505 results on '"HENRY F. SCHAEFER"'
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2. Iron Carbonyl Complexes of [2.2.2]Hericene as a Rigid Tris(1,3-diene) Ligand
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Jinfeng Luo, Haoyu Chen, Huidong Li, Yongxiang Zheng, Qunchao Fan, Robert Bruce King, and Henry F. Schaefer
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Hericenen ,iron carbonyl compounds ,density functional methods ,Organic chemistry ,QD241-441 - Abstract
Hericene is an unusual hexaolefin consisting of three 1,3-diene units located on a rigid bicyclo [2.2.2]octane framework that restricts the geometrical relationships of metal atoms bonded to these olefinic units. In order to explore possible effects of this rigidity limiting metal–metal interaction in polynuclear derivatives possibly stabilizing coordinatively unsaturated species, the structures and energetics of the hericene iron carbonyl complexes (hericene)Fem(CO)n (m = 1, n = 3; m = 2, n = 6, 5; m = 3, n = 9, 8) have been investigated by density functional theory. The lowest-energy (hericene)Fem(CO)3m (m = 1, 2, 3) structures have the cavities of the hericene ligand filled with a single Fe(CO)3 moiety bonded to a 1,3-diolefin unit. Such species have been synthesized by the reaction of Fe2(CO)9 with hericene. For the (hericene)Fe2(CO)5 system, the lowest energy structures are singlet structures with an Fe(CO)3 unit bonded to a 1,3-diene unit in one hericene cavity and an Fe(CO)2 unit in another hericene cavity bonded to three C=C double bonds from two 1,3-diene units. Higher energy (hericene)Fe2(CO)5 structures include a structure in which a single hericene cavity contains a Fe2(CO)4(µ-CO) moiety with each iron atom bonded to a 1,3-diene unit. In addition, both singlet and triplet (hericene)Fe2(CO)5 structures are found in which an Fe(CO)3 moiety and an Fe(CO)2 moiety located in separate hericene cavities are each bonded to a 1,3-diene unit. The lowest-energy (hericene)Fe3(CO)8 structures have two hericene cavities containing Fe(CO)3 moieties fully bonded to 1,3-diene units and a third hericene cavity containing an Fe(CO)2 moiety fully bonded to a 1,3-diene unit.
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- 2024
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3. Trinuclear and Tetranuclear Ruthenium Carbonyl Nitrosyls: Oxidation of a Carbonyl Ligand by an Adjacent Nitrosyl Ligand
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Shengchun Chen, Xuejun Feng, Yaoming Xie, R. Bruce King, and Henry F. Schaefer
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trinuclear and tetranuclear carbonyls ,ruthenium ,density functional theory ,Organic chemistry ,QD241-441 - Abstract
Trinuclear and tetranuclear ruthenium carbonyls of the types Ru3(CO)n(NO)2, Ru3(N)(CO)n(NO), Ru3(N)2(CO)n, Ru3(N)(CO)n(NCO), Ru3(CO)n(NCO)(NO), Ru4(N)(CO)n(NO), Ru4(N)(CO)n(NCO), and Ru4(N)2(CO)n related to species observed experimentally in the chemistry of Ru3(CO)10(µ-NO)2 have been investigated using density functional theory. In all cases, the experimentally observed structures have been found to be low-energy structures. The low-energy trinuclear structures typically have a central strongly bent Ru–Ru–Ru chain with terminal CO groups and bridging nitrosyl, isocyanate, and/or nitride ligands across the end of the chain. The low-energy tetranuclear structures typically have a central Ru4N unit with terminal CO groups and a non-bonded pair of ruthenium atoms bridged by a nitrosyl or isocyanate group.
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- 2024
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4. Mini-Review on Structure–Reactivity Relationship for Aromatic Molecules: Recent Advances
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Boris Galabov, Sonia Ilieva, Diana Cheshmedzhieva, Valya Nikolova, Vassil A. Popov, Boriana Hadjieva, and Henry F. Schaefer
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Chemistry ,QD1-999 - Published
- 2022
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5. The Electronic Structure of Atoms and Molecules Henry F. SCHAEFER III
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Pichanick, Francis
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- 1973
6. Probing the Potential Energy Profile of the I + (H2O)3 → HI + (H2O)2OH Forward and Reverse Reactions: High Level CCSD(T) Studies with Spin-Orbit Coupling Included
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Xinyuan Zhang, Xiaoting Chen, Yan Lin, Yan Meng, Guoliang Li, Yaoming Xie, and Henry F. Schaefer
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iodine atom ,water trimer ,atom–molecule reactions ,potential energy profile ,CCSD(T) computations ,Organic chemistry ,QD241-441 - Abstract
Three different pathways for the atomic iodine plus water trimer reaction I + (H2O)3 → HI + (H2O)2OH were preliminarily examined by the DFT-MPW1K method. Related to previous predictions for the F/Cl/Br + (H2O)3 reactions, three pathways for the I + (H2O)3 reaction are linked in terms of geometry and energetics. To legitimize the results, the “gold standard” CCSD(T) method was employed to investigate the lowest-lying pathway with the correlation-consistent polarized valence basis set up to cc-pVQZ(-PP). According to the CCSD(T)/cc-pVQZ(-PP)//CCSD(T)/cc-pVTZ(-PP) results, the I + (H2O)3 → HI + (H2O)2OH reaction is predicted to be endothermic by 47.0 kcal mol−1. The submerged transition state is predicted to lie 43.7 kcal mol−1 above the separated reactants. The I···(H2O)3 entrance complex lies below the separated reactants by 4.1 kcal mol−1, and spin-orbit coupling has a significant impact on this dissociation energy. The HI···(H2O)2OH exit complex is bound by 4.3 kcal mol−1 in relation to the separated products. Compared with simpler I + (H2O)2 and I + H2O reactions, the I + (H2O)3 reaction is energetically between them in general. It is speculated that the reaction between the iodine atom and the larger water clusters may be energetically analogous to the I + (H2O)3 reaction. The iodine reaction I + (H2O)3 is connected with the analogous valence isoelectronic bromine/chlorine reactions Br/Cl + (H2O)3 but much different from the F + (H2O)3 reaction. Significant difference with other halogen systems, especially for barrier heights, are seen for the iodine systems.
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- 2023
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7. Simulation of the VUV Absorption Spectra of Oxygenates and Hydrocarbons: A Joint Theoretical–Experimental Study
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Addison K. Bralick, Erica C. Mitchell, Anna C. Doner, Annabelle R. Webb, Matthew G. Christianson, Justin M. Turney, Brandon Rotavera, and Henry F. Schaefer
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Physical and Theoretical Chemistry - Published
- 2023
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8. Tensor Hypercontraction Form of the Perturbative Triples Energy in Coupled-Cluster Theory
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Andy Jiang, Justin M. Turney, and Henry F. Schaefer
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Chemical Physics (physics.chem-ph) ,Physics - Chemical Physics ,FOS: Physical sciences ,Physical and Theoretical Chemistry ,Computer Science Applications - Abstract
We present the working equations for a reduced-scaling method of evaluating the perturbative triples (T) energy in coupled-cluster theory, through the tensor hypercontraction (THC) of the triples amplitudes ($t_{ijk}^{abc}$). Through our method we can reduce the scaling of the (T) energy from the traditional O($N^{7}$) to a more modest O($N^{5}$). We also discuss implementation details to aid future research, development, and software realization of this method. Additionally, we show that this method yields sub-millihartree (mEh) differences from CCSD(T) when evaluating absolute energies, and sub-0.1 kcal/mol energy differences when evaluating relative energies. Finally, we demonstrate that this method converges to the true CCSD(T) energy through the systematic increasing of the rank or eigenvalue tolerance of the orthogonal projector, as well as exhibiting sub-linear to linear error growth with respect to system size.
