| 1. |
- Bondesson, Laban, et al.
(author)
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Density functional theory calculations of hydrogen bonding energies of drug molecules
- 2006
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In: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860 .- 1872-8014 .- 0166-1280. ; 776:1-3, s. 61-68
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Journal article (peer-reviewed)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. |
- Bih, H., et al.
(author)
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Raman spectroscopic study of the phase transitions sequence in Li3Fe2(PO4)(3) and Na3Fe2(PO4)(3) at high temperature
- 2009
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In: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860 .- 1872-8014. ; 936, s. 147-155
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Journal article (peer-reviewed)abstract
- The phase transition properties of A3Fe2(PO4)3 (A = Li, Na) were studied by Raman spectroscopy. Several Raman bands change continuously in 25–400 °C temperature range, indicating a phase transition from the γ, β to the α-phase occurring at this range of temperature. Bands caused by vibrations of phosphate anion and different ions have been found. The spectra analysis reveals that the modes, located at low frequency range 100–400 cm−1, near 500 cm−1 at room temperature, are the most thermo-sensitive. In addition, the modes corresponding to bond valence stretching of (PO4) unit in the frequency region 970–1200 cm−1 show also evolution with temperature but less sensitive than the above ones. It is observed that phosphate groups show some ordering with temperature. According to our Raman study, we can state that each of the compounds LiFeP and NaFeP shows two reversible phase transformations in the temperature range studied.
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| 3. |
- Chen, Ruikui, et al.
(author)
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Photoinduced intramolecular charge-transfer state in thiophene-π-conjugated donor-acceptor molecules.
- 2008
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In: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860 .- 1872-8014. ; 876:1-3, s. 102-109
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Journal article (peer-reviewed)abstract
- Novel thiophene-π-conjugated donor-acceptor mols., 5-[2-(1,2,2,4-tetramethyl-1,2,3,4-tetrahydroquinolin-6-yl)-vinyl]-thiophene-2-carbaldehyde (QTC) and (1-cyano-2-{5-[2-(1,2,2,4-tetramethyl-1,2,3,4-tetrahydroquinolin-6-yl)-vinyl]-thiophen-2-yl}-vinyl)-phosphonic acid di-Et ester (QTCP), were designed and synthesized. Combined exptl. and theor. methods were performed to investigate the photoinduced intramol. charge-transfer (ICT) processes of these compds. Steady-state absorption and fluorescence measurements in different solvents indicate the photoinduced ICT characters of QTC and QTCP. Solvent dependency of the large Stokes shifts and high dipole moment of the excited state also support the charge-transfer character of the excited state. Theor. calcns. based on time-dependent d. functional theory (TDDFT) method were performed to investigate ICT states of these compds. The results reveal that the excited states have adopted a distortion of the C=C double bond between the donor moiety and the thiophene-π-bridge. [on SciFinder(R)]
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| 4. |
- Liu, Wei, et al.
(author)
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Geometric and electronic structure of the diphenylamine radical cation : An EPR, ENDOR and MO study
- 2005
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In: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860 .- 1872-8014. ; 733:1-3, s. 13-17
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Journal article (peer-reviewed)abstract
- The geometric and electronic structure of the diphenylamine radical cation Ph2(H)N+ obtained by X-irradiation of diphenylamine in CFCl3 at low temperature have been studied by the methods of EPR and ENDOR combined with theoretical calculations. The 110 K ENDOR spectrum of Ph2(H)N+ is mainly attributed to the ortho and meta phenyl ring protons. The accurate assignment of spectroscopic parameters is based on spectral simulations and theoretical calculations. Close agreement was obtained between the experimental and calculated hyperfine tensors of ortho and meta protons. © 2004 Elsevier B.V. All rights reserved.
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| 5. |
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| 6. |
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| 7. |
- Holmlid, Leif, 1942
(author)
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Rotational spectra of large Rydberg Matter clusters K37, K61 and K91 give trends in K–K bond distances relative to electron orbit radius
- 2008
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In: Journal of Molecular Structure. - : Elsevier BV. - 0022-2860. ; 885:1-3, s. 122-130
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Journal article (peer-reviewed)abstract
- Rotational spectra of planar clusters of Rydberg Matter (RM) have recently been reported for the first time, for clusters K19 in excitation levels nB = 4, 5 and 6 [L. Holmlid, Mol. Phys. 105 (2007) 933–939]. From such spectra, the average bond distances in the clusters can be determined, and good agreement with theoretical predictions is found. K19 is an example of a sixfold symmetric planar RM cluster, while other similar clusters have 37, 61 and 91 atoms. Rotational bands of the heavy clusters K37, K61 and K91 are easily identified since they appear as closely spaced groups of lines on top of electronic, probably spin-flip transitions. The bond lengths for the heavy clusters are in the range 3–10 nm, found with a relative precision of approximately 2 × 10−3. The cluster K37 (nB = 8) is the largest cluster observed with diameter of 58.9 nm and bond length of 9.82 ± 0.02 nm. The dimensional ratio d/rn, i.e. the ratio between the experimental interatomic distance and the theoretical electron orbiting radius, is larger for higher excitation levels, where the classical limit is approached and thus the electronic motion is more strongly confined to the cluster plane. The dimensional ratio is also larger for smaller clusters, which is probably due to larger edge effects giving larger average bond distances. The average value of d/rn is 2.865 ± 0.032, close to the theoretically predicted value 2.9. Intensity alternation for every second rotational line is often observed.
