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An Easy-to-Use Three-Dimensional Molecular Visualization An Easy-to-Use Three-Dimensional Molecular Visualization and Analysis Program: POSMOL

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... The optimized geometries were drawn using the Posmol molecular visualization and analysis package. 95 ...
Article
Various types of interactions between halogen (X) and π moiety (X-π 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 X2 and CX4 (X = Cl/Br) can be intercalated in graphite and bilayer graphene for doping and graphene functionalization/modification. Due to the X-π interactions, though recently highly studied, their structures are still hardly predictable. Here, using the coupled-cluster with single, double, and non-iterative triple excitations (CCSD(T)), the Møller-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 X2 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), X2-Bz is found to have the T-shaped structure where the electro-positive X atom-end of X2 is pointing to the electro-negative 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 X2-Bz (S2/S3) and CX4-Bz (S2) are stabilized primarily by the dispersion interaction, while 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 X2-Bz (S1), while 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-π interactions adequately, close to the CCSD(T)/CBS binding energies (within ~1 kJ/mol). This understanding would be useful to study diverse X-π interaction driven structures such as halogen containing compounds intercalated between 2 dimensional layers.
... The above theorems are the principle theorems for 3D drawing, which should be taken into consideration in 3D visualization. Meanwhile, in 3D molecular technologies, some synthetic software tools have been developed, such as VEGA [36] and POSMOL [37], which provide rich and variable references. However, in molecule networks, all nodes are atoms and the 3D graph expresses their molecular structure. ...
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Compared with 2D technology, the 3D visualization and 3D mapping could provide a new technical methodology for information visualization, knowledge visualization and science mapping. In this article, the 3D visualization and 3D mapping are realized by using software tools Mage and Mayavi while drawing 3D graph. The 3D graph can rotate and move in the space for visualizing knowledge structure, with keeping 3D drawing three theorems. Two cases are shown in the article: one case is the two layers network; the other belongs to three layers network. With the revealing of the 3D core structures of multilayer networks, the information and knowledge visualization and science mapping have the potential to be promoted.
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A hydroiodic acid molecule is dissociated by more than four water molecules. Here, the effect of an excess electron on the hexahydated hydroiodic acid where the dissociated structure [H3O+(H2O)(5)I-] is much more stable than the undissociated one [(H2O)(6)HI], is investigated. Upon binding an excess electron (e(-)), the cluster releases a hydrogen radical and forms the stable hexahydrated iodide [(H2O)(6)I-] when the initial kinetic energy is above similar to 200 K, due to the small transition barrier (similar to 0.5 eV). The system with the hydrogen radical released, [(H2O)(6)I- + H center dot], is much more stable than the systems with an excess electron, [(H3O)(+){e(-)(H2O)5}I-] or [e(-)(H2O)(2)(H3O)(+)(H2O)(3)I-].
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Electron(e)-binding hydrated hydrogen fluoride clusters [e–HF(H2O)n=1–10] have been studied with density functional and ab intio calculations. The hydrofluoric acid in e–HF(H2O)n clusters is found to be undissociated at 0K till n=10. The e–HF(H2O)3 cluster is particularly unstable compared with the corresponding neutral structures, which reflects the particularly unstable antimagic number of e–water tetramer. The characteristic of “magic” numbers of electron–water clusters appears in these e–(HF)(H2O)n clusters. The vertical detachment energies of e–HF(H2O)n are enhanced by the HF acid as compared with those of the e-binding water clusters [e–(H2O)n+1], and the excess electron is surface bound near the terminal water molecule with two dangling hydrogen atoms. The coordination number of HF is one for n=1–4 as a linear structure in contrast to two for n=5–6, and three for n=7–10. The phase transition from 2- to 3-dimensional structures appears at penta-hydrated system in contrast to hepta-hydrated system for neutral HF–water clusters. The structures for e–HF(H2O)n=2,3 are quite different from those of the corresponding e–(H2O)n+1=3,4, and the structures for e–HF(H2O)n=2–6 are quite different from those of the corresponding HF(H2O)n=2–6.