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- 2023
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9. High-Level Coupled-Cluster Study on Substituent Effects in H2 Activation by Low-Valent Aluminyl Anions
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Nery Villegas-Escobar, Preston R. Hoobler, Alejandro Toro-Labbé, and Henry F. Schaefer
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Physical and Theoretical Chemistry - Published
- 2023
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10. Toward the Observation of the Tin and Lead Analogs of Formaldehyde
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Nathaniel L. Kitzmiller, Mark E. Wolf, Justin M. Turney, and Henry F. Schaefer
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Physical and Theoretical Chemistry - Abstract
Heavy aldehyde and ketone analogues, R
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- 2022
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11. Demarcating Noncovalent and Covalent Bond Territories: Imine-CO2 Complexes and Cooperative CO2 Capture
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Sebastian Anila, Cherumuttathu H. Suresh, and Henry F. Schaefer
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Physical and Theoretical Chemistry - Published
- 2022
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12. Tris(Butadiene) Compounds versus Butadiene Oligomerization in Second-Row Transition Metal Chemistry: Effects of Increased Ligand Fields
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Yi Zhao, Qun Chen, Mingyang He, Zhihui Zhang, Xuejun Feng, Yaoming Xie, Robert Bruce King, and Henry F. Schaefer
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butadiene complexes ,transition metals ,density functional theory ,Organic chemistry ,QD241-441 - Abstract
The geometries, energetics, and preferred spin states of the second-row transition metal tris(butadiene) complexes (C4H6)3M (M = Zr–Pd) and their isomers, including the experimentally known very stable molybdenum derivative (C4H6)3Mo, have been examined by density functional theory. Such low-energy structures are found to have low-spin singlet and doublet spin states in contrast to the corresponding derivatives of the first-row transition metals. The three butadiene ligands in the lowest-energy (C4H6)3M structures of the late second-row transition metals couple to form a C12H18 ligand that binds to the central metal atom as a hexahapto ligand for M = Pd but as an octahapto ligand for M = Rh and Ru. However, the lowest-energy (C4H6)3M structures of the early transition metals have three separate tetrahapto butadiene ligands for M = Zr, Nb, and Mo or two tetrahapto butadiene ligands and one dihapto butadiene ligand for M = Tc. The low energy of the experimentally known singlet (C4H6)3Mo structure contrasts with the very high energy of its experimentally unknown singlet chromium (C4H6)3Cr analog relative to quintet (C12H18)Cr isomers with an open-chain C12H18 ligand.
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- 2021
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13. Butterfly, Vinylidene‐Like, Monobridged and Trans Structures of Si 2 H 2 + : Comparison to the Well‐Characterized Neutral Si 2 H 2
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Kailyn M. Schueller, Henry F. Mull, Justin T. Turney, and Henry F. Schaefer
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General Chemistry - Published
- 2023
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14. Highly Strained Pn(CH)3 (Pn = N, P, As, Sb, Bi) Tetrahedranes: Theoretical Characterization
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Justin M. Turney, Henry F. Schaefer, Elizabeth A Doty, and Mark E. Wolf
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010304 chemical physics ,Chemistry ,Electronic structure ,010402 general chemistry ,Antibonding molecular orbital ,01 natural sciences ,0104 chemical sciences ,Crystallography ,Delocalized electron ,chemistry.chemical_compound ,Molecular geometry ,0103 physical sciences ,Molecule ,Physical and Theoretical Chemistry ,Tetrahedrane ,Pnictogen ,Natural bond orbital - Abstract
Recent experimental research by Cummins and co-workers has established the existence of a tetrahedrane molecule with one CH moiety replaced by phosphorus. We present here the first theoretical studies of the entire Pn(CH)3 (Pn = N, P, As, Sb, Bi) class of molecules. Geometries are obtained at the highly reliable CCSD(T)/aug-cc-pwCVTZ(-PP) level of theory. Harmonic vibrational frequencies are determined and analyzed to confirm the nature of each stationary point and provide helpful findings that may aid in the detection of each species. Most notable is the result that the geometric parameters associated with the (CH)3 moiety in the tetrahedranes exhibit little change under pnictogen substitution, while the Pn-C bonds and C-Pn-C bond angles greatly increase and decrease, respectively. Strain energies are predicted and range from 122.3 kcal mol-1 (N(CH)3) to 99.4 kcal mol-1 (Bi(CH)3) at the DF-CCSD(T)//B3LYP-D3/aug-cc-pV(T+d)Z(-PP) level of theory. The obtained geometries are further analyzed with Natural Bond Orbital (NBO) methods to understand the bonding and electronic structure of each species. We also provide insight into how different substituents can help make the tetrahedrane structure more energetically favorable due to electron delocalization into substituent antibonding orbitals. The effect of additional delocalization also weakens the Pn-C bonds, especially for the heavier pnictogens. This work concludes with a list of considerations that summarize our key findings and motivate future work aimed at producing novel pnictogen-substituted tetrahedrane molecules.
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- 2021
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15. The HOX⋯SO 2 (X=F, Cl, Br, I) Binary Complexes: Implications for Atmospheric Chemistry
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Henry F. Schaefer, Mark E. Wolf, Justin M. Turney, and Nathaniel L. Kitzmiller
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chemistry.chemical_classification ,Hydrogen bond ,Chemistry ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Quantum chemistry ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,Pseudopotential ,Crystallography ,Ab initio quantum chemistry methods ,Halogen ,Molecule ,Non-covalent interactions ,Physical and Theoretical Chemistry ,0210 nano-technology ,Natural bond orbital - Abstract
Sulfur dioxide and hypohalous acids (HOX, X = F, Cl, Br, I) are ubiquitous molecules in the atmosphere that are central to important processes like seasonal ozone depletion, acid rain, and cloud nucleation. We present the first theoretical examination of the HOX···SO 2 binary complexes and the associated trends due to halogen substitution. Reliable geometries were optimized at the CCSD(T)/aug-cc-pV(T+d)Z level of theory for HOF and HOCl complexes. The HOBr and HOI complexes were optimized at the CCSD(T)/aug-cc-pV(D+d)Z level of theory with the exception of the Br and I atoms which were modeled with an aug-cc-pwCVDZ-PP pseudopotential. 27 HOX···SO 2 complexes were characterized and the focal point method was employed to produce CCSDT(Q)/CBS interaction energies. Natural Bond Orbital analysis and Symmetry Adapted Perturbation Theory were used to classify the nature of each principle interaction. The interaction energies of all HOX···SO 2 complexes in this study ranged from 1.35 to 3.81 kcal mol -1 . The single-interaction hydrogen bonded complexes spanned a range of 2.62 to 3.07 kcal mol -1 , while the single-interaction halogen bonded complexes were far more sensitive to halogen substitution ranging from 1.35 to 3.06 kcal mol -1 , indicating that the two types of interactions are extremely competitive for heavier halogens. Our results provide insight into the interactions between HOX and SO 2 which may guide further research of related systems.
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- 2020
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16. Isomer‐dependent reaction mechanisms of cyclic ether intermediates:cis‐2,3‐dimethyloxirane andtrans‐2,3‐dimethyloxirane
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Matthew M. Davis, Matthew G. Christianson, Leonid Sheps, Henry F. Schaefer, Anna C. Doner, Craig A. Taatjes, Alanna L. Koritzke, Justin M. Turney, Brandon Rotavera, and David L. Osborn
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Inorganic Chemistry ,Reaction mechanism ,Chemistry ,Cyclic ether ,Organic Chemistry ,Physical and Theoretical Chemistry ,Biochemistry ,Medicinal chemistry - Published
- 2020
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17. A Stable Naked Dithiolene Radical Anion and Synergic THF Ring-Opening
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Gregory H. Robinson, Michael K. Johnson, Henry F. Schaefer, Soshawn A. Blair, Pingrong Wei, Dongtao Cui, Yu-Zhong Wang, and Yaoming Xie
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Anions ,Models, Molecular ,Free Radicals ,chemistry.chemical_element ,Salt (chemistry) ,Sulfides ,010402 general chemistry ,Ring (chemistry) ,01 natural sciences ,Biochemistry ,Medicinal chemistry ,Article ,Catalysis ,Ion ,chemistry.chemical_compound ,Colloid and Surface Chemistry ,Heterocyclic Compounds ,Molar ratio ,Molecule ,Sulfhydryl Compounds ,Furans ,chemistry.chemical_classification ,Molecular Structure ,Extramural ,Imidazoles ,Silylene ,General Chemistry ,0104 chemical sciences ,chemistry ,Solvents ,Lithium - Abstract
Reaction of the lithium dithiolene radical 2(•) with the imidazolium salt [{(Me)CN(i-Pr)}(2)CH](+)[Cl](−) (in a 1:1 molar ratio) gives the first stable naked anionic dithiolene radical 3(•), which, when coupled with hexasulfide, [{(Me)CN(i-Pr)}(2)CH](+)(2)[S(6)](2−) (4), and N-heterocyclic silylene 5, unexpectedly results in synergic THF ring-opening via a radical mechanism.
