| 1. |
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Advances in Quantum Chemistry. vol 81 : Chemical Physics and Quantum Chemistry
- 2020
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Samlingsverk (redaktörskap) (refereegranskat)abstract
- This volume collects 11 selected papers from the scientific contributions presented at the 10th Congress of the International Society for Theoretical Chemical Physics (ISTCP-X), organized by a team led by Professor Kenneth Ruud at the University of Tromsø—The Arctic University of Norway, from July 11 to 17, 2019. The ISTCP-X Congress in Tromsø followed the format established at the nine previous meetings:ISTCP-I: Professor Ramon Carbo-Dorca, Girona (Spain), June 28–July 3, 1993ISTCP-II: Professor Sean P. McGlynn, New Orleans (LA, USA), April 9–13, 1996ISTCP-III: Professor Miguel Castro, Mexico City (DF, Mexico), November 8–13, 1999ISTCP-IV: Professor Jean Maruani, Marly-le-Roi (Paris, France), July 9–16, 2002ISTCP-V: Professor Peter Politzer, New Orleans (LA, USA), July 20–26, 2005ISTCP-VI: Professor Yan Alexander Wang, Vancouver (BC, Canada), July 19–24, 2008ISTCP-VII: Professor Hiromi Nakai, Waseda (Tokyo, Japan), September 2–8, 2011ISTCP-VIII: Professor Péter Surján, Eötvös (Budapest, Hungary), August 25–31, 2013ISTCP-IX: Professor Mark Hoffmann, Grand Forks (ND, USA), July 17–22, 2016For the 10th congress of the ISTCP, there were 543 participants from all around the world. The program consisted of 200 lectures and almost 280 poster presentations, allowing the participants to get a broad view of the most recent advances in almost all subject matters in the field of theoretical chemical physics. With the city of Tromsø being located north of the Arctic Circle, the sun never set during the entire conference, creating a unique and stimulating atmosphere for scientific discussions.The International Society for Theoretical Chemical Physics (ISTCP) was founded in 1990 by Professor János Ladik at the University of Erlangen, Germany. ISTCP has the objectives to promote theoretical developments at the frontier between physics and chemistry. Additionally the goal is to allow younger researchers to interact with leading contributors in the field at regularly organized International Congresses. The Society involves an Honorary Board, a Board of Directors gathering altogether about 60 scientists (including five Nobel Laureates and two Wolf Prize laureates) in the fields of Theoretical Chemistry and Physics, and a Board of National Representatives covering about 35 countries/regions. The current President, since July 2000, is Professor Erkki J. Brändas, from Uppsala University, Sweden.ISTCP congress proceedings have been published regularly in the special issues of the International Journal of Quantum Chemistry (IJQC) and partly (2002, 2008) copublished in special volumes of Progress in Theoretical Chemistry and Physics (PTCP). For the 10th congress, we are very happy to be able to collect a small sample of the science presented at the ISTCP-X as a collection in Advances in Quantum Chemistry. These articles were solicited from researchers in several forefront fields represented at ISTCP-X.The articles cover topics from very accurate calculations using multireference perturbation theories and high-accuracy studies going beyond the Born-Oppenheimer approximation, through the study of interaction of light with molecules and materials—from very short attosecond processes to photophysical processes in chemical and biological systems—to the nature of excited states in anionic systems and the temperature dependence of the mobility of rubrene. Parity violation, fundamental symmetries, and tunneling effects are also covered and the power of machine learning in quantum chemistry is addressed in other chapters. Finally, Maximillian Seel provides some reminiscences of the founder of the ISTCP, Prof. Janos Ladik, who sadly passed away on March 17, 2018.ISTCP-X was organized into 13 thematic symposia, plus a special symposium honoring the late founder of the ISTCP, Prof. Janos Ladik, organized into a set of plenary and keynote lectures as well as parallel sessions covering contributions from the thematic symposia. The very compact conference venue made conversation across disciplines and thematic symposia easy to organize. The coorganizers of each of the symposia had significant freedom in inviting leading scientists in their areas, with attention paid to overall geographical, career stage, and gender balance. It is the careful thought and hard work of the Symposium Organizers that contributed to the success of the congress. The Symposia and their Organizers were:1.From picoseconds to attoseconds: nuclear and electron dynamics (David Clary, Leticia Gonzalez, Fernando Martin)2.Aspects of heavy-element chemistry (Pekka Pyykkö, Trond Saue)3.Emergent electronic structure methods (Stefan Goedecker, Gustavo Scuseria)4.Multiscale modeling