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Intermolecular interactions modulate the electro-optical properties of molecular materials and the nature of low-lying exciton states. Molecular materials composed by oligoacenes are extensively investigated for their semiconducting and optoelectronic properties. Here, we analyze the exciton states derived from time-dependent density functional theory (TDDFT) calculations for two oligoacene model aggregates: naphthalene and anthracene dimers. To unravel the role of inter-molecular interactions, a set of diabatic states is selected, chosen to coincide with local (LE) and charge-transfer (CT) excitations within a restricted orbital space including two occupied and two unoccupied orbitals for each molecular monomer. We study energy profiles and disentangle inter-state couplings to disclose the (CT) character of singlet and triplet exciton states and assess the influence of inter-molecular orientation by displacing one molecule with respect to the other along the longitudinal translation coordinate. The analysis shows that (CT) contributions are relevant, although comparably less effective for triplet excitons, and induce a non-negligible mixed character to the low-lying exciton states for eclipsed monomers and for small translational displacements. Such (CT) contributions govern the La/Lb state inversion occurring for the low-lying singlet exciton states of naphthalene dimer and contribute to the switch from H- to J-aggregate type of the strongly allowed Bb transition of both oligoacene aggregates. [ABSTRACT FROM AUTHOR]

We study the ultrafast photoactivated dynamics of the hydrogen bonded dimer Guanine‐Cytosine in chloroform solution, focusing on the population of the Guanine→Cytosine charge transfer state (GC‐CT), an important elementary process for the photophysics and photochemistry of nucleic acids. We integrate a quantum dynamics propagation scheme, based on a linear vibronic model parameterized through time dependent density functional theory calculations, with four different solvation models, either implicit or explicit. On average, after 50 fs, 30∼40 % of the bright excited state population has been transferred to GC‐CT. This process is thus fast and effective, especially when transferring from the Guanine bright excited states, in line with the available experimental studies. Independent of the adopted solvation model, the population of GC‐CT is however disfavoured in solution with respect to the gas phase. We show that dynamical solvation effects are responsible for this puzzling result and assess the different chemical‐physical effects modulating the population of CT states on the ultrafast time‐scale. We also propose some simple analyses to predict how solvent can affect the population transfer between bright and CT states, showing that the effect of the solute/solvent electrostatic interactions on the energy of the CT state can provide a rather reliable indication of its possible population. [ABSTRACT FROM AUTHOR]

It has previously been shown that human very small embryonic-like (hVSEL) stem cell proliferation occurs rapidly when hVSEL stem cells in platelet rich plasma (PRP) are exposed to Strachan Ovokaitys Node Generator (SONG)-modulated laser light. The surface antigens Oct 3/4, SSEA4 and CXCR4 in the lineage negative (Lin-) compartment were assessed using flow cytometry. Of these three markers, it is known that CXCR4 may be blocked from binding to flow cytometry antibodies by its antagonist ligand, the Endogenous Peptide Inhibitor of CXCR4 (EPI-X4). In this theoretical manuscript, we focus on possible novel methods of unblocking CXCR4 by SONG-modulated laser light to make it readily available for binding by flow cytometry antibodies. We propose that the SONG-modulated red laser penetrates the minor pocket of CXCR4 and thus disrupts the hydrogen bonds and salt bridges binding CXCR4 to EPI-X4. A quantum-mechanical description of the laser interaction with the hydrogen atoms of the hydrogen bonds and salt bridges provides an atom-level illustration of the forces producing stem cell proliferation effects in vitro. This is a novel description of the mechanism of action of SONG-modulated laser light on stem cell antigens at the quantum level which may have wide implications in stem cell biology and regenerative medicine.