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We review various types of hydrogen bond characteristics based on our theoretical work of diverse chemical systems. The systems include water clusters, hydrated clusters, enzymes, ionophores/receptors, and assembled molecules such as organic nanotubes. Special features of weak, normal, short, short strong H-bonding are discussed in terms of structures, interaction energies, and spectra. Various p-type H-bonds are also discussed.
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To understand the hydration phenomena of noble transition metals, we investigated the structures, hydration energies, electronic properties, and spectra of the Cu+(H3O)1–6 and Au+(H2O)1–6 clusters using ab initio calculations. The coordination numbers of these clusters are found to be only two, which is highly contrasted to those of Ag+(H2O)n (which have the coordination numbers of 3–4) as well as the hydrated alkali metal ions (which have the coordination numbers of ∼ 6). For the possible identification of their interesting hydration structures, we predict their IR spectra for the OH stretch modes.
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Using DFT B3LYP/6-31G(d,p) calculation method, stable molecular structures were optimized for the p-tert-butylcalix[4]tube (1) and its alkali-metal-ion complexes. Sodium ion gave 15∼20 kcal/mol better complexation efficiency than the potassium cation toward 1 in both poly-ether tube (exo) and benzene-rings pocket (endo). For two different kinds of complexation mode, the alkali-metal-ion in exo-tube showed much better complexation efficiency than the cation in endo-pocket of 1.
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We have investigated the issue of two-dimensional (2D) versus three-dimensional (3D) structures for neutral-state Au10 and clarified the lowest-energy structure among a few 2D Au10− isomers. Though almost all previous works were based on density functional theory (DFT), we here carried out not only extensive DFT calculations but also high levels of ab initio calculations of Möller-Plesset second order perturbation theory (MP2), and coupled cluster theory with single and double excitations (CCSD) including perturbative triple excitations [CCSD(T)]. While DFT favors 2D structures, MP2 and CCSD(T) favor 3D structures for moderate-sized basis sets. However, we note that the basis-set superposition error (BSSE) corrections make the ab intio results favor 2D structures too. The near-degeneracy (driven by relativistic effects) of 5d and 6s orbitals of gold helps stabilize acute apex gold atoms, resulting in 2D structures. The planar triangular structures of a local minimum Au10 (triplet) and the global minimum Au10− show remarkable spatial charge-spin separation due to their singly occupied molecular orbital(s). By the same reason, Au10− shows much larger vertical detachment energy than other even-numbered gold cluster anions.
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We have reinvestigated the structures of hydrated hydride anion clusters, using density functional theory and high-level ab initio theory. We find new low-lying energy structures for H−(H2O)n=3,4,6 which are compatible with previously reported structures. The binding energies, electronic properties, and IR spectra of these competing low-energy hydrated hydride anion clusters are reported to facilitate experiments. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
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The physical chemistry (PC) articles published in the Bulletin of the Korean Chemical Society (BKCS) from 2003 to 2007 are surveyed, and in-depth content analysis was conducted to classify the PC articles into 12 topics used in The Journal of Physical Chemistry (JPC). The PC articles published in the Journal of the American Chemical Society (JACS) in 2007 are also surveyed. The extensive summary of all PC articles in BKCS for the last five years reveals the current trend of physical chemistry research in Korea. The comparison study with the JACS shows that the proportion of PC articles among all articles published in BKCS (16%) is slightly higher than that of JACS (11%), and the non-Korean authorship ratio of BKCS (12%) is very low compared with the non-US authorship of JACS (52%). From the comparison study with articles published in JPC in 2007, it is found that BKCS disseminates various topics of physical chemistry researches adequately. In particular, BKCS most frequently published PC articles in molecular structure and spectroscopy topics, whereas JPC published surface chemistry and nano-chemistry articles most frequently. It is concluded that BKCS should publish more articles to be a leading journal, and it is suggested that the SCI impact factor of BKCS must be increased by improving the electronic version of BKCS.
