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Raczuk E, Dmochowska B, Samaszko-Fiertek J, Madaj J. Different Schiff Bases-Structure, Importance and Classification. Molecules 2022; 27:787. [PMID: 35164049 PMCID: PMC8839460 DOI: 10.3390/molecules27030787] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/14/2022] [Accepted: 01/14/2022] [Indexed: 11/17/2022] Open
Abstract
Schiff bases are a vast group of compounds characterized by the presence of a double bond linking carbon and nitrogen atoms, the versatility of which is generated in the many ways to combine a variety of alkyl or aryl substituents. Compounds of this type are both found in nature and synthesized in the laboratory. For years, Schiff bases have been greatly inspiring to many chemists and biochemists. In this article, we attempt to present a new take on this group of compounds, underlining of the importance of various types of Schiff bases. Among the different types of compounds that can be classified as Schiff bases, we chose hydrazides, dihydrazides, hydrazones and mixed derivatives such as hydrazide-hydrazones. For these compounds, we presented the elements of their structure that allow them to be classified as Schiff bases. While hydrazones are typical examples of Schiff bases, including hydrazides among them may be surprising for some. In their case, this is possible due to the amide-iminol tautomerism. The carbon-nitrogen double bond present in the iminol tautomer is a typical element found in Schiff bases. In addition to the characteristics of the structure of these selected derivatives, and sometimes their classification, we presented selected literature items which, in our opinion, represent their importance in various fields well.
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Affiliation(s)
| | - Barbara Dmochowska
- Carbohydrate Chemistry Group, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (E.R.); (J.S.-F.); (J.M.)
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Vandenbroucke SST, Levrau E, Minjauw MM, Van Daele M, Solano E, Vos R, Dendooven J, Detavernier C. Study of the surface species during thermal and plasma-enhanced atomic layer deposition of titanium oxide films using in situ IR-spectroscopy and in vacuo X-ray photoelectron spectroscopy. Phys Chem Chem Phys 2020; 22:9262-9271. [DOI: 10.1039/d0cp00395f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
By the powerful combination of in situ FTIR and in vacuo XPS, the surface species during ALD of TDMAT with different reactants could be identified.
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Affiliation(s)
| | - Elisabeth Levrau
- Department of Solid State Sciences
- CoCooN group
- Ghent University
- 9000 Gent
- Belgium
| | - Matthias M. Minjauw
- Department of Solid State Sciences
- CoCooN group
- Ghent University
- 9000 Gent
- Belgium
| | - Michiel Van Daele
- Department of Solid State Sciences
- CoCooN group
- Ghent University
- 9000 Gent
- Belgium
| | - Eduardo Solano
- Department of Solid State Sciences
- CoCooN group
- Ghent University
- 9000 Gent
- Belgium
| | - Rita Vos
- Interuniversity Micro Electronics Center (IMEC)
- 3001 Heverlee
- Belgium
| | - Jolien Dendooven
- Department of Solid State Sciences
- CoCooN group
- Ghent University
- 9000 Gent
- Belgium
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3
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Kwaśniewicz M, Czarnecki MA. The Effect of Chain Length on Mid-Infrared and Near-Infrared Spectra of Aliphatic 1-Alcohols. APPLIED SPECTROSCOPY 2018; 72:288-296. [PMID: 29134818 DOI: 10.1177/0003702817732253] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Effect of the chain length on mid-infrared (MIR) and near-infrared (NIR) spectra of aliphatic 1-alcohols from methanol to 1-decanol was examined in detail. Of particular interest were the spectra-structure correlations in the NIR region and the correlation between MIR and NIR spectra of 1-alcohols. An application of two-dimensional correlation analysis (2D-COS) and chemometric methods provided comprehensive information on spectral changes in the data set. Principal component analysis (PCA) and cluster analysis evidenced that the spectra of methanol, ethanol, and 1-propanol are noticeably different from the spectra of higher 1-alcohols. The similarity between the spectra increases with an increase in the chain length. Hence, the most similar are the spectra of 1-nonanol and 1-decanol. Two-dimensional hetero-correlation analysis is very helpful for identification of the origin of bands and may guide selection of the best spectral ranges for the chemometric analysis. As shown, normalization of the spectra pronounces the intensity changes in various spectral regions and provides information not accessible from the raw data. The spectra of alcohols cannot be represented as a sum of the CH3, CH2, and OH group spectra since the OH group is involved in the hydrogen bonding. As a result, the spectral changes of this group are nonlinear and its spectral profile cannot be properly resolved. Finally, this work provides a lot of evidence that the degree of self-association of 1-alcohols decreases with the increase in chain length because of the growing meaning of the hydrophobic interactions. For butyl alcohol and higher 1-alcohols the hydrophobic interactions are more important than the OH OH interactions. Therefore, methanol, ethanol, and 1-propanol have unlimited miscibility with water, whereas 1-butanol and higher 1-alcohols have limited miscibility with water.
