1
|
Wiik K, Høyvik IM, Unneberg E, Jensen TL, Swang O. Unimolecular Decomposition Reactions of Picric Acid and Its Methylated Derivatives─A DFT Study. J Phys Chem A 2022; 126:2645-2657. [PMID: 35472276 PMCID: PMC9082609 DOI: 10.1021/acs.jpca.1c10770] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
To handle energetic
materials safely, it is important to have knowledge
about their sensitivity. Density functional theory (DFT) has proven
a valuable tool in the study of energetic materials, and in the current
work, DFT is employed to study the thermal unimolecular decomposition
of 2,4,6-trinitrophenol (picric acid, PA), 3-methyl-2,4,6-trinitrophenol
(methyl picric acid, mPA), and 3,5-dimethyl-2,4,6-trinitrophenol (dimethyl
picric acid, dmPA). These compounds have similar molecular structures,
but according to the literature, mPA is far less sensitive to impact
than the other two compounds. Three pathways believed important for
the initiation reactions are investigated at 0 and 298.15 K. We compare
the computed energetics of the reaction pathways with the objective
of rationalizing the unexpected sensitivity behavior. Our results
reveal a few if any significant differences in the energetics of the
three molecules, and thus do not reflect the sensitivity deviations
observed in experiments. These findings point toward the potential
importance of crystal structure, crystal morphology, bimolecular reactions,
or combinations thereof on the impact sensitivity of nitroaromatics.
Collapse
Affiliation(s)
- Kristine Wiik
- Chemistry Department, The Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, 7491 Trondheim, Norway.,Department of Process Technology, SINTEF Industry, P.O. Box 124 Blindern, 0314 Oslo, Norway
| | - Ida-Marie Høyvik
- Chemistry Department, The Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, 7491 Trondheim, Norway
| | - Erik Unneberg
- Norwegian Defence Research Establishment (FFI), P.O. Box 25, 2027 Kjeller, Norway
| | - Tomas Lunde Jensen
- Norwegian Defence Research Establishment (FFI), P.O. Box 25, 2027 Kjeller, Norway
| | - Ole Swang
- Department of Process Technology, SINTEF Industry, P.O. Box 124 Blindern, 0314 Oslo, Norway
| |
Collapse
|
2
|
Prabhakaran EN, Reddy DN, Banerjee S. A kinetic method for detecting intramolecular peptide H-bonds. NEW J CHEM 2021. [DOI: 10.1039/d1nj03544d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The current method for the detection of peptide hydrogen bond (PHB) formation places charge donors/acceptors (D/A) at the N-/C-termini of the peptides involved in the putative PHB.
Collapse
Affiliation(s)
- Erode N. Prabhakaran
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Damodara N. Reddy
- Division of Medicinal and Process Chemistry, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
| | - Shreya Banerjee
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| |
Collapse
|
3
|
Thermochemical behavior of sorghum procyanidin trimers with C4–C8 and C4–C6 interflavan bonds in the reaction with superoxide anion radical and H2O2-forming NADH-oxidase flavoenzyme. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112912] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
4
|
Ganesan M, Paranthaman S. Studies on the structure and conformational flexibility of secondary structures in amyloid beta — A quantum chemical study. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2020. [DOI: 10.1142/s0219633620500145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Density functional theory (DFT) calculations are performed to study the conformational flexibility of secondary structures in amyloid beta (A[Formula: see text]) polypeptide. In DFT, M06-2X/6-31[Formula: see text]G(d, p) method is used to optimize the secondary structures of 2LFM and 2BEG in gas phase and in solution phase. Our calculations show that the secondary structures are energetically more stable in solution phase than in gas phase. This is due to the presence of strong solvent interaction with the secondary structures considered in this study. Among the backbone [Formula: see text] and [Formula: see text] dihedral angles, [Formula: see text] varies significantly in sheet structure. This is due to the absence of intermolecular hydrogen bond (H-bond) interactions in sheets considered in this study. Our calculations show that the conformational transition of helix/coil to sheet or vice-versa is due to the floppiness of the amino acid residues. This is observed from the Ramachandran map of the studied secondary structures. Further, it is noted that the intramolecular H-bond interactions play a significant role in the conformational transition of secondary structures of A[Formula: see text].
