| 1. |
- Aquilante, Francesco, et al.
(author)
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Modern quantum chemistry with [Open]Molcas
- 2020
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In: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:21
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Journal article (peer-reviewed)abstract
- MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.
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| 2. |
- Aquilante, Francesco, et al.
(author)
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Molcas 8 : New capabilities for multiconfigurational quantum chemical calculations across the periodic table
- 2016
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In: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 37:5, s. 506-541
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Journal article (peer-reviewed)abstract
- In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.
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| 3. |
- De Vico, Luca, et al.
(author)
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New general tools for constrained geometry optimizations
- 2005
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In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 1:5, s. 1029-1037
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Journal article (peer-reviewed)abstract
- A modification of the constrained geometry optimization method by Anglada and Bofill (Anglada, J. M.; Bofill, J. M. J. Comput. Chem. 1997, 18, 992-1003) is designed and implemented. The changes include the choice of projection, quasi-line-search, and the use of a Rational Function optimization approach rather than a reduced-restricted-quasi-Newton-Raphson method in the optimization step. Furthermore, we show how geometrical constrains can be implemented in an approach based on nonreclunclant curvilinear coordinates avoiding the inclusion of the constraints in the set of redundant coordinates used to define the internal coordinates. The behavior of the new implementation is demonstrated in geometry optimizations featuring single or multiple geometrical constraints (bond lengths, angles, etc.), optimizations on hyperspherical cross sections (as in the computation of steepest descent paths), and location of energy minima on the intersection subspace of two potential energy surfaces (i.e. minimum energy crossing points). In addition, a novel scheme to determine the crossing point geometrically nearest to a given molecular structure is proposed.
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| 4. |
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| 5. |
- Galván, Ignacio Fdez., et al.
(author)
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OpenMolcas : From Source Code to Insight
- 2019
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In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 15:11, s. 5925-5964
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Journal article (peer-reviewed)abstract
- In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.
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| 6. |
- Gozem, Samer, et al.
(author)
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Dynamic Electron Correlation Effects on the Ground State Potential Energy Surface of a Retinal Chromophore Model
- 2012
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In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 8:11, s. 4069-4080
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Journal article (peer-reviewed)abstract
- The ground state potential energy surface of the retinal chromophore of visual pigments (e.g., bovine rhodopsin) features a low-lying conical intersection surrounded by regions with variable charge-transfer and diradical electronic structures. This implies that dynamic electron correlation may have a large effect on the shape of the force fields driving its reactivity. To investigate this effect, we focus on mapping the potential energy for three paths located along the ground state CASSCF potential energy surface of the penta-2,4-dieniminium cation taken as a minimal model of the retinal chromophore. The first path spans the bond length alternation coordinate and intercepts a conical intersection point. The other two are minimum energy paths along two distinct but kinetically competitive thermal isomerization coordinates. We show that the effect of introducing the missing dynamic electron correlation variationally (with MRCISD) and perturbatively (with the CASPT2, NEVPT2, and XMCQDPT2 methods) leads, invariably, to a stabilization of the regions with charge transfer character and to a significant reshaping of the reference CASSCF potential energy surface and suggesting a change in the dominating isomerization mechanism. The possible impact of such a correction on the photoisomerization of the retinal chromophore is discussed.
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| 7. |
- Gozem, Samer, et al.
(author)
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Shape of Multireference, Equation-of-Motion Coupled-Cluster, and Density Functional Theory Potential Energy Surfaces at a Conical Intersection
- 2014
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In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 10:8, s. 3074-3084
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Journal article (peer-reviewed)abstract
- We report and characterize ground-state and excited-state potential energy profiles using a variety of electronic structure methods along a loop lying on the branching plane associated with a conical intersection (Cl) of a reduced retinal model, the penta-2,4-dieniminium cation (PSB3). Whereas the performance of the equation-of-motion coupled-duster, density functional theory, and multireference methods had been tested along the excited- and ground-state paths of PSB3 in our earlier work, the ability of these methods to correctly describe the potential energy surface shape along a CI branching plane has not yet been investigated. This is the focus of the present contribution. We find, in agreement with earlier studies by others, that standard time-dependent DFT (TDDFT) does not yield the correct two-dimensional (i.e., conical) crossing along the branching plane but rather a one-dimensional (i.e., linear) crossing along the same plane. The same type of behavior is found for SS-CASPT2(IPEA=0), SS-CASPT2(IPEA=0.25), spin-projected SF-TDDFT, EOM-SF-CCSD, and, finally, for the reference MRCISD+Q method. In contrast, we found that MRCISD, CASSCF, MS-CASPT2(IPEA=0), MS-CASPT2(IPEA=0.25), XMCQDPT2, QD-NEVPT2, non-spin-projected SF-TDDFT, and SI-SA-REKS yield the expected conical crossing. To assess the effect of the different crossing topologies (i.e., linear or conical) on the PSB3 photoisomerization efficiency, we discuss the results of 100 semiclassical trajectories computed by CASSCF and SS-CASPT2(IPEA=0.25) for a PSB3 derivative. We show that for the same initial conditions, the two methods yield similar dynamics leading to isomerization quantum yields that differ by only a few percent.
