Extending the MST Model to Large Biomolecular Systems: Parametrization of the ddCOSMO-MST Continuum Solvation Model.

Continuum solvation models such as the polarizable continuum model and the conductor-like screening model are widely used in quantum chemistry, but their application to large biosystems is hampered by their computational cost. Here, we report the parametrization of the Miertus-Scrocco-Tomasi (MST) model for the prediction of hydration free energies of neutral and ionic molecules based on the domain decomposition formulation of COSMO (ddCOSMO), which allows a drastic reduction of the computational cost by several orders of magnitude. We also introduce several novelties in MST, like a new definition of atom types based on hybridization and an automatic setup of the cavity for charged regions.

A Polarizable CASSCF/MM Approach Using the Interface Between OpenMMPol Library and Cfour.

We present a polarizable embedding quantum mechanics/molecular mechanics (QM/MM) framework for ground- and excited-state Complete Active Space Self-Consistent Field (CASSCF) calculations on molecules within complex environments, such as biological systems. These environments are modeled using the AMOEBA polarizable force field. This approach is implemented by integrating the OpenMMPol library with the CFour quantum chemistry software suite.

Cholesky Decomposition in Spin-Free Dirac-Coulomb Coupled-Cluster Calculations.

We present an implementation for the use of Cholesky decomposition (CD) of two-electron integrals within the spin-free Dirac-Coulomb (SFDC) scheme that enables to perform high-accuracy coupled-cluster (CC) calculations at costs almost comparable to those of their nonrelativistic counterparts. While for nonrelativistic CC calculations, atomic-orbital (AO)-based algorithms, due to their significantly reduced disk-space requirements, are the key to efficient large-scale computations, such algorithms are less advantageous in the SFDC case due to their increased computational cost in that case. Here, molecular-orbital (MO)-based algorithms exploiting the CD of the two-electron integrals allow us to reduce disk-space requirements and lead to computational cost in the CC step that is more or less the same as in the nonrelativistic case.

Reference CC3 Excitation Energies for Organic Chromophores: Benchmarking TD-DFT, BSE/, and Wave Function Methods.

To expand the QUEST database of highly accurate vertical transition energies, we consider a series of large organic chromogens ubiquitous in dye chemistry, such as anthraquinone, azobenzene, BODIPY, and naphthalimide. We compute, at the CC3 level of theory, the singlet and triplet vertical transition energies associated with the low-lying excited states. This leads to a collection of more than 120 new highly accurate excitation energies.

Importance of Polarizable Embedding for Computing Optical Rotation: The Case of Camphor in Ethanol.

Solvation effects on optical rotation are notoriously challenging to model for computational chemistry, as the specific rotatory power of a molecule can vary wildly going from apolar to polar or even protic solvents. To address such a problem, we present a polarizable embedding implementation of an electric and magnetic response property based on density functional theory and the AMOEBA polarizable force field, and apply such an implementation to the study of the optical rotation of camphor in ethanol. By comparing a continuum model, and electrostatic and polarizable embedding QM/MM models, we observe that accounting for the environment's polarization gives rise to not only a different quantitative prediction, in very good agreement with experiments for the QM/AMOEBA model, but also to a very different qualitative picture, with the values of the optical rotation computed along a classical molecular dynamics trajectory with electrostatic embedding being statistically uncorrelated to the ones obtained with the polarizable description.

Geometric Optimization of Restricted-Open and Complete Active Space Self-Consistent Field Wave Functions.

We explore Riemannian optimization methods for Restricted-Open-shell Hartree-Fock (ROHF) and Complete Active Space Self-Consistent Field (CASSCF) methods. After showing that ROHF and CASSCF can be reformulated as optimization problems on so-called "flag manifolds", we review Riemannian optimization basics and their application to these specific problems. We compare these methods to traditional ones and find robust convergence properties without fine-tuning of numerical parameters.

Transition Metal-Driven Selectivity in Direct C-H Arylation of Imidazo[2,1-b]Thiazole.

A selective direct arylation of the different Csp2-H bonds of imidazo[2,1-b]thiazole with (hetero) aryl halides can be achieved simply by switching from a palladium catalyst system to the use of stoichiometric amounts of copper. The observed selectivity, also rationalized by DFT calculations, can be explained by a change in the mechanistic pathways between electrophilic palladation and base-promoted C-H metalation.

