Search

CONSPECTUS: In chemical and biological systems, various interactions that govern the chemical and physical properties of molecules, assembling phenomena, and electronic transport properties compete and control the microscopic structure of materials. The well-controlled manipulation of each component can allow researchers to design receptors or sensors, new molecular architectures, structures with novel morphology, and functional molecules or devices. In this Account, we describe the structures and electronic and spintronic properties of π-molecular systems that are important for controlling the architecture of a variety of carbon-based systems. Although DFT is an important tool for describing molecular interactions, the inability of DFT to accurately represent dispersion interactions has made it difficult to properly describe π-interactions. However, the recently developed dispersion corrections for DFT have allowed us to include these dispersion interactions cost-effectively. We have investigated noncovalent interactions of various π-systems including aromatic-π, aliphatic-π, and non-π systems based on dispersion-corrected DFT (DFT-D). In addition, we have addressed the validity of DFT-D compared with the complete basis set (CBS) limit values of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)] and Møller-Plesset second order perturbation theory (MP2). The DFT-D methods are still unable to predict the correct ordering in binding energies within the benzene dimer and the cyclohexane dimer. Nevertheless, the overall DFT-D predicted binding energies are in reasonable agreement with the CCSD(T) results. In most cases, results using the B97-D3 method closely reproduce the CCSD(T) results with the optimized energy-fitting parameters. On the other hand, vdW-DF2 and PBE0-TS methods estimate the dispersion energies from the calculated electron density. In these approximations, the interaction energies around the equilibrium point are reasonably close to the CCSD(T) results but sometimes slightly deviate from them because interaction energies were not particularly optimized with parameters. Nevertheless, because the electron cloud deforms when neighboring atoms/ions induce an electric field, both vdW-DF2 and PBE0-TS seem to properly reproduce the resulting change of dispersion interaction. Thus, improvements are needed in both vdW-DF2 and PBE0-TS to better describe the interaction energies, while the B97-D3 method could benefit from the incorporation of polarization-driven energy changes that show highly anisotropic behavior. Although the current DFT-D methods need further improvement, DFT-D is very useful for computer-aided molecular design. We have used these newly developed DFT-D methods to calculate the interactions between graphene and DNA nucleobases. Using DFT-D, we describe the design of molecular receptors of π-systems, graphene based electronic devices, metalloporphyrin half-metal based spintronic devices as graphene nanoribbon (GNR) analogs, and graphene based molecular electronic devices for DNA sequencing. DFT-D has also helped us understand quantum phenomena in materials and devices of π-systems including graphene.

Experimental vibrational predissociation spectra of the magic NH4(+)(H2O)20 clusters are close to those of the magic H3O(+)(H2O)20 clusters. It has been assumed that the geometric features of NH4(+)(H2O)20 clusters might be close to those of H3O(+)(H2O)20 clusters, in which H3O(+) resides on the surface. Car-Parrinello molecular dynamics simulations in conjunction with density functional theory calculations are performed to generate the infrared spectra of the magic NH4(+)(H2O)20 clusters. In comparison with the experimental vibrational predissociation spectra of NH4(+)(H2O)20, we find that NH4(+) is inside the cage structure of NH4(+)(H2O)20 as opposed to on the surface structure. This shows a clear distinction between the structures of NH4(+)(H2O)20 and H3O(+)(H2O)20 as well as between the hydration phenomena of NH4(+) and H3O(+).

Visual detection: cyclo-Bis(urea-3,6-dichlorocarbazole) (1), the first anion receptor bearing urea, displays a fluorescence quenching effect with pyrophosphate and fluoride ions. Its deprotonated form (12−) acts as a new fluorescent probe that can selectively detect metal cations (Zn2+ and Cu2+) by means of colorimetric changes.