including focused models (Benedetta Mennucci, Lyudmila Slipchenko)5.Large-scale electronic structure models of materials (Thomas Heine, Hiromi Nakai)6.Ultracold chemical physics (Jeremy M. Hutson, Bogumil Jeziorski)7.Molecular properties and interactions (Antonio Rizzo, Krzysztof Szalewicz)8.Computational spectroscopy: From X-rays to microwaves (Attila Csaszar, Hans Ågren)9.90 years of r12: Hylleraas symposium (Wim Klopper, Ed Valeev)10.Machine-learning and data-driven approaches in chemical physics (Alán Aspuru-Guzik, Pavlo Dral)11.Computational biophysics (Fernanda Duarte, Ursula Röthlisberger)12.Path-integral methods (David E. Manolopoulos, Gregory Voth)13.Physical organic chemistry and catalysis (Odile Eisenstein, Vidar R. Jensen)14.Janos Ladik memorial symposium (Erkki Brändas, Kenneth Ruud)In addition to symposia, there were 12 plenary and keynote talks for which all participants were gathered.1.Sharon Hammes-Schiffer, Multicomponent Quantum Chemistry: Integrating Electronic and Nuclear Quantum Effects2.Trygve Helgaker, Egil Hylleraas—A Pioneer of Computational Quantum Mechanics3.Peter Schwerdtfeger, The Year of the Periodic Table—Going Superheavy4.Sylvio Canuto, Environment Contribution to Molecular Spectroscopy, Reactivity and Photochemistry5.Peter Gill, Q-MP2-OS: A New Approach to Correlation Using Quadrature6.Peter Saalfrank, Molecules Driven by Light: Electron and Nuclear Dynamics7.Thomas F. Miller, Classical and Machine-Learning Methods for Quantum Simulation8.Irene Burghardt, High-Dimensional Quantum Dynamics of Functional Organic Polymer Materials: Coherence, Confinement, and Disorder9.Giulia Galli, Simulating Energy Conversion Processes From First Principles10.Zhigang Shuai, Density Matrix Renormalization Group: Time-Dependent Formalism, Light-Emitting, Carrier Transport, and Singlet Fission11.Monica Olvera de la Cruz, Properties of Molecular Electrolytes12.Kersti Hermansson, OH, Seriously, … Molecules + Materials = Difficult!We are grateful to all organizers for their exceptional work. We are indebted to our excellent scientific organizing committee that guided us in producing a well-balanced, global perspective on cutting-edge chemical physics: Aurora Clark, David Clary, Hazel Cox, Peter Gill, Leticia Gonzalez, Kersti Hermansson, Bogumil Jeziorski, Anna Krylov, Shuhua Li, Hiromi Nakai, Oleg Prezhdo, and Thereza Soares, and the local organizing committee: Maarten Beerepoot, Bjørn-Olav Bransdal, Stig Eide, Luca Frediani, Bin Gao, Stephanie Hansen, Kathrin Hopmann, and Michal Repisky. Many thanks also to Karen Dundas for designing the logo of the congress. We are also grateful to all session chairs, speakers, poster presenters, as well as all student volunteers, contributing significantly to the great success of the meeting. For more details regarding the congress we refer to the web site of the congress, http://istcp-2019.org/.The ISTCP-X congress took place at the Clarion Hotel The Edge in downtown Tromsø, located less than 5 km away from the local airport. The compact city center made it easy for participants to engage in discussions in restaurants and cafes, and gave a sense of a workshop with time and space for scientific discussions despite the large number of conference participants. The beautiful surroundings of the city and the never-ending days was exploited by many of the participants, who used the late evenings or early mornings to explore the surroundings through bicycle or hiking trips.We are pleased to express our sincere thanks to our sponsors. We would here in particular like to thank the Research Council of Norway and the University of Tromsø—The Arctic University of Norway for very generous financial support, and the staff at Clarion Hotel The Edge for making sure all practical aspects of the conference went smoothly. We are also grateful to ACS Omega, Journal of Chemical Theory and Computation, The Journal of Physical Chemistry, The Journal of Physical Chemistry Letters, PCCP, International Journal of Quantum Chemistry, Journal of Computational Chemistry, and Elsevier through Advances in Quantum Chemistry for providing poster awards for young researchers. The poster prize winners were selected by the members of the scientific committee, and we are grateful to our sponsors for allowing us to honor many young scientists for their excellent poster contributions at the conference.The guest editors of this special volume, finally, want to thank the authors, who accepted our invitation to contribute to these proceedings, and in so doing provide a perspective of some cutting-edge areas of study in chemical physics. The Xth congress of ISTCP included both these areas and many more. We hope that all researchers with a great interest in theory and methods related to fundamental scientific problems and future progress in our field will appreciate this volume.
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| 2. |
- Aidas, Kestutis, et al.
