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Dorafshan Tabatabai AS, Dehghanian E, Mansouri-Torshizi H, Feizi-Dehnayebi M. Computational and experimental examinations of new antitumor palladium(II) complex: CT-DNA-/BSA-binding, in-silico prediction, DFT perspective, docking, molecular dynamics simulation and ONIOM. J Biomol Struct Dyn 2024; 42:5447-5469. [PMID: 37349936 DOI: 10.1080/07391102.2023.2226715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/12/2023] [Indexed: 06/24/2023]
Abstract
Since the design of metal complexes with better biological activities is important, herein a new palladium(II) complex bearing en and acac (en and acac stand for ethylenediamine and acetylacetonato, respectively) as its ligands, [Pd(en)(acac)]NO3 complex, was synthesized and fully characterized. Quantum chemical computations of the palladium(II) complex were done via DFT/B3LYP method. Cytotoxicity activity of the new compound on leukemia cell line (K562) was assessed via MTT method. The findings indicated that the metal complex has remarkable cytotoxic effect than cisplatin. OSIRIS DataWarrior software was employed to calculate in-silico physicochemical and toxicity parameters of the synthesized complex which rendered significant results. To comprehend the interaction type of new metal compound with macromolecules, the in depth investigation of interaction of mentioned complex with CT-DNA and BSA was accomplished by fluorescence, UV-Visible absorption spectroscopy, viscosity measurement, gel electrophoresis, FRET analysis and circular dichroism (CD) spectroscopy. On the other hand, computational molecular docking was carried out and the obtained data demonstrated that H-bond and van der Waals forces are the dominant forces for the binding of the compound to the mentioned biomolecules. Molecular dynamics simulation was also done and confirmed the stability of best docked pose of palladium(II) complex inside DNA or BSA over the time and in presence of water solvent. Also, Our own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM) methodology based on the hybridization of quantum mechanics and molecular mechanics (QM/MM) methodology was accomplished to inquire about binding of Pd(II) complex with DNA or BSA.HIGHLIGHTSNew biologically active Pd(II) complex was synthesized and characterized.The in silico studies of the designed complex and its ligands were accomplished by OSIRIS DataWarrior softwareInteraction with CT-DNA and BSA was assessed by various spectroscopic methods.Molecular docking simulation supported the interaction with both macromolecules.Based on ONIOM analysis, the structures of the complex and biomolecules are altered after binding. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Effat Dehghanian
- Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
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2
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Dean JLS, Winkler VS, Boyer MA, Sibert EL, Fournier JA. Investigating Intramolecular H Atom Transfer Dynamics in β-Diketones with Ultrafast Infrared Spectroscopies and Theoretical Modeling. J Phys Chem A 2023; 127:9258-9272. [PMID: 37882618 DOI: 10.1021/acs.jpca.3c05417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
The vibrational signatures and ultrafast dynamics of the intramolecular H-bond in a series of β-diketones are investigated with 2D IR spectroscopy and computational modeling. The chosen β-diketones exhibit a range of H atom donor-acceptor distances and asymmetry along the H atom transfer coordinate that tunes the intramolecular H-bond strength. The species with the strongest H-bonds are calculated to have very soft H atom potentials, resulting in highly red-shifted OH stretch fundamental frequencies and dislocation of the H atom upon vibrational excitation. These soft potentials lead to significant coupling to the other normal mode coordinates and give rise to the very broad vibrational signatures observed experimentally. The 2D IR spectra in both the OH and OD stretch regions of the light and deuterated isotopologues reveal broadened and long-lived ground-state bleach signatures of the vibrationally hot molecules. Polarization-sensitive transient absorption measurements in the OH and OD stretch regions reveal notable isotopic differences in orientational dynamics. Orientational relaxation was measured to occur on ∼600 fs and ∼2 ps time scales for the light and deuterated isotopologues, respectively. The orientational dynamics are interpreted in terms of activated H/D atom transfer events driven by collective intramolecular structural rearrangements.
