Stochastic dynamics describes processes in complex systems having the probabilistic nature. They can involve very different dynamical systems and occur on very different temporal and spatial scale. This paper discusses the concept of stochastic dynamics and its implementation in the popular program MBN Explorer. Stochastic dynamics in MBN Explorer relies on the Monte Carlo approach and permits simulations of physical, chemical, and biological processes. The paper presents the basic theoretical concepts underlying stochastic dynamics implementation and provides several examples highlighting its applicability to different systems, such as diffusing proteins seeking an anchor point on a cell membrane, deposition of nanoparticles on a surface leading to structures with fractal morphologies, and oscillations of compounds in an autocatalytic reaction. The chosen examples illustrate the diversity of applications that can be modeled by means of stochastic dynamics with MBN Explorer.

Finding global and local minima on the potential energy surface is a key task for most studies in computational chemistry. Having a set of possible conformations for chemical structures and their corresponding energies, one can judge their chemical activity, understand the mechanisms of reactions, describe the formation of metal-ligand and ligand-protein complexes, and so forth. Despite the fact that the interest in various minima search algorithms in computational chemistry arose a while ago (during the formation of this science), new methods are still emerging. These methods allow to perform conformational analysis and geometry optimization faster, more accurately, or for more specific tasks. This article presents the application of a novel global geometry optimization approach based on the Tree Parzen Estimator method. For benchmarking, a database of small organic molecule geometries in the global minimum conformation was created, as well as a software package to perform the tests.

Methods rooted in the density functional theory and in the coupled cluster ansatz were employed to investigate the cycloaddition reactions to ethylene and acetylene of 1,3-dipolar species including ozone and the derivatives issued from replacement of the central oxygen atom by the valence-isoelectronic sulfur atom, and/or of one or both terminal oxygen atoms by the isoelectronic CH2 group. This gives rise to five different 1,3-dipolar compounds, namely ozone itself (O3 ), sulfur dioxide (SO2 ), the simplest Criegee intermediate (CH2 OO), sulfine (CH2 SO), and thioformaldehyde S-methylide (CH2 SCH2 , TSM). The experimental and accurate theoretical data available for some of those molecules were employed to assess the accuracy of two last-generation composite methods employing conventional or explicitly correlated post-Hartree-Fock contributions (jun-Cheap and SVECV-f12, respectively), which were then applied to investigate the reactivity of TSM. The energy barriers provided by both composite methods are very close (the average values for the two composite methods are 7.1 and 8.3 kcal mol-1 for the addition to ethylene and acetylene, respectively) and comparable to those ruling the corresponding additions of ozone (4.0 and 7.7 kcal mol-1 , respectively). These and other evidences strongly suggest that, at least in the case of cycloadditions, the reactivity of TSM is similar to that of O3 and very different from that of SO2 .

Experimental isotherms of N2 and CO2 on carbon-based porous materials and models of the physisorption of gases on surfaces are used to obtain the pore size distribution (PSD). An accurate modelization of the physisorption of N2 and CO2 on the surface of carbon-based porous materials is important to obtain accurate N2 and CO2 storage capacities and reliable PSDs. Physisorption depends on the dispersion interactions. High precision ab initio methods, such as CCSD(T), consider accurately the dispersion interactions, but they are computationally expensive. Double hybrid, hybrid and DFT-based methods are much less expensive. In the case of graphene, there are experimental data of the adsorption of N2 and CO2 on graphite that can be used to build the Steele interaction potential of these gases on graphene. The goal is to find out hybrid and/or DFT methods that are as accurate as the CCSD(T) on benzene and as accurate as the experimental results on graphene. Calculations of the interaction energy curves of N2 and CO2 on benzene and graphene have been carried out using the CCSD(T) method and several double hybrid, hybrid, and DFT methods that consider the dispersion interactions. The energy curves on benzene have been compared to the CCSD(T) and the energy curves on graphene have been compared with the Steele energy curves. The comparisons indicate that double hybrids with dispersion corrections and ωB97 based DFT methods are accurate enough for benzene. For graphene, only the PBE-XDM functional has a good agreement with the Steele energy curves.