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Andrade LAF, Silla JM, Cormanich RA, Freitas MP. Infrared Fingerprints of n N → σ* NH Hyperconjugation in Hydrazides. J Org Chem 2017; 82:12181-12187. [PMID: 29058903 DOI: 10.1021/acs.joc.7b01985] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An earlier study demonstrated that hyperconjugation operates in hydrazides by analyzing the N-H stretching mode in gas phase infrared (IR) spectroscopy, and then observing two very distinct bands corresponding to isolated isomers experiencing or not the nN → σ*N-H electron delocalization. The present work reports a chemical method to obtain insight on the hyperconjugation in hydrazide derivatives from solution IR spectroscopy. The analogous amides did not show a νN-H red-shifted band, as the electron donor orbital in the above hyperconjugative interaction does not exist. In addition, the effect of electron withdrawing groups bonded to a nitrogen atom, namely the trifluoroacetyl and the methanesulfonyl groups, was analyzed on the conformational isomerism and on the ability to induce a stronger hyperconjugation in the resulting compounds.
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Affiliation(s)
- Laize A F Andrade
- Department of Chemistry, Federal University of Lavras , 37200-000 Lavras, MG, Brazil
| | - Josué M Silla
- Department of Chemistry, Federal University of Lavras , 37200-000 Lavras, MG, Brazil
| | - Rodrigo A Cormanich
- Institute of Chemistry, University of Campinas , P.O. Box 6154, 13083-970, Campinas, SP, Brazil
| | - Matheus P Freitas
- Department of Chemistry, Federal University of Lavras , 37200-000 Lavras, MG, Brazil
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Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
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Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
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Vorobyov I, Anisimov VM, Greene S, Venable RM, Moser A, Pastor RW, MacKerell AD. Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers. J Chem Theory Comput 2015; 3:1120-33. [PMID: 26627431 DOI: 10.1021/ct600350s] [Citation(s) in RCA: 216] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Empirical force field parameters consistent with the CHARMM additive and classical Drude based polarizable force fields are presented for linear and cyclic ethers. Initiation of the optimization process involved validation of the aliphatic parameters based on linear alkanes and cyclic alkanes. Results showed the transfer to cyclohexane to yield satisfactory agreement with target data; however, in the case of cyclopentane direct transfer of the Lennard-Jones parameters was not sufficient due to ring strain, requiring additional optimization of these parameters for this molecule. Parameters for the ethers were then developed starting with the available aliphatic parameters, with the nonbond parameters for the oxygens optimized to reproduce both gas- and condensed-phase properties. Nonbond parameters for the polarizable model include the use of an anisotropic electrostatic model on the oxygens. Parameter optimization emphasized the development of transferable parameters between the ethers of a given class. The ether models are shown to be in satisfactory agreement with both pure solvent and aqueous solvation properties, and the resulting parameters are transferable to test molecules. The presented force field will allow for simulation studies of ethers in condensed phase and provides a basis for ongoing developments in both additive and polarizable force fields for biological molecules.