Collapse
Affiliation(s)
- Mahendiraprabu Ganesan
- Department of Physics and International Research Centre, Kalasalingam Academy of Research and Education (Deemed to be University), Krishnankoil 626126, India
| | - Selvarengan Paranthaman
- Department of Physics and International Research Centre, Kalasalingam Academy of Research and Education (Deemed to be University), Krishnankoil 626126, India
| |
Collapse
|
5
|
Chen Y, Viereck J, Harmer R, Rangan S, Bartynski RA, Galoppini E. Helical Peptides Design for Molecular Dipoles Functionalization of Wide Band Gap Oxides. J Am Chem Soc 2020; 142:3489-3498. [PMID: 31977205 DOI: 10.1021/jacs.9b12001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The use of helical hexapeptides to establish a surface dipole layer on a TiO2 substrate, with the goal of influencing the energy levels of a coadsorbed chromophore, is explored. Two helical hexapeptides, synthesized from 2-amino isobutyric acid (Aib) residues, were protected at the N-terminus with a carboxybenzyl group (Z) and at the C-terminus carried either a carboxylic acid or an isophthalic acid (Ipa) anchor group to form Z-(Aib)6-COOH or Z-(Aib)6-Ipa, respectively. Using a combination of vibrational and photoemission spectroscopies, bonding of the two peptides to TiO2 surfaces (either nanostructured or single-crystal TiO2(110)) was found to be highly dependent on the anchor group, with Ipa establishing a monolayer much more efficiently than COOH. Furthermore, a monolayer of Z-(Aib)6-Ipa on TiO2(110) was exposed for different binding times to a solution of a zinc tetraphenylporphyrin (ZnTPP) derivative terminated with an Ipa anchor group (ZnTPP-P-Ipa). Photoemission spectroscopy revealed that ZnTPP-P-Ipa partly displaced Z-(Aib)6-Ipa, forming a coadsorbed monolayer on the oxide surface. The presence of the peptide molecular dipole shifted the HOMO levels of the ZnTPP group to lower energy by ∼300 meV, in accordance with a simple parallel plate capacitor model. These results suggest that a mixed-layer approach, involving coadsorption of a strong molecular dipole compound with a chromophore, is a versatile method to shift the energy levels of such chromophores with respect to the band edges of the substrate.
Collapse
Affiliation(s)
- Yuan Chen
- Chemistry Department , Rutgers University , 73 Warren Street , Newark , New Jersey 07102 , United States
| | - Jonathan Viereck
- Department of Physics and Astronomy and Laboratory for Surface Modification , Rutgers University , 136 Frelinghuysen Road , Piscataway , New Jersey 08854 , United States
| | - Ryan Harmer
- Chemistry Department , Rutgers University , 73 Warren Street , Newark , New Jersey 07102 , United States
| | - Sylvie Rangan
- Department of Physics and Astronomy and Laboratory for Surface Modification , Rutgers University , 136 Frelinghuysen Road , Piscataway , New Jersey 08854 , United States
| | - Robert A Bartynski
- Department of Physics and Astronomy and Laboratory for Surface Modification , Rutgers University , 136 Frelinghuysen Road , Piscataway , New Jersey 08854 , United States
| | - Elena Galoppini
- Chemistry Department , Rutgers University , 73 Warren Street , Newark , New Jersey 07102 , United States
| |
Collapse
|
6
|
Abstract
Estimating the range of three-dimensional structures (conformations) that are available to a molecule is a key component of computer-aided drug design. Quantum mechanical simulation offers improved accuracy over forcefield methods, but at a high computational cost. The question is whether this increased cost can be justified in a context in which high-throughput analysis of large numbers of molecules is often key. This chapter discusses the application of quantum mechanics to conformational searching, with a focus on three key challenges: (1) the generation of ensembles that include a good approximation to a molecule's bioactive conformation at as prominent a ranking as possible; (2) rational analysis and modification of a pre-established bioactive conformation in terms of its energetics; and (3) approximation of real solution-phase conformational ensembles in tandem with NMR data. The impact of QM on the high-throughput application (1) is debatable, meaning that for the moment its primary application is still lower-throughput applications such as (2) and (3). The optimal choice of QM method is also discussed. Rigorous benchmarking suggests that DFT methods are only acceptable when used with large basis sets, but a trickle of papers continue to obtain useful results with relatively low-cost methods, leading to a dilemma that the literature has yet to fully resolve.