MBE-CASSCF Approach for the Accurate Treatment of Large Active Spaces.

We present a novel implementation of the complete active space self-consistent field (CASSCF) method that makes use of the many-body expanded full configuration interaction (MBE-FCI) method to incrementally approximate electronic structures within large active spaces. On the basis of a hybrid first-order algorithm employing both Super-CI and quasi-Newton strategies for the optimization of molecular orbitals, we demonstrate both computational efficacy and high accuracy of the resulting MBE-CASSCF method. We assess the performance of our implementation on a set of established numerical tests before applying MBE-CASSCF in the investigation of the triplet-quintet spin gap of iron(II) porphyrin with active spaces as large as 50 electrons in 50 orbitals.

Step by step technique of Stentless Florence Robotic Intracorporeal Neobladder (FloRIN), does the ureteral management influence functional outcomes?

Introduction: Benefits and harms of avoid the sent placement during IntraCorporeal Neobladder configuration are still debated. Our objective was to describe the step-by-step technique of Florence intracorporeal neobladder (FloRIN) configuration performed with stentless procedure focusing on perioperative and mid-term functional outcomes.

Materials And Methods: In this single institution prospective randomized 1:1 series all consecutive patients underwent Robot-Assisted Radical Cystectomy (RARC) and FloRIN reconfiguration from January 2021 to March 2021 were enrolled.

Changing aromatic properties through stacking: the face-to-face dimer of Ni(II) bis(pentafluorophenyl)norcorrole.

Nuclear magnetic resonance (NMR) shielding constants have been calculated for Ni(II) bis(pentafluorophenyl)norcorrole and its face-to-face stacked dimer at the Hartree-Fock (HF), second-order Møller-Plesset perturbation theory (MP2), complete-active-space self-consistent-field (CASSCF) levels as well as at density functional theory (DFT) levels using several functionals. The calculated H NMR shielding constants agree rather well with the experimental ones. The shielding constants of N and Ni calculated at DFT, HF, and MP2 levels differ from those obtained in the CASSCF calculations due to near-degeneracy effects at the Ni atom.

The OpenMMPol library for polarizable QM/MM calculations of properties and dynamics.

We present a new library designed to provide a simple and straightforward way to implement QM/AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) and other polarizable QM/MM (Molecular Mechanics) methods based on induced point dipoles. The library, herein referred to as OpenMMPol, is free and open-sourced and is engineered to address the increasing demand for accurate and efficient QM/MM simulations. OpenMMPol is specifically designed to allow polarizable QM/MM calculations of ground state energies and gradients and excitation properties.

Breaking the Rules: On the Relative Stability of Some Methylencyclopropane and Methylcyclopropene Derivatives.

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.

Unraveling Water Solvation Effects with Quantum Mechanics/Molecular Mechanics Semiclassical Vibrational Spectroscopy: The Case of Thymidine.

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.

Cholesky Decomposition-Based Implementation of Relativistic Two-Component Coupled-Cluster Methods for Medium-Sized Molecules.

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.

A novel coupled-cluster singles and doubles implementation that combines the exploitation of point-group symmetry and Cholesky decomposition of the two-electron integrals.

A novel implementation of the coupled-cluster singles and doubles (CCSD) approach is presented that is specifically tailored for the treatment of large symmetric systems. It fully exploits Abelian point-group symmetry and the use of the Cholesky decomposition of the two-electron repulsion integrals. In accordance with modern CCSD algorithms, we propose two alternative strategies for the computation of the so-called particle-particle ladder term.

Linear Response Equations Revisited: A Simple and Efficient Iterative Algorithm.

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.

Heptazine, Cyclazine, and Related Compounds: Chemically-Accurate Estimates of the Inverted Singlet-Triplet Gap.

Molecules that violate Hund's rule and exhibit an inverted gap between the lowest singlet S and triplet T excited states have attracted considerable attention due to their potential applications in optoelectronics. Among these molecules, the triangular-shaped heptazine, and its derivatives, have been in the limelight. However, conflicting reports have arisen regarding the relative energies of S and T.

Assessing Implicit and Explicit Polarizable Solvation Models for Nuclear-Electronic Orbital Systems: Quantum Proton Polarization and Solvation Energetics.

