| 1. |
- Bondesson, Laban, et al.
(författare)
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Density functional theory calculations of hydrogen bonding energies of drug molecules
- 2006
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Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860 .- 1872-8014 .- 0166-1280. ; 776:1-3, s. 61-68
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Tidskriftsartikel (refereegranskat)abstract
- Hydrogen bonding energies of several drug molecules have been calculated using hybrid density functional theory with inclusion of basis set superposition error corrections. The calculated total hydrogen bonding energy of each drug molecule has been compared with the result of a conceptually simple additive model, from which the summation of hydrogen bonding energies of individual polar groups present in the drug molecule are considered. It is shown that the validity of the additive model is strongly conditional, and to some extent predictable: In cases where the hydrogen bonding group is isolated the addition model can be of relevance, while in cases where the hydrogen bonding groups are interconnected through pi-conjugation rings or chains of the drug molecules it introduces substantial errors. It is suggested that such strong cooperative effects of hydrogen bonds should always be taken into account for evaluation of the hydrogen bonding energies of drug molecules.
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| 2. |
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| 3. |
- Klug, Otto, et al.
(författare)
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Raman spectroscopy of aromatic acids adsorbed on oxidised aluminium foil
- 1997
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Ingår i: Journal of Molecular Structure. - 0022-2860 .- 1872-8014. ; 410, s. 183-188
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Tidskriftsartikel (refereegranskat)abstract
- Adsorption of ortho- and para-phthalic acids on oxidised aluminium foil was investigated by Raman and surface-enhanced Raman spectroscopy (SERS). Without any treatment of the foil only a modified method of SERS provided spectroscopic evidence of the adsorption. However, by dissolving the metal aluminium from the Al2O3-Al-Al2O3 structure of the foil, the adsorption could be investigated by Raman spectroscopy without surface-enhanced conditions. The vibrational bands of the adsorbed species, obtained by both types of Raman spectroscopy, are compared to the solid-state spectra of the pure acids and their dipotassium salts. The band shifts suggest that the adsorbed species are essentially in the carboxylate form; however, the Raman and the SER spectra of the same species are not identical indicating a separate chemical reaction occurring at the surface upon depositing the sol. (C) 1997 Elsevier Science B.V.
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| 4. |
- Larsson, Andreas, et al.
(författare)
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Theoretical verification and extension of the McKean relationship between bond lengths and stretching frequencies
- 1999
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Ingår i: Journal of Molecular Structure. - 0022-2860 .- 1872-8014. ; 485-486, s. 385-407
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Tidskriftsartikel (refereegranskat)abstract
- Vibrational spectra contain explicit information on the electronic structure and the bonding situation of a molecule, which can be obtained by transforming the vibrational normal modes of a molecule into appropriate internal coordinate modes, which are localized in a fragment of the molecule and which are associated to that internal coordinate that describes the molecular fragment in question. It is shown that the adiabatic internal modes derived recently (Int. J. Quant. Chem., 67 (1998) 1) are the theoretical counterparts of McKean's isolated CH stretching modes (Chem. Soc. Rev., 7 (1978) 399). Adiabatic CH stretching frequencies obtained from experimental vibrational spectra can be used to determine CH bond lengths with high accuracy. Contrary to the concept of isolated stretching frequencies a generalization to any bond of a molecule is possible as is demonstrated for the CC stretching frequencies. While normal mode frequencies do not provide a basis to determine CC bond lengths and CC bond strengths, this is possible with the help of the adiabatic CC stretching frequencies. Measured vibrational spectra are used to describe different types of CC bonds in a quantitative way. For CH bonds, it is also shown that adiabatic stretching frequency leads to the definition of an ideal dissociation energy, which contrary to the experimentally determined dissociation energy is a direct measure of the bond strength. The difference between measured and ideal dissociation energies gives information on stabilization or destabilization of the radicals formed in a dissociation process
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| 5. |
- Abad, Nadeem, et al.