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Affiliation(s)
- Igor Vorobyov
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Victor M Anisimov
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Shannon Greene
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Richard M Venable
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Adam Moser
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Richard W Pastor
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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Punihaole D, Hong Z, Jakubek RS, Dahlburg EM, Geib S, Asher SA. Glutamine and Asparagine Side Chain Hyperconjugation-Induced Structurally Sensitive Vibrations. J Phys Chem B 2015; 119:13039-51. [PMID: 26392216 PMCID: PMC5065012 DOI: 10.1021/acs.jpcb.5b07651] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We identified vibrational spectral marker bands that sensitively report on the side chain structures of glutamine (Gln) and asparagine (Asn). Density functional theory (DFT) calculations indicate that the Amide III(P) (AmIII(P)) vibrations of Gln and Asn depend cosinusoidally on their side chain OCCC dihedral angles (the χ3 and χ2 angles of Gln and Asn, respectively). We use UV resonance Raman (UVRR) and visible Raman spectroscopy to experimentally correlate the AmIII(P) Raman band frequency to the primary amide OCCC dihedral angle. The AmIII(P) structural sensitivity derives from the Gln (Asn) Cβ-Cγ (Cα-Cβ) stretching component of the vibration. The Cβ-Cγ (Cα-Cβ) bond length inversely correlates with the AmIII(P) band frequency. As the Cβ-Cγ (Cα-Cβ) bond length decreases, its stretching force constant increases, which results in an upshift in the AmIII(P) frequency. The Cβ-Cγ (Cα-Cβ) bond length dependence on the χ3 (χ2) dihedral angle results from hyperconjugation between the Cδ═Oϵ (Cγ═Oδ) π* and Cβ-Cγ (Cα-Cβ) σ orbitals. Using a Protein Data Bank library, we show that the χ3 and χ2 dihedral angles of Gln and Asn depend on the peptide backbone Ramachandran angles. We demonstrate that the inhomogeneously broadened AmIII(P) band line shapes can be used to calculate the χ3 and χ2 angle distributions of peptides. The spectral correlations determined in this study enable important new insights into protein structure in solution, and in Gln- and Asn-rich amyloid-like fibrils and prions.
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Affiliation(s)
- David Punihaole
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Chevron Science Center, Pittsburgh, Pennsylvania 15260, United States
| | - Zhenmin Hong
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Chevron Science Center, Pittsburgh, Pennsylvania 15260, United States
| | - Ryan S. Jakubek
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Chevron Science Center, Pittsburgh, Pennsylvania 15260, United States
| | - Elizabeth M. Dahlburg
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Chevron Science Center, Pittsburgh, Pennsylvania 15260, United States
| | - Steven Geib
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Chevron Science Center, Pittsburgh, Pennsylvania 15260, United States
| | - Sanford A. Asher
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Chevron Science Center, Pittsburgh, Pennsylvania 15260, United States
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Zhu H, Dhinojwala A. Thermal Behavior of Long-Chain Alcohols on Sapphire Substrate. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:6306-6313. [PMID: 26010291 DOI: 10.1021/acs.langmuir.5b01330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Structures of amphiphilic molecules at the liquid/solid and solid/solid interfaces are important in understanding lubrication, colloid stabilization, chromatography, and nucleation. Here, we have used interface-sensitive sum frequency generation (SFG) spectroscopy to characterize the interfacial structures of long-chain alcohols above and below the bulk melting temperature (Tm). The melting temperature of the ordered hexadecanol monolayer was measured to be around 30 °C above the bulk Tm, consistent with the transition temperature reported using X-ray reflectivity [ Phys. Rev. Lett. 2011 , 106 , 137801 ]. The disruption of hydrogen bonds between the sapphire and the alcohol hydroxyl groups was directly measured as a function of temperature. The strength of this hydrogen-bonding interaction, which explained the monolayer thermal stability above Tm, was calculated using the Badger-Bauer equation. Below Tm, the ordered self-assembled monolayer influenced the structure of the interfacial crystalline layer, and the transition from the ordered monolayer to the bulk crystalline phases (α rotator phase, β crystalline phase, and γ crystalline phase) resulted in packing frustrations at the interface.
