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Intermolecular interactions with polycyclic aromatic hydrocarbons (PAHs) represent an important area of physisorption studies. These investigations are often hampered by a size of interacting PAHs, which makes the calculation prohibitively expensive. Therefore, methods designed to deal with large molecules could be helpful to reduce the computational costs of such studies. Recently we have introduced a new systematic approach for the molecular fragmentation of PAHs, denoted as AROFRAG, which decomposes a large PAH molecule into a set of predefined small PAHs with a benzene ring being the smallest unbreakable unit, and which in conjunction with the Molecules-in-Molecules (MIM) approach provides an accurate description of total molecular energies. In this contribution we propose an extension of the AROFRAG, which provides a description of intermolecular interactions for complexes composed of PAH molecules. The examination of interaction energy partitioning for various test cases shows that the AROFRAG3 model connected with the MIM approach accurately reproduces all important components of the interaction energy. An additional important finding in our study is that the computationally expensive long-range electron-correlation part of the interaction energy, that is, the dispersion component, is well described at lower AROFRAG levels even without MIM, which makes the latter models interesting alternatives to existing methods for an accurate description of the electron-correlated part of the interaction energy.
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Intermolecular complexes with calixarenes are intriguing because of multiple possibilities of noncovalent binding for both polar and nonpolar molecules, including docking in the calixarene cavity. In this contribution calix[6]arenes interacting with amino acids are studied with an additional aim to show that tools such as symmetry-adapted perturbation theory (SAPT), functional-group SAPT (F-SAPT), and systematic molecular fragmentation (SMF) methods may provide explanations for different numbers of noncovalent bonds and of their varying strength for various calixarene conformers and guest molecules. The partitioning of the interaction energy provides an easy way to identify hydrogen bonds, including those with unconventional hydrogen acceptors, as well as other noncovalent bonds, and to find repulsive destabilizing interactions between functional groups. Various other features can be explained by energy partitioning, such as the red shift of an IR stretching frequency for some hydroxy groups, which arises from their attraction to the phenyl ring of calixarene. Pairs of hydrogen bonds and other noncovalent bonds of similar magnitude found by F-SAPT explain an increase in the stability of both inclusion and outer complexes.
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Aminoácidos , Calixarenos , Ligação de Hidrogênio , Fenômenos Físicos , HidrogênioRESUMO
Symmetry-adapted perturbation theory (SAPT) and functional-group SAPT (F-SAPT) are applied to examine differences in interaction energies of diastereoisomeric complexes of two chiral molecules of natural origin: (S/R)-carvone with (-)-menthol. The study is extended by including derivatives of menthol with its hydroxy group exchanged by another functional group, thus examining the substituent effect of the interaction and the interaction differences between diastereoisomers. The partitioning of the interaction energy into functional-group components allows one to explain this phenomenon by the mutual cancellation of attractive and repulsive interactions between functional groups. In some cases, one can identify dominant chiral interactions between groups of atoms of carvone and menthol derivatives, while in many other instances, no major interaction can be distinguished and the net chiral difference results from subtle near cancellation of several smaller terms. Our results indicate that the F-SAPT method can be faithfully utilized for such analyses.
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Molpro is a general purpose quantum chemistry software package with a long development history. It was originally focused on accurate wavefunction calculations for small molecules but now has many additional distinctive capabilities that include, inter alia, local correlation approximations combined with explicit correlation, highly efficient implementations of single-reference correlation methods, robust and efficient multireference methods for large molecules, projection embedding, and anharmonic vibrational spectra. In addition to conventional input-file specification of calculations, Molpro calculations can now be specified and analyzed via a new graphical user interface and through a Python framework.
