Project Adamantanes

A computational study of the electronic structure and excited-state relaxation dynamics of pristine and methylated adamantanes.

---

Overview

This project — Nonadiabatic Molecular Dynamics in Pristine and Methylated Adamantanes — combines static electronic-structure calculations with non-adiabatic molecular dynamics (NAMD) simulations to investigate the photophysical properties of adamantane and its methylated derivatives.

The repository contains the complete computational workflow for:

• Quantum-chemistry calculations of the electronic structure of adamantane and its methylated derivatives.
• Non-adiabatic molecular dynamics (NAMD) simulations of excited-state relaxation.
• Analysis of radiative and non-radiative recombination, quantum yields, and their dependence on molecular structure.

In addition to the dynamic trajectory method, a single-optimization approach was also employed.

---

Repository Structure

Project_adamantanes/ ├── LICENSE ├── README.md # This file ├── NAMD/ # NAMD workflow (STEP1 → STEP4) │ ├── STEP1/ # Structure preparation │ ├── STEP2/ # Electronic-structure calculations │ ├── STEP3/ # Vibronic Hamiltonians and NACs │ └── STEP4/ # NAMD simulations and analysis └── Static_Optimization_Structure/ # Optimized geometries and IP/UV-Vis data

---

Workflow Overview

Static Optimization Structure

Optimize the initial crystal structure using the B3LYP functional.

• Input: Optimized CIF files, ORCA and CP2K input files with the appropriate energy_type setting (4 different systems).
• Output: Ground state and TDDFT output files and corresponding Molden files. The TDDFT output files can be further analyzed with Multiwfn to generate UV–Vis spectra in .txt format. Different spectral line shapes and degrees of peak broadening can be obtained by adjusting the full width at half maximum (FWHM).

Related scripts and examples are available in:

Static_Optimization_Structure/UV_Vis_spectra

---

Nonadiabatic Molecular Dynamics Workflow

STEP 1: Adiabatic Molecular Dynamics

• Objective: Obtain equilibrated adiabatic trajectories at 300 K.
• Output: Equilibrated ground-state molecular-dynamics trajectories for subsequent electronic-structure calculations.

Additional Note: Restarting a CP2K MD Simulation:

To continue a previously interrupted CP2K molecular-dynamics simulation, include the following restart settings in the input file:

&EXT_RESTART RESTART_FILE_NAME adamantane_MD-1_5000.restart RESTART_DEFAULT T &END EXT_RESTART

---

STEP 2: TDDFT Calculations

• Input: TDDFT calculations based on a 300 K temperature profile.
• Output: Excited-state energies, oscillator strengths, and Kohn–Sham orbital energies for visualizing electronic entropy and UV-Vis spectra.

---

STEP 3: Vibronic Hamiltonian Construction

• Objective: Generate the time-dependent vibronic Hamiltonian using the Step 2 outputs and the selected active space.
• Active space: Taking adamantane as an example, orbitals 18–46, with orbital 38 as the HOMO and orbital 39 as the LUMO.
• Output: Time-dependent electronic energies, probability distributions, and non-adiabatic couplings for the selected electronic states.

---

STEP 4: Nonadiabatic Molecular Dynamics

• Objective: Perform non-adiabatic molecular-dynamics simulations using the Step 3 Hamiltonian data with four different surface-hopping methods: FSSH, FSSH2, IDA, and MSDM.
• Output: Determine the timescale using relaxation dynamics, and compute PLQY, non-radiative lifetimes, and stretch exponents.

---

Workflow Summary Table

Step	Purpose	Key Outputs
Static Optimization	B3LYP geometry optimization and UV-Vis	CIF, Molden, TDDFT output, spectra
STEP1	Prepare and align molecular structures, run MD at 300 K	aligned.tar.gz, MD trajectories
STEP2	TDDFT calculations along MD trajectories	Kohn–Sham energies, UV-Vis spectra
STEP3	Build vibronic Hamiltonians and non-adiabatic couplings	Hvib_ci_.npz, St_ci_.npz
STEP4	Run NAMD simulations and analyze kinetics	mem_data.hdf, analysis_results.pkl

---

Structures Studied

• Adamantane
• 1-Methyl-adamantane
• 1,3-Dimethyl-adamantane
• 1,3,5-Trimethyl-adamantane

---

Surface Hopping Methods

The NAMD simulations in STEP4 employ four different trajectory surface-hopping (TSH) methods:

Method	Description
FSSH	Fewest Switches Surface Hopping (Tully, 1990)
FSSH2	Alternative FSSH formulation with robust switching
IDA	Instantaneous Decoherence at Attempted hops
MSDM	Simplified Decay of Mixing

---

Dependencies

• Python 3.10+
• numpy, scipy, h5py, matplotlib
• libra_py (Libra library)
• CP2K, ORCA, Multiwfn (for STEP2 / static calculations)

---

Contact

• Qingxin Zhang (qingxin@buffalo.edu)
• Hamid Zabihi Hashjin (h.zabihi@eng.uk.ac.ir)
• Alexey V. Akimov (alexeyak@buffalo.edu)