| 1. |
- Abelev, Betty, et al.
(författare)
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Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV
- 2012
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Ingår i: Journal of High Energy Physics. - 1029-8479. ; :11
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Tidskriftsartikel (refereegranskat)abstract
- The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
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| 2. |
- Abelev, Betty, et al.
(författare)
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Long-range angular correlations on the near and away side in p-Pb collisions at root S-NN=5.02 TeV
- 2013
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Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 719:1-3, s. 29-41
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Tidskriftsartikel (refereegranskat)abstract
- Angular correlations between charged trigger and associated particles are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5 < P-T,P-assoc < P-T,P-trig < 4 GeV/c. The correlations are measured over two units of pseudorapidity and full azimuthal angle in different intervals of event multiplicity, and expressed as associated yield per trigger particle. Two long-range ridge-like structures, one on the near side and one on the away side, are observed when the per-trigger yield obtained in low-multiplicity events is subtracted from the one in high-multiplicity events. The excess on the near-side is qualitatively similar to that recently reported by the CMS Collaboration, while the excess on the away-side is reported for the first time. The two-ridge structure projected onto azimuthal angle is quantified with the second and third Fourier coefficients as well as by near-side and away-side yields and widths. The yields on the near side and on the away side are equal within the uncertainties for all studied event multiplicity and p(T) bins, and the widths show no significant evolution with event multiplicity or p(T). These findings suggest that the near-side ridge is accompanied by an essentially identical away-side ridge. (c) 2013 CERN. Published by Elsevier B.V. All rights reserved.
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| 3. |
- Abelev, Betty, et al.
(författare)
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Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC
- 2012
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Ingår i: Journal of High Energy Physics. - 1029-8479. ; :7
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Tidskriftsartikel (refereegranskat)abstract
- We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.
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| 4. |
- Kumar, Pradeep, et al.
(författare)
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Density functional theoretic studies of host-guest interaction in gas hydrates
- 2014
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Ingår i: Computational and Theoretical Chemistry. - : Elsevier. - 2210-271X .- 2210-2728. ; 1029, s. 26-32
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Tidskriftsartikel (refereegranskat)abstract
- Recently we reported the host-guest interaction between a dodecahedral water cage and a variety of guest species that include diatomic (CO, H-2, N-2, O-2), triatomic (CO2, O-3) and polyatomic (CH4, NH3) molecules at the MP2/CBS limit (Kumar and Sathyamurthy, 2011). Since high computational costs involved in the application of MP2 and CCSD (T) methods limit the size of the clathrate that can be studied, the performance of the density functional theoretic method using functionals like B3LYP, M06-HF, M06-L, M06-2X and BLYP-D3 is evaluated for its ability to predict the interaction energy as well as the geometry. The computed results are compared with the estimated CCSD/CBS values, which were obtained with the help of the MP2/CBS values reported earlier. The DFT/BLYP-D3 method seems to be the best; the functionals M06-2X and M06-HF performed reasonably well, while B3LYP failed to predict any attraction between the guest and the host. (C) 2013 Elsevier B.V. All rights reserved.
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| 5. |
- Kumar, R. P. S. Abhijith, et al.
(författare)
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Stabilization of the C-20 cage by encapsulation of H+ and He2+ ions
- 2014
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Ingår i: Current Science. - 0011-3891. ; 106:9, s. 1255-1259
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Tidskriftsartikel (refereegranskat)abstract
- It is shown by ab initio calculations using second-order Moller-Plesset perturbation theory and 6-31g*, aug-cc-pVDZ and aug-cc-pVTZ basis sets and coupled cluster singles, doubles and perturbative triples method with the 6-31g* basis set, that it is possible to stabilize the cage structure of the smallest fullerene C-20 by encapsulating small cations like H+ and He2+. While the latter stabilizes the cage structure by charge transfer, the former prefers to form a covalent linkage with the carbon atoms.
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| 6. |
- Andersson, C. David, 1978-, et al.