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| 8. |
- Groenhof, Gerrit, et al.
(author)
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Photoactivation of the photoactive yellow protein : why photon absorption triggers a trans-to-cis Isomerization of the chromophore in the protein.
- 2004
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In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 126:13, s. 4228-4233
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Journal article (peer-reviewed)abstract
- Atomistic QM/MM simulations have been carried out on the complete photocycle of Photoactive Yellow Protein, a bacterial photoreceptor, in which blue light triggers isomerization of a covalently bound chromophore. The "chemical role" of the protein cavity in the control of the photoisomerization step has been elucidated. Isomerization is facilitated due to preferential electrostatic stabilization of the chromophore's excited state by the guanidium group of Arg52, located just above the negatively charged chromophore ring. In vacuo isomerization does not occur. Isomerization of the double bond is enhanced relative to isomerization of a single bond due to the steric interactions between the phenyl ring of the chromophore and the side chains of Arg52 and Phe62. In the isomerized configuration (ground-state cis), a proton transfer from Glu46 to the chromophore is far more probable than in the initial configuration (ground-state trans). It is this proton transfer that initiates the conformational changes within the protein, which are believed to lead to signaling.
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| 9. |
- Manni, Giovanni Li, et al.
(author)
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The OpenMolcas Web : A Community-Driven Approach to Advancing Computational Chemistry
- 2023
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In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:20, s. 6933-6991
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Journal article (peer-reviewed)abstract
- The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.
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| 10. |
- Melaccio, Federico, et al.
(author)
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Unique QM/MM potential energy surface exploration using microiterations
- 2011
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In: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 111:13, s. 3339-3346
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Journal article (peer-reviewed)abstract
- The determination and the characterization of important points of a potential energy surface can be carried out routinely using any molecular modelling software based on either a quantum mechanical (QM) or a classical (molecular mechanics, MM) description of the particle interactions. However the coupling of the QM and MM descriptions (QM/MM) gives rise to severe efficiency limitations during a geometry optimization of the whole system, especially when both subsystems are coupled electrostatically. The present work introduces two simple improvements, mainly developed in the framework of the ElectroStatic Potential Fitted (ESPF) method to ensure the uniqueness of the QM/MM potential energy surface. The first one aims to improve the approximate Hessian matrix used in the QM optimization step. The second one tries to recouple electrostatically the QM and MM subsystems when microiterations are used. These methods are tested on a very simple system (a QM water molecule in a MM water box) before to be applied to the investigation of the light absorption in the rhodopsin protein at the multireference second-order perturbation level of theory (CASPT2). This work is dedicated to the memory of Prof. B. O. Roos. He was a great support for the implementation of the QM/MM method in the Molcas package.
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| 11. |
- Schapiro, Igor, et al.
(author)
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A surface hopping algorithm for nonadiabatic minimum energy path calculations
- 2015
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In: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 36:5, s. 312-20
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Journal article (peer-reviewed)abstract
- The article introduces a robust algorithm for the computation of minimum energy paths transiting along regions of near-to or degeneracy of adiabatic states. The method facilitates studies of excited state reactivity involving weakly avoided crossings and conical intersections. Based on the analysis of the change in the multiconfigurational wave function the algorithm takes the decision whether the optimization should continue following the same electronic state or switch to a different state. This algorithm helps to overcome convergence difficulties near degeneracies. The implementation in the MOLCAS quantum chemistry package is discussed. To demonstrate the utility of the proposed procedure four examples of application are provided: thymine, asulam, 1,2-dioxetane, and a three-double-bond model of the 11-cis-retinal protonated Schiff base.
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| 12. |
- Schapiro, Igor, et al.
(author)
-
Synthesis, spectroscopy and QM/MM simulations of a biomimetic ultrafast light-driven molecular motor
- 2019
-
In: Photochemical and Photobiological Sciences. - : Springer Science and Business Media LLC. - 1474-9092 .- 1474-905X. ; 18:9, s. 2259-2269
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Journal article (peer-reviewed)abstract
- A molecular motor potentially performing a continuous unidirectional rotation is studied by a multidisciplinary approach including organic synthesis, transient spectroscopy and excited state trajectory calculations. A stereogenic center was introduced in the N-alkylated indanylidene-pyrroline Schiff base framework of a previously investigated light-driven molecular switch in order to achieve the unidirectional C[double bond, length as m-dash]C rotary motion typical of Feringa's motor. Here we report that the specific substitution pattern of the designed chiral molecule must critically determine the unidirectional efficiency of the light-induced rotary motion. More specifically, we find that a stereogenic center containing a methyl group and a hydrogen atom as substituents does not create a differential steric effect large enough to fully direct the motion in either the clockwise or counterclockwise direction especially along the E→Z coordinate. However, due to the documented ultrafast character and electronic circular dichroism activity of the investigated system, we find that it provides the basis for development of a novel generation of rotary motors with a biomimetic framework and operating on a picosecond time scale.
