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Lawson KE, Evans MN, Dekle JK, Adamczyk AJ. Computing the Differences between Asn-X and Gln-X Deamidation and Their Impact on Pharmaceutical and Physiological Proteins: A Theoretical Investigation Using Model Dipeptides. J Phys Chem A 2023; 127:57-70. [PMID: 36549007 DOI: 10.1021/acs.jpca.2c06511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein deamidation is a degradation mechanism that significantly impacts both pharmaceutical and physiological proteins. Deamidation impacts two amino acids, Asn and Gln, where the net neutral residues are converted into their acidic forms. While there are multiple similarities between the reaction mechanisms of the two residues, the impact of Gln deamidation has been noted to be most significant on physiological proteins while Asn deamidation has been linked to both pharmaceutical and physiological proteins. For this purpose, we sought to analyze the thermochemical and kinetic properties of the different reactions of Gln deamidation relative to Asn deamidation. In this study, we mapped the deamidation of Gln-X dipeptides into Glu-X dipeptides using density functional theory (DFT). Full network mapping facilitated the prediction of reaction selectivity between the two primary pathways, as well as between the two products of Gln-X deamidation as a function of solvent dielectric. To achieve this analysis, we studied a total of 77 dipeptide reactions per solvent dielectric (308 total reactions). Modeled at a neutral pH and using quantum chemical and statistical thermodynamic methods, we computed the following values: enthalpy of reaction (ΔHRXN), entropy (ΔSRXN), Gibbs free energy of reaction (ΔGRXN), activation energy (EA), and the Arrhenius preexponential factor (log(A)) for each dipeptide. Additionally, using chemical reaction principles, we generated a database of computed rate coefficients for all possible N-terminus Gln-X deamidation reactions at a neutral pH, predicted the most likely deamidation reaction mechanism for each dipeptide reaction, analyzed our results against our prior study on Asn-X deamidation, and matched our results against qualitative trends previously noted by experimental literature.
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Affiliation(s)
- Katherine E Lawson
- Department of Chemical Engineering, Auburn University, Auburn, Alabama36830, United States
| | - Megan N Evans
- Department of Chemical Engineering, Auburn University, Auburn, Alabama36830, United States
| | - Joseph K Dekle
- Department of Chemical Engineering, Auburn University, Auburn, Alabama36830, United States
| | - Andrew J Adamczyk
- Department of Chemical Engineering, Auburn University, Auburn, Alabama36830, United States
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Lawson KE, Dekle JK, Adamczyk AJ. Towards pharmaceutical protein stabilization: DFT and statistical learning studies on non-enzymatic peptide hydrolysis degradation mechanisms. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Claveau EE, Choi Y, Adamczyk AJ, Miliordos E. Electronic structure of the ground and excited states of neutral and charged silicon hydrides, SiH x0/+/-, x = 1-4. Phys Chem Chem Phys 2022; 24:11782-11790. [PMID: 35506867 DOI: 10.1039/d2cp00956k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ground and excited electronic states of the titled species are investigated with multi-reference configuration interaction and diffuse basis sets. We found that in addition to the valence orbitals, the inclusion of the 4s, 4p, and especially 3d orbitals (although with minimal population) of silicon in the active space of the reference complete active space self-consistent field wavefunction are necessary for the proper convergence of the calculations. We also demonstrate that the aug-cc-pVTZ basis set provides quite accurate results compared to both larger basis sets and basis set limit results at a lower computational cost. The excited states involve excitations within the 3s and 3p orbitals of silicon (especially for the mono- and di-hydrides), followed by excitations from the Si-H bonding orbitals to either silicon valence or Rydberg (4s, 4p) orbitals. The number of electronic states per energy unit decrease as we add hydrogen atoms, and the first excited state of SiH4 is at 9.0 eV and leads to SiH3 + H. All species have stable ground state structures with all hydrogen atoms bound to silicon, except for SiH4+ and SiH4-. The former dissociates to SiH2+ + H2, while the latter loses an electron or can dissociate forming H2 as well.
