The developments of the open-source chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes can address, while showing that is an attractive platform for state-of-the-art atomistic computer simulations.

We present the SHARC/COBRAMM approach to enable easy and efficient excited-state dynamics simulations at different levels of electronic structure theory in the presence of complex environments using a quantum mechanics/molecular mechanics (QM/MM) setup. SHARC is a trajectory surface-hoping method that can incorporate the simultaneous effects of nonadiabatic and spin–orbit couplings in the excited-state dynamics of molecular systems. COBRAMM allows ground- and excited-state QM/MM calculations using a subtractive scheme, with electrostatic embedding and a hydrogen link-atom approach. The combination of both free and open-source program packages provides a modular and extensive framework to model nonadiabatic processes after light irradiation from the atomistic scale to the nano-scale. As an example, the relaxation of acrolein from S1 to T1 in solution is provided.

Photoelectron imaging of the isolated adenosine-5´-triphosphate dianion excited to the 1 ππ* states reveals that electron emission is predominantly parallel to the polarization axis of the light and arises from subpicosecond electron tunneling through the repulsive Coulomb barrier (RCB). The computed RCB shows that the most probable electron emission site is on the amino group of adenine. This is consistent with the photoelectron imaging: excitation to the 1 ππ* states leads to an aligned ensemble distributed predominantly parallel to the long axis of adenine, the subsequent electron tunneling site is along this axis, and the negatively charged phosphate groups guide the outgoing electron mostly along this axis at long range. Imaging electron tunneling from polyanions combined with computational chemistry may offer a general route to probing the intrinsic photo-oxidation site and dynamics as well as overall structure of complex isolated species.

The impact of different initial conditions in non-adiabatic trajectory surface hopping dynamics within a hybrid quantum mechanical/molecular mechanics scheme is investigated. The influence of a quantum sampling, based on a Wigner distribution, a fully thermal sampling, based on classical molecular dynamics, and a quantum sampled system, but thermally equilibrated with the environment, is investigated on the relaxation dynamics of solvated fulvene after light irradiation. We find that the decay from the first singlet excited state to the ground state shows high dependency on the initial condition and simulation parameters. The three sampling methods lead to different distributions of initial geometries and momenta, which then affect the fate of the excited state dynamics. We evaluated both the effect of sampling geometries and momenta, analysing how the ultrafast decay of fulvene changes accordingly. The results are expected to be of interest to decide how to initialize non-adiabatic dynamics in the presence of the environment. This article is part of the theme issue ‘Chemistry without the Born–Oppenheimer approximation’.

We present a series of new implementations that we recently introduced in COBRAMM, the open-source academic software developed in our group. The goal of these implementations is to offer an automatized workflow and interface to simulate time-resolved transient absorption (TA) spectra of medium-to-big chromophore embedded in a complex environment. Therefore, the excited states absorption and the stimulated emission are simulated along nonadiabatic dynamics performed with trajectory surface hopping. The possibility of treating systems from medium to big size is given by the use of time-dependent density functional theory (TD-DFT) and the presence of the environment is taken into account employing a hybrid quantum mechanics/molecular mechanics (QM/MM) scheme. The full implementation includes a series of auxiliary scripts to properly setup the QM/MM system, the calculation of the wavefunction overlap along the dynamics for the propagation, the evaluation of the transition dipole moment at linear response TD-DFT level, and scripts to setup, run and analyze the TA from an ensemble of trajectories. Altogether, we believe that our implementation will open the door to the easily simulate the time-resolved TA of systems so far computationally inaccessible.

The binding mechanism of the protonated open form of three spiropyran derivatives into a 12-mer (poly-dAT)2 has been unveiled by means of computational methods.

The excited state dynamics of the doubly deprotonated dianion of adenosine-5′-triphosphate, [ATP–H2]2 –, has been spectroscopically explored by time-resolved photoelectron spectroscopy following excitation at 4.66 eV. Time-resolved photoelectron spectra show that two competing processes occur for the initially populated 1ππ* state. The first is rapid electron emission by tunneling through a repulsive Coulomb barrier as the 1ππ* state is a resonance. The second is nuclear motion on the 1ππ* state surface leading to an intermediate that no longer tunnels and subsequently decays by internal conversion to the ground electronic state. The spectral signatures of the features are similar to those observed for other adenine-derivatives, suggesting that this nucleobase is quite insensitive to the nearby negative charges localized on the phosphates, except of course for the appearance of the additional electron tunneling channel, which is open in the dianion.

The recent delivery of af luorescentq uinolizidinesubstituted spiropyran, which is able to switch in vivo and bind to guanineq uadruplexes (G4) at physiological pH values,u rged us to elucidate its molecular switching and bindingm echanism.C ombining multiscale dynamicals tudies and accurate quantum chemical calculations, we show that, both in water and in the G4 environment,t he switching of the spiropyran ring is not promoted by an initial protonatione vent-as expected by the effect of low pH solutions-but that the deprotonated merocyanine form is an intermediate of the reactionl eading to the protonated open species.A dditionally,w ei nvestigate the binding of both deprotonated and protonated open forms of merocyanine to c-MYCG4s. Both species bind to G4s albeit with different hydrogen-bond patterns and provide distinct rotamers around the exocyclic double bond of the merocyanine forms.A ltogether,o ur study sheds light on the pharmacophoric points for the binding of these probes to DNA,a nd thereby,c ontributes to future developments of new G4 binders of the remarkable family of quinolizidine-substituted spiropyrans. Scheme1.Quinolizidine-substituted spiropyrans (QSP) isomerizes to the protonated merocyanine(QMCH) under acid conditions or by DNA G4 binding. Bondsf or the definition of the QMCHi somers are shown in blue (a, b, g).