ren FD, Wang JH, Liu B, Li YX. Theoretical evaluation to improve the performance of composite wax powder: cooperativity effects involving the strong Na+···π/σ and weak hydrogen-bonding interactions in the complex of graphene oxide with Na+ and CH4. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1612106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Le-tao Jiang
- School of Materials Science and Engineering, North University of China, Taiyuan, People’s Republic of China
- College of Gem and Material Technology, Hebei Geo University, Shijiazhuang, People’s Republic of China
| | - Pei-kang Bai
- School of Materials Science and Engineering, North University of China, Taiyuan, People’s Republic of China
| | - Fu-de Ren
- School of Chemical Engineering and Technology, North University of China, Taiyuan, People’s Republic of China
| | - Jian-hong Wang
- School of Materials Science and Engineering, North University of China, Taiyuan, People’s Republic of China
| | - Bin Liu
- School of Materials Science and Engineering, North University of China, Taiyuan, People’s Republic of China
| | - Yu-xin Li
- School of Materials Science and Engineering, North University of China, Taiyuan, People’s Republic of China
| |
Collapse
|
3
|
Pan J, Cao DL, Ren FD, Wang JL, Yang L. Theoretical investigation into the cooperativity effect between the intermolecular π∙π and H-bonding interactions in the curcumin∙cytosine∙H2O system. J Mol Model 2018; 24:298. [DOI: 10.1007/s00894-018-3836-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/14/2018] [Indexed: 12/25/2022]
|
4
|
Zhen JP, Wei XC, Shi WJ, Huang ZY, Jin B, Zhou YK. Cooperativity effect involving drug-DNA/RNA intermolecular interaction: A B3LYP-D3 and MP2 theoretical investigation on ketoprofen⋯cytosine⋯H 2O system. J Biomol Struct Dyn 2017; 36:3587-3606. [PMID: 29092677 DOI: 10.1080/07391102.2017.1400469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In order to examine the origin of the drug action and design new DNA/RNA-targeted drugs, the cooperativity effect involving drug-DNA/RNA intermolecular interaction in ketoprofen⋯cytosine⋯H2O ternary system were investigated by the B3LYP, B3LYP-D3, and MP2 methods with the 6-311++G(2d,p) basis set. The thermodynamic cooperativity was also evaluated at 310.15 K. The N-H⋯O, O-H⋯O, O-H⋯N, C-H⋯N, and C-H⋯O H bonds coexist in ternary complexes. The intermolecular interactions obtained by B3LYP-D3 are close to those calculated by MP2. The steric effects and van der Waals interactions have little influence on the cooperativity effects. The anti-cooperativity effect in ket⋯cyt⋯H2O is far more notable than the cooperativity effect, and the stability of the cyclic structure with anti-cooperativity effect is higher than that of the linear structure with cooperativity effect, as is confirmed by the AIM (atoms in molecules) and RDG (reduced density gradient) analysis. Thus, it can be inferred that, in the presence of H2O, the anti-cooperativity effect plays a dominant role in the drug-DNA/RNA interaction, and the nature of the hydration in the binding of drugs to DNA/RNA bases is the H-bonding anti-cooperativity effect. Furthermore, the drug always links simultaneously with DNA/RNA base and H2O, and only in this way can the biological activity of drugs play a role. In most cases, the enthalpy change is the major factor driving the cooperativity, as is different from most of biomacromolecule complexes.