(författare)
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Gauge-origin independent magnetizabilities from hybrid quantum mechanics/molecular mechanics models: Theory and applications to liquid water
- 2007
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Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614. ; 442:4-6, s. 322-328
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Tidskriftsartikel (refereegranskat)abstract
- The theory of a hybrid quantum mechanics/molecular mechanics (QM/MM) approach for gauge-origin independent calculations of the molecular magnetizability using Hartree-Fock or Density Functional Theory is presented. The method is applied to liquid water using configurations generated from classical Molecular Dynamics simulation to calculate the statistical averaged magnetizability. Based on a comparison with experimental data, treating only one water molecule quantum mechanically appears to be insufficient, while a quantum mechanical treatment of also the first solvation shell leads to good agreement between theory and experiment. This indicates that the gas-to-liquid phase shift for the molecular magnetizability is to a large extent of non-electrostatic nature. (c) 2007 Elsevier B.V. All rights reserved.
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| 3. |
- Aidas, Kestutis, et al.
(författare)
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Solvent effects on NMR isotropic shielding constants. A comparison between explicit polarizable discrete and continuum approaches
- 2007
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Ingår i: The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory. - : American Chemical Society (ACS). - 1520-5215. ; 111:20, s. 4199-4210
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Tidskriftsartikel (refereegranskat)abstract
- The gas-to-aqueous solution shifts of the O-17 and C-13 NMR isotropic shielding constants for the carbonyl chromophore in formaldehyde and acetone are investigated. For the condensed-phase problem, we use the hybrid density functional theory/molecular mechanics approach in combination with a statistical averaging over an appropriate number of solute-solvent configurations extracted from classical molecular dynamics simulations. The PBE0 exchange-correlation functional and the 6-311++G(2d,2p) basis set are used for the calculation of the shielding constants. London atomic orbitals are employed to ensure gauge-origin independent results. The effects of the bulk solvent molecules are found to be crucial in order to calculate accurate solvation shifts of the shielding constants. Very good agreement between the computed and experimental solvation shifts is obtained for the shielding constants of acetone when a polarizable water potential is used. Supermolecular results based on geometry-optimized molecular structures are presented. We also compare the results obtained with the polarizable continuum model to the results obtained using explicit MM molecules to model the bulk solvent effect.
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| 4. |
- Aidas, Kestutis, et al.
(författare)
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The Dalton quantum chemistry program system
- 2014
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Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 4:3, s. 269-284
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Tidskriftsartikel (refereegranskat)abstract
- Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.
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| 5. |
- Badri, Zahra, et al.
(författare)
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All-Metal Aromaticity : Revisiting the Ring Current Model among Transition Metal Clusters
- 2013
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 9:11, s. 4789-4796
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Tidskriftsartikel (refereegranskat)abstract
- We present new insight into the nature of aromaticity in metal clusters. We give computational arguments in favor of using the ring-current model over local indices, such as nucleus independent chemical shifts, for the determination of the magnetic aromaticity. Two approaches for estimating magnetically induced ring currents are employed for this purpose, one based on the quantum theory of atoms in molecules (QTAIM) and the other where magnetically induced current densities (MICD) are explicitly calculated. We show that the two-zone aromaticity/antiaromaticity of a number of 3d metallic clusters (Sc-3(-), Cu-3(+), and Cu-4(2-)) can be explained using the QTAIM-based magnetizabilities. The reliability of the calculated atomic and bond magnetizabilities of the metallic clusters are verified by comparison with MICD computed at the multiconfiguration self-consistent field (MCSCF) and density functional levels of theory. Integrated MCSCF current strength susceptibilities as well as a visual analysis of the calculated current densities confirm the interpretations based on the QTAIM magnetizabilities. In view of the new findings, we suggest a simple explanation based on classical electromagnetic theory to explain the anomalous magnetic shielding in different transition metal clusters. Our results suggest that the nature of magnetic aromaticity/antiaromaticity in transition-metal clusters should be assessed more carefully based on global indices.
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| 6. |
- Bauer, Paul
(författare)
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Computational modelling of enzyme selectivity
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Enantioselective reactions are one of the ways to produce pure chiral compounds. Understanding the basis of this selectivity makes it possible to guide enzyme design towards more efficient catalysts. One approach to study enzymes involved in chiral chemistry is through the use of computational models that are able to simulate the chemical reaction taking place. The potato epoxide hydrolase is one enzyme that is known to be both highly enantioselective, while still being robust upon mutation of residues to change substrate scope. The enzyme was used to investigate the epoxide hydrolysis mechanism for a number of different substrates, using the EVB approach to the reaction both in solution and in several enzyme variants. In addition to this, work has been performed on new ways of performing simulations of divalent transition metals, as well as development of new simulation software.
