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1
المؤلفون: Gopakumar, Geethanjali, 1992, Muchova, E, Unger, Isaak, Malerz, S, Trinter, F, Öhrwall, G, Lipparini, F, Menucci, B, Ceolin, D, Caleman, Carl, Wilkinson, I, Winter, B, Slavicek, P, Hergenhahn, U, Björneholm, Olle
المصدر: Physical Chemistry, Chemical Physics - PCCP. 24(15):8661-8671
الوصف: The decay of core holes is often regarded as a local process, but in some systems, it involves the autoionization of neighbouring atoms or molecules. Here, we explore such non-local autoionization (Intermolecular Coulombic Decay, ICD) of surrounding molecules upon 1s ionization of aqueous-phase Na+, Mg2+ and Al3+ ions. The three ions are isoelectronic but differ in the strength of the ion-water interactions which is manifested in experimental Auger electron spectra by varying intensities. While for strongly interacting Mg2+ and Al3+ the non-local decay is observed, for weakly bound Na+ no signal was measured. Combined with theoretical simulations we provide a microscopic understanding of the non-local decay processes. We assigned the ICD to decay processes ending with two-hole states delocalized between the central ion and neighbouring water. The ICD process is also shown to be highly selective with respect to water molecular orbitals. The ICD lifetime was estimated to be around 40 fs for Mg and 20 fs for Al. Auger spectroscopy thus represents a novel tool for exploring molecules in the liquid phase, providing simultaneously structural and electronic information.
وصف الملف: electronic
الوصول الحر: https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-451685Test
https://doi.org/10.1039/D2CP00227BTest
https://uu.diva-portal.org/smash/get/diva2:1588749/FULLTEXT02.pdfTest -
2تقرير
المؤلفون: Polack, E., Mikhalev, A., Dusson, Geneviève, Stamm, B., Lipparini, F.
مصطلحات موضوعية: Physics - Chemical Physics
الوصف: Repeated computations on the same molecular system, but with different geometries, are often performed in quantum chemistry, for instance, in ab-initio molecular dynamics simulations or geometry optimizations. While many efficient strategies exist to provide a good guess for the self-consistent field procedure, which is usually the main computational task to be performed, little is known on how to efficiently exploit in this direction the abundance of information generated during the many computations. In this article, we present a strategy to provide an accurate initial guess for the density matrix, expanded in a set of localized basis functions, within the self-consistent field iterations for parametrized Hartree-Fock problems where the nuclear coordinates are changed along a few user-specified collective variables, such as the molecule's normal modes. Our approach is based on an offline-stage where the Hartree-Fock eigenvalue problem is solved for some particular parameter values and an online-stage where the initial guess is computed very efficiently for any new parameter value.The method allows non-linear approximations of density matrices, which belong to a non-linear manifold that is isomorphic to the Grassmann manifold.The so-called Grassmann exponential and logarithm map the manifold onto the tangent space and thus provides the correct geometrical setting accounting for the manifold structure when working with subspaces rather than functions itself.Numerical tests on different amino acids show promising initial results.
الوصول الحر: http://arxiv.org/abs/2003.11802Test
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3دورية أكاديمية
المؤلفون: Alessandro R., Gianni' I., Pes F., Nottoli T., Lipparini F.
المساهمون: Alessandro, R., Gianni', I., Pes, F., Nottoli, T., Lipparini, F.
الوصف: We present an algorithm to solve the linear response equations for Hartree-Fock, Density Functional Theory, and the Multiconfigurational Self-Consistent Field method that is both simple and efficient. The algorithm makes use of the well-established symmetric and antisymmetric combinations of trial vectors but further orthogonalizes them with respect to the scalar product induced by the response matrix. This leads to a standard, symmetric block eigenvalue problem in the expansion subspace that can be solved by diagonalizing a symmetric, positive definite matrix half the size of the expansion space. Numerical tests showed that the algorithm is robust and stable.
