MLatom 3: A Platform for Machine Learning-Enhanced Computational Chemistry Simulations and Workflows.

Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program package designed to leverage the power of ML to enhance typical computational chemistry simulations and to create complex workflows.

Recommendations for Velocity Adjustment in Surface Hopping.

This study investigates velocity adjustment directions after hopping in surface hopping dynamics. Using fulvene and a protonated Schiff base (PSB4) as case studies, we investigate the population decay and reaction yields of different sets of dynamics with the velocity adjusted in either the nonadiabatic coupling, gradient difference, or momentum directions. For the latter, in addition to the conventional algorithm, we investigated the performance of a reduced kinetic energy reservoir approach recently proposed.

A multi-descriptor analysis of substituent effects on the structure and aromaticity of benzene derivatives: π-Conjugation versus charge effects.

This work provides a detailed multi-component analysis of aromaticity in monosubstituted (X = CH, C , C , NH, NH, NH, OH, O, and O) and para-homodisubstituted (X = CH, CH, NH, NH, OH, and O) benzene derivatives. We investigate the effects of substituents using single-reference (B3LYP/DFT) and multireference (CASSCF/MRCI) methods, focusing on structural (HOMA), vibrational (AI(vib)), topological (ELF), electronic (MCI), magnetic (NICS), and stability (S-T splitting) properties. The findings reveal that appropriate π-electron-donating and π-electron-accepting substituents with suitable size and symmetry can interact with the π-system of the ring, significantly influencing π-electron delocalization.

Temperature effects on the internal conversion of excited adenine and adenosine.

This work aims to elucidate the dependence of the excited-state lifetime of adenine and adenosine on temperature. So far, it has been experimentally shown that while adenine's lifetime is unaffected by temperature, adenosine's lifetime strongly depends on it. However, the non-Arrhenius temperature dependence has posed a challenge in explaining this phenomenon.

WS22 database, Wigner Sampling and geometry interpolation for configurationally diverse molecular datasets.

Multidimensional surfaces of quantum chemical properties, such as potential energies and dipole moments, are common targets for machine learning, requiring the development of robust and diverse databases extensively exploring molecular configurational spaces. Here we composed the WS22 database covering several quantum mechanical (QM) properties (including potential energies, forces, dipole moments, polarizabilities, HOMO, and LUMO energies) for ten flexible organic molecules of increasing complexity and with up to 22 atoms. This database consists of 1.

Structural stability and the low-lying singlet and triplet states of BN-n-acenes, n = 1-7.

The chemical stability and the low-lying singlet and triplet excited states of BN-n-acenes (n = 1-7) were studied using single reference and multireference methodologies. From the calculations, descriptors such as the singlet-triplet splitting, the natural orbital (NO) occupations and aromaticity indexes are used to provide structural and energetic analysis. The boron and nitrogen atoms form an isoelectronic pair of two carbon atoms, which was used for the complete substitution of these units in the acene series.

Newton-X Platform: New Software Developments for Surface Hopping and Nuclear Ensembles.

Newton-X is an open-source computational platform to perform nonadiabatic molecular dynamics based on surface hopping and spectrum simulations using the nuclear ensemble approach. Both are among the most common methodologies in computational chemistry for photophysical and photochemical investigations. This paper describes the main features of these methods and how they are implemented in Newton-X.

Correction: Modeling the heating and cooling of a chromophore after photoexcitation.

Correction for 'Modeling the heating and cooling of a chromophore after photoexcitation' by Elizete Ventura , , 2022, , 9403-9410, https://doi.org/10.1039/D2CP00686C.

Pre-Dewar structure modulates protonated azaindole photodynamics.

Recent experimental work revealed that the lifetime of the S state of protonated 7-azaindole is about ten times longer than that of protonated 6-azaindole. We simulated the nonradiative decay pathways of these molecules using trajectory surface hopping dynamics after photoexcitation into S to elucidate the reason for this difference. Both isomers mainly follow a common ππ* relaxation pathway involving multiple state crossings while coming down from S to S in the subpicosecond time scale.

Modeling the heating and cooling of a chromophore after photoexcitation.

The heating of a chromophore due to internal conversion and its cooling down due to energy dissipation to the solvent are crucial phenomena to characterize molecular photoprocesses. In this work, we simulated the nonadiabatic dynamics of cytosine, a prototypical chromophore undergoing ultrafast internal conversion, in three solvents-argon matrix, benzene, and water-spanning an extensive range of interactions. We implemented an analytical energy-transfer model to analyze these data and extract heating and cooling times.

Simulations of molecular photodynamics in long timescales.

