| 1. |
- Holmén, Anders, 1967, et al.
(författare)
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Assignment of electronic transition moment directions of adenine from linear dichroism measurements
- 1997
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 119:50, s. 12240-12250
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Tidskriftsartikel (refereegranskat)abstract
- The electronic spectra of a series of adenine derivatives have been investigated with respect to the number of electronic transitions, their intensities, and transition moments. The experimental work includes linear dichroism (LD) measurements on samples partially oriented in stretched polymer poly(vinyl alcohol) films, fluorescence anisotropy (FA), and: magnetic circular dichroism (MCD). The UV spectra of both 7-methyladenine (7MA) and 9-methyladenine (9MA) are resolved into contributions from five pi --> pi* transitions (I-V). Their polarizations relative to the C-4-C-5 axis are for 7MA +45 degrees (I, 36 600 cm(-1)), -16 degrees (II, 39 500 cm(-1)), -28 degrees (III, 42 600 cm(-1)), +76 degrees (IV 45 800 cm(-1)) and similar to-29 degrees (V, similar to 47 700 cm(-1)); and for 9MA +66 degrees (I, 36 700 cm(-1)), +19 degrees (II, 38 820 cm(-1)), -15 degrees (III, 43 400 cm(-1)), -21 degrees (IV, 46 800 cm(-1)), and similar to-64 degrees (V, similar to 48 320 cm(-1)). The experimental results are correlated with results from semiempirical INDO/S and ab initio CIS/6-31G(d) and CASPT2 molecular orbital calculations. The transition moments are found to be conserved when the adenine amino group has been substituted with either one or two methyl groups. In addition, LD and MCD spectra for 6-(dimethylamino)-9-ethylpurine, which is soluble in nonpolar solvents, have been measured in stretched polyethylene film and cyclohexane, respectively. The results indicate that the electronic transition moments of the 9-substituted adenine chromophore are essentially the same in a polar and a nonpolar solvent. On the basis of the. results,for 7MA and 9MA, the reduced LD and absorption spectra of adenine are analyzed in terms of contributions from the 7-H and 9-H tautomers of adenine. By comparison with theoretical and experimental results for purine and 2-aminopurine regarding the position of the lowest n --> pi* transition, we are able to confidently position the lowest n --> pi* transition in 9MA very close to the lowest pi --> pi* transition. The proximity of the first (1)n pi* and (1) pi pi* states in adenine might be related to the efficient nonradiative deactivation of the lowest excited (1) pi pi* state.
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| 2. |
- Holmén, Anders, 1967, et al.
(författare)
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Ir Transition Moments of 1,3-Dimethyluracil - Linear Dichroism Measurements and Ab-Initio Calculations
- 1994
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Ingår i: Journal of Physical Chemistry. - 0022-3654. ; 98:19, s. 4998-5009
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Tidskriftsartikel (refereegranskat)abstract
- The vibrational transition moment directions of 1,3-dimethyluracil (DMU), 1,3-dimethyluracil-5-d (DMU-5-d), and 1,3-dimethyluracil-6-d (DMU-6-d) have been determined from measurements of polarized IR spectra on samples partially aligned in stretched poly(vinyl alcohol) and by ab initio calculations at the HF/6-31G* level of approximation. The agreement between experiments and theory is good. IR spectra of DMU, DMU-5-d, and DMU-6-d in KBr and in D2O form, together with the calculated spectra and the IR polarizations, the basis for some reassignments. Special attention is paid to the double-bond region, where the high-frequency carbonyl stretching mode is assigned to an in-phase vibration of the C4O and the C2O. This vibration is polarized in a direction almost bisecting the angle between the two carbonyl bonds, in agreement with an in-phase assignment. The low-frequency mode is the out-of-phase vibration of the two carbonyl groups, and it is consequently polarized perpendicular to the high-frequency mode. In order to determine the orientation axis of DMU in the polymer matrix, the UV linear dichroism (LD) spectrum was measured and the polarizations of the electronic transitions were estimated from a semiempirical self-consistent reaction field (SCRF) calculation including solvent effects. The combined information from IR LD and UV LD shows that the molecular orientation axis in the stretched film experiment is parallel to the first pi --> pi* transition in DMU.
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| 3. |
- Becker, Hans-Christian, 1971, et al.