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Affiliation(s)
- Emily E Claveau
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849-5312, USA.
| | - Yeseul Choi
- Department of Chemical Engineering, Auburn University, Auburn, AL 36849-5312, USA.
| | - Andrew J Adamczyk
- Department of Chemical Engineering, Auburn University, Auburn, AL 36849-5312, USA.
| | - Evangelos Miliordos
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849-5312, USA.
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Choi Y, Adamczyk AJ. Competitive Hydrogen Migration in Silicon Nitride Nanoclusters: Reaction Kinetics Generalized from Supervised Machine Learning. J Phys Chem A 2022; 126:2677-2689. [PMID: 35452242 DOI: 10.1021/acs.jpca.2c01050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rate coefficients for 52 hydrogen shift reactions for silicon nitrides containing up to 6 atoms of silicon and nitrogen have been calculated using the G3//B3LYP composite method and statistical thermodynamics. The overall reaction of substituted acyclic and cyclic silylenes to their respective silene and imine species by a 1,2-hydrogen shift reaction was sorted by three different types of H shift reactions using overall reaction thermodynamics: (1) endothermic H shift between N and Si:, (2) endothermic H shift between Si and Si:, and (3) exothermic H shift between Si and Si:. Endothermic H shift reactions between Si atoms have one dominant activation barrier where the exothermic H shift reaction between Si atoms has two barriers and a stable intermediate. The rate-determining step was determined to be from the intermediate to the substituted silene, and then kinetic parameters for the overall reaction were calculated for the two-step pathway. The single event pre-exponential factors, Ã, and activation energies, Ea, for the three different classes of hydrogen shift reactions of silicon nitrides were computed. The hydrogen shift reaction was explored for acyclic and cyclic monofunctional silicon nitrides, and the type of hydrogen shift reaction gives the most significant influence on the kinetic parameters. Using a supervised machine learning approach, the models for predicting the energy barrier of three different hydrogen shift reactions were generalized and suggested based on selected descriptors.
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Affiliation(s)
- Yeseul Choi
- Department of Chemical Engineering, Auburn University, 212 Ross Hall, Auburn, Alabama 36830, United States
| | - Andrew J Adamczyk
- Department of Chemical Engineering, Auburn University, 212 Ross Hall, Auburn, Alabama 36830, United States
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Lawson KE, Dekle JK, Evans MN, Adamczyk AJ. Deamidation reaction network mapping of pharmacologic and related proteins: impact of solvation dielectric on the degradation energetics of asparagine dipeptides. REACT CHEM ENG 2022. [DOI: 10.1039/d2re00110a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Asn-X deamidation pathways in the FV region of the monoclonal antibody (mAb).
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Affiliation(s)
| | - Joseph K. Dekle
- Department of Chemical Engineering, Auburn University, Auburn, AL, USA
| | - Megan N. Evans
- Department of Chemical Engineering, Auburn University, Auburn, AL, USA
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Azad T, Torres HF, Auad ML, Elder T, Adamczyk AJ. Isolating key reaction energetics and thermodynamic properties during hardwood model lignin pyrolysis. Phys Chem Chem Phys 2021; 23:20919-20935. [PMID: 34541592 DOI: 10.1039/d1cp02917g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computational studies on the pyrolysis of lignin using electronic structure methods have been largely limited to dimeric or trimeric models. In the current work we have modeled a lignin oligomer consisting of 10 syringyl units linked through 9 β-O-4' bonds. A lignin model of this size is potentially more representative of the polymer in angiosperms; therefore, we used this representative model to examine the behavior of hardwood lignin during the initial steps of pyrolysis. Using this oligomer, the present work aims to determine if and how the reaction enthalpies of bond cleavage vary with positions within the chain. To accomplish this, we utilized a composite method using molecular mechanics based conformational sampling and quantum mechanically based density functional theory (DFT) calculations. Our key results show marked differences in bond dissociation enthalpies (BDE) with the position. In addition, we calculated standard thermodynamic properties, including enthalpy of formation, heat capacity, entropy, and Gibbs free energy for a wide range of temperatures from 25 K to 1000 K. The prediction of these thermodynamic properties and the reaction enthalpies will benefit further computational studies and cross-validation with pyrolysis experiments. Overall, the results demonstrate the utility of a better understanding of lignin pyrolysis for its effective valorization.