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Protonated water clusters H+(H2O)n favor two-dimensional (2D) structures for n < or = 7 at low temperatures. At 0 K, the 2D and three-dimensional (3D) structures for n = 8 are almost isoenergetic, and the 3D structures for n > 9 tend to be more stable. However, for n = 9, the netlike structures are likely to be more stable above 150 K. In this regard, we investigate the case of n = 10 to find which structure is more stable between the 3D structure and the netlike structure around 150 and 250 K. We use density functional theory, Møller-Plesset second-order perturbation theory, and coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)). At the complete basis set limit for the CCSD(T) level of theory, three isomers of 3D cage structure are much more stable in zero point energy corrected binding energy and in free binding energies at 150 K than the lowest energy netlike structures, while the netlike structure would be more stable around approximately 250 K. The predicted vibrational spectra are in good agreement with the experiment. One of the three isomers explains the experimental IR observation of an acceptor (A) type peak of a dangling hydrogen atom.
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We have investigated the structure, interaction energy, electronic properties, and IR spectra of the ammonia-water cation (NH(3)H(2)O)(+) using density functional theory (DFT) and high-level ab initio theory. The ammonia-water cation has three minimum-energy structures of (a) H(2)NH(+)...OH(2), (b) H(3)N(+)...OH(2), and (c) H(3)NH(+)...OH. The lowest-energy structure is (a), followed by (c) and (b). The ammonia dimer cation has two minimum-energy structures [the lowest H(3)NH(+)...NH(2) structure and the second lowest (H(3)N...NH(3))(+) structure]. The minimum transition barrier for the interconversion between (a), (b), and (c) is approximately 6 kcal/mol. Most DFT calculations with various functionals, except a few cases, overstabilize the N...O and N...N binding, predicting different structures from Moller-Plesset second-order perturbation (MP2) theory and the most reliable complete basis set (CBS) limit of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. Thus, the validity test of the DFT functionals for these ionized molecular systems would be of importance.
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We investigated various two-dimensional (2D) and three-dimensional (3D) structures of H (+)(H 2O) 8, using density functional theory (DFT), Moller-Plesset second-order perturbation theory (MP2), and coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)). The 3D structure is more stable than the 2D structure at all levels of theory on the Born-Oppenheimer surface. With the zero-point energy (ZPE) correction, the predicted structure varies depending on the level of theory. The DFT employing Becke's three parameters with Lee-Yang-Parr functionals (B3LYP) favors the 2D structure. At the complete basis set (CBS) limit, the MP2 calculation favors the 3D structure by 0.29 kcal/mol, and the CCSD(T) calculation favors the 3D structure by 0.27 kcal/mol. It is thus expected that both 2D and 3D structures are nearly isoenergetic near 0 K. At 100 K, all the calculations show that the 2D structure is much more stable in free binding energy than the 3D structure. The DFT and MP2 vibrational spectra of the 2D structure are consistent with the experimental spectra. First-principles Car-Parrinello molecular dynamics (CPMD) simulations show that the 2D Zundel-type vibrational spectra are in good agreement with the experiment.
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Density functional and ab intio calculations are employed in order to understand the base dissociation of rubidium hydroxide by water molecules. The hydrated structures, stabilities, thermodynamic quantities, dissociation energies, infrared spectra, and electronic properties of RbOH(H2O)(n = 0-5) are investigated. With the successive addition of water molecules to RbOH, the Rb-OH bond lengthens significantly from 2.45 angstroms for n = 0 to 3.06 angstroms for n = 5. It is interesting to note that four water molecules are needed for the stable dissociation of RbOH (as an almost dissociate conformation) and five water molecules are needed for the complete dissociation without any Rb-OH stretch mode, in contrast to the same group base of CsOH which requires only three water molecules for an almost dissociate conformation and four water molecules for the complete dissociation.
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The structures, energetics, electronic properties, and spectra of hydrated hydroxide anions are studied using density functional and high level ab initio calculations. The overall structures and binding energies are similar to the hydrated anion clusters, in particular, to the hydrated fluoride anion clusters except for the tetrahydrated clusters and hexahydrated clusters. In tetrahydrated system, tricoordinated structures and tetracoordinated structures are compatible, while in pentahydrated systems and hexahydrated systems, tetracoordinated structures are stable. The hexahydrated system is similar in structure to the hydrated chloride cluster. The thermodynamic quantities (enthalpies and free energies) of the clusters are in good agreement with the experimental values. The electronic properties induced by hydration are similar to hydrated chloride anions. The charge-transfer-to-solvent energies of these hydrated-hydroxide anions are discussed, and the predicted ir spectra are used to explain the experimental data in terms of the cluster structures. The low-energy barriers between the conformations along potential energy surfaces are reported.