Accurate simulations of many chemical processes require the inclusion of both nuclear quantum effects and a solvent environment. The nuclear-electronic orbital (NEO) approach, which treats electrons and select nuclei quantum mechanically on the same level, combined with a polarizable continuum model (PCM) for the solvent environment, addresses this challenge in a computationally practical manner. In this work, the NEO-PCM approach is extended beyond the IEF-PCM (integral equation formalism PCM) and C-PCM (conductor PCM) approaches to the SS(V)PE (surface and simulation of volume polarization for electrostatics) and ddCOSMO (domain decomposed conductor-like screening model) approaches.

A Quasi Time-Reversible Scheme Based on Density Matrix Extrapolation on the Grassmann Manifold for Born-Oppenheimer Molecular Dynamics.

This Letter introduces the so-called Quasi Time-Reversible scheme based on Grassmann extrapolation (QTR G-Ext) of density matrices for an accurate calculation of initial guesses in Born-Oppenheimer Molecular Dynamics (BOMD) simulations. The method shows excellent results on four large molecular systems that are representative of real-life production applications, ranging from 21 to 94 atoms simulated with Kohn-Sham (KS) density functional theory surrounded with a classical environment with 6k to 16k atoms. Namely, it clearly reduces the number of self-consistent field iterations while at the same time achieving energy-conserving simulations, resulting in a considerable speed-up of BOMD simulations even when tight convergence of the KS equations is required.

Fast Method for Excited-State Dynamics in Complex Systems and Its Application to the Photoactivation of a Blue Light Using Flavin Photoreceptor.

The excited-state dynamics of molecules embedded in complex (bio)matrices is still a challenging goal for quantum chemical models. Hybrid QM/MM models have proven to be an effective strategy, but an optimal combination of accuracy and computational cost still has to be found. Here, we present a method which combines the accuracy of a polarizable embedding QM/MM approach with the computational efficiency of an excited-state self-consistent field method.

Coarse-Graining ddCOSMO through an Interface between Tinker and the ddX Library.

The domain decomposition conductor-like screening model is an efficient way to compute the solvation energy of solutes within a polarizable continuum medium in a linear scaling computational time. Despite its efficiency, the application to very large systems is still challenging. A possibility to further accelerate the algorithm is resorting to coarse-graining strategies.

A Unique and Stable Polyproline I Helix Sorted out from Conformational Equilibrium by Solvent Polarity.

Polyproline I helical structures are often considered as the hidden face of their most famous geminal sibling, Polyproline II, as PPI is generally spotted only within a conformational equilibrium. We designed and synthesized a stable Polyproline I structure exploiting the striking tendency of ()-indoline-2-carboxylic acid to drive the peptide bond conformation toward the amide isomer, when dissolved in polar solvents. The cooperative effect of only four amino acidic units is sufficient to form a preferential structure in solution.

Trajectory Surface Hopping for a Polarizable Embedding QM/MM Formulation.

We present the implementation of trajectory surface-hopping nonadiabatic dynamics for a polarizable embedding QM/MM formulation. Time-dependent density functional theory was used at the quantum mechanical level of theory, whereas the molecular mechanics description involved the polarizable AMOEBA force field. This implementation has been obtained by integrating the surface-hopping program Newton-X NS with an interface between the Gaussian 16 and the Tinker suites of codes to calculate QM/AMOEBA energies and forces.

Computation of NMR shieldings at the CASSCF level using gauge-including atomic orbitals and Cholesky decomposition.

We present an implementation of coupled-perturbed complete active space self-consistent field (CP-CASSCF) theory for the computation of nuclear magnetic resonance chemical shifts using gauge-including atomic orbitals and Cholesky decomposed two-electron integrals. The CP-CASSCF equations are solved using a direct algorithm where the magnetic Hessian matrix-vector product is expressed in terms of one-index transformed quantities. Numerical tests on systems with up to about 1300 basis functions provide information regarding both the computational efficiency and limitations of our implementation.

A Mountaineering Strategy to Excited States: Revising Reference Values with EOM-CC4.

In the framework of the computational determination of highly accurate vertical excitation energies in small organic compounds, we explore the possibilities offered by the equation-of-motion formalism relying on the approximate fourth-order coupled-cluster (CC) method, CC4. We demonstrate, using an extended set of more than 200 reference values based on CC including up to quadruples excitations (CCSDTQ), that CC4 is an excellent approximation to CCSDTQ for excited states with a dominant contribution from single excitations with an average deviation as small as 0.003 eV.