In the present study, we have investigated the performance of RIJCOSX DLPNO-CCSD(T)-F12 methods for a wide range of systems. Calculations with a high-accuracy option ["DefGrid3 RIJCOSX DLPNO-CCSD(T1 )-F12"] extrapolated to the complete-basis-set limit using the maug-cc-pV[D+d,T+d]Z basis sets provides fairly good agreements with the canonical CCSD(T)/CBS reference for a diverse set of thermochemical and kinetic properties [with mean absolute deviations (MADs) of ~1-2 kJ mol-1 except for atomization energies]. On the other hand, the low-cost "RIJCOSX DLPNO-CCSD(T)-F12D" option leads to substantial deviations for certain properties, notably atomization energies (MADs of up to tens of kJ mol-1 ). With the high-accuracy CBS approach, we have formulated the L-W1X method, which further includes a low-cost core-valence plus scalar-relativistic term. It shows generally good accuracy. For improved accuracies in specific cases, we advise replacing maug-cc-pV(n+d)Z with jun-cc-pV(n+d)Z for the calculation of electron affinities, and using well-constructed isodesmic-type reactions to obtain atomization energies. For medium-sized systems, DefGrid3 RIJCOSX DLPNO-CCSD(T1 )-F12 calculations are several times faster than the corresponding canonical computation; the use of the local approximations (RIJCOSX and DLPNO) leads to a better scaling than that for the canonical calculation (from ~6-7 down to ~2-4 for our test systems). Thus, the DefGrid3 RIJCOSX DLPNO-CCSD(T1 )-F12 method, and the L-W1X protocol that based on it, represent a useful means for obtaining accurate thermochemical quantities for larger systems.

The conductor-like polarizable continuum model (C-PCM), which is a low-cost solvation model, cannot treat characteristic interactions between the solvent and substructure(s) of the solute. Moreover, the error in a charged system is significant. Using machine learning, we clarified that the systematic error of the oxidation potential calculated by the G3B3/C-PCM was correlated with the molecular size of a solute. The G3B3/C-PCM overestimated the Gibbs oxidation energy by averaging 6.94 kcal/mol. According to the performance of related methods reported in previous studies, this error is mainly due to the solvation energy of the charged solute. Additionally, we succeeded in reducing the error to 2.27 kcal/mol (32%)-3.2 kcal/mol (40%) by correction based on the substructure information of the solute. To modify the C-PCM, effects that correlate with the molecular size of the solute in the charged system should be incorporated.

A linearly parameterized functional form for a Cartesian representation of molecular dipole polarizability tensor surfaces (PTS) is described. The proposed expression for the PTS is a linearization of the recently reported power series ansatz of the original Applequist model, which by construction is non-linear in parameter space. This new approach possesses (i) a unique solution to the least-squares fitting problem; (ii) a low level of the computational complexity of the resulting linear regression procedure, comparable to those of the potential energy and dipole moment surfaces; and (iii) a competitive level of accuracy compared to the non-linear PTS model. Calculations of CH4 PTS, with polarizabilities fitted to 9000 training set points with the energies up to 14,000 cm-1 show an impressive level of accuracy of the linear PTS model obtained with ~1600 parameters: ~1% versus 0.3% RMSE for the non-linear vs. linear model on a test set of 1000 configurations.