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A dimerization of methyl chlorophyllide a molecules and a role of water in stabilization and properties of methyl chlorophyllide a dimers were studied by means of symmetry-adapted perturbation theory (SAPT), functional-group SAPT (F-SAPT), density-functional theory (DFT), and time-dependent DFT approaches. The quantification of various types of interactions, such as π-π stacking, coordinative, and hydrogen bonding by applying the F-SAPT energy decomposition scheme shows the major role of the magnesium atom and the pheophytin macrocycle in the stability of the complex. The examination of interaction energy components with respect to a mutual orientation of monomers and in the presence or absence of water molecules reveals that the dispersion energy is the main binding factor of the interaction, while water molecules tend to weaken the attraction between methyl chlorophyllide a species. The dimerization can be seen in computed UV-vis spectra, and results in a doubling of the lowest peaks, as compared to the monomer spectrum, and in an intensity rise of the lowest 1.8 and 2.4 eV peaks at a cost of the 3.5 eV peaks for the majority of dimer configurations. The complexation of water has little effect on the peaks' position; however, it affects the overall shape of simulated spectra through changes in peak intensities, which is strongly dependent on the structure of the complex. The VCD spectra for the dimers show several characteristic features attributed to the interaction of substituting groups and/or water ligand attached to macrocycle groups belonging to different monomers. VCD is sensitive to the type of the formed dimer, but not to the number of water molecules it contains. This and several other features, as well as the differential UV-vis spectra, may serve as the indicator of the presence of a given dimer structure in the experiment.
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Clorofila A/química , Clorofilídeos/química , Dimerização , Modelos Moleculares , Água/química , Ligação de Hidrogênio , Conformação MolecularRESUMO
Despite massive efforts to pinpoint the substituent effects in the so-called cationπ systems, no consensus has been yet reached on how substituents exercise their effects in the interaction of the aromatic molecule with the metal ion. The π-polarization (the Hunter model) and the direct local effect (the Wheeler-Houk model) are two lines of thought applied to this problem, but the justification of both approaches is based on insufficiently proven assumptions and approximations. In order to shed more light on this issue we propose a new approach which enables us to gauge directly the energetic trends resulting from the interaction of the ring with the cation. In our method we add one more partitioning level to the interacting quantum atoms (IQA) scheme and decompose the IQA interaction energies into contributions resulting from σ and π electron densities of the aromatic ring. The new approach, which is named partitioned-IQA, abbreviated as p-IQA, has been applied to complexes of derivatives of benzene or azaborine interacting with a sodium cation. The p-IQA approach reveals that in these systems both σ and π electronic moieties are polarized. Interestingly, for the majority of cases the σ-polarization outweighs the π one, contrary to the Hunter model. However, the Wheeler-Houk model is not precise, either, since the σ-polarization shows some degree of non-locality. In addition, the substituents are found to have a negligible influence on the ring orbital-overlapping capability, i.e. the covalency. Therefore, the substituent effect in the cationπ interaction is a nonlocal classical effect, indicating that neither Hunter model nor Wheeler-Houk model is able to fully describe all the aspects of the substituent effects. The p-IQA conclusions for the considered systems have been compared with the results from the functional-group SAPT (F-SAPT) method. We believe that the presented partitioning in the IQA framework will provide a deeper insight into the substituent effects in the cationπ interactions, which is beyond the σ-π atomic charge population separation.
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The applicability of symmetry-adapted perturbation theory (SAPT) and functional-group SAPT (F-SAPT) to study chiral recognition is investigated on an example of three popular chiral drug molecules: ibuprofen, norepinephrine, and baclofen, interacting with phenethylamine or proline - two molecules that are often used as chiral phases in chromatography. The comparison of the F-SAPT with the interacting quantum atoms (IQA) approach is also provided. Accurate estimation of energetic differences of the non-covalent intermolecular complexes composed of two chiral molecules is a necessary prerequisite for the possibility of a prediction of the chiral recognition. The SAPT method with interacting molecules described on the density functional theory level provides accurate total interaction energies, while the F-SAPT approach is the most useful in determining which functional groups are responsible for strengthening or weakening of the interaction between chiral molecules. The largest difference in the interaction energies has been calculated for the baclofen-phenethylamine and norepinephrine-phenethylamine pairs, while the smallest for the ibuprofen-proline and baclofen-proline ones. In most cases, the intermolecular interaction is found to be composed of a strong directional hydrogen bond, which was stabilized by two or more weaker non-covalent interactions between groups (in accordance with the phenomological three-point rule), but in several cases more subtle factors are responsible for larger stability of one diastereoisomer, like the stabilization of the conformation involving two noninteracting functional groups attached to a chiral atom through intramolecular attraction. Additionally, the simulated IR spectra were analyzed for all pairs of diastereoisomeric complexes and the red- and blue-shifts of characteristic bond vibrations were discussed in the context of inter-group interactions.