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Affiliation(s)
- Jessika L S Dean
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Valerie S Winkler
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mark A Boyer
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin Madison, Madison, Wisconsin 53706, United States
| | - Edwin L Sibert
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin Madison, Madison, Wisconsin 53706, United States
| | - Joseph A Fournier
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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3
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Dean JLS, Fournier JA. Vibrational Dynamics of the Intramolecular H-Bond in Acetylacetone Investigated with Transient and 2D IR Spectroscopy. J Phys Chem B 2022; 126:3551-3562. [PMID: 35536173 DOI: 10.1021/acs.jpcb.2c00793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Acetylacetone (AcAc) has proven to be a fruitful but highly challenging model system for the experimental and computational interrogation of strong intramolecular hydrogen bonds. Key questions remain, however, regarding the identity of the minimum-energy structure of AcAc and the dynamics of intramolecular proton transfer. Here, we investigate the OH/OD stretch and bend regions of the enol tautomer of AcAc and its deuterated isotopologue with transient absorption and 2D IR spectroscopy. The OH bend region reveals a single dominant diagonal transition near 1625 cm-1 with intense cross peaks to lower-frequency modes, demonstrating highly mixed fingerprint transitions that contain OH bend character. The anharmonic coupling of the OH bend results in a highly elongated OH bend excited-state absorption transition that indicates a large manifold of OH bend overtone/combination bands in the OH stretch region that leads to strong bend-stretch Fermi resonance interactions. The OH and OD stretch regions consist of broad ground-state bleach signals, but there is no clear evidence of ω21 excited-state absorptions due to rapid population relaxation arising from strong intramolecular coupling to bending, fingerprint, and low-frequency H-bond modes. Orientational relaxation dynamics persist for timescales longer than the vibrational lifetimes, with polarization anisotropy components decaying within approximately 2 and 10 periods of the O-O oscillation for the OH and OD stretch, respectively. The significant isotopic dependence of the orientational dynamics is discussed in the context of intramolecular mode coupling, diffusional processes, and contributions from proton/deuteron transfer dynamics.
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Affiliation(s)
- Jessika L S Dean
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, United States 63130
| | - Joseph A Fournier
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, United States 63130
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4
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Qu C, Conte R, Houston PL, Bowman JM. Full-dimensional potential energy surface for acetylacetone and tunneling splittings. Phys Chem Chem Phys 2021; 23:7758-7767. [DOI: 10.1039/d0cp04221h] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New, full-dimensional potential energy surface for acetylacetone allows for description of H-tunneling dynamics and characterization of stationary points.
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Affiliation(s)
- Chen Qu
- Department of Chemistry & Biochemistry
- University of Maryland
- College Park
- USA
| | - Riccardo Conte
- Dipartimento di Chimica
- Università Degli Studi di Milano
- 20133 Milano
- Italy
| | - Paul L. Houston
- Department of Chemistry and Chemical Biology
- Cornell University
- Ithaca
- USA
- Department of Chemistry and Biochemistry
| | - Joel M. Bowman
- Cherry L. Emerson Center for Scientific Computations and Department of Chemistry
- Atlanta
- USA
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5
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Hansen PE, Spanget-Larsen J. NMR and IR Investigations of Strong Intramolecular Hydrogen Bonds. Molecules 2017; 22:E552. [PMID: 28353675 PMCID: PMC6154318 DOI: 10.3390/molecules22040552] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/20/2017] [Accepted: 03/24/2017] [Indexed: 11/24/2022] Open
Abstract
For the purpose of this review, strong hydrogen bonds have been defined on the basis of experimental data, such as OH stretching wavenumbers, νOH, and OH chemical shifts, δOH (in the latter case, after correction for ring current effects). Limits for O-H···Y systems are taken as 2800 > νOH > 1800 cm-1, and 19 ppm > δOH > 15 ppm. Recent results as well as an account of theoretical advances are presented for a series of important classes of compounds such as β-diketone enols, β-thioxoketone enols, Mannich bases, proton sponges, quinoline N-oxides and diacid anions. The O···O distance has long been used as a parameter for hydrogen bond strength in O-H···O systems. On a broad scale, a correlation between OH stretching wavenumbers and O···O distances is observed, as demonstrated experimentally as well as theoretically, but for substituted β-diketone enols this correlation is relatively weak.
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Affiliation(s)
- Poul Erik Hansen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, P.O. Box 260, DK-4000 Roskilde, Denmark.
| | - Jens Spanget-Larsen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, P.O. Box 260, DK-4000 Roskilde, Denmark.
