Highly emissive organic molecular crystals find applications in several areas, such as organic electronics, solar cells, and sensors. Understanding the excited-state mechanisms underlying these applications is essential for optimizing and controlling them effectively. Exciton models coupled with nonadiabatic dynamics, particularly quantum dynamics, provide crucial insights into photochemical and photophysical processes in molecular crystals. Nevertheless, there remains a lack of general tools and automated workflows to facilitate such simulations. In this paper, we present a computational strategy to investigate the photoactivated dynamics of organic molecular crystals, bridging methodologies traditionally used for molecular systems and materials science, with a particular focus on the interplay between local excitations and charge transfer (CT) processes. We have implemented an interface between the fromage and Overdia programs, enabling the construction of vibronic Hamiltonians for molecular crystals within an excited-state ONIOM(QM:QM') framework, incorporating long-range electrostatics through a RESP-based Ewald summation. Fragment-based diabatization provides a route to quantum dynamics simulations in weak-to-intermediate coupling regimes. The method was applied to the photophysics of dibenzo[g,p]chrysene (DBC) crystals using time-dependent DFT. The fromage/Overdia interface was employed to compute the couplings of local excitations and CT states for 18 unique DBC dimers in the crystal and to quantify the influence of electrostatic embedding, which was found to be modest (10-20%). Simulations on π-stacked dimers reproduced the small red shift observed experimentally from solution to crystal, attributed to electronic interactions among fixed monomers rather than crystal electrostatics. Quantum dynamics simulations revealed ultrafast population transfer from bright local excitations to CT states. This approach establishes a robust framework linking molecular and solid-state excited-state dynamics, with potential applications for studying excitations, defects, and impurities in molecular crystals.

Recently developed mixed quantum classical (MQC) approaches, which integrate classical molecular dynamics (MD) driven by accurate quantum-mechanically derived force fields with vibronic models, were employed to investigate the absorption spectra in benzene solution of coelenteramide, the chromophore of different photoproteins. Our results confirm that light absorption in this medium is only due to the protonated neutral species 2H. Neglecting the large-amplitude motions of the most flexible modes and adopting local harmonic expansions of the potential energy surfaces around the global minimum, the simulation of the spectrum is straightforward and it even leads to decent agreement with the experiment, indicating only moderate nonadiabatic effects. The complexity of the molecule becomes however evident when trying to accurately describe the effect of molecular flexibility, a key property expected to be very sensitive to the protein environment. MD sampling in fact shows that at room temperature the 2H molecule frequently assumes conformations where its excited electronic states are almost degenerate and hence strongly mix, with drastic redistribution of the oscillator strengths. We document that such mixings are triggered by both stiff vibrations and soft flexible modes and that, in such a complex scenario, methods that do not properly describe nonadiabatic interactions at the quantum vibronic level introduce artifacts in the simulation of the spectrum. We also show that such problems can be cured, at least approximately, by resorting to the parameterization of linear vibronic coupling models specific for the different configurations sampled from the classical MD. A critical discussion of all achieved results is eventually addressed, hence setting up a robust grounding for further development of MQC protocols for electronic spectroscopy of flexible dyes in the condensed phase.

In this work, we study the quantum dynamics of a photoisomerization reaction employing a two-electronic-state three-vibrational-mode model of the 2-cis-penta-2,4-dieniminium cation (cis-PSB3). In particular, we address two main issues: the challenges encountered in properly converging quantum dynamics calculations, even when a reduced-dimensionality molecular model is used; the emergence of a coherent oscillatory behavior in the formation of the trans isomer upon photoexcitation of cis-PSB3. The two issues are strictly related, since only upon reliable convergence, the simulated dynamics is able to capture the large amplitude motion associated to the torsion around the reactive bond, typical of photoisomerizations, which is due to the large amount of kinetic energy acquired by the vibrational modes after light excitation.

In this work, we study the quantum dynamics of the isomerization associated with the primary event in vision employing a model for the 2-cis-penta-2,4-dieniminium cation (cis-PSB3). We aim to demonstrate that the observed relationship between a specific wag mode and the reaction quantum yield emerges naturally from wavepacket propagation. To do so, we address two previously undetected methodological issues related to (i) establishing the appropriate level of convergence of the quantum dynamics calculations, and (ii) describing the emergence of distinct oscillatory behaviors during the formation of the cis and trans isomers in the ground state following cis-PSB3 photoexcitation. The two issues are strictly related, since only upon reliable convergence, the simulated dynamics is able to capture the large amplitude motion associated with the torsional and wag deformations in the region of the reactive bond.