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| 8. |
- Hui, Tong, et al.
(author)
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A Computational Investigation of the Retrocyclization Reaction of Silacyclo-but-2-enes to 1-silabuta-1,3-dienes : Focus on the effect of the substituents
- 2007
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In: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 811:1-3, s. 153-160
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Journal article (peer-reviewed)abstract
- Substituent effects on the reaction profile of the thermal retrocyclization reaction of silacyclobut-2-enes to 1-silabuta-1,3-dienes were studied using B3LYP hybrid density functional theory as well as CCSD and CCSD(T) ab initio calculations. Several different substituents (–CF3, –SiH3, –CN, –OCH3, –OH, and –NH2) were used to investigate their effects on the relative energies of the transition states of the retrocyclization reaction as well as of the 1-silabutadiene products. It was found that π-donor groups at the 4-position greatly reduce the energy barriers, and also stabilize the 1-silabutadienes relative to the silacyclobut-2-enes. Silyl substituents at the silicon atom will facilitate the reaction when compared to alkyl substituents. The results thus indicate that the ring-opening reaction of 4,4-disubstituted 1,1-disilylsilacyclobut-2-enes with π-donor substituents are particularly suitable entries for formation of 1-silabutadienes of low relative energy.
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| 9. |
- Iribarne, F., et al.
(author)
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Interaction energies of nitrofurans with trypanothione reductase and glutathione reductase studied by molecular docking
- 2007
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In: Journal of Molecular Structure. - : Elsevier BV. - 0166-1280. ; 818:1-3, s. 7-22
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Journal article (peer-reviewed)abstract
- A theoretical docking study was conducted on a sample of previously reported nitrofuran derivatives, at the binding sites of Trypanosoma cruzi trypanothione reductase (TR) and human erythrocyte glutathione reductase (GR), in order to examine interaction energies (affinities) towards the parasite enzyme and check for selectivity with respect to the human counterpart. A large proportion of nitrofurans were previously shown to be TR inhibitors and some of them have in vitro trypanocidal action as well. The analysis of data collected from the docking procedure was undertaken both from the numeric and graphical standpoints, including the comparison of force field energies, molecular contacts and spatial location of the different orientations that ligands acquired at the binding sites. The results clearly suggest that nitrofurans are not able to selectively bind at the active site of the parasite TR, attaining even larger interaction energies at GR active site. The reason for inhibitor specificity is two-fold: (a) the nitrofuran group acts as a strong electrostatic anchor in GR; (b) the compounds form more stable complexes when binding at the non-selective dimmer interface. Therefore, these two aspects should be specially considered when seeking good candidates for leaders in regards the development of drugs with selective inhibition of TR.
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| 10. |
- Johansson, Patrik, 1969, et al.
(author)
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A novel field of ab initio studies: complexation of simple anions within neutral cryptands
- 2005
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In: Journal of Molecular Structure: THEOCHEM. - : Elsevier BV. - 0166-1280. ; 717:1-3, s. 215-221
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Journal article (peer-reviewed)abstract
- We present here an ab initio study on anion guest - macrocycle host relationships. The complexation of different simple inorganic anions (F - , Cl - , BF 4 - and ClO 4 - ) with the neutral cryptand, the macrotricycle (H 3 BN) 4 [(CH 2 ) n ] 6 , (n=3-6), has been studied using ab initio Hartree-Fock calculations and density functional theory using the B3LYP hybrid functional. As the side-lengths of the pure cryptands increase with the oligomeric sidechain (n), the cryptand cavity increases as n 3 . F - is the most strongly preferred anion for all cryptands, only for the largest host cavity (n=6) complexes are formed exothermally for all anion guests. Morokuma-Kitaura decomposition has been performed to analyse the total interaction energies within the created supermolecules in physically relevant terms including the importance of treatment of the basis set superposition error. According to this scheme the polarisation/charge transfer parts differ in importance amongst the complexes in facilitating a strong binding of the anion guests, but the dominant balance being that of Coulombic attraction and Pauli repulsion. © 2004 Elsevier B.V. All rights reserved.
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