Transition state optimization based on approximate spin-projection (AP) method

Saitô, Tôru; Nishihara, Satomichi; Kataoka, Yosuke; Nakanishi, Yoshito; Matsui, Tamotsu; Kitagawa, Yasutaka; Kawakami, Takashi; Okumura, Mitsutaka; Yamaguchi, Kizashi

doi:10.1016/j.cplett.2009.10.055

Cited by 80 publications

(93 citation statements)

References 23 publications

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“…Spin‐unrestricted DFT, CCSD(T), and BD(T) calculations of open shell singlets may have significant spin contamination from the lowest triplet states. The energies of spin contaminated broken symmetry (BS) calculations have been corrected using Yamaguchi's approximate spin projection (AP) method . The spin‐projected total energy of a singlet state ( E AP ) is given by Equation :

true E^{A P} = α E^{B S} - β E^{H S}

…”

Section: Methodsmentioning

confidence: 99%

“…Approximate spin projection methods can eliminate the spin contamination from other spin states. In this study, the energies of spin contaminated, broken symmetry (BS) structures are corrected using Yamaguchi's approximate‐spin projection method . A range of methods (CASSCF, NEVPT2, B3LYP, ωB97XD, LC‐BLYP, CCSD(T), and BD(T)) has been used to explore the potential energy surface for singlet oxygen addition to guanine and subsequent reaction with water and lysine.…”

Section: Introductionmentioning

confidence: 99%

“…Several theoretical studies have explored the mechanism of singlet oxygen addition reaction across double bonds by using density functional theory (DFT) and multireference methods. [55][56][57][58][59][60][61][62][63][64][65][66] These studies involve 1,2-or 1,4-type additions of singlet oxygen across double bonds to form an endoperoxide, reactions analogoust ot he current study.C losed shell single-reference calculations cannotd escribe singlet oxygen properly because of its multireference character.B roken symmetry,openshell DFTcalculations struggletoprovide asuitable description of singlet oxygen because of spin contamination from its lower lying triplet state. This can cause sizeable errors in the energy unless spin projection is used to remove the contamination.…”

Section: Introductionmentioning

confidence: 99%

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Computational Study of Oxidation of Guanine by Singlet Oxygen (¹Δ_g) and Formation of Guanine:Lysine Cross‐Links

Thapa

Munk

Burrows

et al. 2017

Chemistry A European J

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Oxidation of guanine in the presence of lysine can lead to guanine-lysine cross-links. The ratio of the C4, C5 and C8 crosslinks depends on the manner of oxidation. Type II photosensitizers such as Rose Bengal and methylene blue can generate singlet oxygen, which leads to a different ratio of products than oxidation by type I photosensitizers or by one electron oxidants. Modeling reactions of singlet oxygen can be quite challenging. Reactions have been explored using CASSCF, NEVPT2, DFT, CCSD(T), and BD(T) calculations with SMD implicit solvation. The spin contamination in open-shell calculations were corrected by Yamaguchi's approximate spin projection method. The addition of singlet oxygen to guanine to form guanine endo- peroxide proceeds step-wise via a zwitterionic peroxyl intermediate. The subsequent barrier for ring closure is smaller than the initial barrier for singlet oxygen addition. Ring opening of the endoperoxide by protonation at C4-O is followed by loss of a proton from C8 and dehydration to produce 8-oxoG . The addition of lysine (modelled by methylamine) or water across the C5=N7 double bond of 8-oxoG is followed by acyl migration to form the final spiro products. The barrier for methylamine addition is significantly lower than for water addition and should be the dominant reaction channel. These results are in good agreement with the experimental results for the formation of guanine-lysine cross-links by oxidation by type II photosensitizers.