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- 2020
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18. Reaction mechanisms of a cyclic ether intermediate: Ethyloxirane
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Alanna L. Koritzke, Matthew M. Davis, Leonid Sheps, Matthew G. Christianson, Henry F. Schaefer, Justin M. Turney, Anna C. Doner, David L. Osborn, Brandon Rotavera, and Craig A. Taatjes
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Inorganic Chemistry ,Reaction mechanism ,Chemistry ,Cyclic ether ,Organic Chemistry ,Polymer chemistry ,Physical and Theoretical Chemistry ,Biochemistry - Published
- 2020
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19. Comparative Study of the Thermal Stabilities of the Experimentally Known High-Valent Fe(IV) Compounds Fe(1-norbornyl)4 and Fe(cyclohexyl)4
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R. Bruce King, Yucheng Hu, Huidong Li, Ze Zhang, Qunchao Fan, Linshen Wang, Di Wan, and Henry F. Schaefer
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Steric effects ,chemistry.chemical_compound ,Crystallography ,chemistry ,Transition metal ,chemistry.chemical_element ,Reactivity (chemistry) ,Singlet state ,Physical and Theoretical Chemistry ,Homoleptic ,Conical intersection ,Carbon monoxide ,Ruthenium - Abstract
The high stability of the experimentally known homoleptic 1-norbornyl derivative (nor)4Fe of iron in the unusual +4 oxidation state is a consequence of the high reaction barriers of the singlet or triplet potential surfaces constrained by the global dispersion attraction and the great steric demands of the norbornyl groups. The much more limited stability of the corresponding cyclohexyl derivative (cx)4Fe may result from the conical intersection between the singlet potential surface and the quintet spin potential surface arising from the weaker dispersion attraction and the reduced steric effect of the cyclohexyl groups relative to the 1-norbornyl groups. In contrast, the high stability of the likewise experimentally known (cx)4M (M = Ru or Os) structures results from the larger ligand field splitting (Δ) of the d-orbital energies for the second and third-row transition metals ruthenium and osmium relative to that of the first-row transition metal iron. The cyclohexyl derivative (cx)4Fe is predicted to be reactive toward carbon monoxide to insert CO into up to two Fe-C bonds. However, the dispersion effect as well as the much larger size of the 1-norbornyl substituents prevents similar reactivity of (nor)4Fe with carbon monoxide.
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- 2020
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20. Substituted Ortho-Benzynes: Properties of the Triple Bond
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Justin M. Turney, Frank Weinhold, Henry F. Schaefer, Ryan K. Maynard, and Mitchell Evan Lahm
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010405 organic chemistry ,Chemistry ,Organic Chemistry ,010402 general chemistry ,Electrostatics ,Resonance (chemistry) ,Triple bond ,01 natural sciences ,Aryne ,0104 chemical sciences ,Crystallography ,Distortion ,Coulomb ,Density functional theory ,Natural bond orbital - Abstract
Ortho-benzyne has been well studied by both experiment and theory. Its substituted variants, however, have been less carefully examined. Benchmark data are computed for unsubstituted ortho-benzyne using several density functional theory functionals and basis sets, up to cc-pVQZ. Optimized geometries for the substituted ortho-benzyne as well as harmonic vibrational frequencies and singlet-triplet splittings are computed using the benchmarked functionals. A proximal (syn)OH substitution causes a mean θ1 distortion of +8.1 ± 1.4° from ortho-benzyne. Substituting in the proximal position with F shifts the singlet-triplet splitting by +4.5 ± 0.4 kcal mol-1 from ortho-benzyne. Natural bond orbital analysis, including natural Coulomb electrostatics, elucidates the presence of three influences from the selected substituents: hyperconjugative, resonance, and electrostatic effects.
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- 2020
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21. Substituent, Solvent, and Dispersion Effects on the Zwitterionic Character and Dimerization Thermochemistry of the Group 6 Fulvene Metal Tricarbonyl Complexes
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Yanshu Wang, Huijie Wang, Huidong Li, Yucheng Hu, Qunchao Fan, R. Bruce King, and Henry F. Schaefer
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Physical and Theoretical Chemistry - Abstract
Dimerizations of fulvene metal tricarbonyl complexes of the type (C
- Published
- 2022
22. Pericyclic reaction benchmarks: hierarchical computations targeting CCSDT(Q)/CBS and analysis of DFT performance
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Pascal Vermeeren, Marco Dalla Tiezza, Mark E. Wolf, Mitchell E. Lahm, Wesley D. Allen, Henry F. Schaefer, Trevor A. Hamlin, and F. Matthias Bickelhaupt
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General Physics and Astronomy ,Physical and Theoretical Chemistry ,Theoretical Chemistry - Abstract
A hierarchical ab initio benchmark up to CCSDT(Q)/CBS in combination with a DFT performance study reveals meta-hybrid M06-2X functional as the best performing functional for accurately describing pericyclic reactions.
- Published
- 2022
23. Mini-Review on Structure-Reactivity Relationship for Aromatic Molecules: Recent Advances
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Boris Galabov, Sonia Ilieva, Diana Cheshmedzhieva, Valya Nikolova, Vassil A. Popov, Boriana Hadjieva, and Henry F. Schaefer
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General Chemical Engineering ,General Chemistry - Abstract
Recent advances in quantifying nucleophilic reactivities in chemical reactions and intermolecular interactions of aromatic molecules are reviewed. This survey covers experimental (IR frequency shifts induced by hydrogen bonding) and theoretical (modeling of potential energy surfaces, atomic charges, molecular electrostatic potential) approaches in characterizing chemical reactivity. Recent advances in software developments assisting the evaluation of the reactive sites for electrophilic aromatic substitution are briefly discussed.
- Published
- 2021
24. Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs
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Johannes Steinmetzer, Daniel A. Smith, C. David Sherrill, Mark S. Gordon, Nuwan De Silva, Jamshed Anwar, Fang Liu, Henry F. Schaefer, Justin M. Turney, Lee-Ping Wang, Maximilian Scheurer, Annabelle Lolinco, Doaa Altarawy, Jiří Šponer, John D. Chodera, Carlos H. Borca, Rollin A. King, Asem Alenaizan, Jeffrey B. Schriber, David Dotson, Jonathon P. Misiewicz, Heather J. Kulik, Andrew C. Simmonett, Jeffrey R. Wagner, Sebastian J. R. Lee, Theresa L. Windus, Taylor A. Barnes, Peter Kraus, Matthew Welborn, Lori A. Burns, Logan Ward, Andreas Dreuw, Holger Kruse, Devin A. Matthews, Jiyoung Lee, Farhad Ramezanghorbani, Jan Hermann, Roberto Di Remigio, Levi N. Naden, Todd J. Martínez, Joshua T. Horton, John F. Stanton, Sebastian Ehlert, Colton B. Hicks, Adrian G. Hurtado, Zachary L. Glick, Alexander G. Heide, and Michael F. Herbst
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Computer science ,Computation ,Interoperability ,General Physics and Astronomy ,010402 general chemistry ,computer.software_genre ,01 natural sciences ,ARTICLES ,Software ,Engineering ,Composability ,0103 physical sciences ,Physical and Theoretical Chemistry ,Chemical Physics ,010304 chemical physics ,Database ,Application programming interface ,business.industry ,Modular design ,Automation ,0104 chemical sciences ,Networking and Information Technology R&D (NITRD) ,Physical Sciences ,Chemical Sciences ,GAMESS ,business ,computer - Abstract
Community efforts in the computational molecular sciences (CMS) are evolving toward modular, open, and interoperable interfaces that work with existing community codes to provide more functionality and composability than could be achieved with a single program. The Quantum Chemistry Common Driver and Databases (QCDB) project provides such capability through an application programming interface (API) that facilitates interoperability across multiple quantum chemistry software packages. In tandem with the Molecular Sciences Software Institute and their Quantum Chemistry Archive ecosystem, the unique functionalities of several CMS programs are integrated, including CFOUR, GAMESS, NWChem, OpenMM, Psi4, Qcore, TeraChem, and Turbomole, to provide common computational functions, i.e., energy, gradient, and Hessian computations as well as molecular properties such as atomic charges and vibrational frequency analysis. Both standard users and power users benefit from adopting these APIs as they lower the language barrier of input styles and enable a standard layout of variables and data. These designs allow end-to-end interoperable programming of complex computations and provide best practices options by default.
