| 1. |
- 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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| 2. |
- Aquilante, Francesco, et al.
(författare)
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MOLCAS-a software for multiconfigurational quantum chemistry calculations
- 2013
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Ingår i: Wiley Interdisciplinary Reviews. Computational Molecular Science. - : Wiley. - 1759-0884 .- 1759-0876. ; 3:2, s. 143-149
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Tidskriftsartikel (refereegranskat)abstract
- At variance, with most of the quantum chemistry software presently available, MOLCAS is a package that is specialized in multiconfigurational wave function theory (MC-WFT) rather than density functional theory (DFT). Given the much higher algorithmic complexity of MC-WFT versus DFT, an extraordinary effort needs to be made from the programming point of view to achieve state-of-the-art performance for large-scale calculations. In particular, a robust and efficient implementation of the Cholesky decomposition techniques for handling two-electron integrals has been developed which is unique to MOLCAS. Together with this 'Cholesky infrastructure', a powerful and multilayer graphical and scripting user interface is available, which is an essential ingredient for the setup of MC-WFT calculations. These two aspects of the MOLCAS software constitute the focus of the present report. (C) 2012 John Wiley & Sons, Ltd.
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| 3. |
- Chakraborty, Pratip, et al.
(författare)
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Time-resolved photoelectron spectroscopy via trajectory surface hopping
- 2024
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Ingår i: Wiley Interdisciplinary Reviews. Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 14:3
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Forskningsöversikt (refereegranskat)abstract
- Time-resolved photoelectron spectroscopy is a powerful pump-probe technique which can probe nonadiabatic dynamics in molecules. Interpretation of the experimental signals however requires input from theoretical simulations. Advances in electronic structure theory, nonadiabatic dynamics, and theory to calculate the ionization yields, have enabled accurate simulation of time-resolved photoelectron spectra leading to successful applications of the technique. We review the basic theory and steps involved in calculating time-resolved photoelectron spectra, and highlight successful applications. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Theoretical and Physical Chemistry > Spectroscopy.
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| 4. |
- Delcey, Mickael G, 1988-
(författare)
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MultiPsi: A python-driven MCSCF program for photochemistry and spectroscopy simulations on modern HPC environments
- 2023
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Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 13:6
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Tidskriftsartikel (refereegranskat)abstract
- We present MultiPsi, an open-source MCSCF program for the calculation of ground and excited states properties of strongly correlated systems. The program currently implements a general MCSCF code with excited states available using either state-averaging or linear response. It is written in a highly modular fashion using Python/C++ which makes it well suited as a development platform, enabling easy prototyping of novel methods, and as a teaching tool using interactive notebooks. The code is also very efficient and designed for modern high-performance computing environments using hybrid OpenMP/MPI parallelization. This efficiency is demonstrated with the calculation of the CASSCF energy and linear response of a molecule with more than 700 atoms as well as a fully optimized conventional CI calculation on more than 400 billion determinants. This article is categorized under: Software > Quantum Chemistry Electronic Structure Theory > Ab Initio Electronic Structure Methods Theoretical and Physical Chemistry > Spectroscopy.
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| 5. |
- Friedman, Ran
(författare)
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Computational studies of protein–drug binding affinity changes upon mutations in the drug target
- 2022
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Ingår i: Wiley Interdisciplinary Reviews. Computational Molecular Science. - : John Wiley & Sons. - 1759-0876 .- 1759-0884. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Mutations that lead to drug resistance limit the efficacy of antibiotics, antiviral drugs, targeted cancer therapies, and other treatments. Accurately calculating protein–drug binding affinity changes upon mutations in the drug target is of high interest as this can yield a better understanding into how such mutations drive drug-resistance, especially when the mutation in question does not directly interfere with binding of the drug. The main aim of this article is to provide an up-to-date reference on the computational tools that are available for the calculation of Gibbs energy (free energy) changes upon mutation, their strengths, and limitations. The methods that are discussed include free energy calculations (free energy perturbation, thermodynamic integration, multistate Bennett acceptance ratio), analysis of molecular dynamics simulations (linear interaction energy, molecular mechanics [MM]/Poisson–Boltzmann solvated area, and MM/generalized Born solvated area), and methods that involve quantum mechanical calculations (including QM/MM). The possibility to use machine learning is also introduced. Given that the benefit of accurately calculating binding affinity changes upon mutation depends on comparing calculated values with experimental measurements, a brief survey on experimental methods and observables is provided. Examples of computational studies that go beyond calculating the Gibbs energy changes are given. Factors that need to be addressed by the computational chemist and potential pitfalls are discussed at length.
