Identification of Torsional Modes in Complex Molecules Using Redundant Internal Coordinates: The Multistructural Method with Torsional Anharmonicity with a Coupled Torsional Potential and Delocalized Torsions.

Identification of internal-rotation modes in the normal-mode analysis of complex molecules is important for accurately describing the thermodynamic properties and kinetics of complex molecules when it is necessary to treat the anharmonicity of torsions and the multiconformer anharmonicity caused by the internal rotations. However, identifying and distinguishing torsional modes are very challenging because they are coupled to one another. In this work, we present a new strategy to automatically identify torsional vibrations and separate them from the other vibrational modes. By combining a redundant-internal-coordinate auto-generation procedure with torsional projection techniques, we automate the procedure of identifying and separating the coupled torsions, and we show that we can obtain robust and consistent results with various reasonable definitions of redundant-internal-coordinate sets. This model has been implemented in a new development version of the MSTor program to reduce the user input needed for multistructural and torsional anharmonicity (MS-T) calculations. The new method is called multistructural and torsional anharmonicity with a coupled torsional potential and delocalized torsions ([MS-T(CD)]. As example applications, we consider MS-T(CD) calculations on three molecules (2-hexyl radical, n-propylbenzene, and 5-hydroperoxy-6-oxohexanoylperoxy radical) that have multiple rotors and that provide challenges to choosing good sets of nonredundant-internal coordinates, and we compare the performance of the new strategy to five other torsion identification methods. The new strategy is demonstrated to be efficient in separating the torsional and nontorsional elements in the Hessian matrix, as well as in providing reasonable projected nontorsional frequencies to be used for calculations of partition function and thermochemistry.

[1]  P. Marshall,et al.  Experimental and computational studies of the kinetics of the reaction of hydrogen peroxide with the amidogen radical. , 2022, The Journal of chemical physics.

[2]  Zhen Huang,et al.  Theoretical study on isomerization, decomposition and ring-closure reaction kinetics of methyl pentanoate radicals , 2022, Combustion and Flame.

[3]  T. V. Alves,et al.  Differences in the torsional anharmonicity between reactant and transition state: the case of 3-butenal + H abstraction reactions. , 2021, Physical chemistry chemical physics : PCCP.

[4]  G. Merino,et al.  The hindered rotor theory: A review , 2021, WIREs Computational Molecular Science.

[5]  Zhen Huang,et al.  Theoretical kinetics of hydrogen abstraction reactions from propanol isomers by hydroperoxyl radical: Implication for combustion modeling , 2021 .

[6]  S. Luo,et al.  Multistructural Variational Reaction Kinetics of the Simplest Unsaturated Methyl Ester: H-Abstraction from Methyl Acrylate by H, OH, CH3, and HO2 Radicals. , 2021, The journal of physical chemistry. A.

[7]  A. Fernández-Ramos,et al.  TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids , 2021, Journal of Cheminformatics.

[8]  Xuefei Xu,et al.  A kinetics study on hydrogen abstraction reactions of cyclopentane by hydrogen, methyl, and ethyl radicals. , 2021, Physical chemistry chemical physics : PCCP.

[9]  Donald G. Truhlar,et al.  Pilgrim: A thermal rate constant calculator and a chemical kinetics simulator , 2020, Comput. Phys. Commun..

[10]  S. M. Sarathy,et al.  Oxidation kinetics of n-pentanol: A theoretical study of the reactivity of the 1‑hydroxy‑1-peroxypentyl radical , 2020, Combustion and Flame.

[11]  D. Truhlar,et al.  Direct dynamics of a large complex hydrocarbon reaction system: The reaction of OH with exo-tricyclodecane (the main component of Jet Propellant-10) , 2020 .

[12]  A. Fernández-Ramos,et al.  A Combined Systematic-Stochastic Algorithm for the Conformational Search in Flexible Acyclic Molecules , 2020, Frontiers in Chemistry.

[13]  D. Truhlar,et al.  Anharmonic kinetics of the cyclopentane reaction with hydroxyl radical† , 2020, Chemical science.

[14]  S. Luo,et al.  Benchmarking dual-level MS-Tor and DLPNO-CCSD(T) methods for H-abstraction from methyl pentanoate by an OH radical. , 2019, Physical chemistry chemical physics : PCCP.

[15]  Y. Guan,et al.  Investigation on the Thermal Dissociation of Vinyl Nitrite with a Saddle Point Involved , 2019, ACS omega.

[16]  T. He,et al.  Effect of hindered internal rotation treatments on predicting the thermodynamic properties of alkanes. , 2019, Physical chemistry chemical physics : PCCP.

[17]  D. Truhlar,et al.  Relative Rates of Hydrogen Shift Isomerizations Depend Strongly on Multiple-Structure Anharmonicity. , 2018, Journal of the American Chemical Society.

[18]  O. Roberto-Neto,et al.  Multipath VTST rate constants for D + methyl formate reactions: Importance of torsional anharmonicity and conformational flexibility for combustion chemistry , 2018, Chemical Physics Letters.

