We present a versatile new code released for open community use, the nonadiabatic excited state molecular dynamics (NEXMD) package. This software aims to simulate nonadiabatic excited state molecular dynamics using several semiempirical Hamiltonian models. To model such dynamics of a molecular system, the NEXMD uses the fewest-switches surface hopping algorithm, where the probability of transition from one state to another depends on the strength of the derivative nonadiabatic coupling. In addition, there are a number of algorithmic improvements such as empirical decoherence corrections and tracking trivial crossings of electronic states. While the primary intent behind the NEXMD was to simulate nonadiabatic molecular dynamics, the code can also perform geometry optimizations, adiabatic excited state dynamics, and single-point calculations all in vacuum or in a simulated solvent. In this report, first, we lay out the basic theoretical framework underlying the code. Then we present the code’s structure and workflow. To demonstrate the functionality of NEXMD in detail, we analyze the photoexcited dynamics of a polyphenylene ethynylene dendrimer (PPE, C30H18) in vacuum and in a continuum solvent. Furthermore, the PPE molecule example serves to highlight the utility of the getexcited.py helper script to form a streamlined workflow. This script, provided with the package, can both set up NEXMD calculations and analyze the results, including, but not limited to, collecting populations, generating an average optical spectrum, and restarting unfinished calculations.

We report results on the growth of an NaCl film on Ag(110) under ultrahigh vacuum conditions. At room temperature, low-energy electron diffraction and scanning tunneling microscopy show that the NaCl film forms a (4×1) superstructure. At RT, the film consists of small-sized islands that coalesce into larger islands at 410 K. These large islands preserve the (4×1) superstructure and cover the entire surface. The apparent heights obtained from the STM images show that the initial thickness of the NaCl islands is one atomic layer, and they present a very small height corrugation. The density functional theory calculations, with and without the inclusion of van der Waals effects, confirm the coexistence of two domains in agreement with the observed structure.

A new open-source high-performance implementation of Born Oppenheimer molecular dynamics based on semiempirical quantum mechanics models using PyTorch called PYSEQM is presented. PYSEQM was designed to provide researchers in computational chemistry with an open-source, efficient, scalable, and stable quantum-based molecular dynamics engine. In particular, PYSEQM enables computation on modern graphics processing unit hardware and, through the use of automatic differentiation, supplies interfaces for model parameterization with machine learning techniques to perform multiobjective training and prediction. The implemented semiempirical quantum mechanical methods (MNDO, AM1, and PM3) are described. Additional algorithms include a recursive Fermi-operator expansion scheme (SP2) and extended Lagrangian Born Oppenheimer molecular dynamics allowing for rapid simulations. Finally, benchmark testing on the nanostar dendrimer and a series of polyethylene molecules provides a baseline of code efficiency, time cost, and scaling and stability of energy conservation, verifying that PYSEQM provides fast and accurate computations.

We report a systematic study of thiophene derivatives on gold surfaces. These molecules are of interest in molecular electronics, and the characracteristics of the thiophene–electrode interface in devices needs to be understood as it affects electron transport characteristics. Some experiments indicated S–C bond scission in contact with metals resulting in disruption of the π-electron system that affects charge transport, which would also be affected by presence of split-off chemisorbed sulfur. We explored this dissociation aspect by photoemission for the case of monocrystalline Au(111) surfaces and Au films grown on mica for a series of polythiophenes molecules (nT, n = 1–4, 6) as well as for α,ω-diquaterthiophene (DH4T) and dihexylsexithiophene (DH6T). The S 2p X-ray photoelectron spectroscopy peaks are found to have complex line shapes corresponding to S atoms with different core level binding energies (CLBE). Density functional theory calculations of adsorption energies and CLBEs were performed for various adsorption configurations of thiophene on a perfect Au(111) plane and for comparison, calculations were also performed for bithiophene, terthiophene, alkenethiol, alkenethiol chain, and a broken thiophene related metallocycle, incorporating an Au adatom and an S atom. On the basis of these results we relate the different contributions to the S 2p peak to intact molecules on different adsorption sites and broken molecules. Calculations in particular show that the CLBEs for intact thiophene (1T) can be the same as for the alkene and alkanethiol cases as opposed to usual assumptions in the literature. The existence of intact thiophenes is confirmed by the presence of clear π resonance peaks in the near edge X-ray fine structure (NEXAFS) spectra. Spontaneous dissociation appears to a variable extent in different samples, and we tentatively relate this to the presence of a more or less large number of steps and defects sites. X-ray induced beam damage was investigated for 1T and 3T using an intense synchrotron beam of 260 eV photons, and showed changes in the S 2p spectra related to S–C bond scission.

We report the results of the first-principles density functional theory calculations for the adsorption of thiophene (C4H4S) on Cu(100) and Ni(100) surfaces. The adsorption properties on these surfaces are evaluated for several adsorption configurations, and the calculations are performed with the inclusion of van der Waals (vdW) interactions invoking the optimized vdW (optB86b-vdW, optB88-vdW, and optPBE-vdW) as well as revPBE-vdW and rPW86-vdW2 functionals. In agreement with the earlier reports, on both surfaces, the most stable adsorption configurations correspond to the hollow-45 at which the thiophene adsorbs parallel to the surface. For the adsorption on Ni(100), in agreement with the experimental observations, we confirm that thiophene spontaneously ruptures via breaking of a C–S bond when the center of the molecule is placed over a bridge site. On the basis of both the bond distribution and charge transfer analysis, we conclude that the rupturing of thiophene observed at the bridge-45 configuration on Ni(100) may result from large charge transfer from the surface. The analyses of the electronic and geometric structures and charge transfer reveal that the interaction of the thiophene molecule with Ni(100) is much stronger than that of the Cu(100) surface. Upon adsorption of the molecule, for the former surface, we observed much larger charge transfer, non-negligible changes in the positions of the surface atoms, and appreciable electronic structure changes (i.e., in the center and width of the d-band). The adsorption of thiophene on Ni(100) also leads to the decrease in the magnetic moment of the surface Ni atoms particularly those in the vicinity of the adsorbed molecule. All these observations considered, we conclude that the nature of bonding on Ni(100) can be classified as strong chemisorption, while on Cu(100) it can be classified between weak and strong physisorption depending on the vdW functional used.