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Shannon RJ, Hornung B, Tew DP, Glowacki DR. Anharmonic Molecular Mechanics: Ab Initio Based Morse Parametrizations for the Popular MM3 Force Field. J Phys Chem A 2019; 123:2991-2999. [PMID: 30793911 DOI: 10.1021/acs.jpca.8b12006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methodologies for creating reactive potential energy surfaces from molecular mechanics force-fields are becoming increasingly popular. To date, molecular mechanics force-fields in biochemistry and small molecule organic chemistry tend to use harmonic expressions to treat bonding stretches, which is a poor approximation in reactive and nonequilibirum molecular dynamics simulations since bonds are often displaced significantly from their equilibrium positions. For such applications there is need for a better treatment of anharmonicity. In this contribution, Morse bonding potentials have been extensively parametrized for the atom types in the MM3 force field of Allinger and co-workers using high level CCSD(T)(F12*) energies. To our knowledge this is among the first instances of a comprehensive parametrization of Morse potentials in a popular organic chemistry force field. In the context of molecular dynamics simulations, these data will: (1) facilitate the fitting of reactive potential energy surfaces using empirical valence bond approaches and (2) enable more accurate treatments of energy transfer.
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Affiliation(s)
- R J Shannon
- School of Chemistry, Cantock's Close , University of Bristol , Bristol BS8 1TS , U.K.,Department of Mechanical Engineering , Stanford University , 452 Escondido Mall , Stanford , California 94305 , United States
| | - B Hornung
- School of Chemistry, Cantock's Close , University of Bristol , Bristol BS8 1TS , U.K
| | - D P Tew
- School of Chemistry, Cantock's Close , University of Bristol , Bristol BS8 1TS , U.K
| | - D R Glowacki
- School of Chemistry, Cantock's Close , University of Bristol , Bristol BS8 1TS , U.K.,Department of Computer Science , University of Bristol , Bristol BS8 1UB , U.K
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Diccianni JB, Hu C, Diao T. N−N Bond Forming Reductive Elimination via a Mixed‐Valent Nickel(II)–Nickel(III) Intermediate. Angew Chem Int Ed Engl 2016; 55:7534-8. [DOI: 10.1002/anie.201602566] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Justin B. Diccianni
- Chemistry Department New York University 100 Washington Square E. New York NY 10003 USA
| | - Chunhua Hu
- Chemistry Department New York University 100 Washington Square E. New York NY 10003 USA
| | - Tianning Diao
- Chemistry Department New York University 100 Washington Square E. New York NY 10003 USA
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Diccianni JB, Hu C, Diao T. N−N Bond Forming Reductive Elimination via a Mixed‐Valent Nickel(II)–Nickel(III) Intermediate. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602566] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Justin B. Diccianni
- Chemistry Department New York University 100 Washington Square E. New York NY 10003 USA
| | - Chunhua Hu
- Chemistry Department New York University 100 Washington Square E. New York NY 10003 USA
| | - Tianning Diao
- Chemistry Department New York University 100 Washington Square E. New York NY 10003 USA
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Sun H, Zhang P, Law CK. Gas-phase kinetics study of reaction of OH radical with CH3NHNH2 by second-order multireference perturbation theory. J Phys Chem A 2012; 116:5045-56. [PMID: 22545789 DOI: 10.1021/jp3021529] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The gas-phase kinetics of H-abstraction reactions of monomethylhydrazine (MMH) by OH radical was investigated by second-order multireference perturbation theory and two-transition-state kinetic model. It was found that the abstractions of the central and terminal amine H atoms by the OH radical proceed through the formation of two hydrogen bonded preactivated complexes with energies of 6.16 and 5.90 kcal mol(-1) lower than that of the reactants, whereas the abstraction of methyl H atom is direct. Due to the