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Affiliation(s)
- He Zhu
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Ali Dhinojwala
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
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Duarte L, Giuliano BM, Reva I, Fausto R. Tautomers and UV-induced photoisomerization of a strongly intramolecularly H-bonded aromatic azo-dye: 1-(cyclopropyl)diazo-2-naphthol. J Phys Chem A 2013; 117:10671-80. [PMID: 24059591 DOI: 10.1021/jp405061b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Aromatic azo compounds have a wide range of industrial applications as dyes in optical and color-changing materials and can also be exploited in the design of new photodynamic molecular systems. The azo derivative 1-(cyclopropyl)diazo-2-naphthol was isolated in low-temperature cryogenic matrices, and its molecular structure, tautomeric equilibrium, and photochemical transformations were characterized by infrared spectroscopy and theoretical calculations. Only azo-enol forms having the OH group involved in a strong intramolecular hydrogen bond, forming a six-membered ring with the azo group, were found experimentally. Irradiation with a narrowband source in the near-UV range generates different rotameric and tautomeric azo-enol and keto-hydrazone forms that can be interconverted at different irradiation wavelengths.
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Affiliation(s)
- Luís Duarte
- Department of Chemistry, University of Coimbra , P-3004-535 Coimbra, Portugal
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10
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Lopes Jesus A, Rosado MT, Redinha J. The structure of mono- and di-amino derivatives of cyclohexane: Energetic and Natural Bond Orbital approaches. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2010.11.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Selenoglycosides in silico: ab initio-derived reparameterization of MM4, conformational analysis using histo-blood group ABH antigens and lectin docking as indication for potential of bioactivity. J Comput Aided Mol Des 2010; 24:1009-21. [PMID: 20976527 DOI: 10.1007/s10822-010-9392-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 10/06/2010] [Indexed: 10/18/2022]
Abstract
The identification of glycan epitopes such as the histo-blood group ABH determinants as docking sites for bacterial/viral infections and signals in growth regulation fuels the interest to develop non-hydrolysable mimetics for therapeutic applications. Inevitably, the required substitution of the linkage oxygen atom will alter the derivative's topology. Our study addresses the question of the impact of substitution of oxygen by selenium. In order to characterize spatial parameters and flexibility of selenoglycosides, we first performed ab initio calculations on model compounds to refine the MM4 force field. The following application of the resulting MM4R version appears to reduce the difference to ab initio data when compared to using the MM4 estimator. Systematic conformational searches on the derivatives of histo-blood group ABH antigens revealed increased flexibility with acquisition of additional low-energy conformer(s), akin to the behavior of S-glycosides. Docking analysis using the Glide program for eight test cases indicated potential for bioactivity, giving further experimental investigation a clear direction to testing Se-glycosides as lectin ligands.
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Computational studies of the role of glycopyranosyl oxacarbenium ions in glycobiology and glycochemistry. Adv Carbohydr Chem Biochem 2009; 62:83-159. [PMID: 19501705 DOI: 10.1016/s0065-2318(09)00004-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Bandoli G, Barreca D, Gasparotto A, Seraglia R, Tondello E, Devi A, Fischer RA, Winter M, Fois E, Gamba A, Tabacchi G. An integrated experimental and theoretical investigation on Cu(hfa)2. TMEDA: structure, bonding and reactivity. Phys Chem Chem Phys 2009; 11:5998-6007. [PMID: 19588023 DOI: 10.1039/b904145a] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The physico-chemical properties of the beta-diketonate diamine Cu(ii) compound with hfa (1,1,1,5,5,5-hexafluoro-2-4-pentanedionate) and TMEDA (N,N,N',N' tetramethylethylenediamine), Cu(hfa)(2).TMEDA, have been thoroughly investigated via an integrated multi-technique experimental-computational approach. In the newly found orthorhombic polymorph, as revealed by low temperature single-crystal X-ray studies, the complex is present as a monomer with a distorted octahedral geometry at the Cu(ii) centre. The compound sublimates, without premature side decompositions, at 343 K and 10(-3) Torr. The structural, vibrational, electronic and thermal behavior of the neutral Cu(hfa)(2).TMEDA complex has been investigated along with its fragmentation pathways, initiated by the release of an anionic hfa ligand with formation of a positive Cu(hfa).TMEDA(+) ion. Joint experimental and theoretical analyses led to the rationalization of the first fragmentation steps in terms of the Cu(ii)-ligands bonding properties and Jahn-Teller distortion. The present study suggests applications of Cu(hfa)(2).TMEDA as a precursor for copper and copper oxide materials by Chemical Vapor Deposition.