- Published
- 2021
25. Kinetic Stability of Pentazole
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Justin M. Turney, Gary E. Douberly, Henry F. Schaefer, and Henry F. Mull
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Range (particle radiation) ,chemistry.chemical_compound ,Transition state theory ,chemistry ,Chemical physics ,Pentazole ,Ab initio ,Physical and Theoretical Chemistry ,Kinetic energy ,Decomposition ,Stability (probability) ,Chemical decomposition - Abstract
The utility of high energy density materials (HEDMs) comes from their thermodynamic properties which arise from specific structural features that contribute to energy storage. Studies of such structural features seek to increase our understanding of these energy storage mechanisms in order to further enhance their properties. High-nitrogen-containing HEDMs are of particular interest because they are less toxic than traditional HEDMs. Pentazole is the largest of the nitrogen rings which has been synthesized and considered for an HEDM; however, few experimental studies exist due to the difficulty involved in the synthesis, and most previous theoretical studies employed composite methods where lower level geometries were used with higher level methods. Here, the decomposition reaction of pentazole is studied. Geometries, fundamental frequencies, and energies for each of the stationary points of the decomposition pathway are computed using ab initio methods up to CCSDT(Q). Decomposition rates are calculated over a range of temperatures using canonical transition state theory in order to determine the kinetic stability of pentazole. Based on the present results, it would be difficult for pentazole to act as an HEDM, requiring temperatures close to 200 K to achieve a suitable level of stability.
- Published
- 2021
26. Catalyzed reaction of isocyanates (RNCO) with water
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Jonathon E. Vandezande, Mark E. Wolf, and Henry F. Schaefer
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chemistry.chemical_classification ,Imidic acid ,Enthalpy ,Substituent ,General Physics and Astronomy ,Catalysis ,Autocatalysis ,chemistry.chemical_compound ,chemistry ,Computational chemistry ,Polar effect ,Molecule ,Physical and Theoretical Chemistry ,Alkyl ,Natural bond orbital - Abstract
The reactions between substituted isocyanates (RNCO) and other small molecules (e.g. water, alcohols, and amines) are of significant industrial importance, particularly for the development of novel polyurethanes and other useful polymers. We present very high-level ab initio computations on the HNCO + H2O reaction, with results targeting the CCSDT(Q)/CBS//CCSD(T)/cc-pVQZ level of theory. Our results affirm that hydrolysis can occur across both the N=C and C=O bonds of HNCO via concerted mechanisms to form carbamate or imidic acid with 0 K enthalpy barrier heights of 38.5 and 47.5 kcal mol^-1 A total of 24 substituted RNCO + H2O reactions were studied. Geometries obtained with a composite method and refined with CCSD(T)/CBS single point energies determine that substituted RNCO species have a significant influence on these barrier heights, with an extreme case like fluorine lowering both barriers by close to 20 kcal mol^-1 and most common alkyl substituents lowering both by approximately 4 kcal mol^-1. Natural Bond Orbital (NBO) analysis provides evidence that the predicted barrier heights are strongly associated with the occupation of the in-plane C-O* orbital of the RNCO reactant. Key autocatalytic mechanisms are considered in the presence of excess water and RNCO species. Additional waters (one or two) are predicted to lower both barriers significantly at the CCSD(T)/aug-cc-pV(T+d)Z level of theory with strongly electron withdrawing RNCO substituents also increasing these effects, similar to the uncatalyzed case. The 298 K Gibbs energies are only marginally lowered by a second catalyst water molecule, indicating that the decreasing 0 K enthalpy barriers are offset by the loss of translational entropy with more than one catalyst water. Two-step 2RNCO + H2O mechanisms are characterized for the formation of carbamate and imidic acid. The second step of these two pathways exhibits the largest barrier and presents no clear pattern with respect to substituent choice. Our results indicate that an additional RNCO molecule might catalyze imidic acid formation but have less influence on the efficiency of carbamate formation. We expect that these results lay a firm foundation for the experimental study of substituted isocyanates and their relationship to the energetic pathways of related systems.
- Published
- 2021
27. Formation of Formic Acid Derivatives through Activation and Hydroboration of CO2 by Low-Valent Group 14 (Si, Ge, Sn, Pb) Catalysts
- Author
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Nery Villegas-Escobar, Alejandro Toro-Labbé, and Henry F. Schaefer
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010304 chemical physics ,Chemistry ,Hydride ,Reaction intermediate ,010402 general chemistry ,01 natural sciences ,Medicinal chemistry ,0104 chemical sciences ,Catalysis ,Hydroboration ,chemistry.chemical_compound ,Main group element ,Catalytic cycle ,0103 physical sciences ,Reactivity (chemistry) ,Physical and Theoretical Chemistry ,Hydrometalation - Abstract
The chemistry of low-valent main group elements has attracted much attention in the past decade. These species are relevant because they have been able to mimic transition metal behavior in catalytic applications, with decreased material costs and diminished toxicity. In this contribution, we study the L1EH catalysts (E = Si(II), Ge(II), Sn(II), and Pb(II); L1 = [ArNC(Me)CHC(Me)NAr] with Ar = 2,6-iPr2C6H3) for the formation of formic acid derivatives through hydroboration of CO2. Detailed characterization of relevant structures on the potential energy surface enabled us to rationalize different paths for the hydroboration of CO2. Interestingly, it was found that according to the activation energies for the whole catalytic cycle, the process of transformation of CO2 becomes more favored going down group 14. However, an effective energetic decrease for the process (taking as the reference the uncatalyzed reaction between CO2 and HBpin) is evidenced just from the germanium analogue. The trend in reactivity found in the present study is a direct consequence of the change in the central main group element, enabling enhanced polar character of the E-H (L1EH in the CO2 activation step) and E-O (metal formates in the hydroboration step) bonds as the atomic radius increases. The transient stabilization of reaction intermediates found in the hydroboration step was rationalized through the non-covalent interaction index (NCI) and symmetry-adapted perturbation theory (SAPT). This computational study highlights the reactivity trends in group-14-based hydride catalysts in hydrometalation and posterior hydroboration to form formic acid intermediates. We hope that this study will motivate further experimental work in low-valent lead chemistry.
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- 2020
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28. Cyclobutyne: Minimum or Transition State?
