35 research outputs found
Role of Molecular Singlet Oxygen in Photochemical Degradation of NTO: DFT Study
NTO (5-nitro-1,2,4-triazol-3-one), an energetic material
used in
military applications, may be released to the environment and dissolved
in surface water and groundwater due to its good water solubility.
Singlet oxygen is an important reactive oxygen species produced in
the aquatic environment under sunlight irradiation. A detailed investigation
of the possible mechanism for NTO decomposition in water induced by
singlet oxygen as one of the pathways for NTO environmental degradation
was performed by a computational study at PCM(Pauling)/M06-2X/6-311++G(d,p)
level. Decomposition of NTO was found to be a multistep process that
may begin with singlet oxygen attachment to the carbon atom of the
CN double bond. The formed intermediate undergoes cycle opening,
and nitrogen gas, nitrous acid, and carbon (IV) oxide elimination.
Isocyanic acid, arisen transiently, hydrolyzes into ammonia and carbon
(IV) oxide. The obtained results show a significant increase in reactivity
of the anionic form of NTO as compared to its neutral form. The calculated
activation energies and high exothermicity of the studied processes
support the contribution of singlet oxygen to NTO degradation into
low-weight inorganic compounds in the environment
Structure and Energetics of (111) Surface of γ‑Al<sub>2</sub>O<sub>3</sub>: Insights from DFT Including Periodic Boundary Approach
The (111) surface
of γ-alumina has been reexamined, and a
new (111) surface model has been suggested. The local structure of
this new surface of γ-alumina, (111)<sub>n</sub>, has been optimized
by the density functionals along with the full electron basis sets
by using periodic boundary condition. This newly modeled (111)<sub>n</sub> surface is characterized by the same stability as that of
the (110) surface, and its surface energy amounts to 2.561 J/m<sup>2</sup>, only about 0.002 J/m<sup>2</sup> larger than that of (110).
Three different types of the tricoordinated Al centers have been identified
on (111)<sub>n</sub>. Molecular orbital (MO) analysis and the population
analysis demonstrate that one type of Al, Al(I), is a nonpaired electron
center. The singly occupied MO on Al(I) center is expected to play
an important role in the catalytic activities of the γ-alumina.
Moreover, the neighboring Al (Al(III)) on the (111)<sub>n</sub> surface
provides suitable acceptance position for the electron donating groups.
The defected surfaces of (111)<sub>n</sub> are found to be having
a similar stability. The detachment of Al(I) from the (111)<sub>n</sub> surface results in disappearance of the nonpaired electron centers.
Meanwhile, the attachment of Al(I) on (111)<sub>n</sub> surface will
produce rich nonpaired electron centers on this new surface. Therefore,
this newly defined surface is expected to attract the research interests
in the catalytic activities of γ-alumina
Toward Selection of Efficient Density Functionals for van der Waals Molecular Complexes: Comparative Study of C–H···π and N–H···π Interactions
We have evaluated the performance
of two of the recently developed
density functionals (M06-2X and B2PLYP-D), which are widely used,
by considering three important prototype systems, including benzene–acetylene,
benzene–methane, and benzene–ammonia, possessing C–H···π
or N–H···π interactions. Computational
results are compared with the available experimental data. Considered
density functionals are from two different classes: hybrid meta density
functional (M06-2X) and double hybrid density functional (B2PLYP-D).
The performance of a range of basis sets (6-31G(d), 6-31+G(d), 6-31+G(d,p),
6-311G(d,p), 6-311+G(d,p), aug-cc-pVXZ (X = D, T, Q)) with the above-mentioned
two density functionals was evaluated. Comparison of the results includes
Pople’s basis sets versus Dunning’s correlation consistent
basis sets with the M06-2X and B2PLYP-D functionals considered in
this study. The basis set effect on geometrical parameters, dissociation
energies, and selected vibrational frequency shifts was thoroughly
analyzed. We have addressed whether the counterpoise corrections with
geometry optimizations and vibrational frequencies are important.
Our computational study reveals that calculations carried out with
smaller basis sets very well reproduce the reported experimental values
of dissociation energies. The present study also shows that using
the very large Dunning’s correlation consistent basis set worsens
the results. The necessity of including counterpoise correction for
binding energies depends on the system and the type of method used.