The massive increase in the amount of carbon dioxide (CO2 ) in the atmosphere has led to serious environmental problems. One of the best ways to tackle this problem is the CO2 capture and its utilization as a C1 carbon source for the production of industrially valuable chemicals. But the thermodynamic stability of the CO2 molecule poses a great challenge in its transformation. Since the last two decades, various metal-based and organic catalysts have been developed for the adsorption and activation of CO2 . Among all the catalysts the Frustrated Lewis pairs (FLPs) have been shown great potential in CO2 capture and conversion. Thus, in the present work, Intramolecular Frustrated Lewis pairs (IFLP) based on N-Heterocycles with boron group functionalization at the α-position to N has been theoretically investigated for CO2 activation. Thorough orbital analysis has been carried out to investigate the reactivity of the proposed catalytic systems. The result shows that the considered IFLPs are capable of activating CO2 with minimum energy requirements. The CO2 activation energy range between 8 and 14 kcal/mol. The non-polar solvent was found to be the suitable medium for the reaction. Also, the reversibility of the adducts formed with the IFLPs can be controlled by appropriate substitution at B atom in the IFLPs.

To improve the transition state (TS) search capability in complex chemical environments, AMK_Mountain is constructed based on the automated reaction mechanisms and kinetics (AutoMeKin) package. AMK_Mountain does not distinguish the reaction type of the TSs, which is beneficial to obtaining a more comprehensive reaction mechanism. In this study, the first step of the alkaline hydrolysis process of nitrocellulose monomer was adopted as the research object, and 730 possible initial configurations are constructed and 22 TSs pass high-level calculations. Energy difference and interaction region indicator reveal that the first step of alkaline hydrolysis is mainly the combination of nitrogen-containing functional groups at the positions α and β with hydroxide anions, followed by the formation of nitric acid and the further loss of protons to form nitrate. Overall, in combination with GFN2 -xTB and ORCA, the AMK_Mountain technique provides a reliable method for the location of the TSs in complex environments.

In the present study, the differential scattering cross-sections, depolarization ratios and Raman shifts of small molecular systems are obtained from configuration iteration wave functions of vibrational self-consistent field (VSCF) states. The transition polarizabilities were modeled using the Placzek approximation, neglecting those contributions not arising from the electric dipole mechanism. This theoretical approach is considered a good approximation for samples that absorb in the UV range if the excitation radiation falls in the visible region, as is the case of the molecules selected for the present study, namely: water, methane, and acetylene. Potential energy and electronic polarizability surfaces are calculated by the CCSD(T) and CC3 methods with aug-cc-p(C)V(T,Q,5)Z basis sets. The vibrational Hamiltonian includes the vibrational angular momentum contribution of the Watson kinetic energy operator. As expected, due to the variational nature of the VSCF and vibrational configuration interaction (VCI) methods, the Raman transition wavenumbers are substantially improved over the harmonic predictions. Surprisingly, the scattering cross-sections obtained using the harmonic approximation or the VSCF method better agrees with the experimental values than those cross-sections predicted using VCI wave functions. The more significant deviations of the VCI results from the experimental reference may be related to the significant uncertainties of the measured cross-sections. Still, it may also indicate that the VCI Raman transition moments may require a more accurate description of the electronic polarizability surface. Finally, the depolarization ratios calculated for H2 O and C2 D2 using harmonic and VCI wave functions have similar accuracy, whereas, for C2 H2 and C2 HD, the VCI results are more accurate.

Considering as test case a family of organic rod like push-pull molecules, we derived and applied density based index enabling the description and diagnostic of the electronic density evolution in real time-time dependent density functional theory (RT-TDDFT) simulations. In particular, both the charge transfer (CT) distance and a diagnostic index, the DCT and MAC RT respectively, were computed on the fly from the density distribution obtained at a given time and the reference ground state density and their mean values were compared with what obtained at Linear Response-TDDFT level. Besides giving a way of analyzing the density redistribution occurring in time, these tools allowed to show how RT-TDDFT, which is definitely a powerful method to model the evolution of the density in CT or charge separation processes, can be affected by the same artifacts known for LR-TDDFT approaches and, particularly, to those related to the use of approximate exchange correlation functionals. The analysis here performed allowed to identify and discard on fly the electronic configurations corresponding to spurious situations.