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Silva TM, Fiuza SM, Marques MPM, Batista de Carvalho LAE, Amado AM. Conformational study and reassessment of the vibrational assignments for Norspermidine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 157:227-237. [PMID: 26774814 DOI: 10.1016/j.saa.2016.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/04/2016] [Indexed: 06/05/2023]
Abstract
The present study presents and discusses the conformational preferences of Norspermidine (NSpd). The effects of varying the dielectric constant on the conformational preferences are discussed, with a view to infer which conformation will correspond to the most stable in the pure condensed liquid phase. Within the same context, a set of NSpd-NH3 molecular adducts were simulated in order to determine the relevance of intermolecular hydrogen bonding on the overall stability and relative positioning of the respective vibrational frequencies. The calculations presently performed allowed a reassessment of the vibrational assignments for NSpd. A full assignment of the NSpd vibrational spectra is presented, with special emphasis being given to the vibrational modes that proved to be most affected by hydrogen bonding. The various inconsistencies of a prior study found in the literature were identified and rectified.
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Affiliation(s)
- T M Silva
- I&D Unit "Química-Física Molecular", Department of Chemistry, Faculty of Science and Technology, University of Coimbra, P-3004-535 Coimbra, Portugal
| | - S M Fiuza
- I&D Unit "Química-Física Molecular", Department of Chemistry, Faculty of Science and Technology, University of Coimbra, P-3004-535 Coimbra, Portugal
| | - M P M Marques
- I&D Unit "Química-Física Molecular", Department of Chemistry, Faculty of Science and Technology, University of Coimbra, P-3004-535 Coimbra, Portugal; Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - L A E Batista de Carvalho
- I&D Unit "Química-Física Molecular", Department of Chemistry, Faculty of Science and Technology, University of Coimbra, P-3004-535 Coimbra, Portugal
| | - A M Amado
- I&D Unit "Química-Física Molecular", Department of Chemistry, Faculty of Science and Technology, University of Coimbra, P-3004-535 Coimbra, Portugal.
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Li S, Kjaergaard HG, Du L. Infrared spectroscopic probing of dimethylamine clusters in an Ar matrix. J Environ Sci (China) 2016; 40:51-9. [PMID: 26969545 DOI: 10.1016/j.jes.2015.09.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 05/15/2023]
Abstract
Amines have many atmospheric sources and their clusters play an important role in aerosol nucleation processes. Clusters of a typical amine, dimethylamine (DMA), of different sizes were measured with matrix isolation IR (infrared) and NIR (near infrared) spectroscopy. The NIR vibrations are more separated and therefore it is easier to distinguish different sizes of clusters in this region. The DMA clusters, up to DMA tetramer, have been optimized using density functional methods, and the geometries, binding energies and thermodynamic properties of DMA clusters were obtained. The computed frequencies and intensities of NH-stretching vibrations in the DMA clusters were used to interpret the experimental spectra. We have identified the fundamental transitions of the bonded NH-stretching vibration and the first overtone transitions of the bonded and free NH-stretching vibration in the DMA clusters. Based on the changes in vibrational intensities during the annealing processes, the growth of clusters was clearly observed. The results of annealing processes indicate that DMA molecules tend to form larger clusters with lower energies under matrix temperatures, which is also supported by the calculated reaction energies of cluster formation.
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Affiliation(s)
- Siyang Li
- Environment Research Institute, Shandong University, Shanda South Road 27, Shandong 250100, China.
| | - Henrik G Kjaergaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Lin Du
- Environment Research Institute, Shandong University, Shanda South Road 27, Shandong 250100, China; Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark.