Described in this work is the kinetics of oxidation of ascorbic acid and hydroquinone by a tetranuclear Mn(IV) oxidant, [Mn(4)(μ-O)(6)(bipy)(6)](4+) (1(4+), bipy =2,2(/)-bipyridine), in aqueous solution over a wide pH range 1.5-6.0. In particular, below pH 3.0, protonation on the oxo-bridge of 1(4+) results in the formation of [Mn(4)(μ-O)(5)(μ-OH)(bipy)(6)](5+) (1H(5+)) as an additional oxidant over 1(4+). Both ascorbic acid and ascorbate whereas only hydroquinone and none of its protolytic species were found to be reactive reducing agents in these reactions. Analysis of the rate data clearly established that the oxo-bridge protonated oxidant 1H(5+) is kinetically far more superior to 1(4+) in oxidizing ascorbic acid and hydroquinone. Rates of these reactions are substantially lowered in D(2)O-enriched media in comparison to that in H(2)O media. An initial one electron one proton transfer electroprotic rate step could be mechanistically conceived. DFT studies established that among the two sets of terminal and central Mn(IV) atoms in the tetranuclear oxidant, one of the two terminal Mn(IV) is reduced to Mn(III) at the rate step that we can intuitively predict considering the probable positive charge distribution on the Mn(IV) atoms.

Given that transition metal-hydrogen systems have been studied as a predecessor for hydrogen storage materials, we have investigated the neutral and multiply charged titanium-H2 systems (Ti-H2, Ti(+)-H2, Ti(2+)-H2, Ti(3+)-H2, and Ti(4+)-H2) using density functional theory (DFT) and high-level ab initio calculations, including coupled cluster theory with single, double, and perturbatively triple excitations [CCSD(T)]. These systems show different types of hydrogenation depending on their charged state. The neutral Ti-H2 system shows dihydride structure with covalent interaction where the Ti-H distance is 1.76 Å, while H2 is dissociated into two neigboring hydride ions by withdrawing electrons from Ti. The charged Ti(+)-H2, Ti(2+)-H2, and Ti(3+)-H2 systems show dihydrogen structures with noncovalent interaction, where the Ti(+)-H, Ti(2+)-H, and Ti(3+)-H distances are 2.00, 2.14, and 2.12 Å, respectively. The main binding energies in these systems arise from the hydrogen polarizability driven interaction by the positive charge of Ti(n+) (n = 1-3). Among Ti(n+)-H2 (n = 1-3) the Ti(+)-H2 has the shortest distance against our common expectation, while Ti(2+)-H2 has the longest distance. The Ti(+)-H2 distance is the shortest because of the d-σ* molecular orbital (MO) interaction which is not present in Ti(2+)-H2 and Ti(3+)-H2. The Ti(4+) ion does not bind H2. In this regard, we have investigated the maximal hydrogen binding capacity by Ti complexes. The coordination of titanium mono- and dications complexed with dihydrogen (H2) [Ti(+)(H2)n and Ti(2+)(H2)m] is studied along with their structures, binding energies, electronic properties, and spectra. The titanium monocations of the quartet ground state have up to the hexacoordinaton, while titanium dications of the triplet ground state have up to the octacoordination at very low temperatures. At room temperature, the monocations favor penta- to hexacoordination, while the dications favor hexacoordination. This information would be useful for the design of hydrogen storage devices of Ti complexes, such as Ti-decorated/dispersed polymer-graphene hybrid materials.

Many ligands have been experimentally designed and tested for their activities as inhibitors against bacterial enoyl-ACP reductase (FabI), ENR. Here the binding energies of the reported ligands with the E. coli ENR- were calculated, analyzed and compared, and their molecular dynamics (MD) simulation study was performed. IDN, ZAM and AYM ligands were calculated to have larger binding energies than TCL and IDN has the largest binding energy among the considered ligands (TCL, S54, E26, ZAM, AYM and IDN). The contribution of residues to the ligand binding energy is larger in E. coli ENR-NAD+-IDN than in E. coli ENR--TCL, while the contribution of is smaller for IDN than for TCL. The large-size ligands having considerable interactions with residues and have many effective functional groups such as aromatic rings, acidic hydroxyl groups, and polarizable amide carbonyl groups in common. The cation- interactions have large binding energies, positively charged residues strongly interact with polarisable amide carbonyl group, and the acidic phenoxyl group has strong H-bond interactions. The residues which have strong interactions with the ligands in common are Y146, Y156, M159 and K163. This study of the reported inhibitor candidates is expected to assist the design of feasible ENR inhibitors.