We present PyCDFT, a Python package to compute diabatic states using constrained density functional theory (CDFT). PyCDFT provides an object‐oriented, customizable implementation of CDFT, and allows for both single‐point self‐consistent‐field calculations and geometry optimizations. PyCDFT is designed to interface with existing density functional theory (DFT) codes to perform CDFT calculations where constraint potentials are added to the Kohn–Sham Hamiltonian. Here, we demonstrate the use of PyCDFT by performing calculations with a massively parallel first‐principles molecular dynamics code, Qbox, and we benchmark its accuracy by computing the electronic coupling between diabatic states for a set of organic molecules. We show that PyCDFT yields results in agreement with existing implementations and is a robust and flexible package for performing CDFT calculations. The program is available at https://dx.doi.org/10.5281/zenodo.3821097. [ABSTRACT FROM AUTHOR]

We present a diabatization method of general applicability, based on the localization of molecular orbitals on user specified groups of atoms. The method yields orthogonal molecular orbitals similar to the canonical ones for the isolated atom groups, that are the basis to build reference spin‐adapted configurations representing localized or charge transfer excitations. An orthogonal transformation from the adiabatic to the quasi‐diabatic basis is defined by requiring maximum overlap with the diabatic references. We present the diabatization algorithm as implemented in the framework of semiempirical configuration interaction based on floating occupation molecular orbitals (FOMO−CI), but the same transformation can also be applied to ab initio wavefunctions, obtained for instance with state‐average CASSCF. The diabatic representation so obtained and the associated hamiltonian matrix are particularly suited to assess quantitatively the interactions that account for charge and energy transfer transitions, and to analyze the results of nonadiabatic dynamics simulations involving such phenomena. [ABSTRACT FROM AUTHOR]

Electronic coupling matrix elements are important to the theoretical description of electron transfer processes. However, they are notoriously difficult to obtain accurately from time-dependent density functional theory (TDDFT). Here, we use the HAB11 benchmark dataset of coupling matrix elements to assess whether TDDFT using optimally tuned range-separated hybrid functionals, already known to be successful for the description of charge transfer excitation energies, also allows for an improved accuracy in the prediction of coupling matrix elements. We find that this approach outperforms all previous TDDFT calculations, based on semi-local, hybrid or non-tuned range-separated hybrid functionals, with a remaining average deviation as low as ∼12%. We discuss potential sources for the remaining error. [ABSTRACT FROM AUTHOR]

The multi-state density functional theory (MSDFT) provides a convenient way to estimate electronic coupling of charge transfer processes based on a diabatic representation. Its performance has been benchmarked against the HAB11 database with a mean unsigned error (MUE) of 17 meV between MSDFT and ab initio methods. The small difference may be attributed to different representations, diabatic from MSDFT and adiabatic from ab initio calculations. In this discussion, we conclude that MSDFT provides a general and efficient way to estimate the electronic coupling for charge-transfer rate calculations based on the Marcus-Hush model. [ABSTRACT FROM AUTHOR]

For the design of efficient singlet fission chromophores, knowledge of the factors that govern the singlet fission rate is important. This rate is approximately proportional to the electronic coupling between the lowest (diabatic) spin singlet state that is populated following photoexcitation state and a so-called 1 TT state. The latter state is characterised by two triplets, each localised on one of two neighbouring molecules, which are coupled into a singlet. Here, we show the applicability of a nonorthogonal configuration interaction approach for the calculation of this electronic coupling. The advantages of this rigorous approach are that (1) the coupling can be calculated directly, (2) it includes important correlation and orbital relaxation effects, and (3) it has a clear chemical interpretation in terms of molecular states. This approach is applied to calculate the electronic coupling for a biradicaloid molecule, viz. the bis(inner salt) of 2,5-dihydroxy-1,4-dimethyl-pyrazinium. The biradicaloid molecule is, based on the energetic criteria, a promising candidate for singlet fission. We show that the electronic coupling between the molecules is also sufficiently large for singlet fission, rendering molecules based on this chemical moiety interesting singlet fission chromophores. [ABSTRACT FROM AUTHOR]

