Reconciling TD-DFT and CASPT2 electronic structure methods for describing the photophysics of DNA

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 onπ π * 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 byn π * trapping due to the tendency of TD-DFT in QM/MM schemes with electrostatic embedding to underestimate the energy of theπ π * state leading to a wrongπ π * / n π * 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.

The mechanisms that control the preantral to early antral follicle transition and the strategies to have efficient culture systems to promote their growth in vitro

Preantral to early antral follicles transition is a complex process regulated by endocrine and paracrine factors, as well as by a precise interaction among oocyte, granulosa cells and theca cells. Understanding the mechanisms that regulate this step of folliculogenesis is important to improve in vitro culture systems, and opens new perspectives to use oocytes from preantral follicles for assisted reproductive technologies. Therefore, this review aims to discuss the endocrine and paracrine mechanisms that control granulosa cell proliferation and differentiation, formation of the antral cavity, estradiol production, atresia, and follicular fluid production during the transition from preantral to early antral follicles. The strategies that promote in vitro growth of preantral follicles are also discussed.

Correction: Computational approaches for XANES, VtC-XES, and RIXS using linear-response time-dependent density functional theory based methods

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.

Computational approaches for XANES, VtC-XES, and RIXS using linear-response time-dependent density functional theory based methods

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.

In Silico Ultrafast Nonlinear Spectroscopy Meets Experiments: The Case of Perylene Bisimide Dye

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.

Resonant Stimulated X-ray Raman Spectroscopy of Mixed-Valence Manganese Complexes

Resonant stimulated X-ray Raman spectroscopy of the bimetallic [Mn^IIIMn^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.

Short Iterative Lanczos Integration in Time-Dependent Equation-of-Motion Coupled-Cluster Theory

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.

CLIFF: A component-based, machine-learned, intermolecular force field

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.

Manipulating valence and core electronic excitations of a transition-metal complex using UV/Vis and X-ray cavities

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.

Resonant Inelastic X-ray Scattering Calculations of Transition Metal Complexes Within a Simplified Time-Dependent Density Functional Theory Framework

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.

iSPECTRON: A simulation interface for linear and nonlinear spectra with ab-initio quantum chemistry software

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).

Revealing the bonding of solvated Ru complexes with valence-to-core resonant inelastic X-ray scattering

Ru-complexes are widely studied because of their use in biological applications and photoconversion technologies. We reveal novel insights into the chemical bonding of a series of Ru(ii)- and Ru(iii)-complexes by leveraging recent advances in high-energy-resolution tender X-ray spectroscopy and theoretical calculations. We perform Ru 2p4d resonant inelastic X-ray scattering (RIXS) to probe the valence excitations in dilute solvated Ru-complexes. Combining these experiments with a newly developed theoretical approach based on time-dependent density functional theory, we assign the spectral features and quantify the metal-ligand bonding interactions. The valence-to-core RIXS features uniquely identify the metal-centered and charge transfer states and allow extracting the ligand-field splitting for all the complexes. The combined experimental and theoretical approach described here is shown to reliably characterize the ground and excited valence states of Ru complexes, and serve as a basis for future investigations of ruthenium, or other 4d metals active sites, in biological and chemical applications.

NWChem: Past, present, and future

Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.

Near-Edge X-ray Absorption Fine Structure Spectroscopy of Heteroatomic Core-Hole States as a Probe for Nearly Indistinguishable Chemical Environments

We demonstrate how the near-edge X-ray absorption fine structure (NEXAFS) spectroscopy of single and double core-hole states created by the ionization of a heteroatom can be used to probe subtle changes in intramolecular chemical environments that are nearly indistinguishable by conventional NEXAFS spectroscopy. Using prototypical organic molecules (2/3-pentanone and pentanal), we show how new spectral features emerge in the C K-edge NEXAFS spectra, when creating single and double core-holes at the oxygen heteroatom site. The effect on the lowest unoccupied molecular orbitals is analyzed by studying the double-core-hole-induced ultrafast valence electron dynamics of the three molecules. The predicted changes from our simulations should be observable with state-of-the-art experiments at X-ray free-electron lasers.

Elucidation of the photoaquation reaction mechanism in ferrous hexacyanide using synchrotron x-rays with sub-pulse-duration sensitivity

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.

Spatial and Spin Symmetry Breaking in Semidefinite-Programming-Based Hartree-Fock Theory

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 ( Ŝ² and Ŝ₃) symmetry breaking properties. When imposing Ŝ² and Ŝ₃ 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-H₂ insertion pathway. We also demonstrate numerically that, upon relaxation of Ŝ² and Ŝ₃ symmetry constraints, the RDM-based approach is equivalent to real-valued generalized Hartree-Fock theory.

Modeling molecule-plasmon interactions using quantized radiation fields within time-dependent electronic structure theory

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.

A Parametrized Coupled-Pair Functional for Molecular Interactions: PCPF-MI

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.

Vero cells infected with the Lederle strain of canine distemper virus have increased Fas receptor signaling expression at 15 h post-infection

We evaluated the expression of the Fas receptor gene in Vero cells infected with the Lederle vaccine strain of canine distemper virus using RT-PCR. Vero cells were plated, and after being grown for 24 h in MEM with 5% FBS, 80-90% confluent monolayer cultures were infected with the virus. The cells were harvested at 3, 6, 9, and 15 h post-infection. Uninfected Vero cells were used as a control. Total RNA was isolated from Vero cells using 1 mL Trizol(®) LS, and RT was performed using 2 μg total RNA. Primer pairs for RT-PCR amplification for the canine distemper virus nucleocapsid gene, the S26 reference gene, and the Vero rFas gene were used to analyze expression in Vero cells. RT-PCR results revealed virus activity at 3, 6, 9, and 15 h in the virus-infected Vero cells. The S26 housekeeping gene was amplified in virus infected and control samples. However, expression of the cell death receptor Fas was detected in Vero cells only at 15 h post-infection. We suggest that the Lederle vaccine induces apoptosis by Fas receptor signaling, possibly through caspase-8 signaling rather than through mitochondrial signaling in the infected cells.