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 hydroxyl groups 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(π)···O and H(π)···π interactions, the protonated dimer involves in H(π)···π interactions, and the deprotonated dimer involves in a strong H(π)···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(-1), respectively. The energy components of the intermolecular interactions for the neutral, protonated and deprotonated dimers are analyzed.

Intermolecular interactions that involve aromatic rings are key pro- cesses in both chemical and biological recognition. It is common knowledge that the existence of anion-p interac- tions between anions and electron-defi- cient (p-acidic) aromatics indicates that electron-rich (p-basic) aromatics are expected to be repulsive to anions due to their electron-donating character. Here we report the first concrete theo- retical and experimental evidence of the anion-p interaction between elec- tron-rich alkylbenzene rings and a fluo- ride ion in CH3CN. The cyclophane cavity bridged with three naphthoimi- dazolium groups selectively complexes a fluoride ion by means of a combina- tion of anion-p interactions and (C H) + ···F-type ionic hydrogen bonds. 1 H NMR, 19 F NMR, and fluorescence spectra of 1 and 2 with fluoride ions are examined to show that only 2 can host a fluoride ion in the cavity be- tween two alkylbenzene rings to form a sandwich complex. In addition, the cage compounds can serve as highly se- lective and ratiometric fluorescent sen- sors for a fluoride ion. With the addi- tion of 1 equiv of F, a strongly in- creased fluorescence emission centered at 385 nm appears at the expense of the fluorescence emission of 2 centered at 474 nm. Finally, isothermal titration calorimetry (ITC) experiments were performed to obtain the binding con- stants of the compounds 1 and 2 with F as well as Gibbs free energy. The 2- F complex is more stable than the 1- F complex by 1.87 kcal mol 1 , which is attributable to the stronger anion-p in- teraction between F and triethylben- zene.

From a red proton complex of aldehyde derivatives of polyaromatic hydrocarbon with strong intermolecular hydrogen bonding, which are novel examples of intermolecular proton-bonded aldehydes of polyaromatic hydrocarbons, we find one-dimensional proton arrangement. The complex formed as 9-antraldehyde (Ant-CHO) reacts with HAuCl(4) to form [(Ant-CHO)(2)H](+)[AuCl(4)](-) under dry condition, which are confirmed by single-crystal structure determination and infrared spectra analysis at varying temperatures. Since the compounds of distinctively hydrophobic nature are soluble only in limited organic polar solvents, the strong hydrogen bonds are clearly observed from both the electron density of X-ray analysis and the characteristic signature of the IR frequency. The proton complex units have the typical O-H(+)-O distance of the strong hydrogen bond similar to the Zundel-like cationic hydrogen bond (where two O atoms share a proton in the midpoint of the short O-O distance of approximately 2.4 A). The chemical shift of 20.18 ppm originated from the protons of the O-H(+)-O hydrogen bonds would be the largest downfield shifted value among those of protons in O-H...O bonds reported in various solid materials, indicating very short strong hydrogen bonds for the O-H(+)-O. The complexes are stabilized with the pi-pi intermolecular interactions of the polyaromatic hydrocarbon ligands, resulting in layered structures. The spectral signatures around approximately 900, approximately 1200, and approximately 1700 cm(-1) for the Zundel-like proton bond are clearly characterized.

Two new binaphthyl derivatives 1 and 2 bearing two imidazolium, or bisurea groups were investigated as fluorescent chemosensors for the chiral anion recognition. Receptors 1 and 2 displayed a better selectivity for (S)-2-phenylbutylate over (R)-2-phenylbutylate. Isothermal titration calorimeter methods, fluorescence as well as theoretical calculations are utilized to explain chiral selectivity.

In this account, we highlight the theoretical investigations of various cluster systems comprising of water clusters, π-containing clusters, and metallic clusters. We illustrate how these investiga...

In this mini-review we briefly describe intermolecular interactions ranging from hydrogen bonding to ionic interactions to aromatic interactions. Manifestation of these interaction forces is in the design and realization of various ionophores with chemo-sensing capability for biologically important cations and anions. We also explain how the understanding of hydrogen bonding and π-interactions has led to the design of self-assembled organic nanotubes. We further discuss the conformational changes between stacked and edge-to-face conformers in benzoquinone-benzene complexes, which are controlled by alternating electrochemical potential. The resulting flapping motion illustrates a promising pathway toward the design of nanomechanical devices.