Collapse
Affiliation(s)
- Jun-Ping Zhen
- a Molecular Imaging Laboratory, Department of Radiology , The Second Hospital of Shanxi Medical University , Taiyuan 030053 , China
| | - Xiao-Chun Wei
- a Molecular Imaging Laboratory, Department of Radiology , The Second Hospital of Shanxi Medical University , Taiyuan 030053 , China
| | - Wen-Jing Shi
- a Molecular Imaging Laboratory, Department of Radiology , The Second Hospital of Shanxi Medical University , Taiyuan 030053 , China
| | - Zhu-Yuan Huang
- a Molecular Imaging Laboratory, Department of Radiology , The Second Hospital of Shanxi Medical University , Taiyuan 030053 , China
| | - Bo Jin
- a Molecular Imaging Laboratory, Department of Radiology , The Second Hospital of Shanxi Medical University , Taiyuan 030053 , China
| | - Yu-Kun Zhou
- a Molecular Imaging Laboratory, Department of Radiology , The Second Hospital of Shanxi Medical University , Taiyuan 030053 , China
| |
Collapse
|
5
|
Theoretical insight into the solvent effect of H 2O and formamide on the cooperativity effect in HMX complex. J Mol Model 2017; 23:237. [PMID: 28735498 DOI: 10.1007/s00894-017-3397-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/25/2017] [Indexed: 01/28/2023]
Abstract
The cooperativity effects of the H-bonding interactions in HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane)∙∙∙HMX∙∙∙FA (formamide), HMX∙∙∙HMX∙∙∙H2O and HMX∙∙∙HMX∙∙∙HMX complexes involving the chair and chair-chair HMX are investigated by using the ONIOM2 (CAM-B3LYP/6-31++G(d,p):PM3) and ONIOM2 (M06-2X/6-31++G(d,p):PM3) methods. The solvent effect of FA or H2O on the cooperativity effect in HMX∙∙∙HMX∙∙∙HMX are evaluated by the integral equation formalism polarized continuum model. The results show that the cooperativity and anti-cooperativity effects are not notable in all the systems. Although the effect of solvation on the binding energy of ternary system HMX∙∙∙HMX∙∙∙HMX is not large, that on the cooperativity of H-bonds is notable, which leads to the mutually strengthened H-bonding interaction in solution. This is perhaps the reason for the formation of different conformation of HMX in different solvent. Surface electrostatic potential and reduced density gradient are used to reveal the nature of the solvent effect on cooperativity effect in HMX∙∙∙HMX∙∙∙HMX. Graphical abstract RDG isosurface and electrostatic potential surface of HMX∙∙∙HMX∙∙∙HMX.
Collapse
|
6
|
Belkova NV, Epstein LM, Filippov OA, Shubina ES. Hydrogen and Dihydrogen Bonds in the Reactions of Metal Hydrides. Chem Rev 2016; 116:8545-87. [PMID: 27285818 DOI: 10.1021/acs.chemrev.6b00091] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The dihydrogen bond-an interaction between a transition-metal or main-group hydride (M-H) and a protic hydrogen moiety (H-X)-is arguably the most intriguing type of hydrogen bond. It was discovered in the mid-1990s and has been intensively explored since then. Herein, we collate up-to-date experimental and computational studies of the structural, energetic, and spectroscopic parameters and natures of dihydrogen-bonded complexes of the form M-H···H-X, as such species are now known for a wide variety of hydrido compounds. Being a weak interaction, dihydrogen bonding entails the lengthening of the participating bonds as well as their polarization (repolarization) as a result of electron density redistribution. Thus, the formation of a dihydrogen bond allows for the activation of both the MH and XH bonds in one step, facilitating proton transfer and preparing these bonds for further transformations. The implications of dihydrogen bonding in different stoichiometric and catalytic reactions, such as hydrogen exchange, alcoholysis and aminolysis, hydrogen evolution, hydrogenation, and dehydrogenation, are discussed.
Collapse
Affiliation(s)
- Natalia V Belkova
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences , Vavilov Street 28, 119991 Moscow, Russia
| | - Lina M Epstein
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences , Vavilov Street 28, 119991 Moscow, Russia
| | - Oleg A Filippov
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences , Vavilov Street 28, 119991 Moscow, Russia
| | - Elena S Shubina
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences , Vavilov Street 28, 119991 Moscow, Russia
| |
Collapse
|
7
|
Derikvand Z, Zabardasti A, Azadbakht A. Intermolecular complexes of nido-C2B3H7 with HF and LiH molecules: the theoretical studies, bonding properties and natural bond orbital (NBO) analysis. Struct Chem 2016. [DOI: 10.1007/s11224-015-0576-x] [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]
|
8
|
Affiliation(s)
- A. Subha Mahadevi
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
| | - G. Narahari Sastry
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
| |
Collapse
|
9
|
Derikvand Z, Zabardasti A, Azadbakht A. Theoretical study of intermolecular interactions in CB4H8-HOX (X=F, Cl, Br, I) complexes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 150:778-785. [PMID: 26103431 DOI: 10.1016/j.saa.2015.06.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 05/25/2015] [Accepted: 06/04/2015] [Indexed: 06/04/2023]
Abstract
The molecular aggregation based on intermolecular interactions between CB4H8 and HOX (X=F, Cl, Br and I) with particular emphasis on their bonding characteristics have been investigated using second order Moller-Plesset perturbation (MP2) method with aug-cc-pVDZ basis set. Different kinds of interactions including hydrogen bond (HB; H⋯O, XH; H⋯X), dihydrogen bond (DiHB; H⋯H) and non-classical B-B⋯H interactions were found between CB4H8 and HOX molecules. The structures of complexes have been analyzed using AIM and natural bond orbital methodologies. Good correlations have been found between the interaction energies (SE), the second-order perturbation energies E((2)), and the charge transfer qCT in the studied systems.