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Affiliation(s)
- Giuliano Bandoli
- Department of Pharmaceutical Sciences, Padova University, 35131 Padova, Italy
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Lii JH, Allinger NL. The important role of lone-pairs in force field (MM4) calculations on hydrogen bonding in alcohols. J Phys Chem A 2008; 112:11903-13. [PMID: 18942820 DOI: 10.1021/jp804581h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An expanded treatment of hydrogen bonding has been developed for MM4 force field calculations, which is an extension from the traditional van der Waals-electrostatic model. It adds explicit hydrogen-bond angularity by the inclusion of lone-pair directionality. The vectors that account for this directionality are placed along the hydrogen acceptor and its chemically intuitive electron pairs. No physical lone-pairs are used in the calculations. Instead, an H-bond angularity function, and a lone-pair directionality function, are incorporated into the hydrogen-bond term. The inclusion of the lone-pair directionality results in improved accuracy in hydrogen-bonded geometries and interaction energies. In this work is described hydrogen bonding in alcohols, and also in water and hydrogen fluoride dimer. The extension to other compounds such as aldehydes, ketones, amides, and so on is straightforward and will be discussed in future work. The conformational energies of ethylene glycol are discussed.
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Affiliation(s)
- Jenn-Huei Lii
- Department of Chemistry, University of Georgia, Athens, Georgia 30602-2526, USA
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Ionescu AR, Whitfield DM, Zgierski MZ. O-2 Substituted pyranosyl oxacarbenium ions are C-2–O-2 2-fold rotors with a strong syn preference. Carbohydr Res 2007; 342:2793-800. [DOI: 10.1016/j.carres.2007.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Revised: 09/14/2007] [Accepted: 09/20/2007] [Indexed: 10/22/2022]
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Chen KH, Lii JH, Fan Y, Allinger NL. Molecular mechanics (MM4) study of amines. J Comput Chem 2007; 28:2391-412. [PMID: 17486561 DOI: 10.1002/jcc.20737] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The MM4 force field has been extended to include aliphatic amines. About 20 amines have been examined to obtain a set of useful molecular mechanics parameters for this class. The vibrational spectra of seven amines (172 frequencies) calculated by MM4 have an overall rms error of 27 cm(-1), compared with corresponding MM4 value of 24 cm(-1) for alkanes. The rms and signed average errors of the moments of inertia of nine simple amines compared with the experimental data were 0.18% and -0.004%, respectively. The heats of formation of 30 amines were also studied. The MM4 weighted standard deviation is 0.41 kcal/mol, compared with experiment. Electronegativity effects occur in the hydrocarbon portion of an amine from the nitrogen, and are accounted for by including electronegativity induced changes in bond lengths and angles, and induced dipole-dipole interactions in the molecule. Negative hyperconjugation results from the presence of the lone pair of electrons on nitrogen, and leads to the Bohlmann bands in the infrared, and also to strong and unusual geometric changes in the molecules (Bohlmann effect), all of which are fairly well accounted for. The conformational energies in amines appear to be less straightforward than those for most other classes of molecules, apparently because of the Bohlmann effect, and these are probably not yet completely understood. In general, the agreement between the MM4 calculated results and the available data is reasonably good.