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| 7. |
- Botvinik-Nezer, Rotem, et al.
(författare)
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Variability in the analysis of a single neuroimaging dataset by many teams
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 582, s. 84-88
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Tidskriftsartikel (refereegranskat)abstract
- Data analysis workflows in many scientific domains have become increasingly complex and flexible. Here we assess the effect of this flexibility on the results of functional magnetic resonance imaging by asking 70 independent teams to analyse the same dataset, testing the same 9 ex-ante hypotheses(1). The flexibility of analytical approaches is exemplified by the fact that no two teams chose identical workflows to analyse the data. This flexibility resulted in sizeable variation in the results of hypothesis tests, even for teams whose statistical maps were highly correlated at intermediate stages of the analysis pipeline. Variation in reported results was related to several aspects of analysis methodology. Notably, a meta-analytical approach that aggregated information across teams yielded a significant consensus in activated regions. Furthermore, prediction markets of researchers in the field revealed an overestimation of the likelihood of significant findings, even by researchers with direct knowledge of the dataset(2-5). Our findings show that analytical flexibility can have substantial effects on scientific conclusions, and identify factors that may be related to variability in the analysis of functional magnetic resonance imaging. The results emphasize the importance of validating and sharing complex analysis workflows, and demonstrate the need for performing and reporting multiple analyses of the same data. Potential approaches that could be used to mitigate issues related to analytical variability are discussed. The results obtained by seventy different teams analysing the same functional magnetic resonance imaging dataset show substantial variation, highlighting the influence of analytical choices and the importance of sharing workflows publicly and performing multiple analyses.
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| 8. |
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| 9. |
- Chen, Xing, et al.
(författare)
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Zero-point vibrational corrections to isotropic hyperfine coupling constants in polyatomic molecules
- 2011
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : RSC Publishing. - 1463-9076 .- 1463-9084. ; 13:2, s. 696-707
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Tidskriftsartikel (refereegranskat)abstract
- The present work addresses isotropic hyperfine coupling constants in polyatomic systems with a particular emphasis on a largely neglected, but a posteriori significant, effect, namely zero-point vibrational corrections. Using the density functional restricted-unrestricted approach, the zero-point vibrational corrections are evaluated for the allyl radical and four of its derivatives. In addition for establishing the numerical size of the zero-point vibrational corrections to the isotropic hyperfine coupling constants, we present simple guidelines useful for identifying hydrogens for which such corrections are significant. Based on our findings, we critically re-examine the computational procedures used for the determination of hyperfine coupling constants in general as well as the practice of using experimental hyperfine coupling constants as reference data when benchmarking and optimizing exchange-correlation functionals and basis sets for such calculations.
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| 10. |
- Ferrighi, Lara, et al.
(författare)
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Density-functional-theory study of the electric-field-induced second harmonic generation (EFISHG) of push-pull phenylpolyenes in solution
- 2006
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Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614 .- 1873-4448. ; 425:4-6, s. 5593-5603
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Tidskriftsartikel (refereegranskat)abstract
- Density-functional theory and the polarizable continuum model have been used to calculate the electric-field-induced second harmonic generation of a series of push-pull phenylpolyenes in chloroform solution. The calculations have been performed using both the Becke 3-parameter Lee-Yang-Parr functional and the recently developed Coulomb-attenuated method functional. Solvation has been investigated by examining the effects of the reaction field, non-equilibrium solvation, geometry relaxation, and cavity field. The inclusion of solvent effects leads to significantly better agreement with experimental observations.
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| 11. |
- Gao, Bin, et al.
(författare)
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Plasmon resonances in linear noble-metal chains
- 2012
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 137:19, s. 194307-
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Tidskriftsartikel (refereegranskat)abstract
- The electronic excitations of three noble-metall chains-copper, silver, and gold-have been investigated at the time-dependent density functional theory level. The reduced single-electron density matrix is propagated according to the Liouville-von Neumann equation in the real-time domain after an impulse excitation. The propagation in the real-time domain enables us to investigate the formation and size evolution of electronic excitations in these metallic chains with different number of atoms, up to a total of 26 atoms. The longitudinal oscillations at lower excitation energies are dominated by s -> p transitions in these chains and have collective or central resonances, while the first peak involving d -> p transitions in the longitudinal mode appears at a higher excitation energy and shows collective resonances. In the transverse oscillations, there are in most cases d -> p transitions in each resonance, which can be attributed to either central or end resonances. Convergence of the oscillations, in particular those involving the collective and central resonances in the three noble-metal chains can only be observed for chains with 18 atoms or more. Different spectroscopic characteristics among these three metallic chains can be attributed to their different electronic structures, in particular the relativistic effects in the gold chains have a dramatic effect on their electronic structures and excitations.