In general, vibrational frequency calculations using these DFT functionals
generate characteristic red shifts for the C–H···π
or N–H···π interactions in the complexes
Role of Hydroxyl Radical in Degradation of NTO: DFT Study
Hydroxyl radicals are important reactive oxygen species
produced
in the aquatic environment under sunlight irradiation. Many organic
pollutants may be decomposed as they encounter hydroxyl radicals,
due to their high oxidative ability. NTO (5-nitro-1,2,4-triazol-3-one),
an energetic material used in military applications, may be released
to the environment and dissolved in surface water and groundwater
due to its good water solubility. A detailed investigation of the
possible mechanism for NTO decomposition in water induced by hydroxyl
radical as one of the pathways for NTO environmental degradation was
performed by computational study at the PCM/M06-2X/6-311++G(d,p) level. Decomposition of NTO was found to be a multistep
process that may begin with an addition of hydroxyl radical to the
carbon atom of CN double bond and consequent release of a
nitrite radical. The formed intermediate undergoes a series of chemical
transformations that include the attachments of hydroxyl radical to
carbon atoms, the transfer of hydrogen to hydroxyl radical, isomerization,
and bond cleavage, leading to low-weight inorganic compounds, such
as ammonia, nitrogen gas, nitrous acid, nitric acid, and carbon(IV)
oxide. The anionic form of NTO is more reactive toward interaction
with the hydroxyl radical as compared with its neutral form. Calculated
activation energies and high exergonicity of the studied process support
the significant contribution of the hydroxyl radical to NTO mineralization
in environment
Electron Attachment to the Cytosine-Centered DNA Single Strands: Does Base Stacking Matter?
Electron attachment to the trimer of nucleotide, dGpdCpdG,
has
been investigated by a quantum mechanical approach at a reliable level
of theory. The study of the electron attached dGpdCpdG species demonstrates
that cytosine contained DNA single strands have a strong tendency
to capture low-energy electrons and to form electronically stable
cytosine-centered radical anions. The comparative study of the model
molecules pdCpdG and dGpdCp reveals that base stacking has little
contribution to the adiabatic electron affinity (AEA) of cytosine
in DNA single strands. Additionally, the base–base stacking
does not affect the vertical detachment energy (VDE) of the cytosine-centered
radicals. Intrastrand H-bonding is found to be critical in increasing
the values of the AEA and VDE. However, base–base stacking
is revealed to be important in enlarging the vertical electron affinity
(VEA) of cytosine. The electron attachment to the cytosine moiety
intensifies the intrastrand H-bonding between the neighboring G and
C bases. This process disrupts the base–base stacking interaction
in the radical anion of dGpdCpdG
On the Stability of Perfluoroalkyl-Substituted Singlet Carbenes: A Coupled-Cluster Quantum Chemical Study
A series
of trifluoromethyl-substituted carbenes R–C(:)–CF<sub>3</sub> (R = NMe<sub>2</sub>, OMe, F, PMe<sub>2</sub>, P(NMe<sub>2</sub>)<sub>2</sub>, P(N(Pr-i)<sub>2</sub>)<sub>2</sub>, SMe, Cl);
(dimethylamino)(perfluoroalkyl)carbenes Me<sub>2</sub>N–C(:)–R (R = CF<sub>3</sub>, C<sub>2</sub>F<sub>5</sub>, <i>n</i>-C<sub>3</sub>F<sub>7</sub>, <i>i</i>-C<sub>3</sub>F<sub>7</sub>, and <i>t</i>-C<sub>4</sub>F<sub>9</sub>) and symmetrically substituted carbenes R–C(:)–R
(R = NMe<sub>2</sub>, OMe, F, PMe<sub>2</sub>, SMe, Cl) have been
investigated by means of quantum chemistry methods. Different levels
of approximation were used, including the CCSD(T) approach also known
in quantum chemistry as the “golden standard”, in combination
with three different basis sets (TZVP, cc-pVDZ, cc-pVTZ). Relative
stabilities of carbenes have been estimated using the differences
between the singlet and triplet ground state energies (Δ<i>E</i><sub>ST</sub>) and energies of the hydrogenation reaction
for the singlet and triplet ground states of the carbenes. The latter
seem to correlate better with stability of carbenes than the Δ<i>E</i><sub>ST</sub> values. The <sup>13</sup>C NMR chemical shifts
of the methylidene carbon indicate the more high-field chemical shift
values in the known, isolable carbenes compared to the unstable ones.