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Azizi-Toupkanloo H, Tayyari SF. Density functional efficiency in the calculations of vibrational frequencies and molecular structures of β-diketones. J STRUCT CHEM+ 2016. [DOI: 10.1134/s002247661601008x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Dolati F, Tayyari SF, Vakili M, Wang YA. Proton transfer in acetylacetone and its α-halo derivatives. Phys Chem Chem Phys 2016; 18:344-50. [DOI: 10.1039/c5cp03845f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A two-dimensional potential energy function has been applied to study the bent intramolecular H-bonds within acetylacetone and its α-halo derivatives. The theoretically predicted proton transfer barrier heights correlate very well with geometrical parameters and electronic properties related to the H-bond strength.
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Affiliation(s)
- Fatemeh Dolati
- Chemistry Department
- Ferdowsi University of Mashhad
- Mashhad
- Iran
| | | | - Mohammad Vakili
- Chemistry Department
- Ferdowsi University of Mashhad
- Mashhad
- Iran
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8
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Howard DL, Kjaergaard HG, Huang J, Meuwly M. Infrared and Near-Infrared Spectroscopy of Acetylacetone and Hexafluoroacetylacetone. J Phys Chem A 2015; 119:7980-90. [DOI: 10.1021/acs.jpca.5b01863] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daryl L. Howard
- Australian Synchrotron, 800 Blackburn
Road, Clayton, Victoria 3168, Australia
- Department
of Chemistry, University of Otago, P.O. Box 56, Dunedin 9016, New Zealand
| | - Henrik G. Kjaergaard
- Department
of Chemistry, University of Otago, P.O. Box 56, Dunedin 9016, New Zealand
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Jing Huang
- Department
of Pharmaceutical Science, University of Maryland, Baltimore, Maryland 21201, United States
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Markus Meuwly
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
- Department
of Chemistry, Brown University, Providence, Rhode Island 01912, United States
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Abstract
Protomeric tautomerism is analyzed in view of the topological charge stabilization rules. Based on Hückel molecular orbital considerations and modern DFT calculations, it was found that the branching of amino or hydroxyl groups significantly contributes to the stability of major species through the first- and second-order perturbations with respect to the isoelectronic hydrocarbon. While amino-imino tautomerism is almost completely dominated by topological charge stabilization, hydroxyl-oxo tautomerism is affected by changes in the resonance integral of C-O/C═O bonds. Nevertheless, apart from side effects such as hydrogen bonds or solvent effects, a quantitative preference rule for the prediction of the tautomeric stability can be developed using topological π-electron energetics. As well as the analyses of simple bases, applications to complex or extended systems are exemplified analyzing purine bases, polyguanide, and polyuret. The present approach can be useful in conjunction with chemical intuition that comes from conventional valence bond theory.
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Affiliation(s)
- Masashi Hatanaka
- School of Engineering, Tokyo Denki University , 5 Senju-Asahi-cho, Adachi-ku, Tokyo 120-8551, Japan
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10
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Favero LB, Evangelisti L, Velino B, Caminati W. Morphing the Internal Dynamics of Acetylacetone by CH3 → CF3 Substitutions. The Rotational Spectrum of Trifluoroacetylacetone. J Phys Chem A 2014; 118:4243-8. [DOI: 10.1021/jp5005727] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laura B. Favero
- Istituto per lo
Studio dei Materiali Nanostrutturati (ISMN), Sezione di Bologna CNR, via Gobetti 101, I-40129 Bologna, Italy
| | - Luca Evangelisti
- Dipartimento
di
Chimica “G. Ciamician” dell’Università
di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - Biagio Velino
- Dipartimento
di
Chimica “G. Ciamician” dell’Università
di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - Walther Caminati
- Dipartimento
di
Chimica “G. Ciamician” dell’Università
di Bologna, Via Selmi 2, I-40126 Bologna, Italy
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11
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Janczak J, Kubiak R. From I‐Ligated and I‐Doped to
O
‐Ligated Hafnium(IV) Phthalocyaninate(2–) Complexes. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201301420] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jan Janczak
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, P. O. Box 1410, Okólna str. 2, 50‐950 Wrocław, Poland, http://www.int.pan.wroc.pl/
| | - Ryszard Kubiak
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, P. O. Box 1410, Okólna str. 2, 50‐950 Wrocław, Poland, http://www.int.pan.wroc.pl/
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12
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Petković M, Etinski M. Intramolecular OHO bonding in dibenzoylmethane: symmetry and spectral manifestations. RSC Adv 2014. [DOI: 10.1039/c4ra05586a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Calculations reveal that both symmetric and asymmetric structures of dibenzoylmethane are present in the gas phase at room temperature.