multireference characters of the transition states, the geometries and ro-vibrational frequencies of the reactant, transition states, reactant complexes, and product complexes were optimized by the multireference CASPT2/aug-cc-pVTZ method, and the energies of the stationary points of the potential energy surface were refined at the QCISD(T)/CBS level via extrapolation of the QCISD(T)/cc-pVTZ and QCISD(T)/cc-pVQZ energies. It was found that the abstraction reactions of the central and two terminal amine H atoms of MMH have the submerged energy barriers with energies of 2.95, 2.12, and 1.24 kcal mol(-1) lower than that that of the reactants respectively, and the abstraction of methyl H atom has a real energy barrier of 3.09 kcal mol(-1). Furthermore, four MMH radical-H(2)O complexes were found to connect with product channels and the corresponding transition states. Consequently, the rate coefficients of MMH + OH for the H-abstraction of the amine H atoms were determined on the basis of a two-transition-state model, with the total energy E and angular momentum J conserved between the two transition-state regions. In units of cm(3) molecule(-1) s(-1), the rate coefficient was found to be k(1) = 3.37 × 10(-16)T(1.295) exp(1126.17/T) for the abstraction of the central amine H to form the CH(3)N(•)NH(2) radical, k(2) = 2.34 × 10(-17)T(1.907) exp(1052.26/T) for the abstraction of the terminal amine H to form the trans-CH(3)NHN(•)H radical, k(3) = 7.41 × 10(-20)T(2.428) exp(1343.20/T) for the abstraction of the terminal amine H to form the cis-CH(3)NHN(•)H radical, and k(4) = 9.13 × 10(-21)T(2.964) exp(-114.09/T) for the abstraction of the methyl H atom to form the C(•)H(2)NHNH(2) radical, respectively. Assuming that the rate coefficients are additive, the total rate coefficient of these theoretical predictions quantitatively agrees with the measured rate constant at temperatures of 200-650 K, with no adjustable parameters.
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Affiliation(s)
- Hongyan Sun
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08544, USA.
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Łodyga W, Makarewicz J. Torsion-wagging tunneling and vibrational states in hydrazine determined from its ab initio potential energy surface. J Chem Phys 2012; 136:174301. [DOI: 10.1063/1.4705267] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Nagy PI, Messer WS. Theoretical studies of the in-solution isomeric protonation of non-aromatic six-member rings with two nitrogens. J Phys Chem B 2011; 115:4758-67. [PMID: 21452810 DOI: 10.1021/jp202241m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For exploring the preferred site for hydrogen bond formation, theoretical calculations have been performed for a number of six-member, nonaromatic rings allowing for alternative protonation on the ring nitrogens. Gas-phase protonation studies for test molecules indicate that the B3LYP/aug-cc-pvtz and QCISD(T)(CBS) calculations approach the experimental values within about 1 kcal/mol with considerable improvement for relative enthalpies and free energies. Relative free energies calculated at the IEF-PCM/B3LYP/aug-cc-pvtz level predict favorable protonation on the tertiary rather than on the secondary nitrogen both in aqueous solution and in a dichloromethane solvent for saturated rings. Protonation on a nitrogen atom next to a C═C bond is disfavored due to a large increase in internal energy. Monte Carlo simulations considering a counterion and Ewald summation for the long-range electrostatic effects for a 0.1 molar model system predict ΔG(solv)/MC values generally less negative than from the IEF-PCM calculations. These results make the protonation on the tertiary nitrogen even more favored. The solute-solvent pair-energy distribution depends sensitively on the applied model. In conclusion, the freely moving anion has been considered as the most relevant model with overall neutrality for the system and applying the least restrictions.
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Affiliation(s)
- Peter I Nagy
- Center for Drug Design and Development, The University of Toledo, Toledo, Ohio 43606-3390, United States.