A brief background on the quantum wave-packet propagation method for the study of photodissociation dynamics of polyatomic molecules is summarized as a short tutorial review. The main emphasis is on reasons to use the wave-packet propagation method, followed by a description about basic considerations for practical application of the wave-packet method to polyatomic molecules. The considerations are divided into six steps in the following sequence: (1) prerequisite information for related states, (2) search for critical points, (3) selection of coordinates and kinetic energy operator, (4) potential energy surface, (5) propagation of wave-packet, and (6) analysis of the propagated results. Limitations of the present review and a very brief perspective are given as concluding remarks. © 2016 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Thermal motions in molecular crystals cause substantial fluctuation of the excitonic coupling between neighboring molecules (dynamic disorder). The effect of such fluctuation on the exciton dynamics in two limiting cases is explored here, exemplified by the crystals of anthracene and a heteropentacene derivative. When the excitonic coupling is small in comparison with the electron-phonon coupling, the exciton diffusion is incoherent and the inclusion of excitonic coupling fluctuation does not alter the exciton physics but can improve the agreement between computed and experimental diffusion coefficients. For large excitonic couplings, when the transport becomes coherent, the thermal motions determine the diffusivity of the exciton, which can be several orders of magnitude larger than in the incoherent case. The coherent regime is less frequent but potentially of great technological importance. [ABSTRACT FROM AUTHOR]

This is the first step of a deactivation pathway observed previously in experiment, which could also be operative in DNA, that was simulated here by using quantum dynamics. Keywords: Charge Transfer; Diabatic States; DNA; MCTDH; Photophysics EN Charge Transfer Diabatic States DNA MCTDH Photophysics 1 1 1 10/17/22 20221012 NES 221012 B Charge transfer in solvent b : Guanine is illustrated transferring an electron to cytosine in chloroform after the absorption of light. Front Cover: Solvent Effects on Ultrafast Charge Transfer Population: Insights from the Quantum Dynamics of Guanine-Cytosine in Chloroform (Chem. Eur. J. 57/2022). [Extracted from the article]

We have recently proposed an approach where chemical transformations can be described as quantum processes involving the modulation of entangled states by an applied external field (Arteca and Tapia in Phys Rev A 84:012115, ). In practical implementations, we gain insight into these processes by using simple quantum-mechanical models derived from diabatic schemes. In this context, reactant, product, and, eventually, intermediate species, are assigned to diabatic basis functions, and then entangled by an external field into a quantum state from which all observable properties of the chemical reaction should emerge. Here, we extend our previous model for bond breaking/formation in diatomic molecules (Arteca et al. in J Math Chem 50:949, ). We consider the entire manifold of semiclassical models defined by only two diabatic basis functions: a harmonic well for the 'molecular' bound state, and an exponential potential energy function for the asymptotically separated fragments (the 'product' channel). Using a two-parameter space to describe all models, we determine how the topology of the total energy function is affected by the shape of the applied field. We show that strong and weak local couplings with the external field modify substantially the occurrence of energy barriers, in contrast to using the uniform (i.e., space-invariant) coupling employed in previous works. [ABSTRACT FROM AUTHOR]

Intermolecular interactions modulate the electro-optical properties of molecular materials and the nature of low-lying exciton states. Molecular materials composed by oligoacenes are extensively investigated for their semiconducting and optoelectronic properties. Here, we analyze the exciton states derived from time-dependent density functional theory (TDDFT) calculations for two oligoacene model aggregates: naphthalene and anthracene dimers. To unravel the role of inter-molecular interactions, a set of diabatic states is selected, chosen to coincide with local ( LE ) and charge-transfer ( CT ) excitations within a restricted orbital space including two occupied and two unoccupied orbitals for each molecular monomer. We study energy profiles and disentangle inter-state couplings to disclose the ( CT ) character of singlet and triplet exciton states and assess the influence of inter-molecular orientation by displacing one molecule with respect to the other along the longitudinal translation coordinate. The analysis shows that ( CT ) contributions are relevant, although comparably less effective for triplet excitons, and induce a non-negligible mixed character to the low-lying exciton states for eclipsed monomers and for small translational displacements. Such ( CT ) contributions govern the L a /L b state inversion occurring for the low-lying singlet exciton states of naphthalene dimer and contribute to the switch from H- to J-aggregate type of the strongly allowed B b transition of both oligoacene aggregates.