We here simulate in the gas phase the population dynamics of guanine/cytosine (GC) and cytosine/guanine (CG) stacked dimers in B-DNA and A-DNA arrangement, following excitation in the lowest-energy band, and considering the four lowest-energy ππ* bright excited states, the three lowest-energy nπ* states, and the G → C charge-transfer (CT) state. We resort to a generalized Linear Vibronic Coupling (LVC) model parametrized with time-dependent density functional theory (TD-DFT) computations, exploiting a fragment-based diabatization and we run nonadiabatic quantum dynamical simulations with the multilayer version of the Multiconfigurational Time-Dependent Hartree (ML-MCTDH) approach. G → C CT results in a major decay process for GC in B-DNA but less in A-DNA arrangement, where also the population transfer to the lowest-energy excited state localized on C is an important intermonomer process. In CG arrangements, mostly intramonomeric decays take place. We simulate the dynamics of several other GC structures whose arrangement is intermediate between B-DNA and A-DNA, obtaining further insights on the effect that the sequence and, especially, the stacking geometry have on the population transfer to the G → C CT.

The Cover Feature presents three conformers of (1Z,4Z)-1,4-dipentene-3-bora-1,5-diol corresponding to local energetic minima. The most energetically stable is the conformer with two intramolecular dihydrogen bonds, DHBs, that possess the same hydride Lewis base centre (bifurcated dihydrogen bond). The opening of one of the intramolecular dihydrogen bonded rings leads to the conformer of the higher energy with the single DHB. The conformer without DHBs is characterised by the highest energy. More information can be found in the Research Article by Samira Gholami, Mohammad Aarabi, and Sławomir J. Grabowski .

Discovered over 50 years ago, bacteriorhodopsin is the first recognized and most widely studied microbial retinal protein. Serving as a light-activated proton pump, it represents the archetypal ion-pumping system. Here we compare the photochemical dynamics of bacteriorhodopsin light and dark-adapted forms with that of the first metastable photocycle intermediate known as “K”. We observe that following thermal double isomerization of retinal in the dark from bio-active all- trans 15-anti to 13- cis, 15-syn , photochemistry proceeds even faster than the ~0.5 ps decay of the former, exhibiting ballistic wave packet curve crossing to the ground state. In contrast, photoexcitation of K containing a 13- cis , 15 -anti chromophore leads to markedly multi-exponential excited state decay including much slower stages. QM/MM calculations, aimed to interpret these results, highlight the crucial role of protonation, showing that the classic quadrupole counterion model poorly reproduces spectral data and dynamics. Single protonation of ASP212 rectifies discrepancies and predicts triple ground state structural heterogeneity aligning with experimental observations. These findings prompt a reevaluation of counter ion protonation in bacteriorhodopsin and contribute to the broader understanding of its photochemical dynamics.

Two-ring intramolecular π-electron delocalization assisted dihydrogen bonds existing in (1Z,4Z)-1,4-dipentene-3-bora-1,5-diol and its symmetrically substituted derivatives have been analysed here since the MP2/6-311++G(d,p) calculations on these systems were performed. The influence of the coexistence of two intramolecular dihydrogen bonded rings in these molecular structures on properties of intramolecular dihydrogen bonds as well as on the π-electron delocalization within these rings was investigated. The comparison with corresponding structures of typical two-ring, so-called resonance-assisted, RAHB, systems was performed. The results of calculations show that such rings' coexistence leads to the weakening of dihydrogen bonds, similarly as for the typical two-ring RAHB systems. The Quantum Theory of ''Atoms in Molecules'' (QTAIM) was also applied here to get more details about the nature of dihydrogen bonds. Correlations between dihydrogen bond strength measures and other energetic, geometrical and topological parameters were also analysed. It was found that characteristics of bond critical points as well as of ring critical points are useful to estimate the strength of intramolecular dihydrogen bonds in two-ring dihydrogen bonded systems discussed here. The Natural Bond Orbital, NBO, approach parameters are also discussed as useful ones to describe properties of dihydrogen bonded systems.

