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Spectroscopy simulations are of paramount importance for the interpretation of experimental electronic spectra, the disentangling of overlapping spectral features, and the tracing of the microscopic origin of the observed signals. Linear and nonlinear simulations are based on the results drawn from electronic structure calculations that provide the necessary parameterization of the molecular systems probed by light. Here, we investigate the applicability of excited-state properties obtained from linear-response time-dependent density functional theory (TDDFT) in the description of nonlinear spectra by employing the pseudowavefunction approach and compare them with benchmarks from highly accurate RASSCF/RASPT2 calculations and with high temporal resolution experimental results. As a test case, we consider the prediction of femtosecond transient absorption and two-dimensional electronic spectroscopy of a perylene bisimide dye in solution. We find that experimental signals are well reproduced by both theoretical approaches, showing that the computationally cheaper TDDFT can be a suitable option for the simulation of nonlinear spectroscopy of molecular systems that are too large to be treated with higher-level RASSCF/RASPT2 methods.

We demonstrate how optical cavities can be exploited to control both valence- and core-excitations in a prototypical model transition metal complex, ferricyanide ([Fe(iii)(CN)6]3-), in an aqueous environment. The spectroscopic signatures of hybrid light-matter polariton states are revealed in UV/Vis and X-ray absorption, and stimulated X-ray Raman signals. In an UV/Vis cavity, the absorption spectrum exhibits the single-polariton states arising from the cavity photon mode coupling to both resonant and off-resonant valence-excited states. We further show that nonlinear stimulated X-ray Raman signals can selectively probe the bipolariton states via cavity-modified Fe core-excited states. This unveils the correlation between valence polaritons and dressed core-excitations. In an X-ray cavity, core-polaritons are generated and their correlations with the bare valence-excitations appear in the linear and nonlinear X-ray spectra.

The Chronus Quantum (ChronusQ) software package is an open source (under the GNU General Public License v2) software infrastructure which targets the solution of challenging problems that arise in ab initio electronic structure theory. Special emphasis is placed on the consistent treatment of time dependence and spin in the electronic wave function, as well as the inclusion of relativistic effects in said treatments. In addition, ChronusQ provides support for the inclusion of uniform finite magnetic fields as external perturbations through the use of gauge-including atomic orbitals. ChronusQ is a parallel electronic structure code written in modern C++ which utilizes both message passing implementation and shared memory (OpenMP) parallelism. In addition to the examination of the current state of code base itself, a discussion regarding ongoing developments and developer contributions will also be provided. This article is categorized under: Software > Quantum Chemistry Electronic Structure Theory > Ab Initio Electronic Structure Methods Electronic Structure Theory > Density Functional Theory.

Time‐dependent density functional theory (TD‐DFT) and multiconfigurational second‐order perturbation theory (CASPT2) are two of the most widely used methods to investigate photoinduced dynamics in DNA‐based systems. These methods sometimes give diverse dynamics in physiological environments usually modeled by quantum mechanics/molecular mechanics (QM/MM) protocol. In this work, we demonstrate for the uridine test case that the underlying topology of the potential energy surfaces of electronic states involved in photoinduced relaxation is similar in both electronic structure methods. This is verified by analyzing surface‐hopping dynamics performed at the QM/MM level on aqueous solvated uridine at TD‐DFT and CASPT2 levels. By constraining the dynamics to remain on ππ* state we observe similar fluctuations in energy and relaxation lifetimes in surface‐hopping dynamics in both TD‐DFT and experimentally validated CASPT2 methods. This finding calls for a systematic comparison of the ES potential energy surfaces of DNA and RNA nucleosides at the single‐ and multi‐reference levels of theory. The anomalous long excited state lifetime at the TD‐DFT level is explained by nπ* trapping due to the tendency of TD‐DFT in QM/MM schemes with electrostatic embedding to underestimate the energy of the ππ* state leading to a wrong ππ*/nπ* energetic order. A study of the FC energetics suggests that improving the description of the surrounding environment through polarizable embedding or by the expansion of QM layer with hydrogen‐bonded waters helps restore the correct state order at TD‐DFT level. Thus by combining TDDFT with an accurate modeling of the environment, TD‐DFT is positioned as the standout protocol to model photoinduced dynamics in DNA‐based aggregates and multimers. [ABSTRACT FROM AUTHOR]