Collapse
Affiliation(s)
- Zohreh Derikvand
- Department of Chemistry, Faculty of Science, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran.
| | - Abedien Zabardasti
- Department of Chemistry, Faculty of Science, Lorestan University, Khorramabad, Iran
| | - Azadeh Azadbakht
- Department of Chemistry, Faculty of Science, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran
| |
Collapse
|
10
|
The B–C and C–C bonds as preferred electron source for H-bond and Li-bond interactions in complex pairing of C4B2H6 with HF and LiH molecules. Struct Chem 2015. [DOI: 10.1007/s11224-015-0586-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
11
|
Derikvand Z, Zabardasti A, Amini N. Theoretical investigation of H···F and H···H intermolecular interactions of nido-CB4H8 with HF molecule. Struct Chem 2014. [DOI: 10.1007/s11224-014-0487-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
12
|
A theoretical investigation into the cooperativity effect involving anionic hydrogen bond, thermodynamic property and aromaticity in Cl−⋯benzonitrile⋯H2O ternary complex. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
13
|
A B3LYP and MP2 theoretical investigation on the cooperativity effect between the XH⋯HM (X=F, Cl, Br; M=Li, Na, K) dihydrogen-bonding and HM⋯π interactions involving C6H6. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.07.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
14
|
A B3LYP and MP2(full) theoretical investigation into the cooperativity effect between dihydrogen-bonding and H–M∙∙∙π (M = Li, Na, K) interactions among HF, MH with the π-electron donor C2H2, C2H4 or C6H6. J Mol Model 2013; 19:3153-63. [DOI: 10.1007/s00894-013-1840-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 03/25/2013] [Indexed: 10/26/2022]
|
15
|
Abstract
Ab initio calculations were used to analyze interactions of with 1–4 molecules of NH3at the MP2/6-311++G(d,p) and the B3LYP/6-311++G(d,p) computational levels. In addition to H3B–H⋯H–NH2dihydrogen bond, the H2N–H⋯NH3hydrogen bonds were also predicted in clusters. Negative cooperativity in clusters constructed from mixed H3B–H⋯H–NH2dihydrogen and H2N–H⋯NH3hydrogen bonds are more remarkable. The negative cooperativity increases with size and number of hydrogen bonds in cluster. The B–H stretching frequencies show blue shifts with respect to cluster formation. Greater blue shift in stretching frequencies was predicted for B–H bonds which did not contribute to dihydrogen bonding with NH3molecules. The structures were analyzed with the atoms in molecules (AIM) methodology.
Collapse
|
16
|
Li Y, Zhang L, Du S, Ren FD, Wang WL. A MP2(full) and CCSD(T) theoretical investigation on the dihydrogen-bonded interactions between HNa and RBBH (R=F, Cl, H, CN, NC and CO). COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.09.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
17
|
Zabardasti A, Zare N, Arabpour M. Theoretical study of dihydrogen bonded clusters of water with tetrahydroborate. Struct Chem 2011. [DOI: 10.1007/s11224-011-9747-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
18
|
A MP2 and CCSD(T) theoretical investigation on the weak dihydrogen-bonded interactions between HBBH (1Δg) and HM (M=Li, Na, K, BeH, MgH or CaH). COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2010.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
19
|
Alkorta I, Blanco F, Elguero J. Dihydrogen Bond Cooperativity in Aza-borane Derivatives. J Phys Chem A 2010; 114:8457-62. [DOI: 10.1021/jp1046694] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain, and Department of Chemistry, Trinity College Dublin, Dublin 2, Ireland
| | - Fernando Blanco
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain, and Department of Chemistry, Trinity College Dublin, Dublin 2, Ireland
| | - Jose Elguero
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain, and Department of Chemistry, Trinity College Dublin, Dublin 2, Ireland
| |
Collapse
|