(författare)
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Unveiling structural features, chemical reactivity, and bioactivity of a newly synthesized purine derivative through crystallography and computational approaches
- 2024
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Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860 .- 1872-8014. ; 1311
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Tidskriftsartikel (refereegranskat)abstract
- We introduce the synthesis and characterization of a novel purine derivative, 2-amino-6‑chloro-N,N-diphenyl-7H-purine-7-carboxamide. X-ray crystallography was utilized to elucidate its molecular and crystal structure. A comprehensive crystal packing analysis uncovered a network of diverse intermolecular interactions, including classical and unconventional hydrogen bonding. Remarkably, a unique halogen···π (C—Cl···π(ring)) interaction was identified and theoretically analyzed within a multi-approach quantum mechanics (QM) framework, revealing its lone-pair⋯π (n→π*) nature. Furthermore, insights into the electronic and chemical reactivity properties are provided by means of Conceptual Density Functional Theory (CDFT) at wB97X-D/aug-cc-pVTZ level. The compound's drug-likeness, pharmacokinetics, and toxicology profiles are assessed using ADMETlab 2.0. Finally, molecular docking simulations were conducted to evaluate its bioactivity as a potential cyclooxygenase-2 (COX-2) inhibitor. This study significantly advances our understanding of purine structure and reactivity, offering valuable insights for the development of targeted purine-based COX-2 inhibitors and anticancer therapeutics.
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| 6. |
- Ajpi Condori, Cesario, et al.
(författare)
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Synthesis and spectroscopic characterization of Fe3+-BDC metal organic framework as material for lithium ion batteries
- 2023
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Ingår i: Journal of Molecular Structure. - : Elsevier B.V.. - 0022-2860 .- 1872-8014. ; 1272
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Tidskriftsartikel (refereegranskat)abstract
- This work presents synthesis and spectroscopic characterization of a new metal-organic framework (MOF). The compound Fe-BDC-DMF was synthetized by the solvothermal method and prepared via a reaction between FeCl3.6H2O and benzene-1,4-dicarboxylic acid (H2BDC) or terephthalic acid using N,N-dimethylformamide (DMF) as solvent. The powder was characterized by powder X-ray diffraction (PXRD), scanning electron microscopy (SEM) and infrared spectroscopy (IR) analysis. The electrochemical properties were investigated in a typical lithium-ion battery electrolyte by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS) and galvanostatic charging and discharging. The synthetized Fe-BDC-DMF metal-organic framework (MOF) contains a mixture of three phases, identified by PXRD as: MOF-235, and MIL-53(Fe) monoclinic with C2/c and P21/c space groups. The structure of the Fe-BDC is built up from Fe3+ ions, terephalates (BDC) bridges and in-situ-generated DMF ligands. The electrochemical measurements conducted in the potential range of 0.5–3.5 V vs. Li+/Li0 show the voltage profiles of Fe-BDC and a plateau capacity of around 175 mAh/g. © 2022 The Author(s)
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| 7. |
- Ajpi Condori, Cesario, et al.
(författare)
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Synthesis and spectroscopic characterization of NiII coordination network : Poly-[tris(µ4-Benzene-1,4-dicarboxylato)-tetrakis(µ1-dimethylformamide-κ1O)-trinickel(II)] as material for lithium ion batteries
- 2022
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Ingår i: Journal of Molecular Structure. - : Elsevier B.V.. - 0022-2860 .- 1872-8014. ; 1265
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Tidskriftsartikel (refereegranskat)abstract
- The compound Ni3(C8H4O4)3(C3H7NO)3, poly-[tris(µ4-Benzene-1,4-dicarboxylato)-tetrakis(µ1-dimethylformamide-κ1O)-trinickel(II)], was synthesized by the solvothermal method prepared via reaction between NiCl2•6H2O and terephthalic acid using N,N-dimethylformamide (DMF) as solvent. The structure was characterized by powder X-ray diffraction and infrared spectroscopy analyses. The electrochemical properties as a potential active material in lithium-ion batteries were characterized by electrochemical impedance spectroscopy and galvanostatic charge-discharge curves in a battery half-cell. The characterization results show that the coordination network contains one independent structure in the asymmetric unit. It is constructed from Ni2+ ions, terephthalate bridges and in-situ-generated DMF ligands, forming two similar two-dimensional (2D) layer structures. These similar 2D layers are in an alternating arrangement and are linked with each other by dense H—H interactions (45%) to generate a three-dimensional (3D) supramolecular framework with ordered and disordered DMF molecules. The electrochemical measurements, conducted in the potential range of 0.5–3.5 V vs Li/Li+, show that Ni3(C8H4O4)3(C3H7NO)4 has good electrochemical properties and can work as anode in lithium-ion batteries. The material presents an initial specific capacity of ∼420 mAh g−1, which drops during consecutive scans but stabilizes at ∼50 mAh g−1. However, due to the wide potential range there are indications of a gradual collapse of the structure. The electrochemical impedance spectroscopy shows an increase of charge transfer resistance from 24 to 1190 Ohms after cycling likely due to this collapse.
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| 8. |
- Akpe, Victor, et al.