Computation of intermolecular interactions is a challenge in drug discovery because accurate ab initio techniques are too computationally expensive to be routinely applied to drug–protein models. Classical force fields are more computationally feasible, and force fields designed to match symmetry adapted perturbation theory (SAPT) interaction energies can remain accurate in this context. Unfortunately, the application of such force fields is complicated by the laborious parameterization required for computations on new molecules. Here, we introduce the component-based machine-learned intermolecular force field (CLIFF), which combines accurate, physics-based equations for intermolecular interaction energies with machine-learning models to enable automatic parameterization. The CLIFF uses functional forms corresponding to electrostatic, exchange-repulsion, induction/polarization, and London dispersion components in SAPT. Molecule-independent parameters are fit with respect to SAPT2+(3)δMP2/aug-cc-pVTZ, and molecule-dependent atomic parameters (atomic widths, atomic multipoles, and Hirshfeld ratios) are obtained from machine learning models developed for C, N, O, H, S, F, Cl, and Br. The CLIFF achieves mean absolute errors (MAEs) no worse than 0.70 kcal mol−1 in both total and component energies across a diverse dimer test set. For the side chain–side chain interaction database derived from protein fragments, the CLIFF produces total interaction energies with an MAE of 0.27 kcal mol−1 with respect to reference data, outperforming similar and even more expensive methods. In applications to a set of model drug–protein interactions, the CLIFF is able to accurately rank-order ligand binding strengths and achieves less than 10% error with respect to SAPT reference values for most complexes. [ABSTRACT FROM AUTHOR]

A time-dependent (TD) formulation of equation-of-motion (EOM) coupled-cluster (CC) theory is developed, which, unlike other similar TD-EOM-CC approaches [D. R. Nascimento and A. E. DePrince III, J. Chem. Theory Comput. 12, 5834–5840 (2016)], can be applied to any type of linear electronic spectroscopy. The TD-EOM-CC method is formally equivalent to the standard frequency-domain formulation of EOM-CC theory, with a potential computational advantage of a comparatively low memory footprint. This general TD-EOM-CC framework is applied to the linear absorption and electric circular dichroism spectra of several small oxirane derivatives. [ABSTRACT FROM AUTHOR]

Ligand substitution reactions are common in solvated transition metal complexes, and harnessing them through initiation with light promises interesting practical applications, driving interest in new means of probing their mechanisms. Using a combination of time-resolved x-ray absorption spectroscopy and hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations and x-ray absorption near-edge spectroscopy calculations, we elucidate the mechanism of photoaquation in the model system iron(ii) hexacyanide, where UV excitation results in the exchange of a CN− ligand with a water molecule from the solvent. We take advantage of the high flux and stability of synchrotron x-rays to capture high precision x-ray absorption spectra that allow us to overcome the usual limitation of the relatively long x-ray pulses and extract the spectrum of the short-lived intermediate pentacoordinated species. Additionally, we determine its lifetime to be 19 (±5) ps. The QM/MM simulations support our experimental findings and explain the ∼20 ps time scale for aquation as involving interconversion between the square pyramidal (SP) and trigonal bipyramidal pentacoordinated geometries, with aquation being only active in the SP configuration. [ABSTRACT FROM AUTHOR]

The emergence of state-of-the-art X-ray light sources has paved the way for novel spectroscopies that take advantage of their atomic specificity to shed light on fundamental physical, chemical, and biological processes both in the static and time domains. The success of these experiments hinges on the ability to interpret and predict core-level spectra, which has opened avenues for theory to play a key role. Over the last two decades, linear-response time-dependent density functional theory (LR-TDDFT), despite various theoretical challenges, has become a computationally attractive and versatile framework to study excited-state spectra including X-ray spectroscopies. In this context, we focus our discussion on LR-TDDFT approaches for the computation of X-ray Near-Edge Structure (XANES), Valence-to-Core X-ray Emission (VtC-XES), and Resonant Inelastic X-ray Scattering (RIXS) spectroscopies in molecular systems with an emphasis on Gaussian basis set implementations. We illustrate these approaches with applications and provide a brief outlook of possible new directions. [ABSTRACT FROM AUTHOR]