The crystal structure of bis((μ2-ethynylsilyloxo)-dichloro-aluminum), BEDCA, and a few related structures are characterized by the occurrence of tetrel bonds that link molecules. Particularly, centosymmetric dimers in such structures occur that are connected by two equivalent Si···π tetrel bonds. The dimer of BEDCA and dimers of other model species that similarly are linked by two equivalent Si···π tetrel bonds are analyzed theoretically. Some of the complexes calculated here are also characterized by the occurrence of triel bonds. Thus, ωB97XD/aug-cc-pVTZ calculations are performed and these DFT results are further supported by calculations with the use of other theoretical approaches: the quantum theory of atoms in molecules, QTAIM; the natural bond orbital, NBO; the energy decomposition analysis, EDA; and the noncovalent interactions method, NCI. The results show that the tetrel bonds analyzed here are rather weak, and they are not detected by the QTAIM approach; however, they are detected by other approaches, like NBO, for example. On the other hand, the triel bonds that occur in a few complexes discussed here are very strong and possess characteristics of covalent bonds.

A quantum-classical protocol that incorporates Jahn-Teller vibronic coupling effects and cluster analysis of molecular dynamics simulations is reported, providing a tool for simulations of absorption spectra and ultrafast nonadiabatic dynamics in large molecular photosystems undergoing aggregation in solution. Employing zinc phthalocyanine dyes as target systems, we demonstrated that the proposed protocol provided fundamental information on vibronic, electronic couplings and thermal dynamical effects that mostly contribute to the absorption spectra lineshape and the fluorescence quenching processes upon dye aggregation. Decomposing the various effects arising upon dimer formation, the structure-property relations associated with their optical responses have been deciphered at atomistic resolution.

MP2/aug-cc-pVTZ calculations were performed on systems containing a proton or a lithium cation located between two pi-electron systems or between pi-electron and sigma-electron units. The proton or the lithium cation attached to the acetylene or its derivative may be treated as the Lewis acid unit while the remaining part of the complex, the pi-electron species or the dihydrogen, act as the Lewis base through their pi-electrons or sigma-electrons, respectively. The complexes analysed here are linked by the pi center dot center dot center dot H+/Li+center dot center dot center dot pi and pi center dot center dot center dot H+/Li+center dot center dot center dot sigma interactions. It is discussed whether these interactions are classified as hydrogen and lithium bonds. Therefore, different definitions of the latter interactions are presented. The Electron Localization Function (ELF) and the Natural Bond Orbital (NBO) approaches were applied to analyse the above-mentioned complexes. The unique properties of interactions with the proton and with the lithium cation that occur in complexes analysed here are described.

In the present study, we have employed a high-level density functional theory (DFT) model to investigate both implicit and explicit effects of solvation (i.e., the bulk solvation effect as well as microhydration) in addition to the effect of distal Histidine on the binding of CO to Ferrous and Ferric-Heme. It has been predicted that the distal N-methylimidazole (MI) in addition to microsolvation, as a simple mode of environment, leads to a significant stabilization on the binding of CO to Heme-Fe-II (by similar to 4 kcal mol(-1)). This is while no clear alteration has been predicted for the implicit solvation model. For the Ferric heme, and in contrast to the Ferrous system, strong destabilization from the environment has been predicted for binding CO to the Ferric heme analog. (C) 2021 Elsevier B.V. All rights reserved.

MP2/aug-cc-pVTZ calculations were carried out on complexes wherein the proton or the lithium cation is located between π-electron systems, or between π-electron and σ-electron units. The acetylene or its fluorine and lithium derivatives act as the Lewis base π-electron species similarly to molecular hydrogen, which acts as the electron donor via its σ-electrons. These complexes may be classified as linked by π-H∙∙∙π/σ hydrogen bonds and π-Li∙∙∙π/σ lithium bonds. The properties of these interactions are discussed, and particularly the Lewis acid units are analyzed, because multi-center π-H or π-Li covalent bonds may occur in these systems. Various theoretical approaches were applied here to analyze the above-mentioned interactions—the Quantum Theory of Atoms in Molecules (QTAIM), the Symmetry-Adapted Perturbation Theory (SAPT) and the Non-Covalent Interaction (NCI) method.