Nonadiabatic dynamics simulations in the long timescale (much longer than 10 ps) are the next challenge in computational photochemistry. This paper delimits the scope of what we expect from methods to run such simulations: they should work in full nuclear dimensionality, be general enough to tackle any type of molecule and not require unrealistic computational resources. We examine the main methodological challenges we should venture to advance the field, including the computational costs of the electronic structure calculations, stability of the integration methods, accuracy of the nonadiabatic dynamics algorithms and software optimization.

Fewest switches surface hopping with Baeck-An couplings.

In the Baeck-An (BA) approximation, first-order nonadiabatic coupling vectors are given in terms of adiabatic energy gaps and the second derivative of the gaps with respect to the coupling coordinate. In this paper, a time-dependent (TD) BA approximation is derived, where the couplings are computed from the energy gaps and their second time-derivatives. TD-BA couplings can be directly used in fewest switches surface hopping, enabling nonadiabatic dynamics with any electronic structure methods able to provide excitation energies and energy gradients.

Choosing the right molecular machine learning potential.

Quantum-chemistry simulations based on potential energy surfaces of molecules provide invaluable insight into the physicochemical processes at the atomistic level and yield such important observables as reaction rates and spectra. Machine learning potentials promise to significantly reduce the computational cost and hence enable otherwise unfeasible simulations. However, the surging number of such potentials begs the question of which one to choose or whether we still need to develop yet another one.

MLatom 2: An Integrative Platform for Atomistic Machine Learning.

Atomistic machine learning (AML) simulations are used in chemistry at an ever-increasing pace. A large number of AML models has been developed, but their implementations are scattered among different packages, each with its own conventions for input and output. Thus, here we give an overview of our MLatom 2 software package, which provides an integrative platform for a wide variety of AML simulations by implementing from scratch and interfacing existing software for a range of state-of-the-art models.

Interplay between Aromaticity and Radicaloid Character in Nitrogen-Doped Oligoacenes Revealed by High-Level Multireference Methods.

Aromaticity is a multivariable concept in organic chemistry that plays a central role for understanding the structure, stability, and reactivity of polycyclic aromatic hydrocarbons (PAHs). Several types of PAHs are characterized as singlet biradicaloid species and their chemical stability is intimately linked to the degree of aromatic character. In this study, theoretically designed routes to tune the biradical character (and thereby its chemical stability) of nitrogen-substituted octacenes have been investigated on the basis of the high-level multireference averaged quadratic coupled-cluster MR-AQCC method necessary for the appropriate description of polyradicaloid systems.

Tuning the Biradicaloid Nature of Polycyclic Aromatic Hydrocarbons: The Effect of Graphitic Nitrogen Doping in Zethrenes.

Zethrenes are interesting polycyclic aromatic hydrocarbons (PAHs), which possess unique optoelectronic and magnetic properties because of their singlet open-shell biradicaloid character, making them promising candidates for application in organic electronics. Tuning their properties is a key task in order to develop efficient compounds for practical use by balancing the desired biradicaloid character against its chemical instability. In this work, high-level theoretical multireference methods appropriate for the correct description of polyradicaloid systems are used to develop rules for doping of zethrenes by means of nitrogen taking heptazethrene (HZ) as a benchmark example.

On the importance of non-covalent interactions for porous membranes: unraveling the role of pore size.

Membrane-based gas separation technology is of crucial importance in the current economy and nanoporous graphene, given its single-atomic layer, is an essential building-block material to achieve efficiency towards permeability and selectivity for such processes. Classically, pore size is the main feature that governs the diffusion energy barrier. Its nature, nevertheless, is also affected by other non-negligible physical mechanisms not yet discussed.

Singlet L and L Bands for N-Acenes (N = 2-7): A CASSCF/CASPT2 Study.

In this work CASPT2 calculations of polyacenes (from naphthalene to heptacene) were performed to find a methodology suitable for calculations of the absorption spectra, in particular of the L (B state) and L (B state) bands, of more extended systems. The effect of the extension of the active space and of freezing σ orbitals was investigated. The MCSCF excitation energy of the B state is not sensitive to the size of the active space used.

How to efficiently tune the biradicaloid nature of acenes by chemical doping with boron and nitrogen.

Acenes are fascinating polyaromatic compounds that combine impressive semiconductor properties with an open-shell character by varying their molecular sizes. However, the increasing chemical instabilities related to their biradicaloid structures pose a great challenge for synthetic chemistry. Modifying the π-bond topology through chemical doping allows modulation of the electronic properties of graphene-related materials.