(författare)
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Ground- and excited-state properties of molecular complexes between adenine and 2,7-diazapyrene and its N-methylated cations
- 1997
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 101:47, s. 8853-8860
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Tidskriftsartikel (refereegranskat)abstract
- It has recently been found that 2,7-diazapyrenes upon interaction with nucleic acids form stacked (''intercalation'') complexes, which for the methylated derivatives exhibit new absorption features assigned as charge-transfer (CT) transitions.' To better understand the basis of these interactions and associated optical properties, the geometries and electronic spectra of complexes of adenine (A) with 2,7-diazapyrene (DAP), N-methyl-2,7-diazapyrenium (MDAP(+)), and N,N-dimethyl-2,7-diazapyrenium (DMDAP(2+)) have been modeled using semiempirical AM1 and PM3 geometry optimizations, ab initio (vacuum and Onsager model) energy calculations, and ZINDO/S calculations. In addition, absorption spectra, fluorescence quenching, and H-1 NMR spectra for the complexes in aqueous solution have been measured. For the A-DAP complex, a coplanar, hydrogen-bonded complex is predicted by the calculations, while A-MDAP(+) and A-DMDAP(2+) complexes should have edge-to-face geometry. The association is predicted to be of electrostatic nature, mainly between the pyridinium nitrogen (MDAP(+), DMDAP(2+)) and N-1/NH2 of adenine. There seems to be a preference (6 kcal/mol) for the hydrogen-bonded A-DAP complex, and the energetic difference between face-to-face and edge-to-face A-MDAP(+) and A-DMDAP(2+) complexes is 3 and 8 kcal/mol, respectively (Onsager ab initio, epsilon = 79.5). By contrast, the H-1 NMR data and experimental absorption spectra in conjunction with calculated spectra instead indicate that all three adenine-diazapyrene complexes assume face-to-face arrangement in water because of hydrophobic effects. In agreement with the putative CT absorption of diazapyrenium-DNA complexes, absorption tails are also observed for A-DMDAP(2+) and A-MDAP(+), however not for the A-DAP complex. Most satisfactorily, charge-transfer transitions are predicted by the calculations to occur in the correct wavelength region for A-DMDAP(2+) (strongest) and A-MDAP(+), while A-DAP is predicted not to have any CT transitions. Correspondingly, the observation of quenching of fluorescence of MDAP(+) and DMDAP(2+) (but not DAP) by adenine can explained by charge transfer from adenine to the diazapyrenium.
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| 4. |
- Johannesson, Petra, et al.
(författare)
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SAR and optimization of trioxoisothiazole-based liver receptor X (LXR) agonists leading to the clinical candidate AZD3971
- 2014
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Ingår i: Division of Medicinal Chemistry. ; , s. 247-247
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Konferensbidrag (refereegranskat)abstract
- The liver X receptors (LXRα and LXRβ) are members of the nuclear receptor family of transcription factors. The activation of LXR induces genes involved in reverse cholesterol transport (RCT), which is believed to be the main effect of LXR agonists in the prevention or treatment of atherosclerosis. However LXR agonists have also been shown to cause hepatic steatosis and hypertriglyceridaemia. The ability to separate beneficial effects from negative effects has been a challenge that so far has hampered the development of LXR agonists for human use. We herein describe the SAR and optimization of a series of trioxoisothiazole-based LXR agonists leading to compounds with nanomolar potencies and a separation of beneficial versus negative effects in vivo. This work ultimately led to the nomination of AZD3971 as a candidate for the treatment of atherosclerosis.
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| 5. |
- Kovyrshin, Arseny, et al.
(författare)
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A quantum computing implementation of nuclearelectronic orbital (NEO) theory: Toward an exact pre-Born-Oppenheimer formulation of molecular quantum systems
- 2023
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Ingår i: Journal of Chemical Physics. - 1089-7690 .- 0021-9606. ; 158:21
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Tidskriftsartikel (refereegranskat)abstract
- Nuclear quantum phenomena beyond the Born-Oppenheimer approximation are known to play an important role in a growing number of chemical and biological processes. While there exists no unique consensus on a rigorous and efficient implementation of coupled electron-nuclear quantum dynamics, it is recognized that these problems scale exponentially with system size on classical processors and, therefore, may benefit from quantum computing implementations. Here, we introduce a methodology for the efficient quantum treatment of the electron-nuclear problem on near-term quantum computers, based upon the Nuclear-Electronic Orbital (NEO) approach. We generalize the electronic two-qubit tapering scheme to include nuclei by exploiting symmetries inherent in the NEO framework, thereby reducing the Hamiltonian dimension, number of qubits, gates, and measurements needed for calculations. We also develop parameter transfer and initialization techniques, which improve convergence behavior relative to conventional initialization. These techniques are applied to H2 and malonaldehyde for which results agree with NEO full configuration interaction and NEO complete active space configuration interaction benchmarks for ground state energy to within 10-6 hartree and entanglement entropy to within 10-4. These implementations therefore significantly reduce resource requirements for full quantum simulations of molecules on near-term quantum devices while maintaining high accuracy.
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| 6. |
- Kovyrshin, Arseny, et al.