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Affiliation(s)
- Milena Petković
- Faculty of Physical Chemistry
- University of Belgrade
- 11 158 Belgrade, Serbia
| | - Mihajlo Etinski
- Faculty of Physical Chemistry
- University of Belgrade
- 11 158 Belgrade, Serbia
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13
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Comparative study of the O···H···O proton transfer in the enol form of a single acetylacetone molecule and acetylacetone incorporated in β-cyclodextrin: a theoretical investigation. MONATSHEFTE FUR CHEMIE 2013. [DOI: 10.1007/s00706-013-0969-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Bak A, Magdziarz T, Polanski J. Pharmacophore-based database mining for probing fragmental drug-likeness of diketo acid analogues. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2012; 23:185-204. [PMID: 22292781 DOI: 10.1080/1062936x.2011.645875] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A number of the structurally diverse chemical compounds with functional diketo acid (DKA) subunit(s) have been revealed by combined online and MoStBiodat 3D pharmacophore-guided ZINC and PubChem database screening. We used the structural data available from such screening to analyse the similarities of the compounds containing the DKA fragment. Generally, the analysis by principal component analysis and self-organizing neural network approaches reveals four families of compounds complying with the chemical constitution (aromatic, aliphatic) of the compounds. From a practical point of view, similar studies may reveal potential bioisosteres of known drugs, e.g. raltegravir/elvitegravir. In this context, it seems that mono-halogenated aryl substructures with para group show the closest similarity to these compounds, in contrast to structures where the aromatic ring is halogenated in both ortho- and para-locations.
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Affiliation(s)
- A Bak
- Department of Organic Chemistry , Institute of Chemistry, University of Silesia, Katowice, Poland.
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15
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Janczak J, Kubiak R. From iodoindium(III) phthalocyanine to the π-radical indium(III) diphthalocyanine and magnetically frustrated indium diacetate hydroxide coordination polymer. Inorganica Chim Acta 2011. [DOI: 10.1016/j.ica.2011.05.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Stare J, Mavri J, Grdadolnik J, Zidar J, Maksić ZB, Vianello R. Hydrogen Bond Dynamics of Histamine Monocation in Aqueous Solution: Car–Parrinello Molecular Dynamics and Vibrational Spectroscopy Study. J Phys Chem B 2011; 115:5999-6010. [DOI: 10.1021/jp111175e] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jernej Stare
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Janez Mavri
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | - Jože Grdadolnik
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | - Jernej Zidar
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | | | - Robert Vianello
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
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17
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Pirc G, Stare J, Mavri J. Car-Parrinello simulation of hydrogen bond dynamics in sodium hydrogen bissulfate. J Chem Phys 2010; 132:224506. [PMID: 20550407 DOI: 10.1063/1.3429251] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We studied proton dynamics of a short hydrogen bond of the crystalline sodium hydrogen bissulfate, a hydrogen-bonded ferroelectric system. Our approach was based on the established Car-Parrinello molecular dynamics (CPMD) methodology, followed by an a posteriori quantization of the OH stretching motion. The latter approach is based on snapshot structures taken from CPMD trajectory, calculation of proton potentials, and solving of the vibrational Schrodinger equation for each of the snapshot potentials. The so obtained contour of the OH stretching band has the center of gravity at about 1540 cm(-1) and a half width of about 700 cm(-1), which is in qualitative agreement with the experimental infrared spectrum. The corresponding values for the deuterated form are 1092 and 600 cm(-1), respectively. The hydrogen probability densities obtained by solving the vibrational Schrodinger equation allow for the evaluation of potential of mean force along the proton transfer coordinate. We demonstrate that for the present system the free energy profile is of the single-well type and features a broad and shallow minimum near the center of the hydrogen bond, allowing for frequent and barrierless proton (or deuteron) jumps. All the calculated time-averaged geometric parameters were in reasonable agreement with the experimental neutron diffraction data. As the present methodology for quantization of proton motion is applicable to a variety of hydrogen-bonded systems, it is promising for potential use in computational enzymology.