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Henry F. Schaefer and Zhi Sun
- Subjects
Cyclobutyne ,chemistry.chemical_compound ,chemistry ,010405 organic chemistry ,Organic Chemistry ,Theoretical methods ,Center (algebra and category theory) ,State (functional analysis) ,Atomic physics ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences - Abstract
A cornucopia of very high-level theoretical methods has been used to study cyclobutyne, a molecule that has been the center of much speculation. We conclude that cyclobutyne is a transition state in its singlet ground state, based on new coupled cluster and multireference computations presented in this research. This is substantially different from other theoretical studies proposing the existence of singlet cyclobutyne as a minimum. The singlet cyclobutyne transition state ( C
- Published
- 2019
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29. Ethyl + O2 in Helium Nanodroplets: Infrared Spectroscopy of the Ethylperoxy Radical
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Gary E. Douberly, Christopher P. Moradi, Joseph T. Brice, Henry F. Schaefer, and Peter R. Franke
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010304 chemical physics ,Chemistry ,Infrared ,Radical ,chemistry.chemical_element ,Infrared spectroscopy ,010402 general chemistry ,01 natural sciences ,Molecular physics ,0104 chemical sciences ,Normal mode ,0103 physical sciences ,Physical and Theoretical Chemistry ,Spectroscopy ,Conformational isomerism ,Basis set ,Helium - Abstract
Helium-solvated ethylperoxy radicals (CH3CH2OO•) are formed via the in situ reaction between 2A' ethyl radical and 3Σg- dioxygen. The reactants are captured sequentially through the droplet pick-up technique. Helium droplets are doped with ethyl radical via pyrolysis of di- tert-amyl peroxide or n-propylnitrite in an effusive, low-pressure source. An infrared spectrum of ethylperoxy, in the CH stretching region, is recorded with species-selective droplet beam depletion spectroscopy. Spectral assignments are made via comparisons to second-order vibrational perturbation theory with resonances (VPT2 + K) based on coupled-cluster full quartic force fields. Cubic and quartic force constants, evaluated using a small basis set, are transformed into the normal coordinate system of the higher level quadratic force constants. This transformation procedure eliminates the mismatch between normal modes, which is a source of error whenever normal coordinate force constants from different levels of theory are combined. The spectrum shows signatures of both the C1 gauche and C s trans rotamers in an approximate 2:1 ratio; this is despite the prediction that the gauche rotamer lies 44 cm-1 lower on the zero-Kelvin enthalpic potential surface for torsional interconversion. Helium droplets are 0.4 K at equilibrium; therefore, in situ ethylperoxy production is highly nonthermal.
- Published
- 2019
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30. A Reflection on Norman Louis Allinger
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Henry F. Schaefer and William L. Jorgensen
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Philosophy ,Art history ,Physical and Theoretical Chemistry ,Reflection (computer graphics) ,Computer Science Applications - Published
- 2021
31. Highly Strained Pn(CH)
- Author
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Mark E, Wolf, Elizabeth A, Doty, Justin M, Turney, and Henry F, Schaefer Iii
- Abstract
Recent experimental research by Cummins and co-workers has established the existence of a tetrahedrane molecule with one CH moiety replaced by phosphorus. We present here the first theoretical studies of the entire Pn(CH)
- Published
- 2021
32. Comparative Study of the Thermal Stabilities of the Experimentally Known High-Valent Fe(IV) Compounds Fe(1-norbornyl)
- Author
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Huidong, Li, Linshen, Wang, Yucheng, Hu, Ze, Zhang, Di, Wan, Qunchao, Fan, R Bruce, King, and Henry F, Schaefer
- Abstract
The high stability of the experimentally known homoleptic 1-norbornyl derivative (nor)
- Published
- 2020
33. Substituted
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Mitchell E, Lahm, Ryan K, Maynard, Justin M, Turney, Frank, Weinhold, and Henry F, Schaefer
- Published
- 2020
34. Binding modes of cabazitaxel with the different human β-tubulin isotypes: DFT and MD studies
- Author
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Cuihong Wang, Ce Song, Xudong Lü, Henry F. Schaefer, Lijuan Zhu, Chao Zhang, Meiling Zhang, and Yaoming Xie
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Paclitaxel ,Antineoplastic Agents ,Theoretical research ,Docetaxel ,macromolecular substances ,Molecular Dynamics Simulation ,Pharmacology ,010402 general chemistry ,Microtubules ,01 natural sciences ,Catalysis ,Inorganic Chemistry ,chemistry.chemical_compound ,Tubulin ,0103 physical sciences ,medicine ,Humans ,Homology modeling ,Physical and Theoretical Chemistry ,010304 chemical physics ,biology ,Chemistry ,Organic Chemistry ,Molecular medicine ,Tubulin Modulators ,0104 chemical sciences ,Computer Science Applications ,Molecular Docking Simulation ,Computational Theory and Mathematics ,Drug Resistance, Neoplasm ,Cabazitaxel ,biology.protein ,Thermodynamics ,Taxoids ,medicine.drug - Abstract
Taxanes (paclitaxel, docetaxel, cabazitaxel) are anticancer drugs as microtubule inhibitors. Following our previous studies on paclitaxel and docetaxel, in this work, we examine cabazitaxel and compare these three taxenes. The binding interaction of three taxanes with various β-tubulin isotypes is studied by homology modeling, molecular docking, and molecular dynamics simulations. The results show that the effects of docetaxel on βI-tubulin (- 29.5 kcal/mol) and of paclitaxel on βIIa-tubulin (- 25.5 kcal/mol) are much stronger than their effects on βIII-tubulin (- 17.8 kcal/mol and - 8.6 kcal/mol, respectively). However, the effect of cabazitaxel on βIII-tubulin (- 23.0 kcal/mol) is comparable with that on βI-tubulin (- 24.0 kcal/mol) and βIIa-tubulin (- 25.9 kcal/mol), consistent with the fact that overexpression of βIII-tubulin increases the drug resistance to paclitaxel and docetaxel, but has little influence for cabazitaxel. This theoretical research supports the use of cabazitaxel for patients who are resistant to the action of paclitaxel and docetaxel.
- Published
- 2020
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35. Psi4 1.4: Open-source software for high-throughput quantum chemistry
- Author
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Bernard R. Brooks, Robert A. Shaw, Uğur Bozkaya, Holger Kruse, C. David Sherrill, Francesco A. Evangelista, Konrad Patkowski, Susi Lehtola, A. Eugene DePrince, Zachary L. Glick, Maximilian Scheurer, Lori A. Burns, Matthew C. Schieber, T. Daniel Crawford, Peter Kraus, Justin M. Turney, Rollin A. King, Jonathon P. Misiewicz, Dominic A. Sirianni, Ashutosh Kumar, Yi Xie, Alexander Yu. Sokolov, Jonathan M. Waldrop, Jeffrey B. Schriber, Edward G. Hohenstein, Andrew C. Simmonett, Daniel G. A. Smith, Robert M. Parrish, Joseph Senan O’Brien, Henry F. Schaefer, Raimondas Galvelis, Roberto Di Remigio, Asem Alenaizan, Andrew M. James, Benjamin P. Pritchard, and Department of Chemistry
- Subjects
Computer science ,Computation ,Interoperability ,116 Chemical sciences ,General Physics and Astronomy ,FRAGMENT POTENTIAL METHOD ,02 engineering and technology ,010402 general chemistry ,computer.software_genre ,01 natural sciences ,DENSITY-FUNCTIONAL THEORY ,ARTICLES ,Software ,CONFIGURATION-INTERACTION ,0103 physical sciences ,Physical and Theoretical Chemistry ,010306 general physics ,Implementation ,computer.programming_language ,010304 chemical physics ,business.industry ,Programming language ,ANALYTIC ENERGY GRADIENTS ,FROZEN NATURAL ORBITALS ,Python (programming language) ,COUPLED-CLUSTER METHODS ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,Workflow ,EXCITED-STATES ,SINGLE-REFERENCE ,Component-based software engineering ,Density functional theory ,EXCITATION-ENERGIES ,ADAPTED PERTURBATION-THEORY ,business ,0210 nano-technology ,computer - Abstract
Psi4 is a free and open-source ab initio electronic structure program providing Hartree–Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of Psi4’s core functionality via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSchema data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCArchive Infrastructure project, make the latest version of Psi4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.
- Published
- 2020
36. Important features of the potential energy surface of the methylamine plus O(1D) reaction
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Preston R. Hoobler, Henry F. Schaefer, Justin M. Turney, and Mark E. Wolf
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Focal point ,Methylamine ,Ab initio ,General Physics and Astronomy ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Stationary point ,Molecular physics ,Transition state ,0104 chemical sciences ,Maxima and minima ,Interstellar medium ,chemistry.chemical_compound ,chemistry ,Potential energy surface ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,0210 nano-technology - Abstract
This research presents an ab initio characterization of the potential energy surface for the methylamine plus 1D oxygen atom reaction, which may be relevant to interstellar chemistry. Geometries and harmonic vibrational frequencies were determined for all stationary points at the CCSD(T)/aug-cc-pVTZ level of theory. The focal point method along with several additive corrections was used to obtain reliable CCSDT(Q)/CBS potential energy surface features. Extensive conformational analysis and intrinsic reaction coordinate computations were performed to ensure accurate chemical connectivity of the stationary points. Five minima were determined to be possible products of this reaction and three novel transition states were found that were previously unreported or mislabeled in the literature. The pathways we present can be used to guide further searches for NH2 containing species in the interstellar medium.