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We consider collisional properties of polyatomic aromatic hydrocarbon molecules immersed into ultracold atomic gases and investigate intermolecular interactions of exemplary benzene, naphthalene, and azulene with alkali-metal (Li, Na, K, Rb, and Cs) and alkaline-earth-metal (Mg, Ca, Sr, and Ba) atoms. We apply the state-of-the-art ab initio techniques to compute the potential energy surfaces (PESs). We use the coupled cluster method restricted to single, double, and noniterative triple excitations to reproduce the correlation energy and the small-core energy-consistent pseudopotentials to model the scalar relativistic effects in heavier metal atoms. We also report the leading long-range isotropic and anisotropic dispersion and induction interaction coefficients. The PESs are characterized in detail, and the nature of intermolecular interactions is analyzed and benchmarked using symmetry-adapted perturbation theory. The full three-dimensional PESs are provided for the selected systems within the atom-bond pairwise additive representation and can be employed in scattering calculations. The present study of the electronic structure is the first step toward the evaluation of prospects for sympathetic cooling of polyatomic aromatic molecules with ultracold atoms. We suggest azulene, an isomer of naphthalene which possesses a significant permanent electric dipole moment and optical transitions in the visible range, as a promising candidate for electric field manipulation and buffer-gas or sympathetic cooling.
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Progress in BN/CC isosterism has opened an overwhelming urge to find prospective applications of this class of materials. Herein, the interaction of three BN isosteres of benzene, i. e. 1,2-, 1,3-, 1,4-azaborines and their mono-substituted derivatives with Na+ and Mg2+ cations has been surveyed in light of symmetry-adapted perturbation theory (SAPT) and interacting quantum atoms method (IQA). We have found that the orientation of the cations towards azaborines depends considerably on boron and nitrogen dispersion pattern. However, this tendency cannot be justified by electrostatics alone, without taking into account the induction as the major stabilizing factor, and Pauli repulsion, which effectively shapes the potential energy surface. Due to the significant role of induction, molecular electrostatic potentials (MEPs) can predict the interaction strength and anisotropy only if they are obtained from densities perturbed by the effective field of the cations. Through-bond and through-space effects of the substituents strongly depend on their position in the ring, where the through-bond effects are dominated by the inductive contribution. The importance of the induction energy even at short distances, and of the non-classical IQA component signify the multi-center covalency character of azaborine-cation interactions. Therefore, a pure classical view on the interaction between the cation and compounds standing on the organic/inorganic border is to a large extent misleading.
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Density-functional theory and symmetry-adapted perturbation theory calculations on complexes of the enantiomers of CHFClBr with the most stable isomer of C82-3 fullerene show that despite the guests being too large for the host cage, they are nevertheless stabilized by electrostatic interactions. The complexation leads to considerable strain on the cage and the guests accompanied by compression of the bonds of the guest molecule, resulting in considerable complexation-induced changes in the infrared (IR), vibrational circular dichroism (VCD), nuclear magnetic resonance (NMR), and UV-vis spectra. The effect of chiral recognition is pronounced only for the 19F signal in the NMR spectra and in a sign reversal of the rotational strength of the νCH stretching vibration of S-CHFClBr@C82-3 in the VCD spectrum as compared to that of the free guest, making the sign of this band for the C82 complexes with the S- and R-guest enantiomers the same. This is a surprising result since vibrational circular dichroism is considered a reliable method for determining the absolute chirality of small molecules and for establishing dominant conformations in biopolymers.
