8 research outputs found
Computational Study of Catalytic Reaction of Quercetin 2,4-Dioxygenase
We present a quantum mechanics/molecular
mechanics (QM/MM) and
QM-only study on the oxidative ring-cleaving reaction of quercetin
catalyzed by quercetin 2,4-dioxygenase (2,4-QD). 2,4-QD has a mononuclear
type 2 copper center and incorporates two oxygen atoms at C2 and C4
positions of the substrate. It has not been clear whether dioxygen
reacts with a copper ion or a substrate radical as the first step.
We have found that dioxygen is more likely to bind to a Cu<sup>2+</sup> ion, involving the dissociation of the substrate from the copper
ion. Then a Cu<sup>2+</sup>-alkylperoxo complex can be generated.
Comparison of geometry and stability between QM-only and QM/MM results
strongly indicates that steric effects of the protein environment
contribute to maintain the orientation of the substrate dissociated
from the copper center. The present QM/MM results also highlight that
a prior rearrangement of the Cu<sup>2+</sup>-alkylperoxo complex and
a subsequent hydrogen bond switching assisted by the movement of Glu73
can facilitate formation of an endoperoxide intermediate selectively
A Density Functional Theory Based Protocol to Compute the Redox Potential of Transition Metal Complex with the Correction of Pseudo-Counterion: General Theory and Applications
We propose an accurate
scheme to evaluate the redox potential of
a wide variety of transition metal complexes by adding a charge-dependent
correction term for a counterion around the charged complexes, which
is based on Generalized Born theory, to the solvation energy. The
mean absolute error (MAE) toward experimental redox potentials of
charged complexes is considerably reduced from 0.81 V (maximum error
1.22 V) to 0.22 V (maximum error 0.50 V). We found a remarkable exchange-correlation
functional dependence on the results rather than the basis set ones.
The combination of Wachters+f (for metal) and 6-31++GĀ(d,p) (for other
atoms) with the B3LYP functional gives the least MAE 0.15 V for the
test complexes. This scheme is applicable to other solvents, and heavier
transition metal complexes such as M<sub>1</sub>(CO)<sub>5</sub>(pycn)
(M<sub>1</sub> = Cr, Mo, W), M<sub>2</sub>(mnt)<sub>2</sub> (M<sub>2</sub> = Ni, Pd, Pt), and M<sub>3</sub>(bpy)<sub>3</sub> (M<sub>3</sub> = Fe, Ru, Os) with the same quality
Novel Formation of Ag/Au Bimetallic Nanoparticles by Physical Mixture of Monometallic Nanoparticles in Dispersions and Their Application to Catalysts for Aerobic Glucose Oxidation
Ag/Au bimetallic nanoparticles (BNPs)
with a size less than 2 nm
were prepared by physical mixture of colloidal dispersions of Ag and
Au nanoparticles (NPs). This provides an example of fabrication of
BNPs with self-organization by the reaction between metal NPs. Although
Ag/Au BNPs having different structures and compositions are one of
the most widely studied bimetallic systems in the literature due to
their wide range of uses such as in catalysis, electronics, plasmonics,
optical sensing, and surface-enhanced Raman scattering, we first prepared
such BNPs by physical mixture and characterized them by UVāvis
spectroscopy, SERS, XPS, TEM, and EDS in HR-STEM. The present fabrication
method has the advantage of avoiding the unfavorable formation of
AgCl precipitates in the reaction process which are always produced
when Ag<sup>+</sup> ions are used as a starting material in combination
with a HAuCl<sub>4</sub> precursor. These Ag/Au BNPs showed high catalytic
activities for aerobic glucose oxidation, and the highest activity
of 11ā510 mol of glucoseĀ·h<sup>ā1</sup>Ā·mol
of metal<sup>ā1</sup> was observed for the BNPs with a Ag/Au
atomic ratio of 1/4; the activity value is about 2 times higher than
that of Au NPs with nearly the same particle size. XPS and DFT calculation
results show that the negatively charged Au atoms due to the electron
charge transfer effects from neighboring Ag atoms and polyĀ(<i>N</i>-vinyl-2-pyrrolidone) act as catalytically active sites