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High-level ab initio calculations were carried out to evaluate the interaction between the hydroquinone and benzene molecules. The intermolecular interaction energy was calculated using the Møller-Plesset second-order perturbation theory at the complete basis set limit and also at the coupled cluster theory with single, double, and perturbatively triple excitations. The calculated binding energy is larger than the benzene dimer interaction energy. The T-shaped cluster (T-a) and the parallel conformation (P-a) are calculated to be nearly isoenergetic. Owing to the large energy gain in the attraction by electron correlation, the dispersion interaction is important for the attraction.
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The edge-to-face interactions for either axially or facially substituted benzenes are investigated by using ab initio calculations. The predicted maximum energy difference between substituted and unsubstituted systems is approximately 0.7 kcal/mol (approximately 1.2 kcal/mol if substituents are on both axially and facially substituted positions). In the case of axially substituted aromatic systems, the electron density at the para position is an important stabilizing factor, and thus the stabilization/destabilization by substitution is highly correlated to the electrostatic energy. This results in its subsequent correlation with the polarization and charge transfer. Thus, the stabilization/destabilization by substitution is represented by the sum of electrostatic energy and induction energy. On the other hand, the facially substituted aromatic system depends on not only the electron-donating ability responsible for the electrostatic energy but also the dispersion interaction and exchange repulsion. Although the dispersion energy is the most dominating interaction in both axial and facial substitutions, it is almost canceled by the exchange repulsion in the axial substitution, whereas in the facial substitution, together with the exchange repulsion it augments the electrostatic energy. The systems with electron-accepting substituents (NO2, CN, Br, Cl, F) favor the axial substituent conformation, while those with electron-donating substituents (NH2, CH3, OH) favor the facial substituent conformation. The interactions for the T-shape complex systems of an aromatic ring with other counterpart such as H2, H2O, HCl, and HF are also studied.
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A m-xylene-bridged imidazolium receptor, 1, has been designed and synthesized. The receptor 1 utilizes two imidazole (C-H)(+)- - -anion hydrogen bonds and one benzene hydrogen- - -anion hydrogen bond. The major driving force of complexation between the receptor 1 and anions comes from two imidazole (C-H)(+)- - -anion hydrogen bonds. However, both NMR experiments and ab initio calculations show that the benzene hydrogen attracts the anion guests, clearly indicating benzene (C-H)- - -anion hydrogen bonding. [reaction: see text]
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The structures, stabilities, thermodynamic quantities, dissociation energies, infrared spectra, and electronic properties of LiOH hydrated by up to seven water molecules are investigated by using the density-functional theory and the Møller-Plesset second-order perturbation theory (MP2). Further accurate analysis based on the coupled-cluster theory with singles, doubles, and perturbative triples excitations agrees with the MP2 results. The Li-OH stretch mode significantly shifts with the increase of water molecules, and it eventually disappears upon dissociation. It is revealed that seven water molecules are needed for the stable dissociation of LiOH (as a completely dissociated conformation), in contrast to the cases of RbOH and CsOH which require four and three water molecules, respectively.
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Using molecular-orbital analysis, we have elucidated the quantum-chemical origin of the intriguing phenomena in sequential hydration energies of the gold cation, which is known to be the most conspicuous among all transition metals. The hydration energy of Au+ with the second water molecule is found to be much larger than that with the first water molecule. Owing to the large relativistic effect of gold (i.e., significant lowering of the 6s orbital energy and significant raising of the 5d orbital energy), the highest occupied molecular orbital of the hydrated gold cation has a large portion of the 6s orbital. As the electron density of the 6s orbital populates in a large outer spherical shell far off the gold nucleus, the p orbitals (or sp hybridized lone-pair orbitals) of the water molecules are able to overlap with the outer part of the 6s orbital in the dihydrated gold cation, resulting in the unusual skewed overlap of p-6s-p orbitals (not the atom-to-atom bond overlap). No previous molecular-orbital analysis has reported this peculiar skewed orbitals overlap. Since this skewed orbitals overlap is saturated with two water molecules, this property is responsible for the low coordination number of the gold ion.