The ability of the valence bond (VB) approach to describe a molecular system in ‘chemical terms’ finds its theoretical justification in the fact that the VB wavefunctions are supposed to be diabatic, i.e. with a well-defined nature, not depending on the nuclear geometry. The intimate nature of the VB wavefunctions is here analysed by computing the non-adiabatic coupling for the simple, paradigmatic case of the hydrogen (H2) molecule. This analysis reveals that the neutral and ionic VB wavefunctions cannot be considered as diabatic states, given that they present a large non-adiabatic coupling. The diabatic states, obtained by a suitable transformation of the VB wavefunctions, are found to be the wavefunctions of the orthogonal VB (OVB) approach, which therefore gains a legitimacy in the analysis of the composition of the adiabatic wavefunctions. Such an analysis has some bearing on the description of the nature of the chemical bond in H2: the neutral structure gives a dissociative curve and the bond is due to the stabilisation brought by the ionic structure that mixes together with the neutral structure in the ground state wavefunction at short internuclear distances. The ability of the (at first glance) neutral VB wavefunction based on the 1sorbitals to describe in a compact way the ground state (and therefore the chemical bond) is ascribed to an almost optimal mixing in this wavefunction of the diabatic neutral and ionic states at all internuclear distances. [ABSTRACT FROM AUTHOR]

The ability to describe seams of conical intersection that couple adiabatic potential energy surfaces is a key issue in describing nonadiabatic processes. This work considers the description of these seams provided by a recently introduced description of coupled adiabatic states using a coupled quasi-diabatic state Hamiltonian, Hd, whose matrix elements are polynomials in the internal coordinates. The conical intersection seam is represented in intersection adapted coordinates. Using the seam of accidental conical intersection of the 1,21A states of NH3 as an example the ability of the proposed algorithm to describe a seam of conical intersection in its full dimensionality is demonstrated. The success of this description is attributable to the use of orthogonal intersection adapted coordinates and to the Lagrange multiplier constraints in our algorithm which enables us to require the locus, energies and local topography of selected points on the Hd determined seam of intersection to agree exactly with the ab initio results. [ABSTRACT FROM AUTHOR]

The modulation of intermolecular interactions upon aggregation induces changes in excited state properties of organic molecules that can be detrimental for some optoelectronic applications but can be exploited for others. The time-dependent density functional theory (TDDFT) is a cost-effective approach to determining the exciton states of molecular aggregates, and it has been shown to provide reliable results when coupled with the appropriate choice of the functional. Here we apply a general procedure to analyze the aggregates' exciton states derived from TDDFT calculations in terms of diabatic states chosen to coincide with local (LE) and charge-transfer (CT) excitations within a restricted orbital space. We apply the approach to study energy profiles, interstate couplings, and the charge-transfer character of singlet and triplet exciton states of perylene di-imide aggregates (PDI). We focus on the intermolecular displacement along the longitudinal translation coordinate, which mimics different amounts of slip-stacking observed in PDI crystals. The analysis, in terms of symmetry-adapted Frenkel excitations (FE) and charge-resonance (CR) states and their interactions, discloses how the interchange of the H/J character for small longitudinal shifts, previously reported for singlet exciton states, also occurs for triplet excitons. [ABSTRACT FROM AUTHOR]

We introduce a protocol to represent quantum states as a linear superposition of model electronic diabatic basis states coupled in an external (static) electric field. By considering an entire family of these models, we uncover trends in reaction-path geometry and the topology of potential-energy surfaces, including all those that can be realized in a two-dimensional configurational space. Our approach can be used as a tool to model the key parameters (e.g., diabatic basis states, external field intensity) that yield desired geometrical characteristics in an actual potential energy surface. In this work, external agents such as laser fields, or a group of neighboring charges, are regarded as essential requirements to prompt, or trigger, the occurrence of a chemical process. In these cases, reaction path geometry can be modulated externally so as to yield processes that would appear to occur far from gas-phase geometries. This phenomenology is intrinsically nonadiabatic. Our present approach accounts for the possibility of such features, i.e., the occurrence of quantum states whose electronic structures resemble products, while at geometries that are more similar to those of reactants. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [ABSTRACT FROM AUTHOR]