and play an important role in the aerobic glucose oxidation
Full-valence density matrix renormalisation group calculations on meta-benzyne based on unrestricted natural orbitals. Revisit of seamless continuation from broken-symmetry to symmetry-adapted models for diradicals
<p>In this work, we show that the natural orbitals of unrestricted hybrid density functional theory (UHDFT) can be used as the active space orbitals to perform multireference (MR) calculations, for example, the density matrix renormalisation group (DMRG) and Mukherjee-type (Mk) MR coupled-cluster (CC) method. By including a sufficiently large number of these natural orbitals, full-valence (FV) active space can be identified without recourse of the expensive self-consistent procedures for DMRG-SCF. Several useful chemical indices are derived based on the occupation numbers of the natural orbitals for seamless continuation from broken-symmetry (BS) to symmetry-adapted (SA) methods. These procedures are used on 1,3-didehydrobenzene (meta-benzyne) to calculate its singlet (S)-triplet (T) gap. We compare our results to available experiments and computational results obtained by several other groups. We see our procedures as a seamless bridge between single-reference BS methods, such as UHDFT, and the SA MR methods, such as FV DMRG and MkMRCC.</p
ĻāConjugated Trinuclear Groupā9 Metalladithiolenes with a Triphenylene Backbone
Previously,
we synthesized Ļ-conjugated trinuclear metalladithiolene complexes
based on benzenehexathiol (<i>J. Chem. Soc., Dalton Trans.</i> <b>1998</b>, 2651; <i>Dalton Trans.</i> <b>2009</b>, 1939; <i>Inorg. Chem.</i> <b>2011</b>, <i>50</i>, 6856). Here we report trinuclear complexes with a triphenylene
backbone. A reaction with triphenylenehexathiol and group 9 metal
precursors in the presence of triethylamine gives rise to trinuclear
complexes <b>9</b>ā<b>11</b>. The planar structure
of <b>11</b> is determined using single crystal X-ray diffraction
analysis. The ligand-to-metal charge transfer bands of <b>9</b>ā<b>11</b> move to longer wavelengths compared with
those of mononuclear <b>12</b>ā<b>14</b>. Electrochemical
measurements disclose that the one-electron and two-electron reduced
mixed-valent states are stabilized thermodynamically. UVāvisāNIR
spectroscopy for the reduced species of <b>9</b> identifies
intervalence charge transfer bands for <b>9</b><sup>ā</sup> and <b>9</b><sup>2ā</sup>, substantiating the existence
of electronic communication among the three metal nuclei. These observations
prove that the triphenylene backbone transmits Ļ-conjugation
among the three metalladithiolene units
Xāray Magnetic Circular Dichroism Investigation of the Electron Transfer Phenomena Responsible for Magnetic Switching in a Cyanide-Bridged [CoFe] Chain
The
cyanide-bridged [CoFe] one-dimensional chain, [Co<sup>II</sup>((<i>R</i>)-pabn)]Ā[Fe<sup>III</sup>(Tp)Ā(CN)<sub>3</sub>]Ā(BF<sub>4</sub>)Ā·MeOHĀ·2H<sub>2</sub>O, where (<i>R</i>)-pabn
= (<i>R</i>)-<i>N</i>2,<i>N</i>(2ā²)-bisĀ(pyridin-2-ylmethyl)-1,1ā²-binaphthyl-2,2ā²-diamine
and Tp = hydrotrisĀ(pyrazolyl)Āborate, exhibits magnetic and electric
bistabilities originating from an electron transfer coupled spin transition
between FeāCNāCo pairs. The use of L-edge X-ray absorption
spectroscopy (XAS) in combination with L-edge X-ray magnetic circular
dichroism (XMCD) is explored for the investigation of the electronic
structure and magnetization of Co and Fe ions separately, in both
diamagnetic and paramagnetic states. It has been established from
susceptibility results that the switching between diamagnetic and
paramagnetic phases emanates from electron transfer between low spin
FeĀ(II) and CoĀ(III), resulting in low spin FeĀ(III) (<i>S</i> = 1/2) and high spin CoĀ(II) (<i>S</i> = 3/2). The XAS
and XMCD results are consistent with the bulk susceptibility measurements,
where greater detail regarding the charge transfer process is determined.