The Hinsberg test to recognize the type of amine (1 degrees -3 degrees amines), which has been established for more than 100 years and well documented in textbooks, is not possible without conducting complicated organic reactions. We report for the first time unique chemosensors that are capable of showing selective color changes toward 1 degrees -3 degrees amines as a color version of the Hinsberg test. This simple and straightforward qualitative analysis, using the synthesized novel compounds herein, can be considered a new innovative tool for discriminating 1 degrees -3 degrees amines as an alternative to the historical Hinsberg test.

For the design of functional molecules and nanodevices, it is very useful to utilize nanorecognition (which is governed mainly by interaction forces such as hydrogen bonding, ionic interaction, π-H/π-π interactions, and metallic interactions) and nanodynamics (involving capture, transport, and release of electrons, photons, or protons). The manifestation of these interaction forces has led us to the design and realization of diverse ionophores/receptors, organic nanotubes, nanowires, molecular mechanical devices, molecular switches, enzyme mimetics, protein folding/unfolding, etc. In this review, we begin with a brief discussion of the interaction forces, followed by some of our representative applications. We discuss ionophores with chemo-sensing capability for biologically important cations and anions and explain how the understanding of hydrogen bonding and π-interactions has led to the design of self-assembled nanotubes from calix[4]hydroquinone (CHQ). The binding study of neutral and cationic transition metals with the redox system of hydroquinone (HQ) and quinone (Q) predicts what kind of nanostructures would form. Finally, we look into the conformational changes between stacked and edge-to-face conformers in π-benzoquinone-benzene complexes controlled by alternating electrochemical potential. The resulting flapping motion illustrates a promising pathway toward the design of mobile nanomechanical devices.

Two new imidazolium systems bearing two pyrene groups have been synthesized and the binding properties of these hosts were examined via fluorescent changes. The fluorescent changes of host 2 upon the addition of anions were also utilized as a NOR logic gate and an INH logic gate.

The intermolecular interaction driven structural change is vital to molecular architecturing. In the Cambridge Structural Database (CSD), we find that the preference for geometrical conformations of electron-deficient π systems is different from those of electron-rich π systems. Indeed, ab initio calculations find that electron-deficient π ring systems should involve different structures and energetics, consistent with the CSD search, due to the electric multipole moments and the decrease in the spatial extent of π-electron density.

We have investigated various types of π-interactions, where one of the interacting π-systems is represented by an aromatic benzene molecule. The system includes Rg-π, CH-π, π-π(D), π-π(T), H-π(T), π(+)-π(D), π(+)-π(T), H(+)-π(T), π(+2)-π(D), M(+)-π, and M(+2)-π complexes, where Rg denotes a rare gas or noble atom, M denotes a metal, and D/T indicates displaced-stacked/T-shaped structure. The microsolvation effect is also considered. We note that the interaction between a cationic π system and a neutral π system (πcation-π interaction) is so far ambiguously considered as either π-π or cation-π interaction. In terms of total binding energy, the πcation-π interaction is weaker than the cation-π interaction, but much stronger than the π-π interaction. When the hydrophilic (N-H)(+) or (C-H)(+) group in a singly charged π(+) system (as in protonated histidine, arginine, pyridine, or dimethyl imidazolium) interacts with a π-system, the complex favors a T-shaped form [π(+)-π(T) complex]. However, in the presence of polar solvating molecules or counteranions, these species interact with the (N-H)(+)/(C-H)(+) group, while the π(+) system interacts with the neutral aromatic ring. Then, the displaced-stacked form [π(+)-π(D) complex] is favored or otherwise nearly isoenergetic to the π(+)-π(T) form. The π(+)-π systems are stabilized mainly by both dispersion and electrostatic energies. Ternary diagrams using either attractive energy components or both attractive and repulsive energy components show that the π(+)-π(D) complexes have more contribution from dispersion energy but less contribution from induction energy than the π(+)-π(T) complexes, while both complexes have similar percentage contributions from electrostatic and exchange energy components. In particular, the π(+)-π(D) complexes are found to be distinctly different from the π-π complexes and the non-π organic or metallic cation-π complexes.