Active site properties in some proteins can be affected by conformational fluctuations of neighbor residues, even when the latter are not involved directly in the binding process. A local environment thus appears to alter the relevant potential energy surface and its reaction paths. Here, some aspects of this phenomenon are simulated within a generalized electronic diabatic (GED) scheme to study the geometry and structural similarity for a class of two-dimensional (2D) energy surfaces. The electronic quantum state is a linear superposition of diabatic basis functions, each of which is taken to represent a single (pure) electronic state for the isolated material system. Here, we describe a model reaction of isomerization by shifts in amplitudes for three diabatic species (reactant, product, and an open-shell transition state) coupled in an external field. The “effective” 2D energy surface in the field is characterized in terms of critical points, and the amplitudes along the main reaction paths. A new feature is the introduction of a phase diagram where all possible potential-energy-surface topologies (consistent with three-state systems in two linear coordinates) are matched with actual model parameters. By varying the coupling strengths between diabatic states, we classify regions of this phase diagram in terms of electronic and structural similarities; some regions comprise models whose reaction paths have geometries that belong to the catchment region of the reactant, yet are electronically akin to the diabatic transition state or product. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [ABSTRACT FROM AUTHOR]

Reaction paths are studied with the help of diabatic potential-energy surfaces coupled in a generic external field. We show that all putative geometrical and topological features of two-dimensional (2D) potential-energy surfaces for an isomerization can be generated with a model consisting of strictly diabatic harmonic 2D wells coupled in a static (yet uniform) external field. For a large class of three-state models, we provide a phase diagram of possible topologies in the relevant parameter space for three-state models. By following the shift in diabatic electronic amplitudes (denoted by {|ck|2}) in coherent quantum states produced in the field, we assess whether the models within each phase can produce reaction paths visiting regions of configurational space that are structurally similar to the diabatic transition state. [ABSTRACT FROM AUTHOR]

Abstract: Contrary to a standard definition of diabatic states (i.e., those without momentum-dependent coupling), based on the construction from adiabatic ones, we defined diabatic states as bright and dark states of a given experiment. Namely, they are defined as states providing maximum, respectively, zero value of electronic transition dipole moments projected to a given polarization vector. Second, the state from (or to) which the optical transition is performed is not from the space of investigated electronic excited state manifold, but it is chosen by the observer. It is shown, for this case, that the inter-state coupling is a general function of vibrational coordinates. The explicit dependence of the inter-state coupling on vibrational coordinates is particularly important for system with strong Stokes shift. The role of exact definitions of bright and dark states as well as the inter-state coupling is discussed with respect to the coherent structure of electronic population observed in optical spectroscopy. [Copyright &y& Elsevier]

We revisit the notion of structural similarity along a reaction path within the context of a generalized electronic diabatic (GED) molecular model. In this approach, a reaction involving two closed-shell stable species is described as the evolution of a quantum state that superimposes at least three diabatic electronic species (reactant, product, and an open-shell transition state) coupled by an external electromagnetic field. Reactant and product amplitudes in this general state are also modulated by changing the geometry of a system of classical positive charges interacting with the electrons. By mapping these amplitudes over nuclear configurational space, we can follow the total quantum state along a reaction coordinate and establish its similarity to each of the diabatic species. As a result, chemical processes, and useful notions such as those of energy barriers and the Hammond postulate, emerge as consequence of Franck–Condon-like transitions between quantum states. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [ABSTRACT FROM AUTHOR]

Nonadiabatic effects play an important role in many areas of physics and chemistry. The coupling between electrons and nuclei may, for example, lead to the formation of a conical intersection between potential energy surfaces, which provides an efficient pathway for radiationless decay between electronic states. At such intersections the Born-Oppenheimer approximation breaks down, and unexpected dynamical processes result, which can be observed spectroscopically. We review the basic theory required to understand and describe conical, and related, intersections. A simple model is presented, which can be used to classify the different types of intersections known. An example is also given using wavepacket dynamics simulations to demonstrate the prototypical features of how a molecular system passes through a conical intersection. [ABSTRACT FROM AUTHOR]