We present a combined cavity quantum electrodynamics/ab initio electronic structure approach for simulating plasmon-molecule interactions in the time domain. The simple Jaynes-Cummings-type model Hamiltonian typically utilized in such simulations is replaced with one in which the molecular component of the coupled system is treated in a fully ab initio way, resulting in a computationally efficient description of general plasmon-molecule interactions. Mutual polarization effects are easily incorporated within a standard ground-state Hartree-Fock computation, and time-dependent simulations carry the same formal computational scaling as real-time time-dependent Hartree-Fock theory. As a proof of principle, we apply this generalized method to the emergence of a Fano-like resonance in coupled molecule-plasmon systems; this feature is quite sensitive to the nanoparticle-molecule separation and the orientation of the molecule relative to the polarization of the external electric field. [ABSTRACT FROM AUTHOR]

We introduce iSPECTRON, a program that parses data from common quantum chemistry software (NWChem, OpenMolcas, Gaussian, Cobramm, etc.), produces the input files for the simulation of linear and nonlinear spectroscopy of molecules with the Spectron code, and analyzes the spectra with a broad range of tools. Vibronic spectra are expressed in term of the electronic eigenstates, obtained from quantum chemistry computations, and vibrational/bath effects are incorporated in the framework of the displaced harmonic oscillator model, where all required quantities are computed at the Franck‐Condon point. The program capabilities are illustrated by simulating linear absorption, transient absorption and two dimensional electronic spectra of the pyrene molecule. Calculations at two levels of electronic structure theory, time‐dependent density functional theory (with NWChem) and RASSCF/RASPT2 (with OpenMolcas) are presented and compared where possible. The iSPECTRON program is available online at https://github.com/ispectrongit/iSPECTRON/ and distributed open source under the terms of the Educational Community License version 2.0 (ECL 2.0). [ABSTRACT FROM AUTHOR]

Variational two-electron reduced-density-matrix (2-RDM) methods can provide a reference-independent description of the electronic structure of strongly correlated molecules and materials. These methods represent one of few ways of performing large active-space-based computations that are beyond the scope of conventional configuration-interaction-based approaches. However, implementations of the method are quite rare, making it difficult for the quantum chemistry community to assess the utility of the approach. Here, we discuss an open-shell implementation of the variational 2-RDM method and explore its ability to describe different spin states in several model systems, including linear hydrogen chains and linear acenes. The largest calculations considered are comparable to complete-active-space computations with 50 electrons in 50 orbitals. [ABSTRACT FROM AUTHOR]

Correction for 'Computational approaches for XANES, VtC-XES, and RIXS using linear-response time-dependent density functional theory based methods' by Daniel R. Nascimento et al., Phys. Chem. Chem. Phys., 2022, 24, 14680–14691, https://doi.org/10.1039/D2CP01132H. [ABSTRACT FROM AUTHOR]

Source-to-sink systems are poorly known in tropical rivers. For the Amazonian rivers, the majority of the provenance studies remain focused on the suspended load, implying a poor understanding of the processes governing production and distribution of sands. In this study, we perform heavy mineral and optically stimulated luminescence (OSL) analysis to cover the entire spectrum (heavy and light minerals fraction) of 29 sand samples of the Lower Madeira river region (Amazon and Madeira rivers), of which the main goal was to find provenance indicators specific to these rivers. Despite the tropical humid climate, the sands of the Amazon and Lower Madeira rivers are rich in unstable heavy minerals as augite, hypersthene, green hornblende and andalusite. The Madeira river is highlighted by its higher content of andalusite, with source attributed to the Amazon Craton (medium-to-high grade metamorphic rocks), while the Amazon river, upstream of the Madeira river mouth, has a signature of augite and hypersthene, that suggests an Andean provenance (volcanic rocks). Sands from the Madeira river can be tracked in the Amazon river by the increasing concentration in andalusite. OSL analysis of the light minerals fraction was used as an index of feldspar concentration and sedimentary history of quartz grains. Lower feldspar concentration and quartz grains with longer sedimentary history (higher OSL sensitivity) also point to a major contribution of cratonic sources for the sands in the Madeira river. While the sands from the Lower Madeira would be mainly supplied by cratonic rocks, previous work recognised that suspended sediments (silt and clay) are derived from Andean rocks. Therefore, we interpret a decoupling between the sources of sand and mud (silt and clay) under transport in the Madeira river. Andean sands (rich in augite and hypersthene) would be trapped in the foreland zones of the Beni and Mamoré tributaries. In the Amazon river sands, the low OSL sensitivity of the quartz, higher content of feldspar and unstable heavy mineral assemblage dominated by augite and hypersthene suggest both a fast transport from Andean sources with fine sediment bypass over foreland areas. [ABSTRACT FROM AUTHOR]