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Yu D, Dong C, Yu Z, Cheng M, Du Y, Zhu Q, Zhang C. Comparison between 1-methylphenylhydrazine and phenylhydrazine in the S1 state: Structure, energies and lifetime. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.09.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Xiao D, Yu D, Xu X, Yu Z, Cheng M, Du Y, Zheng W, Zhu Q, Zhang C. Theoretical and REMPI spectroscopic study on phenylhydrazine and phenylhydrazine-(Ar)n (n=1, 2) van der Waals complexes. Phys Chem Chem Phys 2009; 11:3532-8. [PMID: 19421558 DOI: 10.1039/b818688j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phenylhydrazine and its van der Waals complexes with one or two argon atoms were investigated with theoretical calculations and resonant two photon ionization (R2PI) spectroscopy. The ab initio and DFT calculations found a conversion of the orbital hybridization of the Nbeta atom from sp3-like in the S0 state to sp2-like in the S1 state, suggesting that the lone pair electrons of the Nbeta atom are involved in a super p-p-pi conjugation over the skeleton of phenylhydrazine in the S1 state. The structural change of the hydrazino group in the S1<--S0 electronic transition was reflected by the vibrational excitations of the hydrazino group observed in the 1C-R2PI spectrum. The band origin of the S1<--S0 transition is determined to be 33610 cm(-1) and the adiabatic ionization energy (IE) of phenylhydrazine, measured by 2C-R2PI spectroscopy, is 62829+/-15 cm(-1). The S1<--S0 electronic transitions of phenylhydrazine-Ar and phenylhydrazine-Ar2 complexes were also observed in the 1C-R2PI spectrum, and their band origins are, respectively, red-shifted by 39 and 80 cm(-1) from that of phenylhydrazine.
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Affiliation(s)
- Daoqing Xiao
- The State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, PR China
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Bond D. Computational Methods in Organic Thermochemistry. 2. Enthalpies and Free Energies of Formation for Functional Derivatives of Organic Hydrocarbons. J Org Chem 2007; 72:7313-28. [PMID: 17713954 DOI: 10.1021/jo071213a] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Standard state enthalpies and free energies of formation for nitrogen-, oxygen-, sulfur-, fluorine-, chlorine-, and silicon-containing compounds can be computed with reasonable accuracy (usually within four and often two kJ/mol) using the G3 and G3MP2 model chemistries. In several of the families, compounds with as many as 10 carbon atoms have been computed. Larger errors are found in the free energies of these longer chain molecules which can be reduced by compensating for the presence of multiple conformers having a significant population at 298.15 K. In some instances, those substances showing large deviations are found to have experimental energies that may be erroneous.
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Affiliation(s)
- Douglas Bond
- Computer Chemie Centrum, Friedrich-Alexander-Universität, Erlangen-Nürnberg, Nägelsbach Strasse 25, 91052 Erlangen, Germany.
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Sun H, Law CK. Thermochemical and Kinetic Analysis of the Thermal Decomposition of Monomethylhydrazine: An Elementary Reaction Mechanism. J Phys Chem A 2007; 111:3748-60. [PMID: 17388291 DOI: 10.1021/jp067591l] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reaction kinetics for the thermal decomposition of monomethylhydrazine (MMH) was studied with quantum Rice-Ramsperger-Kassel (QRRK) theory and a master equation analysis for pressure falloff. Thermochemical properties were determined by ab initio and density functional calculations. The entropies, S degrees (298.15 K), and heat capacities, Cp degrees (T) (0 < or = T/K < or = 1500), from vibrational, translational, and external rotational contributions were calculated using statistical mechanics based on the vibrational frequencies and structures obtained from the density functional study. Potential barriers for internal rotations were calculated at the B3LYP/6-311G(d,p) level, and hindered rotational contributions to S degrees (298.15 K) and Cp degrees (T) were calculated by solving the Schrödinger equation with free rotor wave functions, and the partition coefficients were treated by direct integration over energy levels of the internal rotation potentials. Enthalpies of formation, DeltafH degrees (298.15 K), for the parent MMH (CH3NHNH2) and its corresponding radicals CH3N*NH2, CH3NHN*H, and C*H2NHNH2 were determined to be 21.6, 48.5, 51.1, and 62.8 kcal mol(-1) by use of isodesmic reaction analysis and various ab initio methods. The kinetic analysis of the thermal decomposition, abstraction, and substitution reactions of MMH was performed at the CBS-QB3 level, with those of N-N and C-N bond scissions determined by high level CCSD(T)/6-311++G(3df,2p)//MPWB1K/6-31+G(d,p) calculations. Rate constants of thermally activated MMH to dissociation products were calculated as functions of pressure and temperature. An elementary reaction mechanism based on the calculated rate constants, thermochemical properties, and literature data was developed to model the experimental data on the overall MMH thermal decomposition rate. The reactions of N-N and C-N bond scission were found to be the major reaction paths for the modeling of MMH homogeneous decomposition at atmospheric conditions.