In general, anion−π interactions exist between anions and aromatics with a positive quadrupole moment. The interaction between anions and aromatics with a negative quadrupole moment is expected to be unstable due to Coulombic repulsion. However, here we investigated the cases of aromatics with a negative quadrupole moment such as electron-rich alkyl/alkenyl/alkynyl-substituted benzenes and triphenylene, which interact with halides. Favorable binding was demonstrated with coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] at the complete basis set (CBS) limit. Stability increases with chain length, unsaturation, and halogenation. Energy decomposition analysis based on symmetry adapted perturbation theory (SAPT) shows that electrostatic repulsion is overcome by induction effects arising from the alkyl substituents.

We compare aromatic π interactions with aliphatic π interactions of double- and triple-bonded π systems and non-π stacking interactions of single-bonded σ systems. The model dimer systems of acetylene (C2H2)2, ethylene (C2H4)2, ethane (C2H6)2, benzene (C6H6)2, and cyclohexane (C6H12)2 are investigated. The ethylene dimer has large dispersion energy, while the acetylene dimer has strong electrostatic energy. The aromatic π interactions are strong with particularly large dispersion and electrostatic energies, which would explain why aromatic compounds are frequently found in crystal packing and molecular self-engineering. It should be noted that the difference in binding energy between the benzene dimer (aromatic–aromatic interactions) and the cyclohexane dimer (aliphatic–aliphatic interactions) is not properly described in most density functionals.

Structures of neutral metal-dibenzene complexes, M(C6H6)2 (M = Sc-Zn), are investigated by using Møller-Plesset second order perturbation theory (MP2). The benzene molecules change their conformation and shape upon complexation with the transition metals. We find two types of structures: (i) stacked forms for early transition metal complexes and (ii) distorted forms for late transition metal ones. The benzene molecules and the metal atom are bound together by δ bonds which originate from the interaction of π-MOs and d orbitals. The binding energy shows a maximum for Cr(C6H6)2, which obeys the 18-electron rule. It is noticeable that Mn(C6H6)2, a 19-electron complex, manages to have a stacked structure with an excess electron delocalized. For other late transition metal complexes having more than 19 electrons, the benzene molecules are bent or stray away from each other to reduce the electron density around a metal atom. For the early transition metals, the M(C6H6) complexes are found to be more weakly bound than M(C6H6)2. This is because the M(C6H6) complexes do not have enough electrons to satisfy the 18-electron rule, and so the M(C6H6)2 complexes generally tend to have tighter binding with a shorter benzene-metal length than the M(C6H6) complexes, which is quite unusual. The present results could provide a possible explanation of why on the Ni surface graphene tends to grow in a few layers, while on the Cu surface the weak interaction between the copper surface and graphene allows for the formation of a single layer of graphene, in agreement with chemical vapor deposition experiments.

Extended electron-deficient arenes are investigated as potential neutral receptors for polyanions. Anion binds via σ interaction with extended arenes, which are composed solely of C and N ring atoms and CN substituents. As a result, the positive charge on the aromatic C is enhanced, consequently maximizing binding strength. Selectivity is achieved because different charge distributions can be obtained for target anions of a particular geometry. The halides F(-) and Cl(-) form the most stable complex with 6, while the linear N3(-) interacts most favorably with 7. The trigonal NO3(-) and tetrahedral ClO4(-) fit the 3-fold rotational axis of 6 but do not form stable complexes with 5 and 7. The Y-shaped HCOO(-) forms complexes with 4, 5, and 7, with the latter being the most stable. Thus, the anion complexes exhibit strong binding and the best geometrical fit between guest and host, reminiscent of Lego blocks.

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.

Anthracene and binaphthyl derivatives bearing two imidazolium rings, which strongly bind anions and are particularly selective for pyrophosphate, are examined using fluorescence, 1 H NMR analysis, and density functional calculations.