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| 12. |
- Gao, Bin, et al.
(författare)
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Shape-Dependent Electronic Excitations in Metallic Chains
- 2014
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 118:24, s. 13059-13069
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Tidskriftsartikel (refereegranskat)abstract
- The electronic excitations of silver chains with different geometries (linear, circle, arc and zigzag chains) have been investigated at the time-dependent density functional theory level, by solving the equation of motion of the reduced single-electron density matrix in the real-time domain. A scaling parameter 0 <= lambda <= 1 has been introduced to adjust the two-electron contributions during propagation in the time domain in a way that allows us to distinguish different electronic excitations plasmon and single-particle excitations. The dipole responses, in particular the plasmon resonances of these metallic chains to an external delta-pulse, show a strong dependence on their geometric structures. In most cases, the dipole responses of these chains possess great tunability when altering their geometric parameters the radius of the circle and arc chains, and the bond angle of the zigzag chains. Some excitations in these chains also show a wide tunable excitation energy range, more than 1 eV, making it possible to fine-tune the excitations of the metallic chains at an atomic scale.
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| 13. |
- Jiemchooroj, Auayporn, 1978-
(författare)
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Long-range intermolecular dispersion forces and circular dichroism spectra from first-principles calculations
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This work presents first-principles calculations of long-range intermolecular dispersion energies between two atoms or molecules and of electronic circular dichroism spectra of chiral molecules. The former is expressed in terms of the C6 dipole-dipole dispersion coefficients Δε, and the latter is given in terms of the extinction coefficient. In a series of publications, the complex linear polarization propagator method has been shown to be a powerful tool to provide accurate ab initio and first-principles density functional theory results. This was the case not only for the C6 dispersion coefficients but also for the electronic circular dichroism at an arbitrary wavelength ranging from the optical to the X-ray regions of the spectrum. The selected samples for the investigation of dispersion interactions in the electronic ground state are the noble gases, n-alkanes, polyacenes, azabenzenes, alkali-metal clusters, and C60. It is found that the values of C6 for the sodium-cluster-to-fullerene interactions are well within the error bars of the experiment. The proposed method can also be used to determine dispersion energies for species in their respective excited electronic states. The C6 dispersion coefficients for the first π → π* excited state of the azabenzene molecules have been obtained with the adopted method in the multiconfiguration self-consistent field approximation. The dispersion energy of the π → π* excited state is smaller than that of the ground state. It is found that the characteristic frequencies ω1 defined in the London approximation of n-alkanes vary in a narrow range which makes it possible to construct a simple structure-to-property relationship based on the number of π-bonds for the dispersion interaction in these saturated compounds. However, this simple approach is not applicable to the interactions of the π-conjugated systems since, depending on the systems, their characteristic frequencies ω1 can vary greatly. In addition, an accomplishment of calculations of the electronic circular dichroism spectra in the near-edge X-ray absorption has been demonstrated.
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| 14. |
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| 15. |
- Kongsted, Jacob, et al.
(författare)
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Solvent effects on zero-point vibrational corrections to optical rotations and nuclear magnetic resonance shielding constants
- 2008
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Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614. ; 451:4-6, s. 226-232
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Tidskriftsartikel (refereegranskat)abstract
- We present a study of solvent effects on the zero-point vibrational corrections (ZPVC) to optical rotations and nuclear magnetic resonance shielding constants of solvated molecules. The model used to calculate vibrational corrections rely on an expansion of the potential and property surfaces around an effective molecular geometry and includes both harmonic and anharmonic correction. Numerical examples are presented for (S)-propylene oxide in various solvents as well as for acetone and the three diazene molecule. We find that solvent effects on the ZPVCs may be significant and in some cases crucial to accurately predict solvent shifts on molecular properties.
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| 16. |
- Lin, Na, et al.
(författare)
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Differences in Two-Photon and One-Photon Absorption Profiles Induced by Vibronic Coupling : The Case of Dioxaborine Heterocyclic Dye
- 2011
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Ingår i: ChemPhysChem. - : Wiley. - 1439-4235 .- 1439-7641. ; 12:17, s. 3392-3403
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Tidskriftsartikel (refereegranskat)abstract
- A theoretical study of a dioxaborine heterocyclic compound in solution provides a case study for an analysis of the effects induced by the so-called HerzbergTeller (HT) vibronic coupling on the one- (OPA) and two-photon absorption (TPA) spectra. For TPA, the HT vibronic coupling induces differences in the shapes of the absorption band. The study highlights the importance of vibronic coupling as a potentially important mechanism in absorption spectroscopy, able to explain differences in the OPA/TPA spectra.
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| 17. |
- Mohammed, Abdelsalam, et al.