The ωB97-XD/6-311++G(d,p) calculations were carried out on dimers and monomers of salicylic acid and salicylamide as well as on their thiol counterparts; different conformations of these species were considered. The searches through the Cambridge Structural Database were performed to find related structures; thus the analysis of results of these searches is presented. Various approaches were applied to analyze inter- and intramolecular hydrogen bonds occurring in the above-mentioned species: natural bond orbital (NBO) method, symmetry-adapted perturbation theory (SAPT) approach, the quantum theory of atoms in molecules (QTAIM), and the electron localization function (ELF) method. The results of calculations indicate a slight mutual influence of inter- and intramolecular hydrogen bonds. However, the frequent occurrence of both interactions in crystal structures indicates the importance of their coexistence. The occurrence of intramolecular chalcogen bonds for trans conformations of species analyzed is also discussed.

omega B97-XD/aug-cc-pVTZ calculations were performed on dimers of selected thiocarboxylic acids and on analogous carboxylic acids. The sample of calculated thiocarboxylic acids is an extension of the Cambridge Structural Database search that contains only a few such structures. The Natural Bond Orbital (NBO) method, Symmetry-Adapted Perturbation Theory (SAPT) approach, Non-Covalent Interaction (NCI) method and Quantum Theory of Atoms in Molecules (QTAIM) were applied additionally to analyse interactions in dimers of thiocarboxylic and carboxylic acids. The insights into crystal structures as well as into results of calculations show that the formation of S-H horizontal ellipsis O hydrogen bonds between molecules of thiocarboxylic acids is steered by the same mechanisms as the formation of much stronger O-H horizontal ellipsis O hydrogen bonds in carboxylic acids. The intramolecular O-H horizontal ellipsis O and C-H horizontal ellipsis S hydrogen bonds occurring in few considered structures are also analysed.

The interaction of a water molecule with ferric heme-iron protoporphyrin ([PP FeIII]+) has been investigated in the gas phase in an ion trap and studied theoretically by density functional theory. It is found that the interaction of water with ferric heme leads to a stable [PP-FeIII-H2O]+ complex in the intermediate spin state (S = 3/2), in the same state as its unligated [PP-FeIII]+ homologue, without spin crossing during water attachment. Using the Van't Hoff equation, the reaction enthalpy for the formation of a Fe-OH2 bond has been determined for [PP-FeIII-H2O]+ and [PP-FeIII-(H2O)2]+. The corrected binding energy for a single Fe-H2O bond is -12.2 ± 0.6 kcal mol-1, while DFT calculations at the OPBE level yield -11.7 kcal mol-1. The binding energy of the second ligation yielding a six coordinated FeIII atom is decreased with a bond energy of -9 ± 0.9 kcal mol-1, well reproduced by calculations as -7.1 kcal mol-1. However, calculations reveal features of a weaker bond type, such as a rather long Fe-O bond with 2.28 Å for the [PP-FeIII-H2O]+ complex and the absence of a spin change by complexation. Thus despite a strong bond with H2O, the FeIII atom does not show, through theoretical modelling, a strong acceptor character in its half filled 3dz2 orbital. It is also observed that the binding properties of H2O to hemes seem strikingly specific to ferric heme and we have shown, experimentally and theoretically, that the affinity of H2O for protonated heme [H PP-Fe]+, an intermediate between FeIII and FeII, is strongly reduced compared to that for ferric heme.

The binding energy of CO, O2 and NO to isolated ferric heme, [FeIIIP]+, was studied in the presence and absence of a σ donor (N-methylimidazole and histidine) as the trans axial ligand. This study combines the experimental determination of binding enthalpies by equilibrium measurements in a low temperature ion trap using the van't Hoff equation and high level DFT calculations. It was found that the presence of N-methylimidazole as the axial ligand on the [FeIIIP]+ porphyrin dramatically weakens the [FeIIIP-ligand]+ bond with an up to sevenfold decrease in binding energy owing to the σ donation by N-methylimidazole to the FeIII(3d) orbitals. This trans σ donor effect is characteristic of ligation to iron in hemes in both ferrous and ferric redox forms; however, to date, this has not been observed for ferric heme.

Two-ring intramolecular resonance-assisted hydrogen bonds (RAHBs) existing in 1,5-dihydroxy-1,4-diene-3-pentanone and some its symmetrically substituted derivatives have been studied at the MP2/6-311++G∗∗ level of theory. The influence of the coexistence of two intramolecular hydrogen bonded rings in these molecular systems on the structure, intramolecular hydrogen bonding and π-electron delocalization was investigated. The results of calculations show that such coexistence increases the π-electron delocalization but it leads also to the weakening of hydrogen bonding. The Quantum Theory of ‘‘Atoms in Molecules’’ (QTAIM) of Bader was also applied here to get more details about the nature of hydrogen bonds. Correlations between the hydrogen bond strength and different parameters were also analyzed. It was found that topological characteristics of critical points (bond critical points and ring critical points) are also useful to estimate the strength of intramolecular hydrogen bonds in two-ring RAHB systems.