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Affiliation(s)
- Kuo-Hsiang Chen
- Department of Chemistry, Center for Computational Chemistry, Chemistry Annex, University of Georgia, Athens, Georgia 30605-2526, USA
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17
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Tabacchi G, Vanoni MA, Gamba A, Fois E. Does Negative Hyperconjugation Assist Enzymatic Dehydrogenations? Chemphyschem 2007; 8:1283-8. [PMID: 17506039 DOI: 10.1002/cphc.200700085] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Gloria Tabacchi
- Dipartimento di Scienze Chimiche ed Ambientali and INSTM, Università degli Studi dell'Insubria, Via Lucini 3, I-22100 Como, Italy
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Chen KH, Lii JH, Walker GA, Xie Y, Schaefer HF, Allinger NL. Molecular Mechanics (MM4) Study of Fluorinated Hydrocarbons. J Phys Chem A 2006; 110:7202-27. [PMID: 16737272 DOI: 10.1021/jp060430x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A molecular mechanics study of small saturated hydrocarbons (up to C-6) substituted by up to six fluorines has been carried out with the MM4 force field. A parameter set has been developed for use in the calculation of bond lengths, bond angles, torsion angles, conformational energies, barriers to rotation, dipole moments, moments of inertia, and vibrational frequencies for these compounds. The results are mostly in fair to good agreement with experiment and ab initio calculations. The high electronegativity of fluorine leads to serious geometric consequences in these compounds, but these consequences can be dealt with adequately by suitable cross-terms in the force constant matrix, and by recognizing that some of the reference bond lengths and angles (l(0), theta(0)) and the corresponding stretching and bending constant parameters (k(s), k(theta)) that are usually thought of as constants must in fact be treated as functions of the electronegativity of the substituents. Additionally, the heavy mass of the fluorine (relative to the mass of hydrogen in alkanes) leads to large values for other cross-terms that were found to be unimportant in hydrocarbons. Conformational equilibria for polyfluorinated compounds are affected by the delta-two effect well-known in carbohydrates. A few larger fluorinated and polyfluorinated alkanes, including perfluoropropane, perfluorobutane, and Teflon, have also been studied.
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Affiliation(s)
- Kuo-Hsiang Chen
- Center for Computational Chemistry, Chemistry Annex, University of Georgia, Athens, 30602-2526, USA
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Lii JH, Chen KH, Johnson GP, French AD, Allinger NL. The external-anomeric torsional effect. Carbohydr Res 2005; 340:853-62. [PMID: 15780251 DOI: 10.1016/j.carres.2005.01.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2004] [Accepted: 01/25/2005] [Indexed: 11/16/2022]
Abstract
The rotational barrier for a methyl group at the end of an anomeric system is sometimes lower than we might have anticipated. Thus, in the trans-trans conformation of dimethoxymethane, the barrier to methyl rotation is calculated (B3LYP/6-311++G(2d,2p)) to be 2.22 kcal/mol, just slightly smaller than the corresponding barrier to rotation of the methyl group in methyl propyl ether of 2.32 kcal/mol. However, if the methyl being rotated in dimethoxymethane is placed into a gauche conformation, that rotational barrier is reduced to 1.52 kcal/mol. This substantial (0.80 kcal/mol relative to methyl propyl ether) reduction in barrier height in the latter case is attributed mainly to the change in the bond order of the C-O bond to which the methyl is attached, as a function of conformation, which in turn is a result of the anomeric effect. We have called this barrier lowering the external-anomeric torsional effect. This effect is apparently widespread in carbohydrates, and it results in the changing of conformational energies by up to about 2 kcal/mol. If polysaccharide potential surfaces are to be accurately mapped by molecular mechanics, this effect clearly needs to be accounted for.
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Affiliation(s)
- Jenn-Huei Lii
- Center for Computational Chemistry, University of Georgia, Chemistry Annex, Athens, GA 30602-2526, USA
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David S. The evidence for an anomeric effect of the proton. Carbohydr Res 2005; 340:2569-72. [PMID: 16157313 DOI: 10.1016/j.carres.2005.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2004] [Accepted: 04/05/2005] [Indexed: 11/29/2022]
Abstract
The significant excess in conformational free-energy at position 2 of an oxane ring and other chemical and physical properties are explained by an anomeric effect of the proton.
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Affiliation(s)
- Serge David
- Institut de Chimie Minérale et Organique, Bât. 420, F-91405 Orsay cedex, France.
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