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Affiliation(s)
- Gordana Pirc
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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18
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Moyon NS, Chandra AK, Mitra S. Effect of Solvent Hydrogen Bonding on Excited-State Properties of Luminol: A Combined Fluorescence and DFT Study. J Phys Chem A 2009; 114:60-7. [DOI: 10.1021/jp907970b] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Asit Kumar Chandra
- Department of Chemistry, North-Eastern Hill University, Shillong 793 022, India
| | - Sivaprasad Mitra
- Department of Chemistry, North-Eastern Hill University, Shillong 793 022, India
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20
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Fluorescence studies on the photophysical properties and encapsulation behavior of acetaminophen in different environments. Biophys Chem 2008; 138:55-62. [DOI: 10.1016/j.bpc.2008.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Revised: 09/02/2008] [Accepted: 09/03/2008] [Indexed: 11/21/2022]
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21
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Molecular interactions of 1,4-dihydropyridine derivatives with selected organic solvents: A volumetric, spectroscopic and computational study. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2007.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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22
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Stare J, Panek J, Eckert J, Grdadolnik J, Mavri J, Hadži D. Proton Dynamics in the Strong Chelate Hydrogen Bond of Crystalline Picolinic Acid N-Oxide. A New Computational Approach and Infrared, Raman and INS Study. J Phys Chem A 2008; 112:1576-86. [DOI: 10.1021/jp077107u] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jernej Stare
- National Institute of Chemistry, Ljubljana, Slovenia; Center for Non-Linear Studies/Los Alamos Neutron Science Center, Los Alamos National Laboratory, Los Alamos, New Mexico; Faculty of Chemistry, Wrocław University, Wrocław, Poland; and Materials Research Laboratory, University of California, Santa Barbara, California
| | - Jarosław Panek
- National Institute of Chemistry, Ljubljana, Slovenia; Center for Non-Linear Studies/Los Alamos Neutron Science Center, Los Alamos National Laboratory, Los Alamos, New Mexico; Faculty of Chemistry, Wrocław University, Wrocław, Poland; and Materials Research Laboratory, University of California, Santa Barbara, California
| | - Juergen Eckert
- National Institute of Chemistry, Ljubljana, Slovenia; Center for Non-Linear Studies/Los Alamos Neutron Science Center, Los Alamos National Laboratory, Los Alamos, New Mexico; Faculty of Chemistry, Wrocław University, Wrocław, Poland; and Materials Research Laboratory, University of California, Santa Barbara, California
| | - Jože Grdadolnik
- National Institute of Chemistry, Ljubljana, Slovenia; Center for Non-Linear Studies/Los Alamos Neutron Science Center, Los Alamos National Laboratory, Los Alamos, New Mexico; Faculty of Chemistry, Wrocław University, Wrocław, Poland; and Materials Research Laboratory, University of California, Santa Barbara, California
| | - Janez Mavri
- National Institute of Chemistry, Ljubljana, Slovenia; Center for Non-Linear Studies/Los Alamos Neutron Science Center, Los Alamos National Laboratory, Los Alamos, New Mexico; Faculty of Chemistry, Wrocław University, Wrocław, Poland; and Materials Research Laboratory, University of California, Santa Barbara, California
| | - Dušan Hadži
- National Institute of Chemistry, Ljubljana, Slovenia; Center for Non-Linear Studies/Los Alamos Neutron Science Center, Los Alamos National Laboratory, Los Alamos, New Mexico; Faculty of Chemistry, Wrocław University, Wrocław, Poland; and Materials Research Laboratory, University of California, Santa Barbara, California
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23
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Demšar K, Stare J, Mavri J. Structure and vibrational dynamics of hydrogen bond in hydrogenbissulfate anion in the gas phase and in the solid state: A computational study. J Mol Struct 2007. [DOI: 10.1016/j.molstruc.2007.03.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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24
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Matanović I, Došlić N. Theoretical modeling of the formic acid dimer infrared spectrum: Shaping the O–H stretch band. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2007.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Jezierska A, Panek JJ, Koll A, Mavri J. Car-Parrinello simulation of an O-H stretching envelope and potential of mean force of an intramolecular hydrogen bonded system: application to a Mannich base in solid state and in vacuum. J Chem Phys 2007; 126:205101. [PMID: 17552801 DOI: 10.1063/1.2736692] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Car-Parrinello molecular dynamics (CPMD) study was performed for an anharmonic system-an intramolecularly hydrogen bonded Mannich-base-type compound, 4,5-dimethyl-2(N,N-dimethylaminemethyl)phenol, to investigate the vibrational spectrum associated with the O-H stretching. Calculations were carried out for the solid state and for an isolated molecule. The classical CPMD simulation was performed and then the proton potential snapshots were extracted from the trajectory. The vibrational Schrodinger equation for the snapshots was solved numerically, and the (O-H) envelope was calculated as a superposition of the 0-->1 transitions. The potential of mean force for the proton stretching mode was calculated from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling, nuclear quantum effects, and effects of the environment. Perspectives for application of the presented methodology in the computational support of biocatalysis are given in the study.