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Mahalakshmi G, Balachandran V. NBO, HOMO, LUMO analysis and vibrational spectra (FTIR and FT Raman) of 1-Amino 4-methylpiperazine using ab initio HF and DFT methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 135:321-334. [PMID: 25084238 DOI: 10.1016/j.saa.2014.06.157] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 06/17/2014] [Accepted: 06/30/2014] [Indexed: 06/03/2023]
Abstract
Experimental FTIR and FT-Raman spectroscopic analysis of 1-Amino-4-methylpiperazine (1A4MP) have been performed. A detailed quantum chemical calculations have been carried out using ab initio HF and density functional theory calculations (B3LYP) with 6-311+G(d,p) basis set. The atomic charges, electronic exchange interaction and charge delocalization of the molecule have been performed by natural bond orbital (NBO) analysis. Electron density distribution and frontier molecular orbitals (FMOs) have been constructed at B3LYP/6-311+G(d,p) level to understand the electronic properties. The charge density distribution and site of chemical reactivity of the molecule have been obtained by mapping electron density isosurface with electrostatic potential surfaces (ESP). The electronic properties, HOMO and LUMO energies were measured by time-dependent TD-DFT approach. The dipole moment (μ), polarizability (α), anisotropy polarizability (Δα) and hyperpolarizability (β) of the molecule have been reported.
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Affiliation(s)
- G Mahalakshmi
- Department of Physics, Karpagam University, Coimbatore 641021, India; Department of Physics, Government Arts College (Autonomous), Karur 639005, India
| | - V Balachandran
- Research Department of Physics, Arignar Anna Government Arts College, Musiri, Tiruchirapalli 621211, India.
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On the Relevance of Considering the Intermolecular Interactions on the Prediction of the Vibrational Spectra of Isopropylamine. J CHEM-NY 2013. [DOI: 10.1155/2013/682514] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The effects of implicitly considering the effects of hydrogen bonding on the molecular properties, such as vibrational frequencies, were inferred on the basis of DFT calculations. Several clusters of isopropylamine were assembled and theoretically characterized. The results showed that maximum H-bond cooperativity is achieved when the amine group acts simultaneously as donor and acceptor. The effect of H-bond cooperativity manifests itself in the relative cluster stability and on the structural and vibrational frequency predictions. Referring to the vibrational frequencies it was found that theNH2stretching and torsion vibrational modes are the most affected by the amine involvement in hydrogen bonding. Both stretching modes were found to be significantly redshifted relative to the monomer. TheNH2torsional mode, on the other hand, was found to be blueshifted up to 350 cm-1. Finally, the comparative study between the theory levels performed allows to conclude that the small 6-31G* basis set is able to stabilize weakC–H⋯Ninteractions as long as the new dispersion corrected DFT methods are considered. The impairments observed with conventional DFT methods for describing weak interactions may be overcome with the improvement of basis set, but the associated increase of computational costs may turn the calculations unfeasible.
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Du L, Kjaergaard HG. Fourier transform infrared spectroscopy and theoretical study of dimethylamine dimer in the gas phase. J Phys Chem A 2011; 115:12097-104. [PMID: 21950960 DOI: 10.1021/jp206762j] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dimethylamine (DMA) has been studied by gas-phase Fourier transform infrared (FTIR) spectroscopy. We have identified a spectral transition that is assigned to the DMA dimer. The IR spectra of the dimer in the gas phase are obtained by spectral subtraction of spectra recorded at different pressures. The enthalpy of hydrogen bond formation was obtained for the DMA dimer by temperature-dependence measurements. We complement the experimental results with ab initio and anharmonic local mode model calculations of monomer and dimer. Compared to the monomer, our calculations show that in the dimer the N-H bond is elongated, and the NH-stretching fundamental shifts to a lower wavenumber. More importantly, the weak NH-stretching fundamental transition has a pronounced intensity increase upon complexation. However, the first NH-stretching overtone transition is not favored by the same intensity enhancement, and we do not observe the first NH-stretching overtone of the dimer. On the basis of the measured and calculated intensity of the NH-stretching transition of the dimer, the equilibrium constant for dimerization at room temperature was determined.