- Published
- 2019
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37. Reduced Density Matrix Cumulants: The Combinatorics of Size-Consistency and Generalized Normal Ordering
- Author
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Justin M. Turney, Henry F. Schaefer, and Jonathon P. Misiewicz
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Pure mathematics ,010304 chemical physics ,Multiplicative function ,Generating function ,Size consistency and size extensivity ,01 natural sciences ,Computer Science Applications ,Separable space ,Probability theory ,0103 physical sciences ,Key (cryptography) ,Reduced density matrix ,Statistical physics ,Physical and Theoretical Chemistry ,Random variable ,Cumulant ,Axiom ,Generating function (physics) ,Mathematics - Abstract
Reduced density matrix cumulants play key roles in the theory of both reduced density matrices and multiconfigurational normal ordering. We present a new, simpler generating function for reduced density matrix cumulants that is formally identical with equating the coupled cluster and configuration interaction ansätze. This is shown to be a general mechanism to convert between a multiplicatively separable quantity and an additively separable quantity, as defined by a set of axioms. It is shown that both the cumulants of probability theory and the reduced density matrices are entirely combinatorial constructions, where the differences can be associated with changes in the notion of "multiplicative separability" for expectation values of random variables compared to reduced density matrices. We compare our generating function to that of previous works and criticize previous claims of probabilistic significance of the reduced density matrix cumulants. Finally, we present a simple proof of the generalized normal ordering formalism to explore the role of reduced density matrix cumulants therein. While the formalism can be used without cumulants, the combinatorial structure of expressing RDMs in terms of cumulants is the same combinatorial structure on cumulants that allows for a simple extended generalized Wick's theorem.
- Published
- 2020
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38. Fundamental Vibrational Analyses of the HCN Monomer, Dimer and Associated Isotopologues
- Author
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Justin M. Turney, Henry F. Schaefer, Preston R. Hoobler, and Jay Agarwal
- Subjects
Physics ,Dimer ,Enthalpy ,Anharmonicity ,Ab initio ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Molecular physics ,Atomic and Molecular Physics, and Optics ,0104 chemical sciences ,chemistry.chemical_compound ,Coupled cluster ,chemistry ,Isotopologue ,Perturbation theory (quantum mechanics) ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,0210 nano-technology ,Natural bond orbital - Abstract
In this work we provide high level ab initio treatments of the structures, vibrational frequencies, and electronic energies of the HCN monomer and dimer systems along with several isotopologues. The plethora of information related to this system within the literature is summarized and serves as a basis for comparison with the results of this paper. The geometry of the dimer and monomer are reported at the all electroncoupled-cluster singles, doubles, and perturbative triples level of theory [AE-CCSD(T)] with the correlation consistent quadruple-zeta quality basis sets with extra core functions (cc-pCVQZ) from Dunning. The theoretical geometries and electronic structures are further analyzed through the use of the Natural Bond Orbital (NBO) method and Natural Resonance Theory (NRT). At the AE-CCSD(T)/cc-pCVQZ level of theory, the full cubic with semi-diagonal quartic force field for nine dimer and four monomer isotopologues (the parent isotopologue along with 15 N, 13 C, and D derivatives) were obtained to treat the anharmonicity of the vibrations via second order vibrational perturbation theory (VPT2). Lastly, the enthalpy change associated with the formation of the dimer from two monomer units was determined using the focal point analysis. Computations including coupled-cluster through perturbative quadruples as well as basis sets up to six-zeta quality, including core functions (cc-pCVXZ, X=D,T,Q,5,6) were used to extrapolate to the AE-CCSDT(Q)/CBS energy associated with this hydrogen-bond forming process. After appending anharmonic zero-point vibrational, relativistic, and diagonal Born-Oppenheimer corrections, we report a value of -3.93 kcal mol-1 for the enthalpy of formation. To our knowledge, each set of results (geometries, vibrational frequencies, and energetics) reported in this study represents the highest-level and most reliable theoretical predictions reported for this system.
- Published
- 2018
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39. Quantification of Aromaticity of Heterocyclic Systems Using Interaction Coordinates
- Author
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Henry F. Schaefer, Dhivya Manogaran, S. Manogaran, and Soumyadeb Dey
- Subjects
Electron density ,010405 organic chemistry ,Heteroatom ,Aromaticity ,010402 general chemistry ,Ring (chemistry) ,01 natural sciences ,0104 chemical sciences ,Electronegativity ,Delocalized electron ,chemistry.chemical_compound ,chemistry ,Chemical physics ,Atom ,Physical and Theoretical Chemistry ,Benzene - Abstract
Recently, we proposed an aromaticity index based on interaction coordinates (AIBIC) ( J. Phys. Chem. A 2016 , 120 , 2894 - 2901 ). This index works well for the aromatic hydrocarbons. However, in the case of heterocyclic systems, the AIBIC overestimates the aromaticity indicating many of them to be more aromatic than benzene, which seems unlikely. Because of the differences in the electronegativity of the carbon and the other heteroatoms, the electron density is partially localized near the more electronegative atom(s) of the aromatic fragment. This localized electron density does not contribute to the aromaticity that is due to the delocalized electron density over the central ring. To account for this reduction in the delocalized electron density, a correction is introduced based on Pauling's electronegativity equation. When the corrected interaction coordinates are used in the computation of AIBIC, we get a new index-aromaticity index based on interaction coordinates corrected. This new index, when computed for a variety of heterocyclic systems, yields results in line with the expectations, and its usefulness in quantifying aromaticity appears to be very promising.
- Published
- 2018
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40. Prototypical Transition-Metal Carbenes, (CO)5Cr═CH2, (CO)4Fe═CH2, (CO)3Ni═CH2, (CO)5Mo═CH2, (CO)4Ru═CH2, (CO)3Pd═CH2, (CO)5W═CH2, (CO)4Os═CH2, and (CO)3Pt═CH2: Challenge to Experiment
- Author
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Henry F. Schaefer, Marissa L. Estep, and Jared D. Weidman
- Subjects
010405 organic chemistry ,010402 general chemistry ,01 natural sciences ,Dissociation (chemistry) ,0104 chemical sciences ,Catalysis ,Metal ,Bond length ,chemistry.chemical_compound ,chemistry ,Transition metal ,visual_art ,visual_art.visual_art_medium ,Molecule ,Physical chemistry ,Physical and Theoretical Chemistry ,Methylene ,Organometallic chemistry - Abstract
Transition-metal carbenes are useful in organometallic chemistry due to their demonstrated use as catalysts in carbon–carbon bond-forming reactions. Yet the prototypical transition-metal carbenes, consisting of a single metal center doubly bonded to a methylene ligand and surrounded by carbonyls, have been elusive to experimental synthesis. This theoretical work examines the structures and properties of nine prototypical transition-metal carbenes. Optimized values for M═CH2 bond lengths, dissociation energies, and vibrational frequencies are reported. The M═CH2 bond distances range from 1.81 (Ni) to 2.05 A (Pd). The M═CH2 dissociation energies fall in the range of 16.4 (Pd) to 92.3 kcal mol–1 (Os). The spectroscopic observation of several of these molecules should be possible.
- Published
- 2018
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41. Nucleophilic Influences and Origin of the S N 2 Allylic Effect
- Author
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Gergana Koleva, Boris Galabov, Wesley D. Allen, and Henry F. Schaefer
- Subjects
Allyl chloride ,Allylic rearrangement ,010405 organic chemistry ,organic chemicals ,Organic Chemistry ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Medicinal chemistry ,Chloride ,Catalysis ,Transition state ,0104 chemical sciences ,chemistry.chemical_compound ,Nucleophile ,chemistry ,Nucleophilic substitution ,medicine ,SN2 reaction ,Solvent effects ,medicine.drug - Abstract
The potential energy surfaces for the SN 2 reactions of allyl and propyl chlorides with 21 anionic and neutral nucleophiles was studied by using ωB97X-D/6-311++G(3df,2pd) computations. The "allylic effect" on SN 2 barriers was observed for all reactions, and compared with propyl substrates, the energy barriers differed by -0.2 to -4.5 kcal mol-1 in the gas phase. Strong correlations of the SN 2 net activation barriers with cation affinities, proton affinities, and electrostatic potentials at nuclei demonstrated the powerful influence of electrostatic interactions on these reactions. For the reactions of anionic (but not neutral) nucleophiles with allyl chloride, some of the incoming negative charge (0.2-18 %) migrated into the carbon chains, which would provide secondary stabilization of the SN 2 transition states. Activation strain analysis provided additional insight into the allylic effect by showing that the energy of geometric distortion for the reactants to reach the SN 2 transition state was smaller for each allylic reaction than for its propyl analogue. In many cases, the interaction energies between the substrate and nucleophile in this analysis were more favorable for propyl chloride reactions, but this compensation did not overcome the predominant strain energy effect.
