scholarly journals Ab Initio Metadynamics Calculations of Dimethylamine for Probing pKb Variations in Bulk vs. Surface Environments

Author(s):  
Sohag Biswas ◽  
Hyuna Kwon ◽  
Kelley Barsanti ◽  
Nanna Myllys ◽  
James N. Smith ◽  
...  

The basicity constant, or pK<sub>b</sub>, is an intrinsic physical property of bases that gives a measure of its proton affinity in macroscopic environments. While the pKb is typically defined in reference to the bulk aqueous phase, several studies have suggested that this value can differ significantly at the air-water interface (which can have significant ramifications for particle surface chemistry and aerosol growth modeling). To provide mechanistic insight into surface proton affinity, we carried out <i>ab initio</i> metadynamics calculations to (1) explore the free-energy profile of dimethylamine and (2) provide reasonable estimates of the pKb value in different solvent environments. We find that the free-energy profiles obtained with our metadynamics calculations show a dramatic variation, with interfacial aqueous dimethylamine pK<sub>b</sub> values being significantly lower than in the bulk aqueous environment. Furthermore, our metadynamics calculations indicate that these variations are due to reduced hydrogen bonding at the air-water surface. Taken together, our quantum mechanical metadynamics calculations show that the reactivity of dimethylamine is surprisingly complex, leading to pK<sub>b</sub> variations that critically depend on the different atomic interactions occurring at the microscopic molecular level.

2020 ◽  
Author(s):  
Sohag Biswas ◽  
Hyuna Kwon ◽  
Kelley Barsanti ◽  
Nanna Myllys ◽  
James N. Smith ◽  
...  

The basicity constant, or pK<sub>b</sub>, is an intrinsic physical property of bases that gives a measure of its proton affinity in macroscopic environments. While the pKb is typically defined in reference to the bulk aqueous phase, several studies have suggested that this value can differ significantly at the air-water interface (which can have significant ramifications for particle surface chemistry and aerosol growth modeling). To provide mechanistic insight into surface proton affinity, we carried out <i>ab initio</i> metadynamics calculations to (1) explore the free-energy profile of dimethylamine and (2) provide reasonable estimates of the pKb value in different solvent environments. We find that the free-energy profiles obtained with our metadynamics calculations show a dramatic variation, with interfacial aqueous dimethylamine pK<sub>b</sub> values being significantly lower than in the bulk aqueous environment. Furthermore, our metadynamics calculations indicate that these variations are due to reduced hydrogen bonding at the air-water surface. Taken together, our quantum mechanical metadynamics calculations show that the reactivity of dimethylamine is surprisingly complex, leading to pK<sub>b</sub> variations that critically depend on the different atomic interactions occurring at the microscopic molecular level.


2020 ◽  
Author(s):  
Sohag Biswas ◽  
Hyuna Kwon ◽  
Kelley Barsanti ◽  
Nanna Myllys ◽  
James N. Smith ◽  
...  

The basicity constant, or pK<sub>b</sub>, is an intrinsic physical property of bases that gives a measure of its proton affinity in macroscopic environments. While the pKb is typically defined in reference to the bulk aqueous phase, several studies have suggested that this value can differ significantly at the air-water interface (which can have significant ramifications for particle surface chemistry and aerosol growth modeling). To provide mechanistic insight into surface proton affinity, we carried out <i>ab initio</i> metadynamics calculations to (1) explore the free-energy profile of dimethylamine and (2) provide reasonable estimates of the pKb value in different solvent environments. We find that the free-energy profiles obtained with our metadynamics calculations show a dramatic variation, with interfacial aqueous dimethylamine pK<sub>b</sub> values being significantly lower than in the bulk aqueous environment. Furthermore, our metadynamics calculations indicate that these variations are due to reduced hydrogen bonding at the air-water surface. Taken together, our quantum mechanical metadynamics calculations show that the reactivity of dimethylamine is surprisingly complex, leading to pK<sub>b</sub> variations that critically depend on the different atomic interactions occurring at the microscopic molecular level.


2019 ◽  
Author(s):  
Xiaoliang Pan ◽  
Pengfei Li ◽  
Junming Ho ◽  
Jingzhi Pu ◽  
Ye Mei ◽  
...  

An efficient and accurate reference potential simulation protocol is proposed for producing ab initio quantum mechanical molecular mechanical (AI-QM/MM) quality free energy profiles for chemical<br>reactions in a solvent or macromolecular environment. This protocol involves three stages: (a) using force matching to recalibrate a semi-empirical quantum mechanical (SE-QM) Hamiltonian for the specific reaction under study; (b) employing the recalibrated SE-QM Hamiltonian (in combination with molecular mechanical force fields) as the reference potential to drive umbrella samplings along the reaction pathway; and (c) computing AI-QM/MM energy values for collected configurations from the sampling and performing weighted thermodynamic perturbation to acquire AI-QM/MM corrected reaction free energy profile. For three model reactions (identity SN2 reaction, Menshutkin reaction, and glycine proton transfer reaction) in aqueous solution and one enzyme reaction (Claisen arrangement in chorismate mutase), our simulations using recalibrated PM3 SE-QM Hamiltonians well reproduced AI-QM/MM free energy profiles (at the B3LYP/6-31G* level of theory) all within 1 kcal/mol with a 20 to 45 fold reduction in the computer time.


2019 ◽  
Vol 21 (37) ◽  
pp. 20595-20605 ◽  
Author(s):  
Xiaoliang Pan ◽  
Pengfei Li ◽  
Junming Ho ◽  
Jingzhi Pu ◽  
Ye Mei ◽  
...  

An efficient and accurate reference potential simulation protocol is proposed for producing ab initio quantum mechanical/molecular mechanical (AI-QM/MM) quality free energy profiles for chemical reactions in a solvent or macromolecular environment.


2020 ◽  
Vol 22 (45) ◽  
pp. 26265-26277
Author(s):  
Sohag Biswas ◽  
Hyuna Kwon ◽  
Kelley C. Barsanti ◽  
Nanna Myllys ◽  
James N. Smith ◽  
...  

Free energy landscape obtained from ab initio metadynamics calculations for dimethylamine protonation at the air–water interface.


2019 ◽  
Author(s):  
Xiaoliang Pan ◽  
Pengfei Li ◽  
Junming Ho ◽  
Jingzhi Pu ◽  
Ye Mei ◽  
...  

An efficient and accurate reference potential simulation protocol is proposed for producing ab initio quantum mechanical molecular mechanical (AI-QM/MM) quality free energy profiles for chemical<br>reactions in a solvent or macromolecular environment. This protocol involves three stages: (a) using force matching to recalibrate a semi-empirical quantum mechanical (SE-QM) Hamiltonian for the specific reaction under study; (b) employing the recalibrated SE-QM Hamiltonian (in combination with molecular mechanical force fields) as the reference potential to drive umbrella samplings along the reaction pathway; and (c) computing AI-QM/MM energy values for collected configurations from the sampling and performing weighted thermodynamic perturbation to acquire AI-QM/MM corrected reaction free energy profile. For three model reactions (identity SN2 reaction, Menshutkin reaction, and glycine proton transfer reaction) in aqueous solution and one enzyme reaction (Claisen arrangement in chorismate mutase), our simulations using recalibrated PM3 SE-QM Hamiltonians well reproduced AI-QM/MM free energy profiles (at the B3LYP/6-31G* level of theory) all within 1 kcal/mol with a 20 to 45 fold reduction in the computer time.


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