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Affiliation(s)
- Lin Du
- Department of Chemistry, University of Copenhagen, Copenhagen Ø, Denmark
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Amines in the Earth’s Atmosphere: A Density Functional Theory Study of the Thermochemistry of Pre-Nucleation Clusters. ENTROPY 2011. [DOI: 10.3390/e13020554] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Padmaja L, Ravikumar C, James C, Jayakumar VS, Hubert Joe I. Analysis of vibrational spectra of L-alanylglycine based on density functional theory calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2008; 71:252-262. [PMID: 18243781 DOI: 10.1016/j.saa.2007.12.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Revised: 12/10/2007] [Accepted: 12/14/2007] [Indexed: 05/25/2023]
Abstract
FT Raman and IR spectra of the crystallized biologically active molecule, L-alanylglycine (L-Ala-Gly) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies of L-Ala-Gly have been investigated with the help of B3LYP density functional theory (DFT) method. The calculated molecular geometry has been compared with the experimental data. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). The optimized geometry shows the non-planarity of the peptide group of the molecule. Potential energy surface (PES) scan studies has also been carried out by ab initio calculations with B3LYP/6-311+G** basis set. The red shifting of NH3+ stretching wavenumber indicates the formation of N-H...O hydrogen bonding. The change in electron density (ED) in the sigma* antibonding orbitals and E2 energies have been calculated by natural bond orbital analysis (NBO) using DFT method. The NBO analysis confirms the occurrence of strong intermolecular hydrogen bonding in the molecule.
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Affiliation(s)
- L Padmaja
- Centre for Molecular and Biophysics Research, Department of Physics, Mar Ivanios College, Thiruvananthapuram 695 015, Kerala, India
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Koch R, Finnerty JJ, Bruhn T, Borget F, Wentrup C. Reaction of Iminopropadienones with Amines: Mechanistic Explanations of Zwitterionic Intermediate, Ketene and Ketenimine Formation. J Phys Chem A 2008; 112:8999-9004. [DOI: 10.1021/jp803352m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rainer Koch
- Institut für Reine and Angewandte Chemie and Center of Interface Science, Carl von Ossietzky Universität Oldenburg, P.O. Box 2503, 26111 Oldenburg, Germany, Physique des Interactions Ionique et Moléculaire, UMR 6633, Université de Provence et CNRS, Centre de St Jérôme, Case 252, 13397 Marseille cedex 20, France, and Chemistry Building, School of Molecular and Microbial Sciences, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Justin J. Finnerty
- Institut für Reine and Angewandte Chemie and Center of Interface Science, Carl von Ossietzky Universität Oldenburg, P.O. Box 2503, 26111 Oldenburg, Germany, Physique des Interactions Ionique et Moléculaire, UMR 6633, Université de Provence et CNRS, Centre de St Jérôme, Case 252, 13397 Marseille cedex 20, France, and Chemistry Building, School of Molecular and Microbial Sciences, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Torsten Bruhn
- Institut für Reine and Angewandte Chemie and Center of Interface Science, Carl von Ossietzky Universität Oldenburg, P.O. Box 2503, 26111 Oldenburg, Germany, Physique des Interactions Ionique et Moléculaire, UMR 6633, Université de Provence et CNRS, Centre de St Jérôme, Case 252, 13397 Marseille cedex 20, France, and Chemistry Building, School of Molecular and Microbial Sciences, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Fabien Borget
- Institut für Reine and Angewandte Chemie and Center of Interface Science, Carl von Ossietzky Universität Oldenburg, P.O. Box 2503, 26111 Oldenburg, Germany, Physique des Interactions Ionique et Moléculaire, UMR 6633, Université de Provence et CNRS, Centre de St Jérôme, Case 252, 13397 Marseille cedex 20, France, and Chemistry Building, School of Molecular and Microbial Sciences, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Curt Wentrup