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| 6. |
- Herbst, Michael F., et al.
(författare)
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adcc : A versatile toolkit for rapid development of algebraic-diagrammatic construction methods
- 2020
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Ingår i: Wiley Interdisciplinary Reviews. Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 10:6
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Tidskriftsartikel (refereegranskat)abstract
- ADC-connect (adcc) is a hybrid python/C++ module for performing excited state calculations based on the algebraic-diagrammatic construction scheme for the polarization propagator (ADC). Key design goal is to restrict adcc to this single purpose and facilitate connection to external packages, for example, for obtaining the Hartree-Fock references, plotting spectra, or modeling solvents. Interfaces to four self-consistent field codes have already been implemented, namely pyscf, psi4, molsturm, and veloxchem. The computational workflow, including the numerical solvers, is implemented in python, whereas the working equations and other expensive expressions are done in C++. This equips adcc with adequate speed, making it a flexible toolkit for both rapid development of ADC-based computational spectroscopy methods as well as unusual computational workflows. This is demonstrated by three examples. Presently, ADC methods up to third order in perturbation theory are available in adcc, including the respective core-valence separation and spin-flip variants. Both restricted or unrestricted Hartree-Fock references can be employed.This article is categorized under: Software > Simulation Methods Electronic Structure Theory > Ab Initio Electronic Structure Methods Theoretical and Physical Chemistry > Spectroscopy Software > Quantum Chemistry
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| 7. |
- Hu, Wei, et al.
(författare)
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Theoretical modeling of surface and tip-enhanced Raman spectroscopies
- 2017
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Ingår i: Wiley Interdisciplinary Reviews. Computational Molecular Science. - : WILEY. - 1759-0876 .- 1759-0884. ; 7:2
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Forskningsöversikt (refereegranskat)abstract
- Raman spectroscopy is a powerful technique in molecular science because of the ability of providing vibrational 'finger-print'. The developments of the surfaceenhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS) have significantly improved the detection sensitivity and efficiency. However, they also introduce complications for the spectral assignments, for which advanced theoretical modeling has played an important role. Here we summarize some of our recent progresses for SERS and TERS, which generally combine both solid-state physics and quantum chemistry methods with two different schemes, namely the cluster model and the periodic boundary condition (PBC) model. In the cluster model, direct Raman spectra calculations are performed for the cluster taken from the accurate PBC structure. For PBC model, we have developed a quasianalytical approach that enables us to calculate the Raman spectra of entire system. Under the TERS condition, the non-uniformity of plasmonic field in real space can drastically alter the interaction between the molecule and the light. By taking into account the local distributions of the plasmonic field, a new interaction Hamiltonian is constructed and applied to model the super-high-resolution Raman images of a single molecule. It shows that the resonant Raman images reflect the transition density between ground and excited states, which are generally vibrational insensitive. The nonresonant Raman images, on the other hand, allow to visualize the atomic movement of individual vibrational modes in real space. The inclusion of non-uniformity of plasmonic field provides ample opportunities to discover new physics and new applications in the future.
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| 8. |
- Kamerlin, Shina C. L., 1981-, et al.