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The interaction of 1,2-dihydro-1,2-, 1,3-dihydro-1,3- and 1,4-dihydro-1,4-azaborine isomers with one and two water molecules has been studied using a variety of supermolecular (Møller-Plesset = MP, and coupled cluster = CC) as well as perturbational (symmetry-adapted perturbation theory = SAPT) electron-correlation methods in the complete basis-set limit. It has been found that the water molecule binds to azaborine isomers through O-H···π, π-H···O, and dihydrogen bonding linkages. The SAPT interaction energy decomposition shows that these complexes are mostly stabilized by dispersion followed closely by induction contributions. Pauli repulsion hinders water molecule to be polarized by azaborine in the O-H···π type of complexes. According to the interacting-quantum-atoms analysis, the structures with a primary binding of the O-H···π type benefit from an additional stabilization factor resulting from the interaction of the oxygen and the second hydrogen atom of water, i.e., the one which does not point toward the ring, while the interaction of hydrogens from water with azaborines plays a destabilizing role for the π-H···O type. The same method states that the intermolecular bindings between azaborines and the water molecule have a multicenter character with a small bond polarization, and they are classified as closed-shell (noncovalent) by quantum theory of atoms-in-molecules analysis at bond critical points. The complexes of azaborines with two water molecules tend to arrange in a circular fashion with a recognizable water dimer attached to the azaborine molecule. A comparison with the CCSD(T) benchmarks shows that the nonadditive contribution to the interaction energy of the trimers is negative and with a good accuracy can be accounted for by the MP2 method. A good agreement between Hartree-Fock (HF) and MP2 nonadditive energy, as well as the decomposition of HF nonadditive interaction energies divulge the importance of nonadditive induction energy in the trimers. The interaction energies for the azaborine with one water calculated with the SAPT(DFT), MP2, SCS-MP2, and MP2C methods are in satisfactory agreement with each other. Finally, it has been found that the population analysis from the electron localization function offers the most comprehensive explanation of the orientational preferences of the water molecule in the complex.
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We present a hierarchy of local coupled cluster (CC) linear response (LR) methods to calculate ionization potentials (IPs), i.e., excited states with one electron annihilated relative to a ground state reference. The time-dependent perturbation operator V(t), as well as the operators related to the first-order (with respect to V(t)) amplitudes and multipliers, thus are not number conserving and have half-integer particle rank m. Apart from calculating IPs of neutral molecules, the method offers also the possibility to study ground and excited states of neutral radicals as ionized states of closed-shell anions. It turns out that for comparable accuracy IPs require a higher-order treatment than excitation energies; an IP-CC LR method corresponding to CC2 LR or the algebraic diagrammatic construction scheme through second order performs rather poorly. We therefore systematically extended the order with respect to the fluctuation potential of the IP-CC2 LR Jacobian up to IP-CCSD LR, keeping the excitation space of the first-order (with respect to V(t)) cluster operator restricted to the m=½â3/2 subspace and the accuracy of the zero-order (ground-state) amplitudes at the level of CC2 or MP2. For the more expensive diagrams beyond the IP-CC2 LR Jacobian, we employ local approximations. The implemented methods are capable of treating large molecular systems with hundred atoms or more.
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Intermolecular ternary complexes composed of: (1) the centrally placed trifluoroacetonitrile or its higher analogs with central carbon exchanged by silicon or germanium (M = C, Si, Ge), (2) the benzonitrile molecule or its para derivatives on one side, and (3) the boron trifluoride of trichloride molecule (X = F, Cl) on the opposite side as well as the corresponding intermolecular tetrel- and triel-bonded binary complexes, were investigated by symmetry-adapted perturbation theory (SAPT) and the supermolecular Møller-Plesset method (MP2) at the complete basis set limit for optimized geometries. A character of interactions was studied by quantum theory of atoms-in-molecules (QTAIM). A comparison of interaction energies and QTAIM bond descriptors for dimers and trimers reveals that tetrel and triel bonds increase in their strength if present together in the trimer. For the triel-bonded complex, this growth leads to a change of the bond character from closed-shell to partly covalent for Si or Ge tetrel atoms, so the resulting bonding scheme corresponds to a preliminary stage of the SN2 reaction. Limitations of the Lewis theory of acids and bases were shown by its failure in predicting the stability order of the triel complexes. The necessity of including interaction energy terms beyond the electrostatic component for an elucidation of the nature of σ- and π-holes was presented by a SAPT energy decomposition and by a study of differences in monomer electrostatic potentials obtained either from isolated monomer densities, or from densities resulting from a perturbation with the effective field of another monomer.