(författare)
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Nonadiabatic Nuclear-Electron Dynamics: A Quantum Computing Approach
- 2023
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Ingår i: Journal of Physical Chemistry Letters. - 1948-7185. ; 14:31, s. 7065-7072
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Tidskriftsartikel (refereegranskat)abstract
- Coupled quantum electron-nuclear dynamics is oftenassociatedwith the Born-Huang expansion of the molecular wave functionand the appearance of nonadiabatic effects as a perturbation. On theother hand, native multicomponent representations of electrons andnuclei also exist, which do not rely on any a priori approximation.However, their implementation is hampered by prohibitive scaling.Consequently, quantum computers offer a unique opportunity for extendingtheir use to larger systems. Here, we propose a quantum algorithmfor simulating the time-evolution of molecular systems and apply itto proton transfer dynamics in malonaldehyde, described as a rigidscaffold. The proposed quantum algorithm can be easily generalizedto include the explicit dynamics of the classically described molecularscaffold. We show how entanglement between electronic and nucleardegrees of freedom can persist over long times if electrons do notfollow the nuclear displacement adiabatically. The proposed quantumalgorithm may become a valid candidate for the study of such phenomenawhen sufficiently powerful quantum computers become available.
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| 7. |
- Lincoln, Per, 1958, et al.
(författare)
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Diastereomeric DNA-binding geometries of intercalated ruthenium(II) trischelates probed by linear dichroism: [Ru(phen)2DPPZ]2+ and [Ru(phen)2BDPPZ]2
- 1996
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 118:11, s. 2644-2653
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Tidskriftsartikel (refereegranskat)abstract
- Linear dichroism (LD) has been used to probe the binding geometries of the diastereomeric adducts between DNA and the Delta and Lambda enantiomers of [Ru(phen)(2)L](2+) where the chelate ligand L is either dipyrido[3,2-a:2',3'-c]-phenazine (DPPZ) or its benzologue benzodipyrido[a:3,2-h:2'3'-j]phenazine (BDPPZ). By combined use of LD and emission anisotropy excitation spectra measured in highly viscous solution the absorption envelope of the metal-to-ligand charge transfer (MLCT) region has been fur the first time resolved in a complex of this type bound to DNA. The absorption can be described by four effective polarization directions (three almost orthogonal), along one of which any transition is polarized, assignments which are in good agreement with molecular orbital (INDO/S) calculations. The analysis of the LD spectrum provides the orientation of the complex in terms of several angles. Near perpendicularity relative to the DNA helix axis, found for the in-plane long and short axes of BDPPZ and DPPZ, together with extensive hypochromicity of the corresponding intraligand transitions, supports intercalation of the (B)DPPZ ligands between the DNA bases as earlier studies have indicated. MLCT transition moments that make an oblique angle to the molecular plane of the (B)DPPZ chromophores confirm this orientation and, in addition, provide strong evidence for a rotation (roll) of the complex around the pseudo-dyad axis, The roll is small (varying between 5 and 15 degrees), but significant, and has the same sign (clockwise) for both enantiomeric forms of the two complexes studied and shows only minor variations between calf-thymus DNA and alternating GC or AT homopolymer duplexes, It may reflect a property intrinsic of DNA (tilt of bases) or be a result of steric interference of the two phenanthroline ''propeller blades'' with a groove. The roll provides the first example of an angle in a DNA system that has been determined with its sign from LD spectroscopy.
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| 8. |
- Nykänen, Anton, et al.
(författare)
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Toward Accurate Post-Born-Oppenheimer Molecular Simulations on Quantum Computers: An Adaptive Variational Eigensolver with Nuclear-Electronic Frozen Natural Orbitals
- 2023
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Ingår i: Journal of Chemical Theory and Computation. - 1549-9626 .- 1549-9618. ; 19:24, s. 9269-9277
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Tidskriftsartikel (refereegranskat)abstract
- Nuclear quantum effects such as zero-point energy and hydrogen tunneling play a central role in many biological and chemical processes. The nuclear-electronic orbital (NEO) approach captures these effects by treating selected nuclei quantum mechanically on the same footing as electrons. On classical computers, the resources required for an exact solution of NEO-based models grow exponentially with system size. By contrast, quantum computers offer a means of solving this problem with polynomial scaling. However, due to the limitations of current quantum devices, NEO simulations are confined to the smallest systems described by minimal basis sets, whereas realistic simulations beyond the Born-Oppenheimer approximation require more sophisticated basis sets. For this purpose, we herein extend a hardware-efficient ADAPT-VQE method to the NEO framework in the frozen natural orbital (FNO) basis. We demonstrate on H2 and D2 molecules that the NEO-FNO-ADAPT-VQE method reduces the CNOT count by several orders of magnitude relative to the NEO unitary coupled cluster method with singles and doubles while maintaining the desired accuracy. This extreme reduction in the CNOT gate count is sufficient to permit practical computations employing the NEO method─an important step toward accurate simulations involving nonclassical nuclei and non-Born-Oppenheimer effects on near-term quantum devices. We further show that the method can capture isotope effects, and we demonstrate that inclusion of correlation energy systematically improves the prediction of difference in the zero-point energy (ΔZPE) between isotopes.
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