وصف الملف: ELETTRONICO
العلاقة: info:eu-repo/semantics/altIdentifier/pmid/38081062; info:eu-repo/semantics/altIdentifier/wos/WOS:001132934300001; volume:19; issue:24; firstpage:9025; lastpage:9031; numberofpages:7; journal:JOURNAL OF CHEMICAL THEORY AND COMPUTATION; https://hdl.handle.net/11568/1218190Test; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85180078157
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4دورية أكاديمية
المؤلفون: Moscato D., Mandelli G., Bondanza M., Lipparini F., Conte R., Mennucci B., Ceotto M.
المساهمون: Moscato, D., Mandelli, G., Bondanza, M., Lipparini, F., Conte, R., Mennucci, B., Ceotto, M.
الوصف: We introduce a quantum mechanics/molecular mechanics semiclassical method for studying the solvation process of molecules in water at the nuclear quantum mechanical level with atomistic detail. We employ it in vibrational spectroscopy calculations because this is a tool that is very sensitive to the molecular environment. Specifically, we look at the vibrational spectroscopy of thymidine in liquid water. We find that the C═O frequency red shift and the C═C frequency blue shift, experienced by thymidyne upon solvation, are mainly due to reciprocal polarization effects, that the molecule and the water solvent exert on each other, and nuclear zero-point energy effects. In general, this work provides an accurate and practical tool to study quantum vibrational spectroscopy in solution and condensed phase, incorporating high-level and computationally affordable descriptions of both electronic and nuclear problems.
العلاقة: info:eu-repo/semantics/altIdentifier/pmid/38470354; info:eu-repo/semantics/altIdentifier/wos/WOS:001183930300001; volume:146; issue:12; firstpage:8179; lastpage:8188; numberofpages:10; journal:JOURNAL OF THE AMERICAN CHEMICAL SOCIETY; https://hdl.handle.net/11568/1230607Test; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85187712823
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5دورية أكاديمية
المؤلفون: Santalucia D., Bondanza M., Lipparini F., Ripszam M., Rossi N., Mandoli A.
المساهمون: Santalucia, D., Bondanza, M., Lipparini, F., Ripszam, M., Rossi, N., Mandoli, A.
مصطلحات موضوعية: cyclopropane, DFT, isomerization reaction, ketals• coupled cluster
الوصف: The structure of the spirocyclic product obtained by reacting catechol with 1,1-dichloro-2-(chloromethyl)cyclopropane is shown by NMR and X-ray analysis to be that of a 2-methylcyclopropene (MeCP), instead of the previously reported 2-methylenecyclopropane (MCP) one. The study of the equilibration between the two isomeric forms by experimental and computational means (including both Density Functional Theory – DFT – and Coupled Cluster with single, double, and perturbative triple excitations – CCSD(T) – calculations) revealed that, at variance with most of the alkylidenecyclopropane/alkylcyclopropene systems described to date, for the compounds of the present study the MeCP derivative is more stable by≈ 2.5–3.0 Kcal mol−1 than the MCP one. The extension of the DFT and CCSD(T) study to other spiro-MCP/MeCP pairs suggests that the origin of the unexpected shift of the equilibrium position can be tracked back to a combination of electronic and ring-strain effects. These findings lead to re-think a long-standing, and substantially undisputed belief in the area of unsaturated cyclopropane derivatives.
العلاقة: info:eu-repo/semantics/altIdentifier/pmid/38483818; journal:CHEMISTRY-A EUROPEAN JOURNAL; https://hdl.handle.net/11568/1230927Test; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85189876951
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6دورية أكاديمية
المؤلفون: Zhang C., Lipparini F., Stopkowicz S., Gauss J., Cheng L.
المساهمون: Zhang, C., Lipparini, F., Stopkowicz, S., Gauss, J., Cheng, L.