(författare)
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Ab initio study of coherent anti-Stokes Raman scattering (CARS) of the 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) explosive
- 2010
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Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614 .- 1873-4448. ; 485:4-6, s. 320-325
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Tidskriftsartikel (refereegranskat)abstract
- Coherent anti-Stokes Raman scattering (CARS) of the 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) C3H6N6O6 molecule is studied by ab initio methods. The results are compared to available experimental observations and against calculations and experimental observations of the conventional non-resonant Raman spectrum for RDX. It is found that all intense bands in the observed CARS spectrum and all Raman differential cross sections are well reproduced by the calculations. The features of the resonant CARS signal vary strongly from the corresponding Raman signal, and are obtained with a considerably larger cross section, a fact that could further facilitate the use of CARS spectroscopy in applications of stand-off detection of gaseous samples at ultra-low concentrations.
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| 18. |
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| 19. |
- Mohammed, Abdelsalam, et al.
(författare)
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Hyper Raman spectra calculated in a time-dependent Hartree-Fock method
- 2012
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Ingår i: Molecular Physics. - : Informa UK Limited. - 0026-8976 .- 1362-3028. ; 110:19-20, s. 2315-2320
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Tidskriftsartikel (refereegranskat)abstract
- Hyper Raman scattering (HRS) of the benzonitrile (BN) and 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) molecules is studied by means of ab initio calculations. The computational procedure employs a recently developed methodology for the analytic calculations of frequency-dependent polarizability gradients of arbitrary order, including perturbation dependent basis sets. The result are compared to normal Raman scattering (NRS) and coherent anti-Stokes Raman scattering (CARS) that previously have been studied using the same technology. It is found that some suppressed or silent modes in CARS and NRS spectra are clearly seen in HRS, and that although under general excitation conditions the HRS intensities are much lower than for CARS and NRS, HRS provides complementary information useful for target identification.
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| 20. |
- Natarajan Arul, Murugan, et al.
(författare)
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Solvatochromic shift of phenol blue in water from a combined Car-Parrinello molecular dynamics hybrid quantum mechanics-molecular mechanics and ZINDO approach
- 2010
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 132:23, s. 234508-
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Tidskriftsartikel (refereegranskat)abstract
- The present work addresses the solvatochromic shift of phenol blue (PB) dye. For this purpose the results of Car-Parrinello molecular dynamics (CPMD) simulations for PB in gas phase are compared with results obtained for PB in water from CPMD hybrid quantum mechanics-molecular mechanics (CPMD-QM/MM) calculations. The absorption spectra were obtained using the intermediate neglect of differential overlap/spectroscopic-configuration interaction (INDO/CIS) method and were calculated for a multitude of configurations of the trajectory. The calculated lambda(max) for PB in gas phase was found to be about 535 nm, which is considerably lower than the lambda(max) reported for PB in nonpolar solvents. Different solvation shells for PB in water have been defined based on the solute-all-atoms and solvent center of mass radial distribution function (g(r(X-O))). The electronic excitation energies for PB computed in the presence of solvent molecules in an increasing number of solvation shells were calculated in a systematic way to evaluate their contributions to the solvatochrmic shift. The inclusion of solvent molecules in the hydration shell yields a lambda(max) of 640 nm, which contributes to almost 78% of the solvatochromic shift. The inclusion of solvent molecules up to 10 angstrom in the g(r(X-O)) rdf yields a lambda(max) of 670 nm which is in good agreement with the experimentally reported value of 654-684 nm. Overall, the present study suggests that the combined CPMD-QM/MM and INDO-CIS approach can be used successfully to model solvatochromic shifts of organic dye molecules. (C) 2010 American Institute of Physics. [doi:10.1063/1.3436516]
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| 21. |
- Norman, Patrick, et al.
(författare)
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Microscopic theory of nonlinear optics
- 2006
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Ingår i: Nonlinear optical properties of matter. - : Springer. - 9781402048500 ; , s. 1-49
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Bokkapitel (refereegranskat)
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| 22. |
- Olsen, Jogvan Magnus Haugaard, et al.
(författare)
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Dalton Project : A Python platform for molecular- and electronic-structure simulations of complex systems
- 2020
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:21
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Tidskriftsartikel (refereegranskat)abstract
- The Dalton Project provides a uniform platform access to the underlying full-fledged quantum chemistry codes Dalton and LSDalton as well as the PyFraME package for automatized fragmentation and parameterization of complex molecular environments. The platform is written in Python and defines a means for library communication and interaction. Intermediate data such as integrals are exposed to the platform and made accessible to the user in the form of NumPy arrays, and the resulting data are extracted, analyzed, and visualized. Complex computational protocols that may, for instance, arise due to a need for environment fragmentation and configuration-space sampling of biochemical systems are readily assisted by the platform. The platform is designed to host additional software libraries and will serve as a hub for future modular software development efforts in the distributed Dalton community.