The Mundaú sub-basin composes the western segment of the Ceará Basin, which is one of a series of basins of the Brazilian Equatorial Margin that resulted from the breakup of Western Gondwana. This study investigates the origin and maturation of the organic matter preserved in the rocks of the middle and outer shelf of the Mundaú sub-basin, in order to assess the source-rock potential for oil and gas generation. The samples selected for this study are representative of the Mundaú, Paracuru, and Ubarana formations, which correlate with the rift, transition, and drift phases of the Western Gondwana breakup. The results indicate moderate to good potential for oil generation and good potential for gas generation for the Mundaú Formation. Fault activity during the rift phase favored sediment supply. Kerogen type III predominates in shallower portions and probably reflects the contribution from the continent. Good to excellent potential for oil and gas generation is indicated for the Paracuru Formation. Kerogen types I and II predominate, having the marine organic matter been deposited in reducing conditions. The most promising interval for hydrocarbon generation is limited by the top of the Trairí Member and the top of the Paracuru Formation. Moderate to good potential for oil and gas generation is suggested for the Uruburetama Member of the Ubarana Formation. The source rocks located in the middle shelf were deposited under reducing conditions in a transgressive marine environment. Kerogen varies from type II, to a mixture of types II and III, and to subordinate type III. Poor to fair potential for oil generation is indicated for the Itapajé Member of the Ubarana Formation. Kerogen type IV (inert or degraded) is typical in the middle shelf, and kerogen type IV and subordinate type III are typical on the outer shelf. The presence of inert kerogen is related to high-energy, oxidizing depositional environments. The hydrocarbon expulsion threshold estimated for the outer shelf is at 2106-m, for the middle shelf at 1635-m, and for the deep waters at 3632-m depths. Source rocks of the middle and outer shelves occur between 561 m and 4080 m, whereas those in deep waters occur between 2754 m and 5007 m of depth. The Active Source Rock Depth Limits (ASDL) estimated for the outer shelf is below 4500 m, whereas for deep waters, this limit is close to 6000 m. These organic geochemical constraints are important guidelines for oil and gas exploration in the Ceará and adjacent basins. [Display omitted] • Source-rock from Mundaú sub-basin, Ceará Basin, Brazilian Equatorial Margin. • Source-rock characterization by means of organic geochemistry. • Distribution of source rocks via transects and isoline maps. • Aptian to Eocene distribution of organic-rich facies. • Oil potential of the Paracuru Formation – transitional phase of the Ceará Basin. [ABSTRACT FROM AUTHOR]

The Chronus Quantum (ChronusQ) software package is an open source (under the GNU General Public License v2) software infrastructure which targets the solution of challenging problems that arise in ab initio electronic structure theory. Special emphasis is placed on the consistent treatment of time dependence and spin in the electronic wave function, as well as the inclusion of relativistic effects in said treatments. In addition, ChronusQ provides support for the inclusion of uniform finite magnetic fields as external perturbations through the use of gauge‐including atomic orbitals. ChronusQ is a parallel electronic structure code written in modern C++ which utilizes both message passing implementation and shared memory (OpenMP) parallelism. In addition to the examination of the current state of code base itself, a discussion regarding ongoing developments and developer contributions will also be provided. This article is categorized under:Software > Quantum ChemistryElectronic Structure Theory > Ab Initio Electronic Structure MethodsElectronic Structure Theory > Density Functional Theory [ABSTRACT FROM AUTHOR]