- Published
- 2018
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42. A remarkable case of basis set dependence: the false convergence patterns of the methyl anion
- Author
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Henry F. Schaefer, W. James Morgan, Michael C. Bowman, and Boyi Zhang
- Subjects
010304 chemical physics ,Biophysics ,010402 general chemistry ,Condensed Matter Physics ,01 natural sciences ,0104 chemical sciences ,Ion ,0103 physical sciences ,Convergence (routing) ,Applied mathematics ,Physical and Theoretical Chemistry ,Molecular Biology ,Basis set ,Mathematics - Published
- 2018
- Full Text
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43. Spin–Orbit Coupling via Four-Component Multireference Methods: Benchmarking on p-Block Elements and Tentative Recommendations
- Author
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Ryan D. Reynolds, Jonathon E. Vandezande, Henry F. Schaefer, and Boyi Zhang
- Subjects
Physics ,010304 chemical physics ,Four component ,Electronic structure ,Spin–orbit interaction ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Computer Science Applications ,symbols.namesake ,Theoretical physics ,0103 physical sciences ,symbols ,Physical and Theoretical Chemistry ,Hamiltonian (quantum mechanics) ,Basis set - Abstract
Within current electronic structure theory methods, fully relativistic four-component (4c) approaches based on the Dirac Hamiltonian treat spin-orbit coupling with the most rigor. The spin treatment arises naturally from the formulation and does not need to be included ad hoc. Spin-orbit splittings can provide insightful benchmark criteria for the assessment of 4c methods; however, there have not been extensive studies in this respect. Spin-orbit splittings of the p-block elements B-I were computed using the 4c-CASSCF, 4c-CASPT2, and 4c-MR-CISD+Q methods, as recently implemented in BAGEL, with uncontracted Dunning basis sets. Comparison with experiment reveals that the four-component methods yield good results, with most of the computed splittings falling within 15% of the experimental values. A large basis set is needed to obtain accurate splittings of the light elements B-F, while splittings of heavier elements show little basis dependence. The 4c-MR-CISD+Q method gave the best splittings for light elements, while 4c-CASSCF showed the best splittings for elements beyond fluorine. The 4c-CASPT2 method gave the best splittings for group 13 atoms.
- Published
- 2018
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44. Cover Feature: Contrasting the Mechanism of H 2 Activation by Monomeric and Potassium‐Stabilized Dimeric Al I Complexes: Do Potassium Atoms Exert any Cooperative Effect? (Chem. Eur. J. 69/2021)
- Author
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Henry F. Schaefer III, Dr. Nery Villegas-Escobar, and Alejandro Toro-Labbe
- Subjects
Organic Chemistry ,General Chemistry ,Catalysis - Published
- 2021
- Full Text
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45. Alkali-Metal Trihalides: M+X3– Ion Pair or MX–X2 Complex?
- Author
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Henry F. Schaefer, Kirk A. Peterson, Kevin B. Moore, J. Grant Hill, Roald Hoffmann, and Zhi Sun
- Subjects
Physics ,010405 organic chemistry ,Antisymmetric relation ,Matrix isolation ,010402 general chemistry ,01 natural sciences ,Diatomic molecule ,Bond order ,0104 chemical sciences ,Surfaces, Coatings and Films ,Ion ,Crystallography ,Normal mode ,Materials Chemistry ,Thermochemistry ,Molecule ,Physical and Theoretical Chemistry - Abstract
The alkali-metal trihalides MX3 (M = Li, Na, K, Rb, and Cs; X = Cl, Br, and I) are systematically studied using coupled-cluster methods. Benchmarks using CCSD(T) against diatomic experimental results suggest satisfactory performance for the weighted core-valence basis sets (new basis sets for K, Rb, and Cs) selected for predicting reliable structures and harmonic vibrational frequencies. An isomer search using the B3LYP functional yields a planar, yet asymmetric T-shaped C s structure as the global minimum for all MX3 species. Much higher level CCSD(T) computations show a moderate to strong distortion of the X3- anion by the M+ cation in the respective equilibrium geometries. Most obviously, for LiCl3, the two Cl-Cl distances are separated by 0.786 A. Even for CsI3, the structure least distorted from the M+X3- model, the two I-I distances differ by 0.243 A. It does not take much energy to distort the parent anions along an antisymmetric stretch, so this is no surprise. The normal modes of vibration of the MX3 molecules are in better agreement with matrix isolation experiments than previous calculations. And these normal modes reveal that, instead of the well-established antisymmetric and symmetric stretches of the "free" X3- anions, relatively localized and mutually perturbed X-X and M-X stretches are calculated. The suggestion emerges that the MX3 system may be alternatively described as an MX-X2 complex rather than the M+X3- ion pair. This perspective is supported by bonding analyses showing low electron densities at the bond critical points and natural bond orders between the MX and X2 moieties. The thermochemistry of fragmentations of MX3 to MX + X2 versus M+ + X3- also supports the alternative viewpoint of the bonding in this class of molecules.
- Published
- 2017
- Full Text
- View/download PDF
46. The Hydrogen Abstraction Reaction H2S + OH → H2O + SH: Convergent Quantum Mechanical Predictions
- Author
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Yaoming Xie, Zhi Sun, Henry F. Schaefer, Mei Tang, and Xiangrong Chen
- Subjects
010304 chemical physics ,Chemistry ,010402 general chemistry ,Hydrogen atom abstraction ,01 natural sciences ,Bond-dissociation energy ,0104 chemical sciences ,Computational chemistry ,0103 physical sciences ,Physical chemistry ,Density functional theory ,Physical and Theoretical Chemistry ,Single point ,Quantum - Abstract
The hydrogen abstraction reaction H2S + OH → H2O + SH has been studied using the “gold standard” CCSD(T) method along with the Dunning’s aug-cc-pVXZ (up to 5Z) basis sets. For the reactant (entrance) complex, the CCSD(T) method predicts a HSH···OH hydrogen-bonded structure to be lowest-lying, and the other lower-lying isomers, including the two-center three-electron hemibonded structure H2S···OH, have energies within 2 kcal/mol. The similar situation is for the product (exit) complex. With the aug-cc-pV5Z single point energies at the aug-cc-pVQZ geometry, the dissociation energy for the reactant complex to the reactants (H2S + OH) is predicted to be 3.37 kcal/mol, and that for the product complex to the products (H2O + SH) is 2.92 kcal/mol. At the same level of theory, the classical barrier height is predicted to be only 0.11 kcal/mol. Thus, the OH radical will react promptly with H2S in the atmosphere. We have also tested the performance of 29 density functional theory (DFT) methods for this reaction. Mo...