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| 23. |
- Pedersen, Thomas, et al.
(författare)
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On the importance of vibrational contributions to small-angle optical rotation: Fluoro-oxirane in gas phase and solution.
- 2009
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 130:3
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Tidskriftsartikel (refereegranskat)abstract
- The specific optical rotation of (S)-fluoro-oxirane in gas phase and solution is predicted using time-dependent density functional theory (B3LYP functional) and coupled cluster linear response theory. Upon vibrational averaging, the coupled cluster singles and doubles model predicts the gas phase specific optical rotation to be 8.1 degrees (dm g/cm(3))(-1) at 355 nm at room temperature. This is an order of magnitude smaller than the B3LYP result of 68.4 degrees (dm g/cm(3))(-1). The main source of this discrepancy is the electronic contribution at the equilibrium geometry. The effects of cyclohexane and acetonitrile solvents are calculated for both the electronic and vibrational contributions with the B3LYP functional. The specific optical rotation is estimated to change significantly depending on the polarity of the solvent, increasing in cyclohexane and decreasing in acetonitrile.
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| 24. |
- Ringholm, Magnus, et al.
(författare)
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Analytic calculations of hyper-Raman spectra from density functional theory hyperpolarizability gradients
- 2014
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 141:13, s. 134107-
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Tidskriftsartikel (refereegranskat)abstract
- We present the first analytic calculations of the geometrical gradients of the first hyperpolarizability tensors at the density-functional theory (DFT) level. We use the analytically calculated hyperpolarizability gradients to explore the importance of electron correlation effects, as described by DFT, on hyper-Raman spectra. In particular, we calculate the hyper-Raman spectra of the all-trans and 11-cis isomers of retinal at the Hartree-Fock (HF) and density-functional levels of theory, also allowing us to explore the sensitivity of the hyper-Raman spectra on the geometrical characteristics of these structurally related molecules. We show that the HF results, using B3LYP-calculated vibrational frequencies and force fields, reproduce the experimental data for all-trans-retinal well, and that electron correlation effects are of minor importance for the hyper-Raman intensities.
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| 25. |
- Rinkevicius, Zilvinas, et al.
(författare)
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Degenerate perturbation theory for electronic g tensors : leading-order relativistic effects
- 2008
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 4:11, s. 1810-1828
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Tidskriftsartikel (refereegranskat)abstract
- A new approach for the evaluation of the leading-order relativistic corrections to the electronic g tensors of molecules with a doublet ground state is presented. The methodology is based on degenerate perturbation theory and includes all relevant contributions to the g tensor shift up to order theta(alpha(4)) originating from the one-electron part of the Breit-Pauli Hamiltonian-that is, it allows for the treatment of scalar relativistic, spin-orbit, and mixed corrections to the spin and orbital Zeeman effects. This approach has been implemented in the framework of spin-restricted density functional theory and is in the present paper, as a first illustration of the theory, applied to study relativistic effects on electronic g tensors of dihalogen anion radicals X-2(-) (X = F, Cl, Br, I). The results indicate that the spin-orbit interaction is responsible for the large parallel component of the g tensor shift of Br-2(-) and I-2(-), and furthermore that both the leading-order scalar relativistic and spin-orbit corrections are of minor importance for the perpendicular component of the g tensor in these molecules since they effectively cancel each other. In addition to investigating the g tensors of dihalogen anion radicals, we also critically examine the importance of various relativistic corrections to the electronic g tensor of linear molecules with Sigma-type ground states and present a two-state model suitable for an approximate estimation of the g tensor in such molecules.
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| 26. |
- Steindal, Arnfinn Hykkerud, et al.
(författare)
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Open-ended response theory with polarizable embedding : multiphoton absorption in biomolecular systems
- 2016
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 18:40, s. 28339-28352
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Tidskriftsartikel (refereegranskat)abstract
- We present the theory and implementation of an open-ended framework for electric response properties at the level of Hartree-Fock and Kohn-Sham density functional theory that includes effects from the molecular environment modeled by the polarizable embedding (PE) model. With this new state-of-the-art multiscale functionality, electric response properties to any order can be calculated for molecules embedded in polarizable atomistic molecular environments ranging from solvents to complex heterogeneous macromolecules such as proteins. In addition, environmental effects on multiphoton absorption (MPA) properties can be studied by evaluating single residues of the response functions. The PE approach includes mutual polarization effects between the quantum and classical parts of the system through induced dipoles that are determined self-consistently with respect to the electronic density. The applicability of our approach is demonstrated by calculating MPA strengths up to four-photon absorption for the green fluorescent protein. We show how the size of the quantum region, as well as the treatment of the border between the quantum and classical regions, is crucial in order to obtain reliable MPA predictions.