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Molecular complexes of a fullerene analogue B12N12 with hydrogen halides (HCl, HBr, and HI) were studied with symmetry-adapted perturbation theory with density-functional theory applied for a description of monomers (SAPT(DFT)), Møller-Plesset theory to the second order (MP2), and its spin-component-scaled variant (SCS-MP2) in a limit of a complete basis set. For each halide five symmetry-distinct minimum structures of the complex have been found on the potential energy hypersurface, with interaction energies ranging from -6 to -18 kJ/mol. The natural bond orbital and the atom-in-molecules analysis of noncovalent bonds resulted in a division of these configurations into three categories: hydrogen-bonded, halogen-bonded, and those of a mixed type, involving simultaneously a hydrogen bonding and a π-hole bonding between halogen and boron atoms. A comparison of various approaches for the calculation of interaction energies shows that the SCS-MP2 supermolecular method gives results which are in a close agreement with SAPT(DFT), while the MP2 interaction energies are systematically more negative than the SAPT values. The ability of the B12N12 nanocage to bind hydrogen halides through several active sites on its surface puts under question the selectivity of the binding necessary in crystal engineering, especially for the hydrogen bromide and hydrogen iodide cases, which show small differences in stabilization energies for their minimum structures. The directionality of noncovalent bonds is explained on grounds of the anisotropy of some SAPT components, like electrostatics and induction, as well as by the σ-hole and π-hole models.
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Binding energies for the complexes of the S12L database by Grimme [Chem. Eur. J. 18, 9955 (2012)] were calculated using intermolecular symmetry-adapted perturbation theory combined with a density-functional theory description of the interacting molecules. The individual interaction energy decompositions revealed no particular change in the stabilisation pattern as compared to smaller dimer systems at equilibrium structures. This demonstrates that, to some extent, the qualitative description of the interaction of small dimer systems may be extrapolated to larger systems, a method that is widely used in force-fields in which the total interaction energy is decomposed into atom-atom contributions. A comparison of the binding energies with accurate experimental reference values from Grimme, the latter including thermodynamic corrections from semiempirical calculations, has shown a fairly good agreement to within the error range of the reference binding energies.
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We present a new systematic fragmentation scheme of polycyclic aromatic hydrocarbons (PAHs), including fullerenes and nanotubes, based on an idea to treat a sextet ring as a single unbreakable unit so that the basic unit of aromaticity remains preserved upon fragmentation. In the approach, denoted as AROFRAG (from aromatic fragmentation), a set of predefined elementary subsystems, such as naphthalene and biphenyl in the first model and larger PAHs in the second and third models, is generated with appropriate weights with the aim of reproducing the structure of the original molecule. The energies of the molecules are approximated as weighted sums of the energies of these subsystems. For symmetric cases, e.g., fullerenes, the point-group symmetry is preserved during the decomposition. The AROFRAG is used in conjunction with the molecule-in-molecule (MIM) technique to obtain an accurate description of the electronic energies. The new approach has been applied for selected graphene structures and fullerene doped with boron and nitrogen atoms, for which isomerization energies were calculated, as well as for several nanotubes and regular fullerene molecules. The combination of the third AROFRAG model and the MIM approach leads to the reproduction of electronic energies with a few milli-hartree accuracy at a fraction of the computational cost of the original method.
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We perform electronic structure calculations of the potential energy surface of the He···BeO((1)Σ(+)) complex. We use several different methods to characterize this unusual interaction. We apply coupled cluster singles, doubles, and noniterative triples [CCSD(T)] and the multireference configuration interaction [MRCI] levels of theory. The nature of the interaction is studied with symmetry-adapted perturbation theory (SAPT) based on DFT and CCSD description of the intramonomer electron densities. Our best estimate of the well depth is 1876.5 cm(-1) at the CCSD(T) level, while the dissociation energy, corrected for the zero-point energy, is equal to 1446.7 cm(-1). The global minimum is located for the collinear He···Be-O geometry at Re = 4.45a0. The rotational constant of the He-BeO complex in its ground state is 0.863 cm(-1). We also calculate bound states of the He···BeO complex for J = 0 and J = 1 (total angular momentum).