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The structures, stabilities, thermodynamic quantities, dissociation energies, infrared spectra, and electronic properties of CsF hydrated by water molecules are investigated by using density functional theory, Møller-Plesset second-order perturbation theory (MP2), coupled cluster theory with singles, doubles, and perturbative triples excitations (CCSD(T)), and ab initio molecular dynamic (AIMD) simulations. It is revealed that at 0 K three water molecules (as a global minimum structure) begin to half-dissociate the Cs-F, and six water molecules (though not a global minimum energy structure) can dissociate it. By the combination of the accurate CCSD(T) conformational energies for Cs(H2O)6 at 0 K with the AIMD thermal energy contribution, it reveals that the half-dissociated structure is the most stable at 0 K, but this structure (which is still the most stable) changes to the dissociated structure above 50 K. The spectra of CsF(H2O)(1-6) from MP2 calculations and the power spectra of CsF(H2O)6 from 50 and 100 K AIMD simulations are also reported.
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The conformational (cis and trans) stability and electronic structures of (C(60)CHCOO)(2)-Sn(IV) porphyrin, recently synthesized as a novel fullerene-porphyrin-fullerene triad linked by metal axial coordination, have been studied by ab initio calculations. The cis conformer was found to be slightly more stable than the trans by 1.38 kcal/mol in the neutral compound. Upon the addition of an electron to the triad, the relative stability of the cis conformer was found to be higher (3.29 kcal/mol) than that in the neutral one. From the investigation of frontier molecular orbitals, for the cis conformer, it was found that the electrons are localized in HOMO of the porphyrin, while the electrons are localized in LUMO of the syn-fullerene. For the trans conformer, it was found that the electrons are localized in HOMO of the porphyrin, while the electrons are localized in LUMO of one of the two fullerene moieties, and the electrons are localized in LUMO2 of the other fullerene moiety, but the LUMO and LUMO2 have the same orbital energy. Thus, the PET may take place unidirectionally in the cis conformer from the porphyrin to the syn-fullerene, while it is bidirectional from the porphyrin to both of the fullerene moieties.
Article
The hydration and dissociation phenomena of HF(H(2)O)(n)() (n < or = 10) clusters have been studied by using both the density functional theory with the 6-311++G[sp] basis set and the Møller-Plesset second-order perturbation theory with the aug-cc-pVDZ+(2s2p/2s) basis set. The structures for n > or = 8 are first reported here. The dissociated form of the hydrogen-fluoric acid in HF(H(2)O)(n) clusters is found to be less stable at 0 K than the undissociated form until n = 10. HF may not be dissociated at 0 K solely by water molecules because the HF H bond is stronger than the OH H bond, against the expectation that the dissociated HF(H(2)O)(n) would be more stable than the undissociated one in the presence of a number of water molecules. The dissociation would be possible for only a fraction of a number of hydrated HF clusters by the Boltzmann distribution at finite temperatures. This is in sharp contrast to other hydrogen halide acids (HCl, HBr, HI) showing the dissociation phenomena at 0 K for n > or = 4. The IR spectra of dissociated and undissociated structures of HF(H(2)O)(n) are compared. The structures and binding energies of HF(H(2)O)(n) are found to be similar to those of (H(2)O)(n+1). It is interesting that HF(H(2)O)(n=5,6,10) are slightly less stable compared with other sizes of clusters, just like the fact that (H(2)O)(n=6,7,11) are slightly less stable. The present study would be useful for the experimental/spectroscopic investigation of not only the dissociation phenomena of HF but also the similarity of the HF-water clusters to the water clusters.
