1
|
Kim YL, Evans JW, Gordon MS. Molecular interactions in diffusion-controlled aldol condensation with mesoporous silica nanoparticles. Phys Chem Chem Phys 2022; 24:10475-10487. [PMID: 35441640 DOI: 10.1039/d2cp00952h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The aldol reaction of p-nitrobenzaldehyde in amino-catalyzed mesoporous silica nanoparticles (MSN) has revealed varying catalytic activity with the size of the pores of MSN. The pore size dependence related to the reactivity indicates that the diffusion process is important. A detailed molecular-level analysis for understanding diffusion requires assessment of the noncovalent interactions of the molecular species involved in the aldol reaction with each other, with the solvent, and with key functional groups on the pore surface. Such an analysis is presented here based upon the effective fragment potential (EFP). The EFP method can calculate the intermolecular interactions, decomposed into Coulomb, polarization, dispersion, exchange-repulsion, and charge-transfer interactions. In this study, the potential energy surfaces corresponding to each intermolecular interaction are analyzed for homo- and hetero-dimers with various configurations. The monomers that compose dimers are five molecules such as p-nitrobenzaldehyde, acetone, n-hexane, propylamine, and silanol. The results illustrate that the dispersion interaction is crucial in most dimers.
Collapse
Affiliation(s)
- Yu Lim Kim
- Ames Laboratory - US Department of Energy, Iowa State University, Ames, Iowa 50011, USA.,Department of Chemistry, Iowa State University, Ames, Iowa 50010, USA
| | - James W Evans
- Ames Laboratory - US Department of Energy, Iowa State University, Ames, Iowa 50011, USA.,Department of Physics, Iowa State University, Ames, Iowa 50011, USA
| | - Mark S Gordon
- Ames Laboratory - US Department of Energy, Iowa State University, Ames, Iowa 50011, USA.,Department of Chemistry, Iowa State University, Ames, Iowa 50010, USA
| |
Collapse
|
2
|
Affiliation(s)
- Rundong Zhao
- Materials and Energy Division, Beijing Computational Science Research Center, Beijing, China
| | - Rui-Qin Zhang
- Materials and Energy Division, Beijing Computational Science Research Center, Beijing, China
- Department of Physics, City University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
3
|
Nishio M, Umezawa Y, Fantini J, Weiss MS, Chakrabarti P. CH-π hydrogen bonds in biological macromolecules. Phys Chem Chem Phys 2015; 16:12648-83. [PMID: 24836323 DOI: 10.1039/c4cp00099d] [Citation(s) in RCA: 335] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP themed issue on "Weak Hydrogen Bonds - Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.
Collapse
Affiliation(s)
- Motohiro Nishio
- The CHPI Institute, 705-6-338, Minamioya, Machida-shi, Tokyo 194-0031, Japan.
| | | | | | | | | |
Collapse
|
4
|
Lavanya P, Ramaiah S, Anbarasu A. Binding site residues in β-lactamases: role in non-classical interactions and metal binding. J COORD CHEM 2014. [DOI: 10.1080/00958972.2014.956661] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- P. Lavanya
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, India
| | - Sudha Ramaiah
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, India
| | - Anand Anbarasu
- Medical & Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, India
| |
Collapse
|
5
|
Lavanya P, Ramaiah S, Anbarasu A. Computational analysis of N–H⋯π interactions and its impact on the structural stability of β-lactamases. Comput Biol Med 2014; 46:22-8. [DOI: 10.1016/j.compbiomed.2013.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 12/12/2013] [Accepted: 12/15/2013] [Indexed: 10/25/2022]
|
6
|
C-H…pi interactions in proteins: prevalence, pattern of occurrence, residue propensities, location, and contribution to protein stability. J Mol Model 2014; 20:2136. [DOI: 10.1007/s00894-014-2136-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 01/02/2014] [Indexed: 11/25/2022]
|
7
|
Borozan SZ, Dimitrijević BP, Stojanović SĐ. Cation−π interactions in high resolution protein−RNA complex crystal structures. Comput Biol Chem 2013; 47:105-12. [DOI: 10.1016/j.compbiolchem.2013.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/01/2013] [Accepted: 08/19/2013] [Indexed: 12/27/2022]
|
8
|
Vaideeswaran S, Ramaiah S. Investigations on the role of π-π interactions and π-π networks in eNOS and nNOS proteins. Bioorg Chem 2013; 49:16-23. [PMID: 23845761 DOI: 10.1016/j.bioorg.2013.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 04/16/2013] [Accepted: 06/03/2013] [Indexed: 10/26/2022]
Abstract
π-π Interactions play an important role in the stability of protein structures. In the present study, we have analyzed the influence of π-π interactions in eNOS and nNOS proteins. The contribution of these π-π interacting residues in sequential separation, secondary structure involvement, solvent accessibility and stabilization centers has been evaluated. π-π interactions stabilize the core regions within eNOS and nNOS proteins. π-π interacting residues are evolutionary conserved. There is a significant number of π-π interactions in spite of the lesser natural occurrences of π-residues in eNOS and nNOS proteins. In addition to π-π interactions, π residues also form π-π networks in both eNOS and nNOS proteins which might play an important role in the structural stability of these protein structures.
