Differences in structure, energy, and spectrum between neutral, protonated, and deprotonated phenol dimers: comparison of various density functionals with <i>ab initio</i> theory

Kołaski, Maciej,Kumar, Anupriya,Singh, N. Jiten,Kim, Kwang S. The Royal Society of Chemistry 2011 Physical chemistry chemical physics Vol.13 No.3

<P>We have carried out extensive calculations for neutral, cationic protonated, anionic deprotonated phenol dimers. The structures and energetics of this system are determined by the delicate competition between H-bonding, H–π interaction and π–π interaction. Thus, the structures, binding energies and frequencies of the dimers are studied by using a variety of functionals of density functional theory (DFT) and Møller–Plesset second order perturbation theory (MP2) with medium and extended basis sets. The binding energies are compared with those of highly reliable coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)) at the complete basis set (CBS) limit. The neutral phenol dimer is unique in the sense that its experimental rotational constants have been measured. The geometry of the neutral phenol dimer is governed by the hydrogen bond formed by two hydroxylgroups and the H–π interaction between two aromatic rings, while the structure of the protonated/deprotonated phenol dimers is additionally governed by the electrostatic and induction effects due to the short strong hydrogen bond (SSHB) and the charges populated in the aromatic rings in the ionic systems. Our salient finding is the substantial differences in structure between neutral, protonated, and deprotonated phenol dimers. This is because the neutral dimer involves in both H<SUB>π</SUB>⋯O and H<SUB>π</SUB>⋯π interactions, the protonated dimer involves in H<SUB>π</SUB>⋯π interactions, and the deprotonated dimer involves in a strong H<SUB>π</SUB>⋯O interaction. It is important to compare the reliability of diverse computational approaches employed in quantum chemistry on the basis of the calculational results of this system. MP2 calculations using a small cc-pVDZ basis set give reasonable structures, but those using extended basis sets predict wrong π-stacked structures due to the overestimation of the dispersion energies of the π–π interactions. A few new DFT functionals with the empirical dispersion give reliable results consistent with the CCSD(T)/CBS results. The binding energies of the neutral, cationic protonated, and anionic deprotonated phenol dimers are estimated to be more than 28.5, 118.2, and 118.3 kJ mol<SUP>−1</SUP>, respectively. The energy components of the intermolecular interactions for the neutral, protonated and deprotonated dimers are analyzed.</P> <P>Graphic Abstract</P><P>Superimposed predicted structures of the neutral (gray), protonated (brown), and deprotonated (blue) phenol dimers. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c003008b'> </P>

Structures, Energetics, and IR Spectra of Monohydrated Inorganic Acids: Ab initio and DFT Study

Kołaski, Maciej,Zakharenko, Aleksey A.,Karthikeyan, S.,Kim, Kwang S. American Chemical Society 2011 Journal of chemical theory and computation Vol.7 No.10

<P>We carried out extensive calculations of diverse inorganic acids interacting with a single water molecule, through a detailed analysis of many possible conformations. The optimized structures were obtained by using density functional theory (DFT) and the second order Møller–Plesset perturbation theory (MP2). For the most stable conformers, we calculated the interaction energies at the complete basis set (CBS) limit using coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The −OH stretching harmonic and anharmonic frequencies are provided as fingerprints of characteristic conformers. The zero-point energy (ZPE) uncorrected/corrected (Δ<I>E</I><SUB>e</SUB>/Δ<I>E</I><SUB>0</SUB>) interaction energies and the enthalpies/free energies (Δ<I>H</I><SUB>r</SUB>/Δ<I>G</I><SUB>r</SUB> at room temperature and 1 bar) are reported. Various comparisons are made between many diverse inorganic acids (H<SUB><I>m</I></SUB>XO<SUB><I>n</I></SUB> where X = B/N/P/Cl/Br/I, <I>m</I> = 1–3, and <I>n</I> = 0–4) as well as other simple inorganic acids. In many cases, we find that the dispersion-driven van der Waals interactions between X in inorganic acid molecules and O in water molecules as well as the X<SUP>+</SUP>···O<SUP>–</SUP> electrostatic interactions are important.</P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/ct100428z'>ACS Electronic Supporting Info</A></P>

Aromatic Excimers: <i>Ab Initio</i> and TD-DFT Study

Kołaski, Maciej,Arunkumar, C. R.,Kim, Kwang S. American Chemical Society 2013 Journal of chemical theory and computation Vol.9 No.1

<P>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 ωPBEh 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.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jctcce/2013/jctcce.2013.9.issue-1/ct300350m/production/images/medium/ct-2012-00350m_0007.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/ct300350m'>ACS Electronic Supporting Info</A></P>

Comparison of cationic, anionic and neutral hydrogen bonded dimers

Lee, Han Myoung,Kumar, Anupriya,Kołaski, Maciej,Kim, Dong Young,Lee, Eun Cheol,Min, Seung Kyu,Park, Mina,Choi, Young Cheol,Kim, Kwang S. Royal Society of Chemistry 2010 Physical chemistry chemical physics Vol.12 No.23

<P>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 Møller–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 <I>r</I>(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.</P> <P>Graphic Abstract</P><P>The H-bond energy is roughly inversely proportional to the fourth power of the <I>r</I>(O/N⋯H) distance in the diverse cation/anion/neutral H-bonds. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=b925551f'> </P>

Halogen−π Interactions between Benzene and X₂/CX₄ (X = Cl, Br): Assessment of Various Density Functionals with Respect to CCSD(T)

Youn, Il Seung,Kim, Dong Yeon,Cho, Woo Jong,Madridejos, Jenica Marie L.,Lee, Han Myoung,Kołaski, Maciej,Lee, Joonho,Baig, Chunggi,Shin, Seung Koo,Filatov, Michael,Kim, Kwang S. American Chemical Society 2016 The Journal of physical chemistry A Vol.120 No.46

<P>Various types of interactions between halogen (X) and pi moiety (X-pi 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-2 and CX4 (X = Cl/Br) can be intercalated in graphite and bilayer graphene for doping and graphene functionalization/modification. Due to the X-pi interactions, though recently highly studied, their structures are still hardly predictable. Here, using the coupled-cluster with single, double, and noniterative triple excitations (CCSD(T)), the Moller-Plesset 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-2 and CX4 (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-2-Bz is found to have the T-shaped structure where the electropositive X atom-end of X-2 is pointing to the electronegative midpoint of CC bond of the Bz ring, and CX4-Bz has the stacked structure. In addition to this CX4 Bz (S1), other low energy conformers of X-2-Bz (S2/S3) and CX4-Bz (S2) are stabilized primarily by the dispersion interaction, whereas the electrostatic interaction is substantial. Most of the density functionals show noticeable deviations from the CCSD(T) complete basis set (CBS) limit binding energies, especially in the case of strongly halogen-bonded conformers of X-2-Bz (S1), whereas the deviations are relatively small for CX4-Bz 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-TS (Tkatchenko-Scheffler)/D3 are well suited to describe the X-pi interactions adequately, close to the CCSD(T)/CBS binding energies (within similar to 1 kJ/mol). This understanding would be useful to study diverse X-pi interaction driven structures such as halogen containing compounds intercalated between 2-dimensional layers.</P>