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| 13. |
- Schapiro, Igor, et al.
(author)
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The Ultrafast Photoisomerizations of Rhodopsin and Bathorhodopsin Are Modulated by Bond Length Alternation and HOOP Driven Electronic Effects
- 2011
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In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 133:10, s. 3354-3364
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Journal article (peer-reviewed)abstract
- Rhodopsin (Rh) and bathorhodopsin (bathoRh) quantum-mechanics/molecular-mechanics models based on ab initio multiconfigurational wave functions are employed to look at the light induced π-bond breaking and reconstitution occurring during the RhfbathoRh and bathoRhfRh isomerizations. More specifically, semiclassical trajectory computations are used to compare the excited (S1) and ground (S0) state dynamics characterizing the opposite steps of the Rh/bathoRh photochromic cycle during the first 200 fs following photoexcitation. We show that the information contained in these data provide an unprecedented insight into the sub-picosecond π-bond reconstitution process which is at the basis of the reactivity of the protein embedded 11-cis and all-trans retinal chromophores.More specifically, the data point to the phase and amplitude of the skeletal bond length alternation stretchingmode as the key factor switching the chromophore to a bonding state. It is also confirmed/found that the phase and amplitude of the hydrogen-out-of-plane mode controls the stereochemical outcome of the forward and reverse photoisomerizations.
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| 14. |
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| 15. |
- Strambi, Angela, et al.
(author)
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Anabaena sensory rhodopsin is a light-driven unidirectional rotor
- 2010
-
In: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences of the United States of America. - 0027-8424 .- 1091-6490. ; 107:50, s. 21322-21326
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Journal article (peer-reviewed)abstract
- The implementation of multiconfigurational quantum chemistry methods into a quantum-mechanics/molecular-mechanics protocol has allowed the construction of a realistic computer model for the sensory rhodopsin of the cyanobacterium Anabaena PCC 7120. The model, which reproduces the absorption spectra of both the all-trans and 13-cis forms of the protein and their associated K and L intermediates, is employed to investigate the light-driven steps of the photochromic cycle exhibited by the protein. It is found that the photoisomerizations of the all-trans and 13-cis retinal chromophores occur through unidirectional, counterclockwise 180 deg rotations of the =C14-C15= moiety with respect to the Lys210-linked end of the chromophore axis. Thus, the sequential interconversions of the all-trans and 13-cis forms during a single photochromic cycle yield a complete (360 deg) unidirectional rotation of the =C14-C15= moiety. This finding implies that Anabaena sensory rhodopsin is a biological realization of a light-driven molecular rotor.
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| 16. |
- Söderhjelm, Pär, et al.
(author)
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Protein Influence on Electronic Spectra Modeled by Multipoles and Polarizabilities
- 2009
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In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 5:3, s. 649-658
-
Journal article (peer-reviewed)abstract
- We have developed automatic methods to calculate multipoles and anisotropic polarizabilities for all atoms and bond centers in a protein and to include such a model in the calculation of electronic properties at any level of quantum mechanical theory. This approach is applied for the calculation of the electronic spectra of retinal in rhodopsin at the CASPT2//CASSCF level (second-order multiconfigurational perturbation theory) for the wild-type protein, as well as two mutants and isorhodopsin in QM/MM structures based on two crystal structures. We also perform a detailed investigation of the importance and distance dependence of the multipoles and the polarizabilities for both the absolute and the relative absorption energies. It is shown that the model of the surrounding protein strongly influences the spectrum and that different models give widely different results. For example, the Amber 1994 and 2003 force fields give excitation energies that differ by up to 16 kJ/mol. For accurate excitation energies, multipoles up to quadrupoles and anisotropic polarizabilities are needed. However, interactions with residues more than 10 A from the chromophore can be treated with a standard polarizable force field without any dipoles or quadrupoles.
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| 17. |
- Valentini, Alessio, et al.
(author)
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Optomechanical Control of Quantum Yield in Trans-Cis Ultrafast Photoisomerization of a Retinal Chromophore Model
- 2017
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In: Angewandte Chemie International Edition. - : WILEY-V C H VERLAG GMBH. - 1433-7851 .- 1521-3773. ; 56:14, s. 3842-3846
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Journal article (peer-reviewed)abstract
- The quantum yield of a photochemical reaction is one of the most fundamental quantities in photochemistry, as it measures the efficiency of the transduction of light energy into chemical energy. Nature has evolved photoreceptors in which the reactivity of a chromophore is enhanced by its molecular environment to achieve high quantum yields. The retinal chromophore sterically constrained inside rhodopsin proteins represents an outstanding example of such a control. In a more general framework, mechanical forces acting on a molecular system can strongly modify its reactivity. Herein, we show that the exertion of tensile forces on a simplified retinal chromophore model provokes a substantial and regular increase in the trans-to-cis photoisomerization quantum yield in a counter-intuitive way, as these extension forces facilitate the formation of the more compressed cis photoisomer. A rationale for the mechanochemical effect on this photoisomerization mechanism is also proposed.
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