ab inito md - astrochemistry of titan's atmosphere - danilo perez and dr. juan lopez

8/9/2019 Ab Inito MD - Astrochemistry of Titan's Atmosphere - Danilo Perez and Dr. Juan Lopez

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• Introduction• What is Titan, why do we care, and how do Ab initio

molecular dynamics relate to its atmosphere?• Previous Research

• What do we know about the problem so far?• Project Objectives

• What do we hope to learn about the problem?•

Methodology• How do we propose to reach these objectives?• Progress• Future Work

Outline


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Cause of Interest


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Atmospheric Constituents


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• Ab initio , meaning ‘first principle’, refers to a solutionthat is derived from natural laws, and assumes noparticularities of the system. In our case, these first

principles relate to the electronic structure of theatoms, as dictated by the laws of electrostatics andquantum mechanics.

• Molecular dynamics relates these studies to the classical

studies of N-body systems.

Ab initio molecular dynamics


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• Direct experimentation can be costly, and currently, thebudget allocation for Space Exploration is at an all-time

low since the end of the Space Race.• To alleviate investments in instrumentation and

equipment, computational studies assist giving directionbefore continuing on in a mission that could be in vane.

Studying without direct experimentation


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Studying without direct experimentation

Kaiser, R. I.; Balucani, N. The Formation of Nitriles in Hydrocarbon-Rich Atmospheres ofPlanets and Their Satellites: Laboratory Investigations by the Crossed Molecular BeamTechnique. Acc. Chem. Res. 2001 , 34, 699-706

•

The utility of solving problems from the standpoint of a ‘firstprinciple’, is that it allows for generalizability and great power inthe conclusions.

• Therefore, these computations allow us to interpret the scarcedata obtained experimentally, and generate new data withinteresting consequences if proven true.


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• Reconcile the experiments of Kaiser and Balucani with

previously reported kinetic analysis in terms oftemperature.

• Determine the reaction’s feasibility and how itprogresses, in terms of Gibb’s Free Energy, instead ofthe system’s Potential Energy.

•

Understand the reaction’s ability to proceed, thereaction dynamics should be studied in terms of thesystem’s free energy.

Objectives


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Computational flow

NWChem• Supercomputer• ECF selection• Basis Set

selection

Python• Input Translation• Verlet Algorithm• Output Formating

Run-determiningScript

Java/Python• Reaction Movie• Structure report•

Energeticprofiling

M-Studio

• Initial Structures• ZPE Determination


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• The reactants, as well as certain predicted products andintermediates were constructed in materials studio.

• 2 Basis sets (6-311+G** and 6-31+G**) and 3 ExchangeCorrelation Functionals (PW91, PBE, and B3LYP) weretested to verify which method was most appropriate forthe problem at hand.

• NIST Chemistry database was consulted as part of this

comparison.

Materials Studio/ECF & Basis Set selection


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ECF & Basis Set selection Results

B3LYP PBE PD91

6-31+G** 0.289118 0.319531 0.755596-311+G** 0.325489 0.402271 0.471182

Table 1. Bond-Length Error Percentages for BS/ECF Pairs.

B3LYP PBE PD91

6-31+G** 4.247380 5.53418 2.9256336-311+G** 4.788858 4.91811 2.940885

Table 2. Frequency Error Percentages for BS/ECF Pairs.

• Statistical significance testing would not deemsignificant most differences between these pairs.


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Python Scripting

• The code must be able to read in gradients (equation 2)

from NWChem, and proceed to implement thisacceleration in the Verlet Algorithm.• The code for this step-wise algorithm has already been

created, and it is able to read gradients and produce

results that are interpretable by NWChem.• However, the run-determining script has not been

written as of yet, for which reason full-fledgedmolecular dynamics cannot be determined.

(1) Verlet Algorithm

(2) Gradient implementation


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Progress so-far and Future Work

NWChem• Supercomputer• ECF selection• Basis Set

selection

Python• Input Translation• Verlet Algorithm• Output Formating

Run-determiningScript

Java/Python• Reaction Movie• Structure report•

Energeticprofiling

M-Studio

• Initial Structures• ZPE Determination


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A dreamer is one who can only find his way bymoonlight…

and his reward is that he sees the

dawn before the rest of the world- Oscar Wild

‘ The Critic as Artist ’

ab inito md - astrochemistry of titan's atmosphere - danilo perez and dr. juan lopez

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