Collapse
Affiliation(s)
- Sivasakthi Vaideeswaran
- Bioinformatics Division, School of Biosciences and Technology, VIT University, Vellore 632 014, Tamil Nadu, India
| | | |
Collapse
|
9
|
Non-canonical H-bonds in β-lactamases: importance of C–H···π interactions. J Biol Inorg Chem 2013; 18:539-45. [DOI: 10.1007/s00775-013-0998-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 03/17/2013] [Indexed: 10/27/2022]
|
10
|
Sivasakthi V, Anbarasu A, Ramaiah S. π–π Interactions in Structural Stability: Role in RNA Binding Proteins. Cell Biochem Biophys 2013; 67:853-63. [DOI: 10.1007/s12013-013-9573-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
11
|
Flick JC, Kosenkov D, Hohenstein EG, Sherrill CD, Slipchenko LV. Accurate Prediction of Noncovalent Interaction Energies with the Effective Fragment Potential Method: Comparison of Energy Components to Symmetry-Adapted Perturbation Theory for the S22 Test Set. J Chem Theory Comput 2012; 8:2835-43. [DOI: 10.1021/ct200673a] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Joanna C. Flick
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United
States
| | - Dmytro Kosenkov
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United
States
| | - Edward G. Hohenstein
- Center for Computational
Molecular
Science and Technology, School of Chemistry and Biochemistry, and
School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
United States
| | - C. David Sherrill
- Center for Computational
Molecular
Science and Technology, School of Chemistry and Biochemistry, and
School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
United States
| | - Lyudmila V. Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United
States
| |
Collapse
|
12
|
Sumpter BG, Meunier V. Can computational approaches aid in untangling the inherent complexity of practical organic photovoltaic systems? ACTA ACUST UNITED AC 2012. [DOI: 10.1002/polb.23075] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
13
|
Stojanović SĐ, Isenović ER, Zarić BL. Contribution of Non-Canonical Interactions to the Stability of Sm/LSm Oligomeric Assemblies. Mol Inform 2011; 30:430-42. [DOI: 10.1002/minf.201000176] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 02/14/2011] [Indexed: 11/06/2022]
|
14
|
Burns LA, Mayagoitia ÁV, Sumpter BG, Sherrill CD. Density-functional approaches to noncovalent interactions: A comparison of dispersion corrections (DFT-D), exchange-hole dipole moment (XDM) theory, and specialized functionals. J Chem Phys 2011; 134:084107. [DOI: 10.1063/1.3545971] [Citation(s) in RCA: 543] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
|
15
|
Ghosh D, Kosenkov D, Vanovschi V, Williams CF, Herbert JM, Gordon MS, Schmidt MW, Slipchenko LV, Krylov AI. Noncovalent interactions in extended systems described by the effective fragment potential method: theory and application to nucleobase oligomers. J Phys Chem A 2010; 114:12739-54. [PMID: 21067134 DOI: 10.1021/jp107557p] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The implementation of the effective fragment potential (EFP) method within the Q-CHEM electronic structure package is presented. The EFP method is used to study noncovalent π-π and hydrogen-bonding interactions in DNA strands. Since EFP is a computationally inexpensive alternative to high-level ab initio calculations, it is possible to go beyond the dimers of nucleic acid bases and to investigate the asymptotic behavior of different components of the total interaction energy. The calculations demonstrated that the dispersion energy is a leading component in π-stacked oligomers of all sizes. Exchange-repulsion energy also plays an important role. The contribution of polarization is small in these systems, whereas the magnitude of electrostatics varies. Pairwise fragment interactions (i.e., the sum of dimer binding energies) were found to be a good approximation for the oligomer energy.
Collapse
Affiliation(s)
- Debashree Ghosh
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Elumalai P, Rajasekaran M, Liu HL, Chen C. Investigation of cation-π interactions in sugar-binding proteins. PROTOPLASMA 2010; 247:13-24. [PMID: 20379838 DOI: 10.1007/s00709-010-0132-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 03/02/2010] [Indexed: 05/29/2023]
Abstract
Cation-π interaction is a non-covalent binding force that plays a significant role in protein stability and drug-receptor interactions. In this work, we have investigated the structural role of cation-π interactions in sugar-binding proteins (SBPs). We observed 212 cation-π interactions in 53 proteins out of 59 SBPs in dataset. There is an average one energetically significant cation-π interaction for every 66 residues in SBPs. In addition, Arg is highly preferred to form cation-π interactions, and the average energy of Arg-Trp is high among six pairs. Long-range interactions are predominant in the analyzed cation-π interactions. Comparatively, all interaction pairs favor to accommodate in strand conformations. The analysis of solvent accessible area indicates that most of the aromatic residues are found on buried or partially buried whereas cationic residues were found mostly on the exposed regions of protein. The cation-π interactions forming residues were found that around 43% of cation-π residues had highly conserved with the conservation score ≥6. Almost cationic and π-residues equally share in the stabilization center. Sugar-binding site analysis in available complexes showed that the frequency of Trp and Arg is high, suggesting the potential role of these two residues in the interactions between proteins and sugar molecules. Our observations in this study could help to further understand the structural stability of SBPs.
Collapse
Affiliation(s)
- Pavadai Elumalai
- Graduate Institute of Biotechnology, National Taipei University of Technology, 1 Sec. 3 ZhongXiao E. Rd., Taipei, Taiwan
| | | | | | | |
Collapse
|
17
|
Anand S, Anbarasu A, Sethumadhavan R. Exploring the C–H…O Interactions in Glycoproteins. Appl Biochem Biotechnol 2009; 159:343-54. [DOI: 10.1007/s12010-008-8518-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Accepted: 12/29/2008] [Indexed: 11/24/2022]
|
18
|
Sherrill CD. Computations of Noncovalent π Interactions. REVIEWS IN COMPUTATIONAL CHEMISTRY 2009. [DOI: 10.1002/9780470399545.ch1] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
|
19
|
Nishio M, Umezawa Y, Honda K, Tsuboyama S, Suezawa H. CH/π hydrogen bonds in organic and organometallic chemistry. CrystEngComm 2009. [DOI: 10.1039/b902318f] [Citation(s) in RCA: 481] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|