(författare)
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Physical Mechanisms Governing Substituent Effects on Arene-Arene Interactions in a Protein Milieu
- 2020
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 124:30, s. 6529-6539
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Tidskriftsartikel (refereegranskat)abstract
- Arene-arene interactions play important roles in protein-ligand complex formation. Here, we investigate the characteristics of arene-arene interactions between small organic molecules and aromatic amino acids in protein interiors. The study is based on X-ray crystallographic data and quantum mechanical calculations using the enzyme acetylcholinesterase and selected inhibitory ligands as a model system. It is shown that the arene substituents of the inhibitors dictate the strength of the interaction and the geometry of the resulting complexes. Importantly, the calculated interaction energies correlate well with the measured inhibitor potency. Non-hydrogen substituents strengthened all interaction types in the protein milieu, in keeping with results for benzene dimer model systems. The interaction energies were dispersion-dominated, but substituents that induced local dipole moments increased the electrostatic contribution and thus yielded more strongly bound complexes. These findings provide fundamental insights into the physical mechanisms governing arene-arene interactions in the protein milieu and thus into molecular recognition between proteins and small molecules.
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| 7. |
- Berg, Lotta, et al.
(författare)
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The Nature of Activated Non-classical Hydrogen Bonds : A Case Study on Acetylcholinesterase-Ligand Complexes
- 2016
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Ingår i: Chemistry - A European Journal. - : Wiley-VCH Verlagsgesellschaft. - 0947-6539 .- 1521-3765. ; 22:8, s. 2672-2681
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Tidskriftsartikel (refereegranskat)abstract
- Molecular recognition events in biological systems are driven by non-covalent interactions between interacting species. Here, we have studied hydrogen bonds of the CHY type involving electron-deficient CH donors using dispersion-corrected density functional theory (DFT) calculations applied to acetylcholinesterase-ligand complexes. The strengths of CHY interactions activated by a proximal cation were considerably strong; comparable to or greater than those of classical hydrogen bonds. Significant differences in the energetic components compared to classical hydrogen bonds and non-activated CHY interactions were observed. Comparison between DFT and molecular mechanics calculations showed that common force fields could not reproduce the interaction energy values of the studied hydrogen bonds. The presented results highlight the importance of considering CHY interactions when analysing protein-ligand complexes, call for a review of current force fields, and opens up possibilities for the development of improved design tools for drug discovery.
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| 8. |
- Karthikeyan, S., et al.
(författare)
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Influence of the Substituents on the CH...pi Interaction : Benzene-Methane Complex
- 2013
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 117:30, s. 6687-6694
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Tidskriftsartikel (refereegranskat)abstract
- Recently we showed that the binding energy of the benzene...acetylene complex could be tuned up to 5 kcal/mol by substituting the hydrogen atoms of the benzene molecule with multiple electron-donating/electron-withdrawing groups (J. Chem. Theory Comput. 2012, 8, 1935). In continuation, we have here examined the influence of various substituents on the CH...pi interaction present in the benzene...methane complex using the CCSD(T) method at the complete basis set limit. The influence of multiple fluoro substituents on the interaction strength of the benzene...methane complex was found to be insignificant, while the interaction strength linearly increases with successive addition of methyl groups. The influence of other substituents such as CN, NO2, COOH, Cl, and OH was found to be negligible. The NH2 group enhances the binding strength similarly to the methyl group. Energy decomposition analysis predicts the dispersion energy component to be on an average three times larger than the electrostatic energy component. Multidimensional correlation analysis shows that the exchange-repulsion and dispersion terms are correlated very well with the interaction distance (r) and with a combination of the interaction distance (r) and molar refractivity (MR), while the electrostatic component correlates well when the Hammett constant is used in combination with the interaction distance (r). Various recently developed DFT methods were used to assess their ability to predict the binding energy of various substituted benzene...methane complexes, and the M06-2X, B97-D, and B3LYP-D3 methods were found to be the best performers, giving a mean absolute deviation of similar to 0.15 kcal/mol.
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| 9. |
- Larsson, Malin, et al.
(författare)
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On the use of electronic descriptors for QSAR modelling of PCDDs, PCDFs and dioxin-like PCBs£ :
- 2013
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Ingår i: SAR and QSAR in environmental research (Print). - : Taylor & Francis Group. - 1062-936X .- 1029-046X. ; 24:6, s. 461-479
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Tidskriftsartikel (refereegranskat)abstract
- The electronic properties of 29 polychlorinated dibenzo-p-dioxins and dibenzofurans and dioxin-like polychlorinated biphenyls that have been included in the toxic equivalency factor system have been investigated and used to derive quantum mechanical (QM) chemical descriptors for QSAR modelling. Their utility in this context was investigated alongside descriptors based on ultraviolet absorption data and traditional 2D descriptors including log Kow, polarizability, molecular surface properties, van der Waals volume and selected connectivity indices. The QM descriptors were calculated using the semi-empirical AM1 method and the density functional theory method B3-LYP/6-31G(∗∗). Atom-specific and molecular quantum chemical descriptors were calculated to compare the electronic properties of dioxin-like compounds regardless of their chemical class, with particular emphasis on the lateral positions. Multivariate analysis revealed differences between the chemical classes in terms of their electronic properties and also highlighted differences between congeners. The results obtained demonstrated the importance of considering molecular orbital energies, but also indicated that the ratios of the coefficients of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) at the lateral carbons were important. In addition, the digitalized UV spectra contained chemical information that provided crucial insights into dioxin-like activity.