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Affiliation(s)
- Aneta Jezierska
- Faculty of Chemistry, University of Wroclaw, 14 F. Joliot-Curie, 50-383 Wroclaw, Poland
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Mohacek-Grosev V, Furić K, Ivanković H. Luminescence and Raman Spectra of Acetylacetone at Low Temperatures. J Phys Chem A 2007; 111:5820-7. [PMID: 17566988 DOI: 10.1021/jp067157j] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Raman spectra of acetylacetone were recorded for molecules isolated in an argon matrix at 10 K and for a polycrystalline sample. In the solid sample, broad bands appear superimposed on a much weaker Raman spectrum corresponding mainly to the stable enol form. The position of these bands depends on the excitation wavelength (514.5 and 488.8 nm argon ion laser lines were used), sample temperature, and cooling history. They are attributed to transitions from an excited electronic state to various isomer states in the ground electronic state. Laser photons have energies comparable to energies of a number of excited triplet states predicted for a free acetylacetone molecule (Chen, X.-B.; Fang, W.-H.; Phillips, D. L. J. Phys. Chem. A 2006, 110, 4434). Since singlet-to-triplet photon absorption transitions are forbidden, states existing in the solid have mixed singlet/triplet character. Their decay results in population of different isomer states, which except for the lowest isomers SYN enol, TS2 enol (described in Matanović I.; Doslić, N. J. Phys. Chem. A 2005, 109, 4185), and the keto form, which can be detected in the Raman spectra of the solid, are not vibrationally resolved. Differential scanning calorimetry detected two signals upon cooling of acetylacetone, one at 229 K and one at 217 K, while upon heating, they appear at 254 and 225 K. The phase change at higher temperature is attributed to a freezing/melting transition, while the one at lower temperature seems to correspond to freezing/melting of keto domains, as suggested by Johnson et al. (Johnson, M. R.; Jones, N. H.; Geis, A; Horsewill. A. J.; Trommsdorff, H. P. J. Chem. Phys. 2002, 116, 5694). Using matrix isolation in argon, the vibrational spectrum of acetylacetone at 10 K was recorded. Strong bands at 1602 and 1629 cm(-1) are assigned as the SYN enol bands, while a weaker underlying band at 1687 cm(-1) and a medium shoulder at 1617 cm(-1) are assigned as TS2 enol bands.
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Affiliation(s)
- Vlasta Mohacek-Grosev
- Ruder Bosković Institute, P.O. Box 180, Bijenicka c. 54, 10002 Zagreb, Croatia, and Faculty of Chemical Engineering and Technology, Marulićev trg 19, 10000 Zagreb, Croatia.
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27
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Dolin S, Levin A, Polyakov E, Khrulev A, Mikhailova T. Hydrogen-bonded materials based on organic tautomeric molecules: Theoretical treatment. J Mol Struct 2006. [DOI: 10.1016/j.molstruc.2005.09.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Coussan S, Ferro Y, Trivella A, Rajzmann M, Roubin P, Wieczorek R, Manca C, Piecuch P, Kowalski K, Włoch M, Kucharski SA, Musiał M. Experimental and Theoretical UV Characterizations of Acetylacetone and Its Isomers. J Phys Chem A 2006; 110:3920-6. [PMID: 16539413 DOI: 10.1021/jp056834r] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Cryogenic matrix isolation experiments have allowed the measurement of the UV absorption spectra of the high-energy non-chelated isomers of acetylacetone, these isomers being produced by UV irradiation of the stable chelated form. Their identification has been done by coupling selective UV-induced isomerization, infrared spectroscopy, and harmonic vibrational frequency calculations using density functional theory. The relative energies of the chelated and non-chelated forms of acetylacetone in the S0 state have been obtained using density functional theory and coupled-cluster methods. For each isomer of acetylacetone, we have calculated the UV transition energies and dipole oscillator strengths using the excited-state coupled-cluster methods, including EOMCCSD (equation-of-motion coupled-cluster method with singles and doubles) and CR-EOMCCSD(T) (the completely renormalized EOMCC approach with singles, doubles, and non-iterative triples). For dipole-allowed transition energies, there is a very good agreement between experiment and theory. In particular, the CR-EOMCCSD(T) approach explains the blue shift in the electronic spectrum due to the formation of the non-chelated species after the UV irradiation of the chelated form of acetylacetone. Both experiment and CR-EOMCCSD(T) theory identify two among the seven non-chelated forms to be characterized by red-shifted UV transitions relative to the remaining five non-chelated isomers.