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true E^{A P} = α E^{B S} - β E^{H S}

…”

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Computational Study of Oxidation of Guanine by Singlet Oxygen (¹Δ_g) and Formation of Guanine:Lysine Cross‐Links

Thapa

Munk

Burrows

et al. 2017

Chemistry A European J

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“…In some cases, KS theory works well for open-shell singlet spin states, and in others, the performance of calculated properties can be improved by spin projection techniques. Yamaguchi and co-workers introduced a spin projection scheme and have applied it widely [25][26][27][28][29][30][31][32][33][34][35].…”

Section: Introductionmentioning

confidence: 99%

Singlet–triplet competition in the low-lying energy states of C4O4−n S n (n = 1–3) molecules

Varga

Truhlar

2015

Struct Chem

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Cyclobutanetetrone, C 4 O 4 , has a triplet ground state, although the ground state of C 4 S 4 is singlet. This computational study focuses on the mono-, di-, and trithiosquarate, C 4 O 4-n S n (n = 1-3), molecules as transition stages between the two ending points (C 4 O 4 and C 4 S 4 ), and investigates the trends for the changes in the energies, geometry, partial atomic charges, partial spin densities, as well as orbital energies of the four low-lying electronic states. As the number of the sulfur atoms is increasing, the singlet spin state becomes energetically more and more preferred. For C 4 O 3 S molecule, where only one oxygen atom is substituted by sulfur, the CCSD(T) calculations predict a triplet ground state, but the error of the calculations is most likely higher than the calculated 0.5 kcal/mol singlet-triplet energy gap.

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“…[18][19][20] Whereas AP energies have been used in studies for the last couple of decades, approximate AP gradient formulations were only reported in the mid-2000s. [21][22][23][24] Most recently, our group reported 21 the first complete and efficient gradient theory based on the z-vector scheme, 25 allowing efficient a) Electronic mail: hhratchian@ucmerced.edu exploration of the potential energy surface (PES) in its spin pure state. While the availability of analytic forces enhances the study of contaminated and broken-symmetry states, second derivatives will be necessary for efficiently characterizing stationary points and carrying out geometry optimization on flat PESs.…”

Section: Introductionmentioning

confidence: 99%

Second derivatives for approximate spin projection methods

Thompson

Hratchian

2015

The Journal of Chemical Physics

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The use of broken-symmetry electronic structure methods is required in order to obtain correct behavior of electronically strained open-shell systems, such as transition states, biradicals, and transition metals. This approach often has issues with spin contamination, which can lead to significant errors in predicted energies, geometries, and properties. Approximate projection schemes are able to correct for spin contamination and can often yield improved results. To fully make use of these methods and to carry out exploration of the potential energy surface, it is desirable to develop an efficient second energy derivative theory. In this paper, we formulate the analytical second derivatives for the Yamaguchi approximate projection scheme, building on recent work that has yielded an efficient implementation of the analytical first derivatives.

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Transition state optimization based on approximate spin-projection (AP) method

Cited by 80 publications

References 23 publications

Computational Study of Oxidation of Guanine by Singlet Oxygen (¹Δ_g) and Formation of Guanine:Lysine Cross‐Links

Computational Study of Oxidation of Guanine by Singlet Oxygen (¹Δ_g) and Formation of Guanine:Lysine Cross‐Links

Singlet–triplet competition in the low-lying energy states of C4O4−n S n (n = 1–3) molecules

Second derivatives for approximate spin projection methods

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Transition state optimization based on approximate spin-projection (AP) method

Cited by 80 publications

References 23 publications

Computational Study of Oxidation of Guanine by Singlet Oxygen (1Δg) and Formation of Guanine:Lysine Cross‐Links

Computational Study of Oxidation of Guanine by Singlet Oxygen (1Δg) and Formation of Guanine:Lysine Cross‐Links

Singlet–triplet competition in the low-lying energy states of C4O4−n S n (n = 1–3) molecules

Second derivatives for approximate spin projection methods

Contact Info

Product

Resources

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Computational Study of Oxidation of Guanine by Singlet Oxygen (¹Δ_g) and Formation of Guanine:Lysine Cross‐Links

Computational Study of Oxidation of Guanine by Singlet Oxygen (¹Δ_g) and Formation of Guanine:Lysine Cross‐Links