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Selected points on the potential energy surface for the complexes Rg@C(60) (Rg = He, Ne, Ar, Kr) are calculated with various theoretical methods, like symmetry-adapted perturbation theory with monomers described by density functional theory (DFT-SAPT), supermolecular Møller-Plesset theory truncated on the second order (MP2), spin-component-scaled MP2 (SCS-MP2), supermolecular density functional theory with empirical dispersion correction (DFT+Disp), and the recently developed MP2C method that improves the MP2 method for long-range electron correlation effects. A stabilization of the endohedral complex is predicted by all methods, but the depth of the potential energy well is overestimated by the DFT+Disp and MP2 approaches. On the other hand, the MP2C model agrees well with DFT-SAPT, which serves as the reference. The performance of SCS-MP2 is mixed: it produces too low interaction energies for the two heavier guests, while its accuracy for He@C(60) and Ne@C(60) is similar to that of MP2C. Fitting formulas for the main interaction energy components, i.e. the dispersion and first-order repulsion energies are proposed, which are applicable for both endo- and exohedral cases. For all examined methods density fitting is used to evaluate two-electron repulsion integrals, which is indispensable to allow studies of noncovalent complexes of this size. It has been found that density-fitting auxiliary basis sets cannot be used in a black-box fashion for the calculation of the first-order SAPT electrostatic energy, and that the quality of these basis sets should be always carefully examined in order to avoid an unphysical long-range behavior.
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State-of-the-art ab initio techniques have been applied to compute the potential energy surface for the lithium atom interacting with the lithium hydride molecule in the Born-Oppenheimer approximation. The interaction potential was obtained using a combination of the explicitly correlated unrestricted coupled-cluster method with single, double, and noniterative triple excitations [UCCSD(T)-F12] for the core-core and core-valence correlation and full configuration interaction for the valence-valence correlation. The potential energy surface has a global minimum 8743 cm(-1) deep if the Li-H bond length is held fixed at the monomer equilibrium distance or 8825 cm(-1) deep if it is allowed to vary. In order to evaluate the performance of the conventional CCSD(T) approach, calculations were carried out using correlation-consistent polarized valence X-tuple-zeta basis sets, with X ranging from 2 to 5, and a very large set of bond functions. Using simple two-point extrapolations based on the single-power laws X(-2) and X(-3) for the orbital basis sets, we were able to reproduce the CCSD(T)-F12 results for the characteristic points of the potential with an error of 0.49% at worst. The contribution beyond the CCSD(T)-F12 model, obtained from full configuration interaction calculations for the valence-valence correlation, was shown to be very small, and the error bars on the potential were estimated. At linear LiH-Li geometries, the ground-state potential shows an avoided crossing with an ion-pair potential. The energy difference between the ground-state and excited-state potentials at the avoided crossing is only 94 cm(-1). Using both adiabatic and diabatic pictures, we analyze the interaction between the two potential energy surfaces and its possible impact on the collisional dynamics. When the Li-H bond is allowed to vary, a seam of conical intersections appears at C(2v) geometries. At the linear LiH-Li geometry, the conical intersection is at a Li-H distance which is only slightly larger than the monomer equilibrium distance, but for nonlinear geometries it quickly shifts to Li-H distances that are well outside the classical turning points of the ground-state potential of LiH. This suggests that the conical intersection will have little impact on the dynamics of Li-LiH collisions at ultralow temperatures. Finally, the reaction channels for the exchange and insertion reactions are also analyzed and found to be unimportant for the dynamics.
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A new coupled cluster model of the polarization propagator, denoted as XCC2, is presented. The XCC2 approach employs time-independent coupled cluster theory of polarization propagators of Moszynski et al. [Collect. Czech. Chem. Commun., 2005, 70, 1109] and excitation operators from the time-dependent (TD) CC2 method. The performance of XCC2 was investigated by calculating static and dynamic dipole polarizabilities for a test set of over 20 molecules and comparing them with TD-CCSD results. The quality of XCC2 dispersion coefficients for several noncovalent molecular complexes was also tested against the benchmark values. This numerical study reveals that the average percent error of XCC2 is significantly reduced in comparison to the TD-CC2 method (4-fold reduction for the mean polarizabilities and 2-fold reduction for anisotropic polarizabilities is observed). Since the computational requirements of both XCC2 and TD-CC2 methods are virtually the same, the new XCC2 method can be viewed as a practical alternative for TD-CC2 for property calculations, giving the second-order polarization propagators of near-CCSD quality in many cases, but retaining at the same time the lower computational cost of the TD-CC2 model.