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Affiliation(s)
- S Coussan
- Laboratoire Physique des Interactions Ioniques et Moléculaires, UMR 6633, Université de Provence-CNRS, Centre St-Jérôme, 13397 Marseille Cedex 20, France.
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29
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Musin RN, Mariam YH. An integrated approach to the study of intramolecular hydrogen bonds in malonaldehyde enol derivatives and naphthazarin: trend in energetic versus geometrical consequences. J PHYS ORG CHEM 2006. [DOI: 10.1002/poc.1102] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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30
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Abstract
It has often been postulated that the lowest energy enolic form of Acetylacetone (AcAc) assumes C(s) symmetry, i.e., has a double-minimum potential possibly exhibiting a low barrier to internal proton transfer and not a single minimum, C(2v). Recent theoretical calculations and experimental work support the C(s) hypothesis but the literature on this fascinating molecule is divided. Toward this objective, the high-resolution rotational spectra of enolic acetylacetone and 3 isotopologues have been obtained, revealing C(2v) symmetry. The two methyl groups exhibit a very low barrier to internal rotation, thus making AcAc internally highly dynamic.
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Affiliation(s)
- Walther Caminati
- Dipartimento di Chimica, G. Ciamician dell'Università, Via Selmi 2, I-40126 Bologna, Italy.
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31
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Delchev VB, Mikosch H. H-bonded complexes between acetylacetone and two molecules of methanol: HF and DFT level study. J Mol Model 2005; 11:474-80. [PMID: 16044289 DOI: 10.1007/s00894-005-0241-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2004] [Accepted: 01/04/2005] [Indexed: 11/30/2022]
Abstract
Five stable H-bonded complexes (supersystems) between acetylacetone and two methanol molecules were investigated at the B3LYP and HF levels of theory using the 6-311G** and 6-11++G** basis sets. The most stable complex was found as the one with the highest relative bonding and interaction energies. All vibrational frequencies resulting from calculations with the 6-311++G** basis set were compared with the recorded IR spectrum of acetylacetone/methanol mixture in a molar ratio 1:2.
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Affiliation(s)
- Vassil B Delchev
- Department of Physical Chemistry, University of Plovdiv, Plovdiv, Bulgaria.
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32
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Klähn M, Schlitter J, Gerwert K. Theoretical IR spectroscopy based on QM/MM calculations provides changes in charge distribution, bond lengths, and bond angles of the GTP ligand induced by the Ras-protein. Biophys J 2005; 88:3829-44. [PMID: 15805169 PMCID: PMC1305617 DOI: 10.1529/biophysj.104.058644] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2004] [Accepted: 03/21/2005] [Indexed: 11/18/2022] Open
Abstract
The GTPase Ras p21 is a crucial switch in cellular signal transduction. Fourier transform infrared (FTIR) spectra of the substrate guanosine triphosphate (GTP) show remarkable changes when it binds to the enzyme. The reduced band widths indicate that the flexible GTP molecule is guided by the protein into a preferred conformation. The delocalized phosphate vibrations of unbound GTP become localized. The frequency shifts show an electron movement toward beta-phosphate, which probably contributes to catalysis by reducing the free activation energy. To quantify these qualitative observations we performed QM/MM molecular dynamics simulations of Ras.GTP and GTP in water. The triphosphate part of GTP was treated quantum mechanically using density functional theory (DFT). Vibrational spectra were calculated in harmonic approximation with an average deviation of 3% from the experimental frequencies. This provides a high confidence in the computational results as vibrational spectra are highly sensitive to conformation and charge distribution. As compared to GTP in water, Ras-bound GTP shows a shift of negative charge of approximately 0.2 e toward the beta-phosphate from gamma-phosphate and from alpha-phosphate due to the positive charge of the magnesium ion, to a lesser extent of Lys-16, and surprisingly without any effect of the P-loop backbone. Magnesium and Gly-13 twist and bend the gamma-O-beta bonds such that the crucial bond is stretched before cleaving.