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Affiliation(s)
- Tanzina Azad
- Department of Chemical Engineering, Auburn University, Auburn, AL, USA.
| | - Hazl F Torres
- Department of Chemical Engineering, Auburn University, Auburn, AL, USA.
| | - Maria L Auad
- Department of Chemical Engineering, Auburn University, Auburn, AL, USA. .,Center for Polymer and Advanced Composites, Auburn, AL, USA
| | - Thomas Elder
- United States Department of Agriculture (USDA) Forest Service, Southern Research Station, Auburn, AL, USA
| | - Andrew J Adamczyk
- Department of Chemical Engineering, Auburn University, Auburn, AL, USA.
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Choi Y, Preston TJ, Adamczyk AJ. Data-Driven Investigation of Monosilane and Ammonia Co-Pyrolysis to Silicon-Nitride-Based Ceramic Nanomaterials. Chemphyschem 2020; 21:2627-2642. [PMID: 32853448 DOI: 10.1002/cphc.202000561] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/26/2020] [Indexed: 11/12/2022]
Abstract
With its high strength, high thermal stability, low density, and high electrical resistance, silicon-nitride-based ceramics have been widely used as gate insulating layers, oxidation masks, and passivation layers. Employing SiN nanomaterials in anode applications also improves rate performances and cycling stability of the lithium-ion batteries. However, a fundamental understanding of the SiN synthetic process remains elusive. SiN gas-phase synthesis can be tailored with a comprehensive understanding of the underlying thermodynamics. In comparison to the characterization data available for solid-state SiN materials, high-level theoretical studies on gas-phase materials possessing Si-N bonds and comprehensive investigation of the SiN chemistry, particularly for nanoclusters, are very uncommon. Thus, we performed a theoretical study of Si and SiN alloy acyclic hydrides and polycyclic clusters to predict electronic structures and thermochemistry using quantum chemical calculation and statistical thermodynamics. Electronic properties by way of highest and lowest occupied molecular orbital energy gap and natural bonding orbitals analysis were calculated to explore the influence of elemental composition and geometry on the stability. Our studies provide characteristic data of SiN species for a data-driven approach to map the design space for discovery of novel silicon-nitride-based ceramic materials for advanced electronic and coating applications.
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Affiliation(s)
- Yeseul Choi
- Auburn University, Department of Chemical Engineering, Auburn, AL 36849, USA
| | - Thomas J Preston
- Institute for Energy Technology (IFE), Department of Solar Energy and Battery Technology, P.O. Box 40, 2027, Kjeller, Norway
| | - Andrew J Adamczyk
- Auburn University, Department of Chemical Engineering, Auburn, AL 36849, USA
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Lozano-Blanco G, Tatarchuk BJ, Adamczyk AJ. Building a Microkinetic Model from First Principles for Higher Amine Synthesis on Pd Catalyst. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b03577] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gisela Lozano-Blanco
- Department of Chemical Engineering, Auburn University, Auburn, Alabama 36849-5127, United States
| | - Bruce J. Tatarchuk
- Department of Chemical Engineering, Auburn University, Auburn, Alabama 36849-5127, United States
| | - Andrew J. Adamczyk
- Department of Chemical Engineering, Auburn University, Auburn, Alabama 36849-5127, United States
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Bhattacharyya P, Rai DK, Shukla A. Systematic First-Principles Configuration-Interaction Calculations of Linear Optical Absorption Spectra in Silicon Hydrides: Si 2H 2n ( n = 1-3). J Phys Chem A 2019; 123:8619-8631. [PMID: 31508955 DOI: 10.1021/acs.jpca.9b06054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have performed first-principles electron-correlated calculations employing large basis sets to optimize the geometries and to compute linear optical absorption spectra of various low-lying conformers of silicon hydrides: Si2H2n, n = 1, 2, 3. The geometry optimization for various isomers was carried out at the coupled-cluster singles-doubles-perturbative-triples [CCSD(T)] level of theory, while their excited states and absorption spectra were computed using a large-scale multireference singles-doubles configuration-interaction approach, which includes electron-correlation effects at a sophisticated level. Our calculated spectra are the first ones for Si2H2 and Si2H4 conformers, while for Si2H6, we obtain excellent agreement with the experimental measurements, suggesting that our computational approach is reliable. Our calculated absorption spectra exhibit a strong structure-property relationship, suggesting the possibility of identifying various conformers based on their optical absorption fingerprints. Furthermore, we have also performed geometry optimization for the selected optically excited states, providing insights into their character.