الوصف: A Cholesky decomposition (CD)-based implementation of relativistic two-component coupled-cluster (CC) and equation-of-motion CC (EOM-CC) methods using an exact two-component Hamiltonian augmented with atomic-mean-field spin-orbit integrals (the X2CAMF scheme) is reported. The present CD-based implementation of X2CAMF-CC and EOM-CC methods employs atomic-orbital-based algorithms to avoid the construction of two-electron integrals and intermediates involving three and four virtual indices. Our CD-based implementation extends the applicability of X2CAMF-CC and EOM-CC methods to medium-sized molecules with the possibility to correlate around 1000 spinors. Benchmark calculations for uranium-containing small molecules were performed to assess the dependence of the CC results on the Cholesky threshold. A Cholesky threshold of 10-4 is shown to be sufficient to maintain chemical accuracy. Example calculations to illustrate the capability of the CD-based relativistic CC methods are reported for the bond-dissociation energy of the uranium hexafluoride molecule, UF6, with up to quadruple-ζ basis sets, and the lowest excitation energy in the solvated uranyl ion [UO22+(H2O)12].
العلاقة: info:eu-repo/semantics/altIdentifier/pmid/38198515; info:eu-repo/semantics/altIdentifier/wos/WOS:001148149700001; volume:20; issue:2; firstpage:787; lastpage:798; numberofpages:12; journal:JOURNAL OF CHEMICAL THEORY AND COMPUTATION; https://hdl.handle.net/11568/1223490Test; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85182555983
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7دورية أكاديمية
المؤلفون: Gopakumar, G., Muchov , E., Unger, I., Malerz, S., Trinter, F., Öhrwall, G., Lipparini, F., Mennucci, B., C olin, D., Caleman, C., Wilkinson, I., Winter, B., Slav cek, P., Hergenhahn, U., Björneholm, O.
مصطلحات موضوعية: Photoelectron spectroscopy, liquid microjet, intermolecular Coulombic Decay, Ultrafast dynamics
الوصف: Non local analogues of Auger decay are increasingly recognized as important relaxation processes in the condensed phase. Here, we explore non local autoionization, specifically Intermolecular Coulombic Decay ICD , of a series of aqueous phase isoelectronic cations following 1s core level ionization. In particular, we focus on Na , Mg2 , and Al3 ions. We unambiguously identify the ICD contribution to the K edge Auger spectrum. The different strength of the ion water interactions is manifested by varying intensities of the respective signals the ICD signal intensity is greatest for the Al3 case, weaker for Mg2 , and absent for weakly solvent bound Na . With the assistance of ab initio calculations and molecular dynamics simulations, we provide a microscopic understanding of the non local decay processes. We assign the ICD signals to decay processes ending in two hole states, delocalized between the central ion and neighbouring water. Importantly, these processes are shown to be highly selective with respect to the promoted water solvent ionization channels. Furthermore, using a core hole clock analysis, the associated ICD timescales are estimated to be around 76 fs for Mg2 and 34 fs for Al3 . Building on these results, we argue that Auger and ICD spectroscopy represents a unique tool for the exploration of intra and inter molecular structure in the liquid phase, simultaneously providing both structural and electronic information
وصف الملف: application/pdf
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8دورية أكاديمية
المؤلفون: Nottoli T., Gauss J., Lipparini F.
المساهمون: Nottoli, T., Gauss, J., Lipparini, F.
مصطلحات موضوعية: Cholesky decomposition, Hartree–Fock, Levenberg–Marquardt, second-order, self-consistent field
الوصف: We present the implementation of a quadratically convergent self-consistent field (QCSCF) algorithm based on an adaptive trust-radius optimisation scheme for restricted open-shell Hartree–Fock (ROHF), restricted Hartree–Fock (RHF), and unrestricted Hartree–Fock (UHF) references. The algorithm can exploit Cholesky decomposition (CD) of the two-electron integrals to allow calculations on larger systems. The most important feature of the QCSCF code lies in its black-box nature–probably the most important quality desired by a generic user. As shown for pilot applications, it does not require one to tune the self-consistent field (SCF) parameters (damping, Pulay's DIIS, and other similar techniques) in difficult-to-converge molecules. Also, it can be used to obtain a very tight convergence with extended basis sets–a situation often needed when computing high-order molecular properties–where the standard SCF algorithm starts to oscillate. Nevertheless, trouble may appear even with a QCSCF solver. In this respect, we discuss what can go wrong, focusing on the multiple UHF solutions of ortho-benzyne.