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Affiliation(s)
- Marco Klähn
- Ruhr-Universität Bochum, Lehrstuhl für Biophysik ND 04, Bochum, Germany.
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33
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Matanović I, Doslić N. Infrared Spectroscopy of the Intramolecular Hydrogen Bond in Acethylacetone: A Computational Approach. J Phys Chem A 2005; 109:4185-94. [PMID: 16833744 DOI: 10.1021/jp044695s] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The intramolecular hydrogen bond in the enol-acethylacetone (ACAC) is investigated by performing reduced-dimensional quantum calculations. To analyze the shared proton vibrations, two sets of coordinates were employed: normal mode coordinates describing the motion in the vicinity of the most stable configuration, and internal coordinates accounting for the double minimum proton motion. It is proved that the extreme broadness of the OH-stretch band in ACAC is a consequence of the coexistence of two enol-ACAC structures: the global minimum and the transition state for rotation of the distal methyl group. Further, a ground-state tunneling splitting of 116 cm(-1) is found, and it is shown that the inclusion of the kinematic coupling is mandatory when treating large-amplitude proton motion. In the OH-stretch direction a splitting of 853 cm(-1) was predicted.
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Affiliation(s)
- I Matanović
- Department of Physical Chemistry, R. Bosković Institute, Bijenicka 54, 10000 Zagreb, Croatia
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34
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Vianello R, Kovačević B, Ambrožič G, Mavri J, Maksić ZB. Hydrogen bonding in complex of serine with histidine: computational and spectroscopic study of model compounds. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.10.089] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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35
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Matanović I, Došlić N, Mihalić Z. Exploring the potential energy surface for proton transfer in acetylacetone. Chem Phys 2004. [DOI: 10.1016/j.chemphys.2004.07.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Žagar E, Grdadolnik J. An infrared spectroscopic study of H-bond network in hyperbranched polyester polyol. J Mol Struct 2003. [DOI: 10.1016/s0022-2860(03)00286-2] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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37
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WU CC, CHAUDHURI C, JIANG JC, LEE YT, CHANG HC. Hydration-induced conformational changes in protonated 2,4-pentanedione in the gas phase. Mol Phys 2003. [DOI: 10.1080/0026897021000054835] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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38
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Coussan S, Manca C, Ferro Y, Roubin P. UV and IR photoisomerizations of an intramolecularly H-bonded molecule: acetylacetone trapped in nitrogen matrix. Chem Phys Lett 2003. [DOI: 10.1016/s0009-2614(03)00037-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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39
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40
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Kržan A, Mavri J. Nitroso-naphthol quinone-monooxime tautomeric equilibrium revisited: evidence for oximo group isomerization. Chem Phys 2002. [DOI: 10.1016/s0301-0104(02)00282-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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41
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Nagashima N, Kudoh S, Takayanagi M, Nakata M. UV-Induced Photoisomerization of Acetylacetone and Identification of Less-Stable Isomers by Low-Temperature Matrix-Isolation Infrared Spectroscopy and Density Functional Theory Calculation. J Phys Chem A 2001. [DOI: 10.1021/jp012557m] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Naoko Nagashima
- Graduate School of BASE (Bio-Applications and Systems Engineering), Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Satoshi Kudoh
- Graduate School of BASE (Bio-Applications and Systems Engineering), Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Masao Takayanagi
- Graduate School of BASE (Bio-Applications and Systems Engineering), Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Munetaka Nakata
- Graduate School of BASE (Bio-Applications and Systems Engineering), Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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42
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Mavri J, Grdadolnik J. Proton Transfer Dynamics in Acetylacetone: A Mixed Quantum-Classical Simulation of Vibrational Spectra. J Phys Chem A 2001. [DOI: 10.1021/jp003671s] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Janez Mavri
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Jože Grdadolnik
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
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