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| 10. |
- Majumder, Moumita, et al.
(författare)
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CH center dot center dot center dot pi and pi center dot center dot center dot pi interaction in benzene-acetylene clusters
- 2013
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Ingår i: Chemical Physics Letters. - : Elsevier. - 0009-2614 .- 1873-4448. ; 557, s. 59-65
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Tidskriftsartikel (refereegranskat)abstract
- Ab initio calculations at the MP2/aug-cc-pVXZ (where, X = D, T and Q) and CCSD(T)/aug-cc-pVDZ levels of theory and certain density functional theoretic calculations were carried out for different configurations of benzene-acetylene clusters. The interaction energy was estimated at the CCSD(T)/CBS limit. For the 1:1 complex, the T-shaped geometry (C-6v symmetry) was found to be the most stable (-2.72 kcal/mol) and the pi center dot center dot center dot pi stacked structure was the least stable (-0.58 kcal/mol). For the 1:2 complex, the ring-shaped (-5.87 kcal/mol) and the double T-shaped (-5.23 kcal/mol) geometries were found to be the most stable and the second most stable, respectively.
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| 11. |
- Mishra, Brijesh Kumar, et al.
(författare)
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Tuning the C-H center dot center dot center dot pi Interaction by Different Substitutions in Benzene-Acetylene Complexes
- 2012
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 8:6, s. 1935-1942
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Tidskriftsartikel (refereegranskat)abstract
- The influence of substitutions in aromatic moieties on the binding strength of their complexes is a subject of broad importance. Using a set of various substituted benzenes, Sherrill and co-workers (J. Am. Chem. Soc. 2011, 133, 13244; J. Phys. Chem. A 2003, 107, 8377) recently showed that the strength of a stacking interaction (pi...pi interaction) is enhanced by adding substituents regardless of their nature. Although the binding strength of an activated C-H...pi interaction is comparable to that of a stacking interaction, a similar systematic study is hitherto unknown in the literature. We have computed the stabilization energies of the C-H...pi complex of acetylene and multiple fluoro-/methyl-substituted benzenes at the coupled-cluster single and double (triple) excitation [CCSD(T)]/complete basis set (CBS) limit. The trend for interaction energies was found to be hexafluorobenzene-acetylene < sym-tetrafluorobenzene-acetylene < sym-trifluorobenzene-acetylene < sym-difluorobenzene-acetylene < benzene-acetylene < sym-dimethylbenzene-acetylene < sym-trimethylbenzene-acetylene < sym-tetramethylbenzene-acetylene < hexamethylbenzene-acetylene. Therefore, contrary to the case of stacking interaction (Hohenstein et al. J. Am. Chem. Soc. 2011, 133, 13244), we show here that electron-withdrawing groups weaken the dimer while electron-donating groups trengthen the interaction energy of the dimer. Various recently developed density functional theoretic (DFT) methods were assessed for their performance and the M05-2X, M06-2X, and omega B97X-D methods were found to be the best performers. These best DFT performers were employed in determining the influence of other representative substituents (-NO2, -CN, -COOH, -Br, -Cl, -OH, and -NH2) as an extension to the above work. The results for the complex of acetylene and various para-disubstituted benzenes revealed a trend in binding energies that is in accordance with the ring-activating/deactivating capacity of each of these groups. The stabilization energy was partitioned via the DFT symmetry-adapted perturbation theory (SAPT) method, and both dispersion and electrostatic interactions were seen to be major driving forces for the complex stabilization. Interestingly, the sum of the energy contributors such as dispersion, exchange, induction, etc., is close to zero and the total energy follows the trend of the electrostatic energy. We observe an excellent linear correlation between the optimized intermolecular separation of the different complexes and the exchange/dispersion interaction.
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