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| 27. |
- Telyatnyk, Lyudmyla, et al.
(författare)
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Electronic g-tensors of solvated molecules using the polarizable continuum model
- 2004
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 121, s. 5051-
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Tidskriftsartikel (refereegranskat)abstract
- We present the implementation of density functional response theory combined with the polarizable continuum model (PCM), enabling first principles calculations of molecular g-tensors of solvated molecules. The calculated g-tensor shifts are compared with experimental g-tensor shifts obtained from electron paramagnetic resonance spectra for a few solvated species. The results indicate qualitative agreement between the calculations and the experimental data for aprotic solvents, whereas PCM fails to reproduce the electronic g-tensor behavior for protic solvents. This failure of PCM for protic solvents can be resolved by including into the model those solvent molecules which are involved in hydrogen bonding with the solute. The results for the protic solvents show that the explicit inclusion of the solvent molecules of the first solvation sphere is not sufficient in order to reproduce the behavior of the electronic g-tensor in protic solvents, and that better agreement with experimental data can be obtained by including the long-range electrostatic effects accounted for by the PCM approach on top of the explicit hydrogen-bonded complexes.
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| 28. |
- Thorvaldsen, Andreas J., et al.
(författare)
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Analytic ab initio calculations of coherent anti-Stokes Raman scattering (CARS)
- 2009
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 11:13, s. 2293-2304
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Tidskriftsartikel (refereegranskat)abstract
- We present a theory for the analytic calculation of frequency-dependent polarizability gradients, and apply the methodology to the calculation of coherent anti-Stokes Raman scattering (CARS). The formalism used is based on an open-ended theory for the calculation of frequency-dependent molecular response properties of arbitrary order, also including contributions from perturbation-dependent basis sets. An important feature of our approach is the close connection between the formalism-which is fully matrix-based in an atomic orbital basis-and the implementation, allowing for the rapid implementation of higher-order molecular properties. Care is taken to allow the formalism to be utilized with linearly-scaling Hartree-Fock and density-functional theory codes. By avoiding the evaluation of responses due to geometry distortions, only 9 response equations need to be solved for the calculation of the CARS intensities, independent of the size of the molecular system. The theory is illustrated by calculations on a set of polyaromatic hydrocarbons using a DFT/B3LYP force field and Hartree-Fock polarizability gradients. Good agreement with the experimental CARS spectra of these compounds is obtained.
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| 29. |
- Yang, Hsiao-yin, et al.
(författare)
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Cell type and transfection reagent-dependent effects on viability, cell content, cell cycle and inflammation of RNAi in human primary mesenchymal cells
- 2014
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Ingår i: European Journal of Pharmaceutical Sciences. - : Elsevier BV. - 0928-0987 .- 1879-0720. ; 53, s. 35-44
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Tidskriftsartikel (refereegranskat)abstract
- The application of RNA interference (RNAi) has great therapeutic potential for degenerative diseases of cartilaginous tissues by means of fine tuning the phenotype of cells used for regeneration. However, possible non-specific effects of transfection per se might be relevant for future clinical application. In the current study, we selected two synthetic transfection reagents, a cationic lipid-based commercial reagent Lipofectamine RNAiMAX and polyethylenimine (PEI), and two naturally-derived transfection reagents, namely the polysaccharides chitosan (98% deacetylation) and hyaluronic acid (20% amidation), for siRNA delivery into primary mesenchymal cells including nucleus pulposus cells, articular chondrocytes and mesenchymal stem cells (MSCs). Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as an endogenous model gene to evaluate the extent of silencing by 20 nM or 200 nM siRNA at day 3 and day 6 post-transfection. In addition to silencing efficiency, non-specific effects such as cytotoxicity, change in DNA content and differentiation potential of cells were evaluated. Among the four transfection reagents, the commercial liposome-based agent was the most efficient reagent for siRNA delivery at 20 nM siRNA, followed by chitosan. Transfection using cationic liposomes, chitosan and PEI showed some decrease in viability and DNA content to varying degrees that was dependent on the siRNA dose and cell type evaluated, but independent of GAPDH knockdown. Some effects on DNA content were not accompanied by concomitant changes in viability. However, changes in expression of marker genes for cell cycle inhibition or progression, such as p21 and PCNA, could not explain the changes in DNA content. Interestingly, aspecific upregulation of GAPDH activity was found, which was limited to cartilaginous cells. In conclusion, non-specific effects should not be overlooked in the application of RNAi for mesenchymal cell transfection and may need to be overcome for its effective therapeutic application.
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