(författare)
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The empirical valence bond model : theory and applications
- 2011
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Ingår i: Wiley Interdisciplinary Reviews. Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 1:1, s. 30-45
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Tidskriftsartikel (refereegranskat)abstract
- Recent years have seen an explosion in computer power, allowing for the examination of ever more challenging problems. For instance, a recent simulation study, which was the first of its kind, was able to actually explore the dynamical nature of enzyme catalysis on a millisecond timescale (Pisliakov AV, Cao J, Kamerlin SCL, Warshel A. Proc Natl Acad Sci U S A 2009, 106:17359.), something that as recently as a year or two ago would have been considered impossible. However, the questions that need addressing are nevertheless very complex, and experimental approaches can unfortunately often be inconclusive (Åqvist J, Kolmodin K, Florián J, Warshel A, Chem Biol 1999, 6:R71.) in answering them. Therefore, it is essential to have an approach that is both reliable and able to capture complex systems in order to resolve long-standing controversies [particularly with regards to questions such as the origin of enzyme catalysis, where the relevant energy contributions cannot be separated without some computational models (Warshel A, Sharma PK, Kato M, Xiang Y, Liu H, Olsson MHM, Chem Rev 2006, 106:3210.)]. Herein, we will present the empirical valence bond (EVB) approach, which, at present, is arguably the most powerful tool for examining chemical reactivity in the condensed phase. We will illustrate the effectiveness of the EVB method when evaluating, for instance, catalytic effects and demonstrate that it is currently the optimal tool for elucidating challenging problems such as understanding the catalytic power of enzymes. Finally, the increasing appreciation of this approach can maybe best illustrated not only by its proliferation but also by attempts to capture its basic chemistry under a different name, as will be discussed in this work.
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| 9. |
- Larsson, Per, 1972-, et al.
(författare)
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Algorithm improvements for molecular dynamics simulations
- 2011
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Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 1:1, s. 93-108
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Tidskriftsartikel (refereegranskat)abstract
- High-performance implementations of molecular dynamics (MD) simulations play an important role in the study of macromolecules. Recent advances in both hardware and simulation software have extended the accessible time scales significantly, but the more complex algorithms used in many codes today occasionally make it difficult to understand the program flow and data structures without at least some knowledge about the underlying ideas used to improve performance. In this review, we discuss some of the currently most important areas of algorithm improvement to accelerate MD, including floating-point maths, techniques to accelerate nonbonded interactions, and methods to allow multiple or extended time steps. There is also a strong trend of increased parallelization on different levels, including both distributed memory domain decomposition, stream processing algorithms running, e. g., on graphics processing units hardware, and last but not least techniques to decouple simulations to enable massive parallelism on next-generation supercomputers or distributed computing. We describe some of the impacts these algorithms are having in current performance, and also how we believe they can be combined in the future.
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| 10. |
- Pedersen, Thomas Bondo, et al.
(författare)
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The versatility of the Cholesky decomposition in electronic structure theory
- 2024
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Ingår i: Wiley Interdisciplinary Reviews. Computational Molecular Science. - : John Wiley & Sons. - 1759-0876 .- 1759-0884. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- The resolution-of-the-identity (RI) or density fitting (DF) approximation for the electron repulsion integrals (ERIs) has become a standard component of accelerated and reduced-scaling implementations of first-principles Gaussian-type orbital electronic-structure methods. The Cholesky decomposition (CD) of the ERIs has also become increasingly deployed across quantum chemistry packages in the last decade, even though its early applications were mostly limited to high-accuracy methods such as coupled-cluster theory and multiconfigurational approaches. Starting with a summary of the basic theory underpinning both the CD and RI/DF approximations, thus underlining the extremely close relation of the CD and RI/DF techniques, we provide a brief and largely chronological review of the evolution of the CD approach from its birth in 1977 to its current state. In addition to being a purely numerical procedure for handling ERIs, thus providing robust and computationally efficient approximations to the exact ERIs that have been found increasingly useful on modern computer platforms, CD also offers highly accurate approaches for generating auxiliary basis sets for the RI/DF approximation on the fly due to the deep mathematical connection between the two approaches. In this review, we aim to provide a concise reference of the main techniques employed in various CD approaches in electronic structure theory, to exemplify the connection between the CD and RI/DF approaches, and to clarify the state of the art to guide new implementations of CD approaches across electronic structure programs.
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