(författare)
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Photophysical and photochemical parameters of octakis (benzylthio) phthalocyaninato zinc, aluminium and tin : Red shift index concept in solvent effect on the ground state absorption of zinc phthalocyanine derivatives
- 2010
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Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860 .- 1872-8014. ; 984:1-3, s. 1-14
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Tidskriftsartikel (refereegranskat)abstract
- This paper addresses the synthesis of octa-substituted benzylthio metallophthalocyanines (OBTMPcs) that contain the central metal ions of Zn2+, Al3+ and Sn4+. The ground state absorption of ZnPc(SR)(8) (OBTZnPc) along with the ZnPc derivatives, well documented in literature were used to study a new concept called the red shift index (RsI). The concept is based on the empirical values of RsI of the different complexes in solvent media. Unequivocally, parameters used in this paper show strong correlations that are consistent with the results obtained. For instance, 12,1 of the complexes tend to increase as the refractive index, n(D), and solvent donor, DN, of solvent increases. Photodegradation (photobleaching) quantum yield, phi(d) measurements of these compounds show that they are highly photostable, phi(d) (0.03-0.33 x 10(-5)). The triplet quantum yield, phi(T) (0.40-0.53) and the triplet lifetime, tau(T) (610-810 mu s) are within the typical range for metallophthalocyanines in DMSO. The photosensitisation efficiency. S-Delta, is relatively high for all the molecules (0.74-0.90). (C) 2010 Elsevier B.V. All rights reserved.
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| 9. |
- Ashraf, Sajda, et al.
(författare)
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Synthesis, spectroscopic characterization, DFT and molecular docking of N-(3-cyano-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl) naphthalene-1-sulfonamide derivatives
- 2024
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Ingår i: Journal of Molecular Structure. - : Elsevier B.V.. - 0022-2860 .- 1872-8014. ; 1312
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Tidskriftsartikel (refereegranskat)abstract
- Liver pyruvate kinase (PKL) is a key player in controlling metabolic pathways and ATP production within the liver's glycolysis pathway. Since PKL modulators have been identified as a promising target for treating hepatocellular carcinoma (HCC) and non-alcoholic fatty liver disease (NAFLD), our research is centered on the development and synthesis of derivatives of N-(3-cyano-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl) naphthalene-1-sulfonamide with the aim of modulating PLK. To improve PKL specificity, we used structural analysis and modeling as a guide. Notably, compound PKL-05 became the series' only active ingredient. DFT, Hirshfeld surface analysis, and molecular docking were used in our study to thoroughly examine the connection between compound structures and their computational functions. The global hardness and softness energy values, as well as the HOMO-LUMO energy gap value, were computed in order to forecast the chemical reactivity of this newly synthesized molecule. These energy values indicate that this molecule tends to be chemically stable and has little chemical reactivity. The results demonstrated a strong agreement between theoretical forecasts and experimental findings. In particular, PKL-05 exhibits encouraging traits that establish it as a useful starting point for additional research in the search for innovative PKL modulators to tackle the treatment issues associated with NAFLD and HCC.
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| 10. |
- Azdouz, M, et al.
(författare)
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Synthesis, Rietveld refinements and Raman spectroscopy studies of the solid solution Na1-xKxPb4(VO4)(3) (0 <= x <= 1)
- 2010
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Ingår i: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860 .- 1872-8014. ; 963:2-3, s. 258-266
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Tidskriftsartikel (refereegranskat)abstract
- In the present study we report the synthesis, crystal structure and Raman spectroscopy studies of Na1-xKxPb4(VO4)(3) orthovanaclates solid solutions (0 <= x <= 1). Rielveld refinements showed that this solid solution is continuous adopting P6(3)/m (no. 176) space group. Some of Pb(II) cations are located in the (6 h) sites. The ninefold coordination sites (4f) are equally occupied by the other lead cations and the K+ and Na+ monovalent ions. The structure can be described as built up from [VO4](3-) tetrahedral and Ph2+ of sixfold coordination cavities (6 h positions), which delimit void hexagonal tunnels running along [0 0 1]. These tunnels are connected by cations of mixed sites (4f) half occupied by Pb(II) and half by Na+/K+ mixed cations. The existence of this type of lacunar apatite seems to be conditioned by the presence of lone pair cations Pb(II). Raman spectra of all the compositions are similar and show some linear shifts in band positions as a function of the composition toward high values due the substitutions of Na+ by K+ with a larger radius. No considerable changes in the temperature dependence of the Raman modes and the corresponding FWHM are observed and thus no temperature induced phase transition is observed in Na0.5K0.5Pb4(VO4)(3) up to 650 K.
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