This is the first report on the expected chemical shifts in the highly
unstable singlet carbenes. Using these criteria, some carbene structures
from the studied series (as, for instance, Me<sub>2</sub>N–C(:)–CF<sub>3</sub>, Me<sub>2</sub>N–C(:)–C<sub>3</sub>F<sub>7</sub>-<i>i</i>) are proposed as good candidates for the experimental
preparation
Geometric, Magnetic, and Adsorption Properties of Cross-Linking Carbon Nanotubes: A Computational Study
Cross-linking carbon nanotubes (CLCNTs) composed of three
axially
confined single-walled carbon nanotubes (SWCNTs) of the (10,0) type
are investigated by plane-wave density functional theory (DFT). Three
CLCNT models, differing from each other by the structure of the contact
regions of the three SWCNT constituents, are explored in terms of
their geometric, electronic, and magnetic properties. Various magnetic
phases, as obtained by combining finite SWCNTs in ferromagnetic (FM)
or antiferromagnetic (AFM) coordination, are distinguished. The characteristics
of these phases are shown to depend on the contact region geometry
which plays an essential role in defining the order of their stabilities.
For a selected CLCNT, adsorption of hydrogen atoms is discussed. The
magnetic features of the CLCNTs turn out to hold the key for understanding
the site dependence of the hydrogen atom adsorption energies
Binding of Alkali Metal Ions with 1,3,5-Tri(phenyl)benzene and 1,3,5-Tri(naphthyl)benzene: The Effect of Phenyl and Naphthyl Ring Substitution on Cation−π Interactions Revealed by DFT Study
The effect of substitution
of phenyl and naphthyl rings to benzene
was examined to elucidate the cation−π interactions involving
alkali metal ions with 1,3,5-tri(phenyl)benzene (TPB) and 1,3,5-tri(naphthyl)benzene
(TNB). Benzene, TPB, and four TNB isomers (with ααα,
ααβ, αββ, and βββ
types of fusion) and their complexes with Li<sup>+</sup>, Na<sup>+</sup>, K<sup>+</sup>, Rb<sup>+</sup>, and Cs<sup>+</sup> were optimized
using DFT approach with B3LYP and M06-2X functionals in conjunction
with the def2-QZVP basis set. Higher relative stability of β,β,β-TNB
over α,α,α-TNB can be attributed to <i>peri</i> repulsion, which is defined as the nonbonding repulsive interaction
between substituents in the 1- and the 8-positions on the naphthalene
core. Binding energies, distances between ring centroid and the metal
ions, and the distance to metal ions from the center of other six-membered
rings were compared for all complexes. Our computational study reveals
that the binding affinity of alkali metal cations increases significantly
with the 1,3,5-trisubstitution of phenyl and naphthyl rings to benzene.
The detailed computational analyses of geometries, partial charges,
binding energies, and ligand organization energies reveal the possibility
of favorable C–H···M<sup>+</sup> interactions
when a α-naphthyl group exists in complexes of TNB structures.
Like benzene-alkali metal ion complexes, the binding affinity of metal
ions follows the order: Li<sup>+</sup> > Na<sup>+</sup> > K<sup>+</sup> > Rb<sup>+</sup> > Cs<sup>+</sup> for any considered
1,3,5-trisubstituted
benzene systems. In case of TNB, we found that the strength of interactions
increases as the fusion point changes from α to β position
of naphthalene
Interaction of 2′-Deoxyadenosine with <i>cis</i>-2-Butene-1,4-dial: Computational Approach to Analysis of Multistep Chemical Reactions
The computational analysis of multistep chemical interactions
between
2′-deoxyadenosine and <i>cis</i>-2-butene-1,4-dial
has been performed. The applied protocol includes generation of a
multistep Gibbs free-energy reaction profile (PCM/M05-2X/6-311+G(d)
level) for the transformations of the reagents to products, followed
by evaluation of the rate constants, construction of the corresponding
kinetic equations, and solving them. Such a procedure allows one to
significantly extend the number of experimentally determined steps
by addition of the ones computationally predicted. The primary products
of the reaction are found to be four diastereomeric adducts characterized
by virtually the same stability. The acid-catalyzed dehydration of
these adducts leads to a more stable secondary product. Computational
verification of UV and NMR spectra has also been performed. It has
been revealed that simulated UV and NMR spectra of primary and secondary
2′-deoxyadenosine adducts of <i>cis</i>-2-butene-1,4-dial
are in agreement with the experimental observations
How the “Liquid Drop” Approach Could Be Efficiently Applied for Quantitative Structure–Property Relationship Modeling of Nanofluids
The main goal of this paper is the
evaluation of the applicability
of the geometrical “liquid drop” model (LDM) to describe
physicochemical properties of nanofluids in quantitative structure–property
relationship (QSPR) modeling. LDM-based descriptors are size-dependent,
which allows them to be applied for a series of nanoparticles with
the same chemical composition but different sizes. Thermal conductivity
of nanofluids as the target property was investigated. Random forest
regression as a nonparametric approach was utilized to determine important
structural features of nanofluids responsible for enhancing their
thermal conductivity