In earlier studies, the interactions of isolated ionic species with various solvents were investigated using ab initio calculations. The ionic species investigated included cations (proton, hydronium, ammonium, and metal cations) and anions (single electron, hydroxide, and halide anions). However in the present study, we investigate the interactions of these ionic species with the solvent in the presence of other competing ionic species. We also elaborate on how the information obtained from these extensive studies have been employed in designing and synthesizing various kinds of novel ionophores and receptors.

Function of nicotine, which induces activation of all parts of the body including our brain, has been receiving much attention for a long period of time and also been actively studied by researchers for its pharmacological actions in the central nervous system. The modulation of nicotine concentration and the inhibition of nicotine binding on target receptors in the brain are the key factors for smoking addiction therapy. In previous studies showed that influx of nicotine at the blood-brain barrier was through the pyrilamine-sensitive organic cation transporters. But the direct interacting mechanism of pyrilamine on the nicotine binding target receptors has not yet been clarified. The aim of the present study is to investigate the direct binding mechanisms of a pyrilamine on the nicotinic acetylcholine receptors (nAChRs). We found that pyrilamine shares the same ligand binding pocket of nicotine (NCT) on nAChRs but interacts with more amino acid residues than NCT does. The extended part of pyrilamine interacts with additional residues in the ligand binding pocket of nAChRs which are located nearby the entrance of the binding pocket. The catecholamine (CA) secretion induced by nAChR agonist (NCT') was significantly inhibited by the pyrilamine pretreatment. Real time carbon-fiber amperometry confirmed the inhibition of the NCT'-induced exocytosis by pyrilamine in a single cell level. We also found that pyrilamine inhibited the NCT'-induced [Ca(2+)]i. In contrast, pyrilamine did not affect the increase in calcium induced by high K(+). Overall, these data suggest that pyrilamine directly docks into the ligand binding site of nAChRs and specifically inhibits the nAChR-mediated effects thereby causing inhibition of CA secretion. Therefore, pyrilamine may play an important role to explore new treatments to aid smoking cessation.

A series of novel coronands having a 2n-crown-n topology based on trioxane (6-crown-3) derivatives are designed and characterized. These neutral hosts can sense anions through pure aliphatic C–H hydrogen bonding (HB) in condensed phases due to the unusual topology of 2n-crown-n. C–H bonds are strongly polarized by two adjacent oxygen atoms in this scaffold. These hosts provide a rare opportunity to modulate anion binding strength by changing the electronic nature of aliphatic C–H bonds and offer ease of synthesis.

Interaction between positively charged aromatic groups (π(+)-π(+)) is characterized by anti-parallel, displaced-stacked structures in the presence of counteranions. Binding energies of pyridinium, N-methylpyridinium and N-methylimidazolium dimers are much larger than that of benzene-pyridine (π-π) and pyridinium-benzene (π(+)-π). Stabilization is attributed to attractive electrostatic interaction with significant dispersion contribution.

We have synthesized self-assembled red-colored proton complexes of the aldehyde derivatives of polyaromatic hydrocarbon with strong intermolecular hydrogen bonding. These intermolecularly proton-bonded polyaromatic aldehydes formed as 1-pyrenecarbaldehyde (Py-CHO) reacted with HAuCl(4) to produce [(Py-CHO)(2)H][AuCl(4)] under dry conditions. The formation of [(Py-CHO)(2)H][AuCl(4)] was confirmed by single-crystal structure determination and IR spectral analysis at various temperatures. The compounds are distinctively hydrophobic in nature and are soluble only in a few organic polar solvents. The proton bonds are clearly observed from both the electron density in X-ray analysis and the characteristic IR frequency signature. The proton complex units have an O-H(+)-O distance of the typical Zundel-like cationic hydrogen bond (in which two O atoms share a proton-like H in the midpoint of the short O-O distance of ≈2.4 A). The proton bonds are thermally stable, even over 100 °C, because the complexes are stabilized in layered structures with π-π intermolecular interactions of the polyaromatic hydrocarbon ligands. The IR signatures at around 900, 1200, and 1700 cm(-1) for the Zundel-like proton bond are clearly characterized.