[19]  D. Truhlar,et al.  Hydrogen shift isomerizations in the kinetics of the second oxidation mechanism of alkane combustion. Reactions of the hydroperoxypentylperoxy OOQOOH radical , 2018, Combustion and Flame.

[20]  M. Natália D. S. Cordeiro,et al.  Q2DTor: A program to treat torsional anharmonicity through coupled pair torsions in flexible molecules , 2018, Comput. Phys. Commun..

[21]  Y. Guan,et al.  Thermodynamic Properties of the Methylmethoxy Radical with Intricate Treatment of Two-Dimensional Hindered Internal Rotations , 2018, Journal of Chemical & Engineering Data.

[22]  S. M. Sarathy,et al.  Theoretical kinetic study of the formic acid catalyzed Criegee intermediate isomerization: multistructural anharmonicity and atmospheric implications. , 2018, Physical chemistry chemical physics : PCCP.

[23]  D. Truhlar,et al.  Kinetics of the Methanol Reaction with OH at Interstellar, Atmospheric, and Combustion Temperatures. , 2018, Journal of the American Chemical Society.

[24]  D. Truhlar,et al.  Variational transition state theory: theoretical framework and recent developments. , 2017, Chemical Society reviews.

[25]  F. Zhang,et al.  Degradation of Carbonyl Hydroperoxides in the Atmosphere and in Combustion. , 2017, Journal of the American Chemical Society.

[26]  Rubén Meana-Pañeda,et al.  Anharmonicity of Coupled Torsions: The Extended Two-Dimensional Torsion Method and Its Use To Assess More Approximate Methods. , 2017, Journal of chemical theory and computation.

[27]  C. Law,et al.  Kinetics and branching fractions of the hydrogen abstraction reaction from methyl butenoates by H atoms. , 2017, Physical chemistry chemical physics : PCCP.

[28]  D. Truhlar,et al.  Path-dependent variational effects and multidimensional tunneling in multi-path variational transition state theory: rate constants calculated for the reactions of HO2 with tert-butanol by including all 46 paths for abstraction at C and all six paths for abstraction at O. , 2016, Physical chemistry chemical physics : PCCP.

[29]  D. Truhlar,et al.  Kinetics of the Hydrogen Abstraction Reaction From 2-Butanol by OH Radical. , 2015, The journal of physical chemistry. A.

[30]  D. Truhlar,et al.  Nanodusty plasma chemistry: a mechanistic and variational transition state theory study of the initial steps of silyl anion-silane and silylene anion-silane polymerization reactions. , 2015, Physical chemistry chemical physics : PCCP.

[31]  Michael J Pilling,et al.  Theoretical chemical kinetics in tropospheric chemistry: methodologies and applications. , 2015, Chemical reviews.

[32]  D. Truhlar,et al.  Entropic Effects on the Free Energies of Clusters in Silane Plasmas , 2015 .

[33]  P. Marshall,et al.  Computational study of the thermochemistry of N₂O₅ and the kinetics of the reaction N₂O₅ + H₂O → 2 HNO₃. , 2014, The journal of physical chemistry. A.

[34]  H. Kjaergaard,et al.  The formation of highly oxidized multifunctional products in the ozonolysis of cyclohexene. , 2014, Journal of the American Chemical Society.

[35]  D. Truhlar,et al.  Prediction of experimentally unavailable product branching ratios for biofuel combustion: the role of anharmonicity in the reaction of isobutanol with OH. , 2014, Journal of the American Chemical Society.

[36]  D. Truhlar,et al.  Large entropic effects on the thermochemistry of silicon nanodusty plasma constituents. , 2014, Journal of the American Chemical Society.

[37]  M. Jamróz.  Vibrational energy distribution analysis (VEDA): scopes and limitations. , 2013, Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy.

[38]  D. Truhlar,et al.  Vibrational configuration interaction using a tiered multimode scheme and tests of approximate treatments of vibrational angular momentum coupling: a case study for methane. , 2013, The journal of physical chemistry. A.

[39]  D. Truhlar,et al.  Quantum Thermochemistry: Multistructural Method with Torsional Anharmonicity Based on a Coupled Torsional Potential. , 2013, Journal of chemical theory and computation.

[40]  D. Truhlar,et al.  Biofuel combustion. Energetics and kinetics of hydrogen abstraction from carbon-1 in n-butanol by the hydroperoxyl radical calculated by coupled cluster and density functional theories and multistructural variational transition-state theory with multidimensional tunneling. , 2012, The journal of physical chemistry. A.

[41]  D. Truhlar,et al.  Multistructural variational transition state theory: kinetics of the hydrogen abstraction from carbon-2 of 2-methyl-1-propanol by hydroperoxyl radical including all structures and torsional anharmonicity. , 2012, The journal of physical chemistry. A.

[42]  D. Truhlar,et al.  Thermochemistry of radicals formed by hydrogen abstraction from 1-butanol, 2-methyl-1-propanol, and butanal. , 2012, The Journal of chemical physics.