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Affiliation(s)
- Pritam Bhattacharyya
- Department of Physics , Indian Institute of Technology Bombay , Powai , Mumbai 400076 , India
| | - Deepak Kumar Rai
- Department of Physics , Indian Institute of Technology Bombay , Powai , Mumbai 400076 , India
| | - Alok Shukla
- Department of Physics , Indian Institute of Technology Bombay , Powai , Mumbai 400076 , India
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Choi Y, Adamczyk AJ. Tuning Hydrogenated Silicon, Germanium, and SiGe Nanocluster Properties Using Theoretical Calculations and a Machine Learning Approach. J Phys Chem A 2018; 122:9851-9868. [PMID: 30484641 DOI: 10.1021/acs.jpca.8b09797] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There are limited studies available that predict the properties of hydrogenated silicon-germanium (SiGe) clusters. For this purpose, we conducted a computational study of 46 hydrogenated SiGe clusters (Si xGe yH z, 1 < X + Y ≤ 6) to predict the structural, thermochemical, and electronic properties. The optimized geometries of the Si xGe yH z clusters were investigated using quantum chemical calculations and statistical thermodynamics. The clusters contained 6 to 9 fused Si-Si, Ge-Ge, or Si-Ge bonds, i.e., bonds participating in more than one 3- to 4-membered rings, and different degrees of hydrogenation, i.e., the ratio of hydrogen to Si/Ge atoms varied depending on cluster size and degree of multifunctionality. Our studies have established trends in standard enthalpy of formation, standard entropy, and constant pressure heat capacity as a function of cluster composition and structure. A novel bond additivity correction model for SiGe chemistry was regressed from experimental data on seven acyclic Si/Ge/SiGe species to improve the accuracy of the standard enthalpy of formation predictions. Electronic properties were investigated by analysis of the HOMO-LUMO energy gap to study the effect of elemental composition on the electronic stability of Si xGe yH z clusters. These properties will be discussed in the context of tailored nanomaterials design and generalized using a machine learning approach.
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Affiliation(s)
- Yeseul Choi
- Auburn University , Department of Chemical Engineering , Auburn , Alabama 36849 , United States
| | - Andrew J Adamczyk
- Auburn University , Department of Chemical Engineering , Auburn , Alabama 36849 , United States
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Mottet M, Tecmer P, Boguslawski K, Legeza Ö, Reiher M. Quantum entanglement in carbon–carbon, carbon–phosphorus and silicon–silicon bonds. Phys Chem Chem Phys 2014; 16:8872-80. [DOI: 10.1039/c4cp00277f] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We present a quantum entanglement analysis to dissect the bond orders in polyatomic molecules.
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Affiliation(s)
- Matthieu Mottet
- ETH Zürich
- Laboratory of Physical Chemistry
- CH-8093 Zürich, Switzerland
| | - Paweł Tecmer
- ETH Zürich
- Laboratory of Physical Chemistry
- CH-8093 Zürich, Switzerland
| | | | - Örs Legeza
- Strongly Correlated Systems “Lendület” Research Group
- Wigner Research Center for Physics
- H-1525 Budapest, Hungary
| | - Markus Reiher
- ETH Zürich
- Laboratory of Physical Chemistry
- CH-8093 Zürich, Switzerland
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