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The West Nile virus (WNV) NS3 serine protease, which plays an important role in assembly of infective virion, is an attractive target for anti-WNV drug development. Cofactors NS2B and NS4A increase the catalytic activity of NS3 in dengue virus and Hepatitis C virus, respectively. Recent studies on the WNV-NS3 characterize the catalytically active form of NS3 by tethering the 40-residue cofactor NS2B. It is suggested that NS2B is essential for the NS3 activity in WNV, while there is no information of the WNV-NS3-related crystal structure. To understand the role of NS2B/substrate in the NS3 catalytic activity, we built a series of models: WNV-NS3 and WNV-NS3-NS2B and WNV-NS3-NS2B-substrate using homology modeling and molecular modeling techniques. Molecular dynamics (MD) simulations were performed for 2.75 ns on each model, to investigate the structural stabilization and catalytic triad motion of the WNV NS3 protease with and without NS2B/substrate. The simulations show that the NS3 rearrangement occurs upon the NS2B binding, resulting in the stable D75-OD1...H51-NH hydrogen bonding. After the substrate binds to the NS3-NS2B active site, the NS3 protease becomes more stable, and the catalytic triad is formed. These results provide a structural basis for the activation and stabilization of the enzyme by its cofactor and substrate.
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Despite intensive studies of the neutral tropyl radical, none of its structure, energetics, and vibrational modes are still clear. This system has puzzled scientists for over a decade since one vibrational mode frequency sharply varies from imaginary number 3000i cm-1 to the real number 6000 cm-1, depending on the calculation methods employed. We find that the origin of this peculiar mode is due to the pseudorotation (omegairot) involved in the interconversion of two nearly isoenergetic Jahn-Teller configurations (elongated structure 2B1 and compressed structure 2A2 with C2v symmetry). Here, we first report that this interconversion is not via D7h or C2v symmetry configuration but via Cs symmetry (i.e., by changing the C2v axis). This interconversion barrier is found negligibly small. Thus, the two conformers are considered to be not two different structures but a dynamically identical structure with partial quantum statistical distributions on the potential energy surface. Owing to the nearly barrierless pseudorotation, the overall structure in a short time scale (less than femtosecond) would be Cs-like between 2A2 and 2B1 configurations with small fluctuation of bond distances. However, the dynamical transitions between the 2B1 and 2A2 configurations via 14 different pseudorotation pathways would make the tropyl radical have the effective D7h structure in either a nonshort time scale (greater than femtosecond) or at nonlow temperatures, which explains the high temperature electron spin resonance experiments.
Article
The hydrated structures, dissociation energies, thermodynamic quantities, infrared spectra, and electronic properties of alkali-metal hydroxides (MOH, M = Na and K) hydrated by up to six water molecules [MOH(H(2)O)(n=1-6)], are investigated by using the density functional theory and Møller-Plesset second-order perturbation theory. Further accurate analysis based on the coupled cluster theory with singles, doubles, and perturbative triples excitations is more consistent with the MP2 results. NaOH shows a peculiar trend in dissociation: it begins to form a partially dissociated structure for n = 3, and it dissociates for n = 4 and 6, whereas it is undissociated for n = 5. However, for n = 5, the dissociated structure is nearly isoenergetic to the undissociated structure. For KOH, it begins to show partial dissociation for n = 5, and complete dissociation for n = 6.
Article
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On the basis of density functional theory (DFT) and high level ab initio theory, we report the structures, binding energies, thermodynamic quantities, IR spectra, and electronic properties of the hydride anion hydrated by up to six water molecules. Ground state DFT molecular dynamics simulations (based on the Born-Oppenheimer potential surface) show that as the temperature increases, the surface-bound hydride anion changes to the internally bound structure. Car-Parrinello molecular dynamics simulations are also carried out for the spectral analysis of the monohydrated hydride. Excited-state ab initio molecular dynamics simulations show that the photoinduced charge-transfer-to-solvent phenomena are accompanied by the formation of the excess electron-water clusters and the detachment of the H radical from the clusters. The dynamics of the detachment process of a hydrogen radical upon the excitation is discussed.