This paper presents an integration of the process of environmental licensing applied to Rio de Janeiro (Brazil) through the document Study and Report of Environmental Impact (EIA/RIMA). Also, the study analyzes the structuring of the recommendations of project management practices according to the Project Management Institute in the stages of initiation, planning, execution, control and closure. This is done to identify the efficiency in integration processes, stakeholders, scope, time, quality, cost and communication in the document project management plan EIA/RIMA. The contextualization of the national, state and local environmental licensing policies in Brazil was done. These are crucial in the making of the Environmental Impact Study. The integration of project management and environmental management documents contributes to form teams that are more committed with environmental responsibilities present in the work plans of environmental projects. [ABSTRACT FROM AUTHOR]

Resonant stimulated X-ray Raman spectroscopy of the bimetallic [Mn III Mn IV (μ-O) 2 (μ-OAC)(tacn) 2 ] 2+ manganese complex is investigated in a simulation study. Essential biological processes, including water oxidation in photosynthesis, involve charge transfer between manganese sites of different oxidation states. We study a prototypical binuclear mixed-valence transition-metal complex with two Mn atoms in different oxidation states surrounded by ligand structures and employ a pump-probe sequence of resonant X-ray Raman excitations to follow the charge transfer occurring in the molecule. This allows us to generate and monitor valence-electron wave packets at selected regions in the molecule by exploiting element-specific core-excited states. A two-color protocol is presented, with pump and probe pulses tuned to the Mn and N K-edges. A natural orbital decomposition allows the visualization of the electron dynamics underlying the signal.

A time-dependent (TD) formulation of equation-of-motion coupled-cluster (EOM-CC) theory can provide excited-state information over an arbitrarily wide energy window with a reduced memory footprint relative to conventional, frequency-domain EOM-CC theory. However, the floating-point costs of the time-integration required by TD-EOM-CC are generally far larger than those of the frequency-domain form of the approach. This work considers the potential of the short iterative Lanczos (SIL) integration scheme [ J. Chem. Phys. 1986 , 85 , 5870-5876] to reduce the floating-point costs of TD-EOM-CC simulations. Low-energy and K-edge absorption features for small molecules are evaluated using TD-EOM-CC with single and double excitations, with the time-integrations carried out via SIL and fourth-order Runge-Kutta (RK4) schemes. Spectra derived from SIL- and RK4-driven simulations are nearly indistinguishable, and with an appropriately chosen subspace dimension, the SIL requires far fewer floating-point operations than are required by RK4. For K-edge spectra, SIL is the more efficient scheme by an average factor of 7.2.

We present a time-dependent density functional theory (TDDFT) approach to compute the light-matter couplings between two different manifolds of excited states relative to a common ground state in the context of 4d transition metal systems. These quantities are the necessary ingredients to solve the Kramers-Heisenberg (KH) equation for resonant inelastic X-ray scattering (RIXS) and several other types of two-photon spectroscopies. The procedure is based on the pseudo-wavefunction approach, where the solutions of a TDDFT calculation can be used to construct excited-state wavefunctions, and on the restricted energy window approach, where a manifold of excited states can be rigorously defined based on the energies of the occupied molecular orbitals involved in the excitation process. Thus, the present approach bypasses the need to solve the costly TDDFT quadratic-response equations. We illustrate the applicability of the method to 4d transition metal molecular complexes by calculating the 2p4d RIXS maps of three representative ruthenium complexes and comparing them to experimental results. The method can capture all the experimental features in all three complexes to allow the assignment of the experimental peaks, with relative energies correct to within ∼0.6 eV at the cost of two independent TDDFT calculations.

Psi4NumPy demonstrates the use of efficient computational kernels from the open-source Psi4 program through the popular NumPy library for linear algebra in Python to facilitate the rapid development of clear, understandable Python computer code for new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods, including self-consistent field (SCF), SCF response, many-body perturbation theory, coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation theory. Furthermore, several reference codes have been integrated into Jupyter notebooks, allowing background, underlying theory, and formula information to be associated with the implementation. Psi4NumPy tools and associated reference implementations can lower the barrier for future development of quantum chemistry methods. These implementations also demonstrate the power of the hybrid C++/Python programming approach employed by the Psi4 program.

