10 research outputs found
Ground state structures and excited state dynamics of pyrrole-water complexes: Ab initio
Aromatic Excimers: <i>Ab Initio</i> and TD-DFT Study
Excited dimers (excimers) formed by aromatic molecules
are important
in biological systems as well as in chemical sensing. The structure
of many biological systems is governed by excimer formation. Since
theoretical studies of such systems provide important information
about mutual arrangement of aromatic molecules in structural biology,
we carried out extensive calculations on the benzene excimer using
EOM-CCSD, RI-CC2, CASPT2, and TD-DFT approaches. For the benzene excimer,
we evaluate the reliability of the TD-DFT method based on the B3LYP,
PBE, PBE0, and ĻPBEh functionals. We extended the calculations
to naphthalene, anthracene, and pyrene excimers. We find that nearly
parallel stacked forms are the minimum energy structure. On the basis
of the benzene to pyrene excimers, we might roughly estimate the equilibrium
layer-to-layer distance for bilayer-long arenes in the first singlet
excited state, which is predicted to be bound
Insights into the structures, energetics, and vibrations of aqua-rubidium(I) complexes: Ab Initio
Insights into the Structures, Energetics, and Vibrations of Monovalent Cationā(Water) 1
HalogenāĻ Interactions between Benzene and X<sub>2</sub>/CX<sub>4</sub> (X = Cl, Br): Assessment of Various Density Functionals with Respect to CCSD(T)
Various
types of interactions between halogen (X) and Ļ moiety
(XāĻ interaction) including halogen bonding play important
roles in forming the structures of biological, supramolecular, and
nanomaterial systems containing halogens and aromatic rings. Furthermore,
halogen molecules such as X<sub>2</sub> and CX<sub>4</sub> (X = Cl/Br)
can be intercalated in graphite and bilayer graphene for doping and
graphene functionalization/modification. Due to the XāĻ
interactions, though recently highly studied, their structures are
still hardly predictable. Here, using the coupled-cluster with single,
double, and noniterative triple excitations (CCSDĀ(T)), the MĆøllerāPlesset
second-order perturbation theory (MP2), and various flavors of density
functional theory (DFT) methods, we study complexes of benzene (Bz)
with halogen-containing molecules X<sub>2</sub> and CX<sub>4</sub> (X = Cl/Br) and analyze various components of the interaction energy
using symmetry adapted perturbation theory (SAPT). As for the lowest
energy conformers (S1), X<sub>2</sub>āBz is found to have the
T-shaped structure where the electropositive X atom-end of X<sub>2</sub> is pointing to the electronegative midpoint of CC bond of the Bz
ring, and CX<sub>4</sub>āBz has the stacked structure. In addition
to this CX<sub>4</sub>āBz (S1), other low energy conformers
of X<sub>2</sub>āBz (S2/S3) and CX<sub>4</sub>āBz (S2)
are stabilized primarily by the dispersion interaction, whereas the
electrostatic interaction is substantial. Most of the density functionals
show noticeable deviations from the CCSDĀ(T) complete basis set (CBS)
limit binding energies, especially in the case of strongly halogen-bonded
conformers of X<sub>2</sub>āBz (S1), whereas the deviations
are relatively small for CX<sub>4</sub>āBz where the dispersion
is more important. The halogen bond shows highly anisotropic electron
density around halogen atoms and the DFT results are very sensitive
to basis set. The unsatisfactory performance of many density functionals
could be mainly due to less accurate exchange. This is evidenced from
the good performance by the dispersion corrected hybrid and double
hybrid functionals. B2GP-PLYP-D3 and PBE0-TSĀ(Tkatchenko-Scheffler)/D3
are well suited to describe the XāĻ interactions adequately,
close to the CCSDĀ(T)/CBS binding energies (within ā¼1 kJ/mol).
This understanding would be useful to study diverse XāĻ
interaction driven structures such as halogen containing compounds
intercalated between 2-dimensional layers
Comparison of cationic, anionic and neutral hydrogen bonded dimers
Short Strong Hydrogen Bonds (SSHBs) play an important role in many fields of physics, chemistry and biology. Since it is known that SSHBs exist in many biological systems, the role of hydrogen bonding motifs has been particularly interesting in enzyme catalysis, bio-metabolism, protein folding and proton transport phenomena. To explore the characteristic features of neutral, anionic and cationic hydrogen bonds, we have carried out theoretical studies of diverse homogeneous and heterogeneous hydrogen bonded dimers including water, peroxides, alcohols, ethers, aldehydes, ketones, carboxylic acids, anhydrides, and nitriles. Geometry optimization and harmonic frequency calculations are performed at the levels of Density Functional Theory (DFT) and Moller-Plesset second order perturbation (MP2) theory. First principles Car-Parrinello molecular dynamics (CPMD) simulations are performed to obtain IR spectra derived from velocity-and dipole-autocorrelation functions. We find that the hydrogen bond energy is roughly inversely proportional to the fourth power of the r(O/N-H) distance. Namely, the polarization of the proton accepting O/N atom by the proton-donating H atom reflects most of the binding energy in these diverse cation/anion/neutral hydrogen bonds. The present study gives deeper insight into the nature of hydrogen-bonded dimers including SSHBs.close151
Differences in structure, energy, and spectrum between neutral, protonated, and deprotonated phenol dimers: comparison of various density functionals with ab initio theory
Aromatic Excimers: Ab Initio and TD-DFT Study
Excited dimers (excimers) formed by aromatic molecules are important in biological systems as well as in chemical sensing. The structure of many biological systems is governed by excimer formation. Since theoretical studies of such systems provide important information about mutual arrangement of aromatic molecules in structural biology, we carried out extensive calculations on the benzene excimer using EOM-CCSD, RI-CC2, CASPT2, and TD-DFT approaches. For the benzene excimer, we evaluate the reliability of the TD-DFT method based on the B3LYP, PBE, PBE0, and ??PBEh functionals. We extended the calculations to naphthalene, anthracene, and pyrene excimers. We find that nearly parallel stacked forms are the minimum energy structure. On the basis of the benzene to pyrene excimers, we might roughly estimate the equilibrium layer-to-layer distance for bilayer-long arenes in the first singlet excited state, which is predicted to be bound.close7