Engineering topics

Martínez, Todd J.

Publications and source records attributed to Martínez, Todd J..

5 records

DOE OSTI2024

Photoinduced hydrogen dissociation in thymine predicted by coupled cluster theory

The fate of thymine upon excitation by ultraviolet radiation has been the subject of intense debate. Today, it is widely believed that its ultrafast excited state gas phase decay stems from a radiationless transition from the bright ππ* state to a dark nπ* state. However, conflicting theoretical predictions have made the experimental data difficult to interpret. Here we simulate the early gas phase ultrafast dynamics in thymine at the highest level of theory to date. This is made possible by performing wavepacket dynamics with a recently developed coupled cluster method. Our simulation confirms an ultrafast ππ* to nπ* transition (τ = 41 ± 14 fs). Furthermore, the predicted oxygen-edge X-ray absorption spectra agree quantitatively with experiment. We also predict an as-yet uncharacterized πσ* channel that leads to hydrogen dissociation at one of the two N-H bonds. Similar behavior has been identified in other heteroaromatic compounds, including adenine, and several authors have speculated that a similar pathway may exist in thymine. However, this was never confirmed theoretically or experimentally. This prediction calls for renewed efforts to experimentally identify or exclude the presence of this channel.

Kjønstad, Eirik F.↗

DOE OSTI2024

Extending GPU-accelerated Gaussian integrals in the TeraChem software package to f type orbitals: Implementation and applications

Here, the increasing availability of graphics processing units (GPUs) for scientific computing has prompted interest in accelerating quantum chemical calculations through their use. However, the complexity of integral kernels for high angular momentum basis functions often limits the utility of GPU implementations with large basis sets or for metal containing systems. In this work, we report the implementation of f function support in the GPU-accelerated TeraChem software package through the development of efficient kernels for the evaluation of Hamiltonian integrals. The high efficiency of the resulting code is demonstrated through density functional theory (DFT) calculations on increasingly large organic molecules and transition metal complexes, as well as coupled cluster singles and doubles calculations on water clusters. Preliminary investigations into Ni(I) catalysis with DFT and the photochemistry of MnH(CH 3 ) with complete active space self-consistent field are also carried out. Overall, our GPU-accelerated software appears to be well-suited for fast simulation of large transition metal containing systems, as well as organic molecules.

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DOE OSTI2024

Attosecond Probing of Coherent Vibrational Dynamics in CBr 4

A coherent vibrational wavepacket is launched and manipulated in the symmetric stretch (a1) mode of CBr 4 , by impulsive stimulated Raman scattering (ISRS) from nonresonant 400 nm laser pump pulses with various peak intensities on the order of tens of 10 12 W/cm 2 . Extreme ultraviolet (XUV) attosecond transient absorption spectroscopy (ATAS) records the wavepacket dynamics as temporal oscillations in XUV absorption energy at the bromine M 4,5 3d 3/2,5/2 edges around 70 eV. The results are augmented by nuclear timedependent Schrödinger equation simulations. Slopes of the (Br 3d 3/2,5/2 ) –1 10a 1 * core-excited state potential energy surface (PES) along the a 1 mode are calculated to be –9.4 eV/Å from restricted open-shell Kohn–Sham calculations. Using analytical relations derived for the small-displacement limit and the calculated slopes of the core-excited state PES, a deeper insight into the vibrational dynamics is obtained by retrieving the experimental excursion amplitude of the vibrational wavepacket and the amount of population transferred to the vibrational first-excited state as a function of pump-pulse peak intensity. Experimentally, the results show that XUV ATAS is capable of resolving oscillations in the XUV absorption energy on the order of a few to tens of meV with tens of femtosecond time precision. This corresponds to change in C–Br bond length on the order of 10 –4 to 10 –3 Å. The results and the analytic relationships offer a clear physical picture, on multiple levels of understanding, of how the pump-pulse peak intensity controls the vibrational dynamics launched by nonresonant ISRS in the small-displacement limit.

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DOE OSTI2024

Prediction of photodynamics of 200 nm excited cyclobutanone with linear response electronic structure and ab initio multiple spawning

Simulations of photochemical reaction dynamics have been a challenge to the theoretical chemistry community for some time. In an effort to determine the predictive character of current approaches, we predict the results of an upcoming ultrafast diffraction experiment on the photodynamics of cyclobutanone after excitation to the lowest lying Rydberg state (S 2 ). A picosecond of nonadiabatic dynamics is described with ab initio multiple spawning. Herein we use both time dependent density functional theory (TDDFT) and equation-of-motion coupled cluster singles and doubles (EOM-CCSD) theory for the underlying electronic structure theory. We find that the lifetime of the S 2 state is more than a picosecond (with both TDDFT and EOM-CCSD). The predicted ultrafast electron diffraction spectrum exhibits numerous structural features, but weak time dependence over the course of the simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Conical Intersection Accessibility Dictates Brightness in Red Fluorescent Proteins

Red fluorescent protein (RFP) variants are highly sought after for in-vivo imaging since longer wavelengths improve depth and contrast in fluorescence imaging. However, the lower energy emission wavelength usually correlates with a lower fluorescent quantum yield compared to their green emitting counterparts. To guide the rational design of bright variants, we have theoretically assessed two variants (mScarlet and mRouge) which are reported to have very different brightness. Using an α-CASSCF QM/MM framework (chromophore and all protein residues within 6 Å of it in the QM region, for a total of more than 450 QM atoms), we identify key points on the ground and first excited state potential energy surfaces. The brighter variant mScarlet has a rigid scaffold, and the chromophore stays largely planar on the ground state. The dimmer variant mRouge shows more flexibility and can accommodate a pre-twisted chromophore conformation which provides easier access to conical intersections. Notably, the main difference between the variants lies in the intersection seam regions, which appear largely inaccessible in mScarlet but partially accessible in mRouge. This observation is mainly related with changes in the cavity charge distribution, the hydrogen-bonding network involving the chromophore and a key ARG/THR mutation (which changes both charge and steric hindrance).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