The Hartree-Fock problem was recently recast as a semidefinite optimization over the space of rank-constrained two-body reduced-density matrices (RDMs) [ Phys. Rev. A 2014 , 89 , 010502(R) ]. This formulation of the problem transfers the nonconvexity of the Hartree-Fock energy functional to the rank constraint on the two-body RDM. We consider an equivalent optimization over the space of positive semidefinite one-electron RDMs (1-RDMs) that retains the nonconvexity of the Hartree-Fock energy expression. The optimized 1-RDM satisfies ensemble N-representability conditions, and ensemble spin-state conditions may be imposed as well. The spin-state conditions place additional linear and nonlinear constraints on the 1-RDM. We apply this RDM-based approach to several molecular systems and explore its spatial (point group) and spin ( Ŝ 2 and Ŝ 3 ) symmetry breaking properties. When imposing Ŝ 2 and Ŝ 3 symmetry but relaxing point group symmetry, the procedure often locates spatial-symmetry-broken solutions that are difficult to identify using standard algorithms. For example, the RDM-based approach yields a smooth, spatial-symmetry-broken potential energy curve for the well-known Be-H 2 insertion pathway. We also demonstrate numerically that, upon relaxation of Ŝ 2 and Ŝ 3 symmetry constraints, the RDM-based approach is equivalent to real-valued generalized Hartree-Fock theory.

An explicitly time-dependent (TD) approach to equation-of-motion (EOM) coupled-cluster theory with single and double excitations (CCSD) is implemented for simulating near-edge X-ray absorption fine structure in molecular systems. The TD-EOM-CCSD absorption line shape function is given by the Fourier transform of the CCSD dipole autocorrelation function. We represent this transform by its Padé approximant, which provides converged spectra in much shorter simulation times than are required by the Fourier form. The result is a powerful framework for the blackbox simulation of broadband absorption spectra. K-edge X-ray absorption spectra for carbon, nitrogen, and oxygen in several small molecules are obtained from the real part of the absorption line shape function and are compared with experiment. The computed and experimentally obtained spectra are in good agreement; the mean unsigned error in the predicted peak positions is only 1.2 eV. We also explore the spectral signatures of protonation in these molecules.

We report an explicitly time-dependent approach to the generation of linear absorption spectra for molecular systems within the framework of equation-of-motion (EOM) coupled-cluster (CC) theory. While most time-dependent CC approaches consider the perturbation and time-evolution of a CC wave function, the present work considers the time-evolution of a CC dipole function. The dipole function formalism introduces no approximations and requires the evolution of only one time-dependent quantity, either the left or right dipole function. This time-dependent framework can be used to compute linear absorption spectra for molecules with a high density of states over a broad spectral range, a case for which conventional frequency-domain computations may become impractical. We validate the approach by comparing absorption spectra for small molecules computed at EOM second-order approximate CC (CC2) and time-dependent EOM-CC2 (TD-EOM-CC2) levels of theory. TD-EOM-CC2 computations are also used to predict extreme ultraviolet absorption spectra for third-row ions that are in reasonable agreement with experiment.

We present a parametrized coupled-pair functional, optimized to describe molecular interactions (PCPF-MI). The method has the same computational cost as singles and doubles configuration interaction, is size extensive, and yields energies that are stationary with respect to variations in all of its excitation coefficients. This last property facilitates the construction of density matrices and the evaluation of one- and two-electron properties. For the S22, HSG, S66, and A24 databases of van der Waals dimers, PCPF-MI computations yield interaction energies with mean unsigned errors of 0.326, 0.149, 0.214, and 0.044 kcal mol(-1), respectively, relative to benchmark computations. PCPF-MI interaction energies consistently improve upon those obtained from several other coupled-pair methods, including the averaged coupled-pair functional (ACPF), the coupled electron-pair approximation [CEPA(n), n = 0,1,3], and averaged quadratic coupled cluster (AQCC). Optimal parameters for spin-component-scaled (SCS) variants of each of these methods are also presented. SCS-CEPA(0), SCS-CEPA(1), SCS-ACPF, and SCS-PCPF-MI all perform similarly, with average errors for the four databases of roughly 0.1 kcal mol(-1). The PCPF-MI method, without additional SCS parametrization, has an average error of 0.192 kcal mol(-1) over the four databases and, when compared to the SCS-parametrized coupled-pair methods, has the added benefit that the energy is stationary with respect to variations in all its excitation coefficients.