[43]  M. Pilling,et al.  MESMER: an open-source master equation solver for multi-energy well reactions. , 2012, The journal of physical chemistry. A.

[44]  Kenneth L. Clarkson,et al.  MSTor: A program for calculating partition functions, free energies, enthalpies, entropies, and heat capacities of complex molecules including torsional anharmonicity , 2012, Comput. Phys. Commun..

[45]  D. Truhlar,et al.  Multi-structural variational transition state theory: kinetics of the 1,5-hydrogen shift isomerization of the 1-butoxyl radical including all structures and torsional anharmonicity. , 2012, Physical chemistry chemical physics : PCCP.

[46]  D. Truhlar,et al.  Statistical thermodynamics of 1-butanol, 2-methyl-1-propanol, and butanal. , 2012, The Journal of chemical physics.

[47]  D. Truhlar,et al.  Statistical thermodynamics of the isomerization reaction between n-heptane and isoheptane. , 2012, Physical chemistry chemical physics : PCCP.

[48]  D. Truhlar,et al.  Multipath variational transition state theory: rate constant of the 1,4-hydrogen shift isomerization of the 2-cyclohexylethyl radical. , 2012, The journal of physical chemistry. A.

[49]  Donald G Truhlar,et al.  Kinetics of the Hydrogen Abstraction from Carbon-3 of 1-Butanol by Hydroperoxyl Radical: Multi-Structural Variational Transition-State Calculations of a Reaction with 262 Conformations of the Transition State. , 2012, The journal of physical chemistry letters.

[50]  Donald G Truhlar,et al.  Practical methods for including torsional anharmonicity in thermochemical calculations on complex molecules: the internal-coordinate multi-structural approximation. , 2011, Physical chemistry chemical physics : PCCP.

[51]  William H Green,et al.  Intramolecular hydrogen migration in alkylperoxy and hydroperoxyalkylperoxy radicals: accurate treatment of hindered rotors. , 2010, The journal of physical chemistry. A.

[52]  M. Head‐Gordon,et al.  Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections. , 2008, Physical chemistry chemical physics : PCCP.

[53]  D. Truhlar,et al.  The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals , 2008 .

[54]  Jim Pfaendtner,et al.  The 1-D hindered rotor approximation , 2007 .

[55]  Benjamin A. Ellingson,et al.  Statistical thermodynamics of bond torsional modes: tests of separable, almost-separable, and improved Pitzer-Gwinn approximations. , 2006, The Journal of chemical physics.

[56]  V Van Speybroeck,et al.  An extended hindered-rotor model with incorporation of Coriolis and vibrational-rotational coupling for calculating partition functions and derived quantities. , 2006, The Journal of chemical physics.

[57]  D. Truhlar,et al.  High-precision quantum thermochemistry on nonquasiharmonic potentials: converged path-integral free energies and a systematically convergent family of generalized Pitzer-Gwinn approximations. , 2005, The journal of physical chemistry. A.

[58]  F. Weigend,et al.  Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy. , 2005, Physical chemistry chemical physics : PCCP.

[59]  Michel Waroquier,et al.  Why does the uncoupled hindered rotor model work well for the thermodynamics of n-alkanes? , 2005 .

[60]  Walter Thiel,et al.  Linear scaling geometry optimisation and transition state search in hybrid delocalised internal coordinates , 2000 .

[61]  N. Handy,et al.  Extensions and tests of “multimode”: a code to obtain accurate vibration/rotation energies of many-mode molecules , 1998 .

[62]  Philippe Y. Ayala,et al.  Identification and treatment of internal rotation in normal mode vibrational analysis , 1998 .

[63]  Jon Baker,et al.  The generation and use of delocalized internal coordinates in geometry optimization , 1996 .

[64]  M. Frisch,et al.  Using redundant internal coordinates to optimize equilibrium geometries and transition states , 1996, J. Comput. Chem..

[65]  T. Dunning,et al.  Electron affinities of the first‐row atoms revisited. Systematic basis sets and wave functions , 1992 .

[66]  B. C. Garrett,et al.  Critical tests of variational transition state theory and semiclassical tunneling methods for hydrogen and deuterium atom transfer reactions and use of the semiclassical calculations to interpret the overbarrier and tunneling dynamics , 1991 .

[67]  G. Natanson.  Separation and semiclassical quantization of bending motion near linear geometries of a triatom , 1990 .

[68]  Donald G. Truhlar,et al.  Importance of quartic anharmonicity for bending partition functions in transition-state theory , 1979 .

[69]  Kenneth S. Pitzer,et al.  Energy Levels and Thermodynamic Functions for Molecules with Internal Rotation. III. Compound Rotation , 1949 .

[70]  Kenneth S. Pitzer,et al.  Energy Levels and Thermodynamic Functions for Molecules with Internal Rotation: II. Unsymmetrical Tops Attached to a Rigid Frame , 1946 .

[71]  Kenneth S. Pitzer,et al.  Energy Levels and Thermodynamic Functions for Molecules with Internal Rotation I. Rigid Frame with Attached Tops , 1942 .