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Affiliation(s)
- Hongyan Sun
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08544, USA.
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Song JW, Lee HJ, Choi YS, Yoon CJ. Origin of Rotational Barriers of the N−N Bond in Hydrazine: NBO Analysis. J Phys Chem A 2006; 110:2065-71. [PMID: 16451044 DOI: 10.1021/jp055755c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrazine passes through two transition states, TS1 (phi = 0 degrees ) and TS2 (phi = 180 degrees ), in the course of internal rotation around its N-N bond. The origin of the corresponding rotational barriers in hydrazine has been extensively studied by experimental and theoretical methods. Here, we used natural bond orbital (NBO) analysis and energy decomposition of rotational barrier energy (DeltaE(barrier)) to understand the origin of the torsional potential energy profile of this molecule. DeltaE(barrier) was dissected into structural (DeltaE(struc)), steric exchange (DeltaE(steric)), and hyperconjugative (DeltaE(deloc)) energy contributions. In both transition states, the major barrier-forming contribution is DeltaE(deloc). The TS2 barrier is lowered by pyramidalization of nitrogen atoms through lowering DeltaE(struc), not by N-N bond lengthening through lowering DeltaE(steric). Higher pyramidality of nitrogen atoms of TS2 than that of TS1 explains well why the N-N bond of TS2 is longer than that of TS1. Finally, the steric repulsion between nitrogen lone pairs does not determine the rotational barrier; nuclear-nuclear Coulombic repulsion between outer H/H atoms in TS1 plays an important role in increasing DeltaE(struc). Taken together, we explain the reason for the different TS1 and TS2 barriers. We show that NBO analysis is a useful tool for understanding structures and potential energy surfaces of compounds containing the N-N bond.
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Affiliation(s)
- Jong-Won Song
- Department of Chemistry, Korea University, 1 Anam-dong, Seoul 136-701, Korea
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Ichimura K, Futami Y, Kudoh S, Nakata M. Hydrogen-atom inversion of 1,2-dimethylhydrazine in low-temperature rare-gas matrices. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.03.155] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Durig JR, Zheng C. On the vibrational spectra and conformational stability of 1,1-dimethylhydrazine from temperature dependent FT-IR spectra of krypton solutions and ab initio calculations. J Mol Struct 2004. [DOI: 10.1016/j.molstruc.2003.11.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Machado FB, Roberto-Neto O. An ab initio study of the equilibrium geometry and vibrational frequencies of hydrazine. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(01)01434-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Tšubrik O, Burk P, Pehk T, Mäeorg U. Conformational analysis of 1-acetyl-2-methylhydrazine. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0166-1280(01)00436-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Graña A, Mosquera R. The evolution of the atomic and bond properties during internal rotation of the hydrazine molecule. J Mol Struct 2000. [DOI: 10.1016/s0022-2860(00)00652-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Schäfer L, Cao M, Ramek M, Teppen BJ, Newton SQ, Siam K. Conformational geometry functions: additivity and cooperative effects. J Mol Struct 1997. [DOI: 10.1016/s0022-2860(97)00023-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Armstrong DA, Yu D, Rauk A. Gas Phase and Aqueous Thermochemistry of Hydrazine and Related Radicals and the Energy Profiles of Reactions with H• and OH•: An ab Initio Study. J Phys Chem A 1997. [DOI: 10.1021/jp964057c] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D. A. Armstrong
- Department of Chemistry, The University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - D. Yu
- Department of Chemistry, The University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - A. Rauk
- Department of Chemistry, The University of Calgary, Calgary, Alberta, Canada T2N 1N4
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