- Published
- 2017
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47. Enhanced Relative Stability of Metallabenzenes versus Metallocenes upon Ring Perfluorination: Nickel, Palladium, and Platinum Systems
- Author
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Guoliang Li, Henry F. Schaefer, Yaoming Xie, Jing Li, and R. Bruce King
- Subjects
010405 organic chemistry ,Inorganic chemistry ,Fluorobenzene ,chemistry.chemical_element ,010402 general chemistry ,Ring (chemistry) ,01 natural sciences ,0104 chemical sciences ,Inorganic Chemistry ,chemistry.chemical_compound ,Crystallography ,Nickel ,Transition metal ,chemistry ,Reagent ,Platinum ,Metallocene ,Palladium - Abstract
Perfluorination of one η5-C5H5 ring in the MC10H10 system (M = Ni, Pd, Pt) to give an MC10H5F5 system greatly destabilizes structures containing a perfluorinated pentahapto η5-C5F5 ring. As a result, the metallapentafluorobenzene structures (η5-C5H5)(MC5F5) are the lowest energy structures for all three metals with energy differences of 1.4, 6.2, and 16.2 kcal/mol for nickel, palladium, and platinum, respectively. In addition, for palladium and platinum isomeric metalla-tetrafluorocyclopentadiene structures with a complexed fluorobenzene ring, i. e., (C6H5F)(MC4F4) (M = Pd, Pt), are lower energy structures than the lowest energy metallocene structures. Furthermore, for palladium and platinum the lowest energy metallocene structures are slipped metallocenes with a trihapto rather than a pentahapto pentafluorocyclopentadienyl ring. These theoretical results suggest the pentafluoro¬cyclopentadienyl anion as a reagent for synthesizing metallapentafluoro-benzene derivatives by reactions with (η5-C5R5)M(CO)X, (η5-C5R5)2M2(µ-CO)2, or (η5-C5R5)2Ni (R = H, Me; M = Ni, Pt).
- Published
- 2017
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48. Stabilizing a different cyclooctatetraene stereoisomer
- Author
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Roald Hoffmann, Henry F. Schaefer, Longfei Li, Bo Chen, Ming Lei, and Yaoming Xie
- Subjects
Steric effects ,Multidisciplinary ,010405 organic chemistry ,Chemistry ,Stereochemistry ,Aromaticity ,010402 general chemistry ,Ring (chemistry) ,01 natural sciences ,Frustrated Lewis pair ,0104 chemical sciences ,chemistry.chemical_compound ,Cyclooctatetraene ,Physical Sciences ,Thiophene ,Electronic effect ,Isomerization - Abstract
An unconventional cis-cis-cis-trans or (Z,Z,Z,E) structure B of cyclooctatetraene (COT) is calculated to lie only 23 kcal/mol above the well-known tub-shaped (Z,Z,Z,Z) isomer A; one example of this type of structure is known. The barrier for B returning to A is small, 3 kcal/mol. However, by suitable choice of substituents, the (Z,Z,Z,E) isomer can be made to lie in energy below the tub-shaped structure. Steric, clamping, and electronic strategies are proposed for achieving this. In the steric strategy, the C8H4(CH3)2(C(tBu)3)2 structure B is predicted to lie 21 kcal/mol below structure A, which is separated from form B only by a small barrier. A simple clamping strategy, effective for COT planarization, does not influence the A/B isomerization much. But, if the clamping group is aromatic (a fused benzene, pyrrole, thiophene, furan), the subtle interplay of potential aromaticity with clamping can be used to confer persistence if not stability on the (Z,Z,Z,E) isomer. An electronic strategy of a different kind, push–pull substitution on the COT ring, was not very effective in stabilizing the B form. However, it led us to vicinal amine–borane-substituted normal COTs that proved to be quite good at activating H2 in a frustrated Lewis pair scenario.
- Published
- 2017
- Full Text
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49. <scp>Psi4</scp> 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability
- Author
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Daniel G. A. Smith, Harley R. McAlexander, Konrad Patkowski, A. Eugene DePrince, Ashutosh Kumar, Prakash Verma, Andrew M. James, Edward G. Hohenstein, Alexander Yu. Sokolov, Francesco A. Evangelista, Andrew C. Simmonett, Lori A. Burns, Jérôme F. Gonthier, T. Daniel Crawford, Justin M. Turney, Rollin A. King, C. David Sherrill, Xiao Wang, Robert M. Parrish, Roberto Di Remigio, Ryan M. Richard, Masaaki Saitow, Uğur Bozkaya, Edward F. Valeev, Henry F. Schaefer, and Benjamin P. Pritchard
- Subjects
Computer science ,Interoperability ,010402 general chemistry ,Energy minimization ,01 natural sciences ,Article ,Computational science ,Computer Software ,Theoretical and Computational Chemistry ,0103 physical sciences ,Physical and Theoretical Chemistry ,computer.programming_language ,Chemical Physics ,010304 chemical physics ,business.industry ,Python (programming language) ,Automation ,0104 chemical sciences ,Computer Science Applications ,Workflow ,Coupled cluster ,Density functional theory ,Biochemistry and Cell Biology ,business ,computer ,Cholesky decomposition - Abstract
Psi4 is an ab initio electronic structure program providing methods such as Hartree-Fock, density functional theory, configuration interaction, and coupled-cluster theory. The 1.1 release represents a major update meant to automate complex tasks, such as geometry optimization using complete-basis-set extrapolation or focal-point methods. Conversion of the top-level code to a Python module means that Psi4 can now be used in complex workflows alongside other Python tools. Several new features have been added with the aid of libraries providing easy access to techniques such as density fitting, Cholesky decomposition, and Laplace denominators. The build system has been completely rewritten to simplify interoperability with independent, reusable software components for quantum chemistry. Finally, a wide range of new theoretical methods and analyses have been added to the code base, including functional-group and open-shell symmetry adapted perturbation theory (F-SAPT and O-SAPT), density-fitted coupled cluster with frozen natural orbitals [DF-FNO-CCSD(T)], orbital-optimized perturbation and coupled-cluster methods (e.g., OO-MP2 and OO-CCSD), density-fitted multiconfigurational self-consistent field (DF-MCSCF), density cumulant functional theory (DCT), algebraic-diagrammatic construction [ADC(2)] excited states, improvements to the geometry optimizer, and the “X2C” approach to relativistic corrections, among many other improvements.
- Published
- 2017
- Full Text
- View/download PDF
50. Decomposition of the Electronic Activity in Competing [5,6] and [6,6] Cycloaddition Reactions Between C60 and Cyclopentadiene
- Author
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Nery Villegas-Escobar, Alejandro Toro-Labbé, Albert Poater, Henry F. Schaefer, and Miquel Solà
- Subjects
Physics ,Reaction mechanism ,Cyclopentadiene ,Fullerene ,Chemical substance ,General Physics and Astronomy ,02 engineering and technology ,Electron ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Kinetic energy ,01 natural sciences ,Cycloaddition ,0104 chemical sciences ,Addition reactions ,chemistry.chemical_compound ,chemistry ,Chemical physics ,Reaccions d'addició ,Physical and Theoretical Chemistry ,0210 nano-technology ,Electronic density - Abstract
Fullerenes, in particular C60, are important molecular entities in many areas, ranging from material science to medicinal chemistry. However, chemical transformations have to be done in order to transform C60 in added-value compounds with increased applicability. The most common procedure corresponds to the classical Diels-Alder cycloaddition reaction. In this research, a comprehensive study of the electronic activity that takes place in the cycloaddition between C60 and cyclopentadiene toward the [5,6] and [6,6] reaction pathways is presented. These are competitive reaction mechanisms dominated by σ and π fluctuating activity. To better understand the electronic activity at each stage of the mechanism, the reaction force (RF) and the symmetry-adapted reaction electronic flux (SA-REF, JΓi(ξ)) have been used to elucidate whether π or σ bonding changes drive the reaction. Since the studied cycloaddition reaction proceeds through a Cs symmetry reaction path, two SA-REF emerge: JA'(ξ) and JA''(ξ). In particular, JA'(ξ) mainly accounts for bond transformations associated with π bonds, while JA''(ξ) is sensitive toward σ bonding changes. It was found that the [6,6] path is highly favored over the [5,6] with respect to activation energies. This difference is primarily due to the less intensive electronic reordering of the σ electrons in the [6,6] path, as a result of the pyramidalization of carbon atoms in C60 (sp2 → sp3 transition). Interestingly, no substantial differences in the π electronic activity from the reactant complex to the transition state structure were found when comparing the [5,6] and [6,6] paths. Partition of the kinetic energy into its symmetry contributions indicates that when a bond is being weakened/broken (formed/strengthened) non-spontaneous (spontaneous) changes in the electronic activity occur, thus prompting an increase (decrease) of the kinetic energy. Therefore, contraction (expansion) of the electronic density in the vicinity of the bonding change is expected to take place.
- Published
- 2020
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