We report the highly improved version of quencher-free molecular beacon (QF-MB) system by using graphene oxide (GO) as an external quencher. This QF-MB/GO system provided a higher S/B ratio (31.0) relative to that (2.2) of the same system in the absence of GO, while retaining a high selectivity for fully matched over single-base-mismatched targets.

Triclosan (5-chloro-2-(2,4-dichloro-phenoxy)-phenol, TCL) is a well known inhibitor against enoyl–acyl carrier protein reductase (ENR), an enzyme critical for cell-wall synthesis of bacteria. The inhibitory concentration at 50% inhibition (IC 50 ) of TCL against the Escherichia coli ENR is 150 nM for wild type (WT), 380, 470 and 68,500 nM for Ala, Ser and Val mutants, respectively. To understand this high TCL resistance in the G93V mutant, we obtained the crystal structures of mutated ENRs complexed with TCL and NAD + . The X-ray structural analysis along with the ab initio calculations and molecular dynamics simulations explains the serious consequence in the G93V mutant complex. The major interactions around TCL due to the aromatic(cation)–aromatic and hydrogen bonding interactions are found to be conserved both in WT and mutant complexes. Thus, the overall structural change of protein is minimal except that a flexible α-helical turn around TCL is slightly pushed away due to the presence of the bulky valine group. However, TCL shows substantial edge-to-face aromatic (π)-interactions with both the flexible R192-F203 region and the residues in the close vicinity of G93. The weakening of some edge-to-face aromatic interactions around TCL in the G93V mutant results in serious resistance to TCL. This understanding is beneficial to design new generation of antibiotics which will effectively act on the mutant ENRs.

Given that half-metals are promising futuristic materials for spintronics, organic materials showing half-metal character are highly desirable for spintronic devices, not only owing to their weak spin-orbit and hyperfine interactions, but also their light and flexible properties. We predict that a two-dimensional organic 2,4,6-tri-(1,3,5-triazinyl)methyl radical polymer has half-metallic properties as well as a spontaneous magnetic ordering at ambient temperature. The quantum transmission is studied based on the nonequilibrium Green function theory coupled with density functional theory. The half-metallic property in the triazine-based polymer depends mainly on the nature of the p-band in contrast to of conventional half metals in which the nature of the d-band is more important.

Protonated and deprotonated adipic acids (PAA: HOOC-(CH(2))(4)--COOH(2) (+) and DAA: HOOC-(CH(2))(4)-COO(-)) have a charged hydrogen bond under the influence of steric constraint due to the molecular skeleton of a circular ring. Despite the similarity between PAA and DAA, it is surprising that the lowest energy structure of PAA is predicted to have (H(2)O...H...OH(2))(+) Zundel-like symmetric hydrogen bonding, whereas that of DAA has H(3)O(+) Eigen-like asymmetric hydrogen bonding. The energy profiles show that direct proton transfer between mirror image structures is unfavorable. Instead, the chiral transformation is possible by subsequent backbone twistings through stepwise proton transfer along multistep intermediate structures, which are Zundel-like ions for PAA and Eigen-like ions for DAA. This type of chiral transformation by multistep intramolecular proton transfers is unprecedented. Several prominent OH...O short hydrogen-bond stretching peaks are predicted in the range of 1000-1700 cm(-1) in the Car-Parrinello molecular dynamics (CPMD) simulations, which show distinctive signatures different from ordinary hydrogen-bond peaks. The O-H-O stretching peaks in the range of 1800-2700 cm(-1) become insignificant above around 150 K and are almost washed out at about 300 K.

The pi(+)-pi interactions are utilized to design the solid-state assembly of host-guest complexes where guests are anions. The doubly protonated MPTPH(2) (MPTP = 4'-(4-methoxyphenyl)-2,2':6',2''-terpyridine) complexed with H(2)O and Cl(-) or Br(-) are synthesized, crystallized, and characterized by X-ray analysis. By using the density functional theory calculations which can properly describe the dispersion energy, the assembling phenomena are analyzed in terms of pi(+)-pi and pi-pi interactions as well as H-bonding interactions. The planar structure of MPTPH(2)(Cl)(2).2H(2)O or MPTPH(2)(Br)(2).2H(2)O facilitates the crystal packing, since the pi(+)-pi interactions play an important role in the solid-state assembly.