العلاقة: info:eu-repo/semantics/altIdentifier/wos/WOS:000695333100001; volume:119; issue:21-22; journal:MOLECULAR PHYSICS; https://hdl.handle.net/11568/1109663Test; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85114460022
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9دورية أكاديمية
المؤلفون: Macaluso V., Hashem S., Nottoli M., Lipparini F., Cupellini L., Mennucci B.
المساهمون: Macaluso, V., Hashem, S., Nottoli, M., Lipparini, F., Cupellini, L., Mennucci, B.
الوصف: Ultrafast transient infrared (TRIR) spectroscopy is widely used to measure the excitation-induced structural changes of protein-bound chromophores. Here, we design a novel and general strategy to compute TRIR spectra of photoreceptors by combining μs-long MM molecular dynamics with ps-long QM/AMOEBA Born-Oppenheimer molecular dynamics (BOMD) trajectories for both ground and excited electronic states. As a proof of concept, the strategy is here applied to AppA, a blue-light-utilizing flavin (BLUF) protein, found in bacteria. We first analyzed the short-time evolution of the embedded flavin upon excitation revealing that its dynamic Stokes shift is ultrafast and mainly driven by the internal reorganization of the chromophore. A different normal-mode representation was needed to describe ground- and excited-state IR spectra. In this way, we could assign all of the bands observed in the measured transient spectrum. In particular, we could characterize the flavin isoalloxazine-ring region of the spectrum, for which a full and clear description was missing.
العلاقة: info:eu-repo/semantics/altIdentifier/pmid/34476939; info:eu-repo/semantics/altIdentifier/wos/WOS:000697332700020; volume:125; issue:36; firstpage:10282; lastpage:10292; numberofpages:11; journal:JOURNAL OF PHYSICAL CHEMISTRY. B, CONDENSED MATTER, MATERIALS, SURFACES, INTERFACES & BIOPHYSICAL; info:eu-repo/grantAgreement/EC/H2020/786714; http://hdl.handle.net/11568/1109657Test; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85114883016
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10دورية أكاديمية
المؤلفون: Nottoli M., Bondanza M., Lipparini F., Mennucci B.
المساهمون: Nottoli, M., Bondanza, M., Lipparini, F., Mennucci, B.
الوصف: We present an extension of the polarizable quantum mechanical (QM)/AMOEBA approach to enhanced sampling techniques. This is achieved by connecting the enhanced sampling PLUMED library to the machinery based on the interface of Gaussian and Tinker to perform QM/AMOEBA molecular dynamics. As an application, we study the excited state intramolecular proton transfer of 3-hydroxyflavone in two solvents: methanol and methylcyclohexane. By using a combination of molecular dynamics and umbrella sampling, we find an ultrafast component of the transfer, which is common to the two solvents, and a much slower component, which is active in the protic solvent only. The mechanisms of the two components are explained in terms of intramolecular vibrational redistribution and intermolecular hydrogen-bonding, respectively. Ground and excited state free energies along an effective reaction coordinate are finally obtained allowing for a detailed analysis of the solvent mediated mechanism.
العلاقة: info:eu-repo/semantics/altIdentifier/wos/WOS:000692818800002; volume:154; issue:18; numberofpages:10; journal:THE JOURNAL OF CHEMICAL PHYSICS; info:eu-repo/grantAgreement/EC/H2020/786714; http://hdl.handle.net/11568/1101532Test; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85105844112