Collapse
|
7
|
Marik T, Tyagi C, Racić G, Rakk D, Szekeres A, Vágvölgyi C, Kredics L. New 19-Residue Peptaibols from Trichoderma Clade Viride. Microorganisms 2018; 6:microorganisms6030085. [PMID: 30103563 PMCID: PMC6165201 DOI: 10.3390/microorganisms6030085] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 12/14/2022] Open
Abstract
Trichoderma koningiopsis and T. gamsii belong to clade Viride of Trichoderma, the largest and most diverse group of this genus. They produce a wide range of bioactive secondary metabolites, including peptaibols with antibacterial, antifungal, and antiviral properties. The unusual amino acid residues of peptaibols, i.e., α-aminoisobutyric acid (Aib), isovaline (Iva), and the C-terminal 1,2-amino alcohol make them unique among peptides. In this study, the peptaibiomes of T. koningiopsis and T. gamsii were investigated by HPLC-ESI-MS. The examined strains appeared to produce 19-residue peptaibols, most of which are unknown from literature, but their amino acid sequences are similar to those of trikoningins, tricholongins, trichostrigocins, trichorzianins, and trichorzins. A new group of peptaibols detected in T. koningiopsis are described here under the name “Koningiopsin”. Trikoningin KA V, the closest peptaibol compound to the peptaibols produced by these two strains, was selected for structural investigation by short MD simulation, which revealed that many residues show high preference for left handed helix formation. The bioactivity of the peptaibol mixtures produced by T. koningiopsis and T. gamsii was tested on agar plates against bacteria, yeasts, and filamentous fungi. The results revealed characteristic differences in bioactivities towards the different groups of target microorganisms, which can be explained with the differences in their cell wall structures.
Collapse
Affiliation(s)
- Tamás Marik
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - Chetna Tyagi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary.
| | - Gordana Racić
- Faculty of Environmental Protection, Educons University, Vojvode Putnika 87, 21208 Sremska Kamenica, Serbia.
| | - Dávid Rakk
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary.
| | - András Szekeres
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| |
Collapse
|
8
|
Exploring the effect of oxygen-containing functional groups on the water-holding capacity of lignite. J Mol Model 2018; 24:130. [PMID: 29736591 DOI: 10.1007/s00894-018-3653-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/11/2018] [Indexed: 10/17/2022]
Abstract
Graphene oxide with different degrees of oxidation was prepared and selected as a model compound of lignite to study quantitatively, using both experiment and theoretical calculation methods, the effect on water-holding capacity of oxygen-containing functional groups. The experimental results showed that graphite can be oxidized, and forms epoxy groups most easily, followed by hydroxyl and carboxyl groups. The prepared graphene oxide forms a membrane-state as a single layer structure, with an irregular surface. The water-holding capacity of lignite increased with the content of oxygen-containing functional groups. The influence on the configuration of water molecule clusters and binding energy of water molecules of different oxygen-containing functional groups was calculated by density functional theory. The calculation results indicated that the configuration of water molecule clusters was totally changed by oxygen-containing functional groups. The order of binding energy produced by oxygen-containing functional groups and water molecules was as follows: carboxyl > edge phenol hydroxyl >epoxy group. Finally, it can be concluded that the potential to form more hydrogen bonds is the key factor influencing the interaction energy between model compounds and water molecules.
Collapse
|