The FeāCNāCo electron transfer pathway is highlighted
by a strongly XMCD dependent transition to a cyanide back bonding
orbital, giving evidence for strong hybridization with FeĀ(III) t<sub>2g</sub> orbitals. In addition to thermally induced and photoinduced
switching, [CoFe] is found to exhibit a switching by grinding induced
dehydration. Analysis of XAS shows that on grinding diamagnetic [CoFe],
75% of metal ions lock into the magnetic CoĀ(II)ĀFeĀ(III) phase. Density
functional theory calculations based on the [CoFe] crystal structure
in the magnetic and nonmagnetic phases aid the spectroscopic results
and provide a complementary insight into the electronic configuration
of the [CoFe] 3d shells, quantifying the change in ligand field around
Co and Fe centers on charge transfer
Bistable Multifunctionality and Switchable Strong Ferromagnetic-to-Antiferromagnetic Coupling in a One-Dimensional Rhodium(I)āSemiquinonato Complex
We
present a comprehensive study of the synthesis, heat capacity,
crystal structures, UVāvisāNIR and mid-IR spectra, DFT
calculations, and magnetic and electrical properties of a one-dimensional
(1D) rhodiumĀ(I)āsemiquinonato complex, [RhĀ(3,6-DBSQ-4,5-(MeO)<sub>2</sub>)Ā(CO)<sub>2</sub>]<sub>ā</sub> (<b>3</b>), where
3,6-DBSQ-4,5-(MeO)<sub>2</sub><sup>ā¢ā</sup> represents
3,6-di-<i>tert</i>-butyl-4,5-dimethoxy-1,2-benzosemiquinonato
radical anion. The compound <b>3</b> comprises neutral 1D chains
of complex molecules stacked in a staggered arrangement with short
RhāRh distances of 3.0796(4) and 3.1045(4) Ć
at 226 K
and exhibits unprecedented bistable multifunctionality with respect
to its magnetic and conductive properties in the temperature range
of 228ā207 K. The observed bistability results from the thermal
hysteresis across a first-order phase transition, and the transition
accompanies the exchange of the interchain CāHĀ·Ā·Ā·O
hydrogen-bond partners between the semiquinonato ligands. The strong
overlaps of the complex molecules lead to unusually strong ferromagnetic
interactions in the low-temperature (LT) phase. Furthermore, the magnetic
interactions in the 1D chain drastically change from strongly ferromagnetic
in the LT phase to antiferromagnetic in the room-temperature (RT)
phase with hysteresis. In addition, the compound <b>3</b> exhibits
long-range antiferromagnetic ordering between the ferromagnetic chains
and spontaneous magnetization because of spin canting (canted antiferromagnetism)
at a transition temperature <i>T</i><sub>N</sub> of 14.2
K. The electrical conductivity of <b>3</b> at 300 K is 4.8 Ć
10<sup>ā4</sup> S cm<sup>ā1</sup>, which is relatively
high despite Rh not being in a mixed-valence state. The temperature
dependence of electrical resistivity also exhibits a clear hysteresis
across the first-order phase transition. Furthermore, the ferromagnetic
LT phase can be easily stabilized up to RT by the application of a
relatively weak applied pressure of 1.4 kbar, which reflects the bistable
characteristics and demonstrates the simultaneous control of multifunctionality
through external perturbation