Article
Structures of the ground state pyrrole-(H2O)n clusters are investigated using ab initio calculations. The charge-transfer driven femtosecond scale dynamics are studied with excited state ab initio molecular dynamics simulations employing the complete-active-space self-consistent-field method for pyrrole-(H2O)n clusters. Upon the excitation of these clusters, the charge density is located over the farthest water molecule which is repelled by the depleted pi-electron cloud of pyrrole ring, resulting in a highly polarized complex. For pyrrole-(H2O), the charge transfer is maximized (up to 0.34 a.u.) around approximately 100 fs and then oscillates. For pyrrole-(H2O)2, the initial charge transfer occurs through the space between the pyrrole and the pi H-bonded water molecule and then the charge transfer takes place from this water molecule to the sigma H-bonded water molecule. The total charge transfer from the pyrrole to the water molecules is maximized (up to 0.53 a.u.) around approximately 100 fs.
Article
High level ab initio calculations are employed to investigate the excess electron attachment to the hydrated hydrohalogen acids. The excess electron leads to the dissociation of hydrogen halide acids, which results in the release of a hydrogen radical. Neutral HCl, HBr, and HI are dissociated by tetrahydration. Upon binding an excess electron, these hydrated hydrohalogen acids show that (i) the H-X bond strength weakens with redshifted H-X stretching frequencies, (ii) HX can have a bound-electron state, a dissociated structure, or a zwitter-ionic structure, and (iii) HClHBr is dissociated by tri/mono-hydration, while HI is dissociated even without hydration. This dissociation is in contrast to the case of electron attachment to hydrated hydrogen fluoric acids for which HF is not dissociated by more than ten water molecules.
Article
Ab initio calculations with various large basis sets have been performed on the water dimer in order to study the structure, energetics, spectra, and electrical properties. As a reference system, the calculations of the water monomer were also performed. The second order M0ller-Plesset perturbation theory (MP2) using a large basis set (O:13s,8p,4d,2j/H:8s,4p,2d) well reproduces various water monomer experimental data except for the somewhat underestimated absolute energy and hyperpolarizability. The monomer energy calculated with the fourth-order M0ller-Plesset perturbation theory (MP4) with the above basis set is -76.407 hartrees, which is only 0.073 hartree above the experimental energy. To compare the theoretical and experimental dimer structures and thermal energies accurately, we summarized the quantum statistical thermodynamic quantities with corrections for anharmonic vibration, rotation, rotation-vibration coupling, and internal rotation. With the correction for the anharmonic binding potential and rotation, the predicted interoxygen distance of the dimer is 2.958 A, which is so far the closest to the experimental value -2.976 A. The predicted dimer dipole moment is 2.612 D, which is the first agreement with experiment (2.60--2.64 D). The predicted frequency shift of the dimer with respect to the monomer is in good agreement with experiment. With the MP2 calculation using the large basis set, the basis set superposition error correction (BSSEC) of the dimer is only 0.33 kcal/mol, which is by far the smallest among the MP2 results reported. Without BSSEC, the predicted binding energy, enthalpy, free energy, and entropy are all in good agreement with experiment within the error bounds, whereas with BSSEC, some of them seem to be slightly off the experimental error bounds. Nevertheless, the results with BSSEC can be more reliable than those without BSSEC.
Article
Using the computer-aided molecular design approach, we recently reported the synthesis of calix[4]hydroquinone (CHQ) nanotube arrays self-assembled with infinitely long one-dimensional (1-D) short hydrogen bonds (H-bonds) and aromatic−aromatic interactions. Here, we assess various calculation methods employed for both the design of the CHQ nanotubes and the study of their assembly process. Our calculations include ab initio and density functional theories and first principles calculations using ultrasoft pseudopotential plane wave methods. The assembly phenomena predicted prior to the synthesis of the nanotubes and details of the refined structure and electronic properties obtained after the experimental characterization of the nanotube crystal are reported. For better characterization of intriguing 1-D short H-bonds and exemplary displaced π−π stacks, the X-ray structures have been further refined with samples grown in different solvent conditions. Since X-ray structures do not contain the positions of H atoms, it is necessary to analyze the system using quantum theoretical calculations. The competition between H-bonding and displaced π−π stacking in the assembling process has been clarified. The IR spectroscopic features and NMR chemical shifts of 1-D short H-bonds have been investigated both experimentally and theoretically. The dissection of the two most important interaction components leading to self-assembly processes would help design new functional materials and nanomaterials.
  • D.-J Kim
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