- Institut für Reine and Angewandte Chemie and Center of Interface Science, Carl von Ossietzky Universität Oldenburg, P.O. Box 2503, 26111 Oldenburg, Germany, Physique des Interactions Ionique et Moléculaire, UMR 6633, Université de Provence et CNRS, Centre de St Jérôme, Case 252, 13397 Marseille cedex 20, France, and Chemistry Building, School of Molecular and Microbial Sciences, The University of Queensland, Brisbane, Qld 4072, Australia
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Cabaleiro-Lago EM, Hermida-Ramón JM, Rodríguez-Otero J. Computational Study of the Interaction in (CH3)2X Dimer and Trimer (X = O, S). J Phys Chem A 2004. [DOI: 10.1021/jp0377679] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Enrique M. Cabaleiro-Lago
- Departamento de Química Física, Facultade de Ciencias, Universidade de Santiago de Compostela, Campus de Lugo, Avda Alfonso X El Sabio s/n, 27002 Lugo, Galicia, Spain
| | - Jose M. Hermida-Ramón
- Departamento de Química Física, Facultade de Ciencias, Universidade de Vigo, Campus Lagoas Marcosende, 36200 Vigo, Galicia, Spain
| | - Jesús Rodríguez-Otero
- Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Avda das Ciencias s/n, 15706 Santiago, Galicia, Spain
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Okuno Y, Yokoyama T, Yokoyama S, Kamikado T, Mashiko S. Theoretical study of benzonitrile clusters in the gas phase and their adsorption onto a Au(111) surface. J Am Chem Soc 2002; 124:7218-25. [PMID: 12059248 DOI: 10.1021/ja011744v] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We made theoretical calculations for a benzonitrile molecule and its clusters in the gas phase and as adsorbed on the Au(111) surface, to explain the observation by scanning tunneling microscope, that is, the trimer formation of cyanophenyl porphyrins adsorbed onto the Au(111) surface. With regard to the gas-phase species, ab initio calculations showed that (1) the benzonitrile dimer has a single stable structure that is planar and antiparallel; (2) the trimer has two isoenergetic stable structures, that is, a planar and cyclic structure and an antiparallel and nonplanar one; (3) the clusters are more stable, at low temperatures, than the monomer. For the adsorbed species, we made quantum mechanical/molecular mechanical calculations in which the interaction between the adsorbates and the surface is evaluated in a molecular-mechanical way by using analytical potential functions and an image charge model. Because the stable structures were found to be similar to those in the gas phase, the cluster formation of adsorbed cyanophenyl porphyrins was attributed to the interaction between cyanophenyl groups, which is barely affected by adsorbate-surface interaction. It was also found that the adsorbed cyclic benzonitrile trimer is more stable than the monomer and the dimer because the relative stability is dependent on enthalpy alone. We therefore concluded that the preferential formation of trimers by the adsorbed cyanophenyl porphyrins is due to the negligible contribution of entropy to the relative stability of the adsorbed species and that the adsorption hardly changes the situation found in the gas phase.
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Affiliation(s)
- Yoshishige Okuno
- Communications Research Laboratory, 588-2 Iwaoka Iwaoka-cho, Nishi-ku, Kobe 651-2492, Japan.
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Mmereki BT, Donaldson DJ. Ab Initio and Density Functional Study of Complexes between the Methylamines and Water. J Phys Chem A 2002. [DOI: 10.1021/jp013694m] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Baagi T. Mmereki
- Department of Chemistry and University of Toronto at Scarborough, University of Toronto, Toronto, Ontario, Canada M5S 3H6
| | - D. J. Donaldson
- Department of Chemistry and University of Toronto at Scarborough, University of Toronto, Toronto, Ontario, Canada M5S 3H6
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Vorobyov I, Yappert MC, DuPré DB. Hydrogen Bonding in Monomers and Dimers of 2-Aminoethanol. J Phys Chem A 2002. [DOI: 10.1021/jp013211e] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Igor Vorobyov
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - M. Cecilia Yappert
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - Donald B. DuPré
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
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