A pincer-like benzene-bridged sensor 1 with a pyrene excimer as a signal source and imidazolium as a phosphate anion receptor was synthesized and investigated for ATP sensing. A unique switch of excimer vs monomer pyrene fluorescence of 1 is observed in the presence of ATP due to the charcteristic sandwich pi-pi stacking of pyrene-adenine-pyrene. On the other hand, four other bases of nucleoside triphosphates such as GTP, CTP, UTP, and TTP can interact only from the outside with the already stabilized stacked pyrene-pyrene dimer of 1, resulting in excimer fluorescence quenching. The fluorescent intensity ratio of monomer-to-excimer for 1 upon binding with ATP (I(375)/I(487)) is much larger than that upon binding with ADP and AMP. This difference is large enough to discriminate ATP from ADP and AMP. As one of the biological applications, sensor 1 is successfully applied to the ATP staining experiments. Sensor 1 is also applied to monitor the hydrolysis of ATP and ADP by apyrase. The results indicate that 1 is a useful fluorescent sensor for investigations of ATP-relevant biological processes.

The development of visible-light-active photocatalysts is being investigated through various approaches. In this study, C(60)-based sensitized photocatalysis that works through the charge transfer (CT) mechanism is proposed and tested as a new approach. By employing the water-soluble fullerol (C(60)(OH)(x)) instead of C(60), we demonstrate that the adsorbed fullerol activates TiO(2) under visible-light irradiation through the "surface-complex CT" mechanism, which is largely absent in the C(60)/TiO(2) system. Although fullerene and its derivatives have often been utilized in TiO(2)-based photochemical conversion systems as an electron transfer relay, their successful photocatalytic application as a visible-light sensitizer of TiO(2) is not well established. Fullerol/TiO(2) exhibits marked visible photocatalytic activity not only for the redox conversion of 4-chlorophenol, I(-), and Cr(VI), but also for H(2) production. The photoelectrode of fullerol/TiO(2) also generates an enhanced anodic photocurrent under visible light as compared with the electrodes of bare TiO(2) and C(60)/TiO(2), which confirms that the visible-light-induced electron transfer from fullerol to TiO(2) is particularly enhanced. The surface complexation of fullerol/TiO(2) induced a visible absorption band around 400-500 nm, which was extinguished when the adsorption of fullerol was inhibited by fluorination of the surface of TiO(2). The transient absorption spectroscopic measurement gave an absorption spectrum ascribed to fullerol radical cations (fullerol(*+)) the generation of which should be accompanied by the proposed CT. The theoretical calculation regarding the absorption spectra for the (TiO(2) cluster+fullerol) model also confirmed the proposed CT, which involves excitation from HOMO (fullerol) to LUMO (TiO(2) cluster) as the origin of the visible-light absorption.

Hydrogen storage: In lithium amidoboranes an initial molecule of H2 is released by the formation of LiH, followed by a redox reaction of the dihydrogen bond formed between LiHδ− and NHδ+. In this dehydrogenation process, an intermolecular NB bond forms through the catalytic effect of a Li cation. After releasing the first molecule of H2, a Li cation binds to a nitrogen atom, lowering the energy barrier for the second H2 loss per lithium amidoborane dimer (see figure). Alkali-metal amidoboranes have been recently highlighted as materials that satisfy many of the criteria required to make hydrogen-storage media. It is, therefore, crucial for us to understand the dehydrogenation mechanism of these materials for further development towards making successful hydrogen-storage media. In the present study, we attempt to shed light on the mechanisms involved in the loss of one molar equivalent of H2 from solid lithium amidoboranes by using high-level ab initio calculations of monomeric and dimeric compounds in the gas phase. In the lithium amidoborane dimer, H2 is released by the formation of LiH, which is followed by a redox reaction of the dihydrogen bond formed between the strongly basic H− in LiH and Hδ+ bonded to N. In the dehydrogenation process, the Li cation catalyzes the intermolecular NB bond formation; this could lead to new pathways for NB polymerization. After the release of the first molecule of H2, a Li cation binds to a nitrogen atom, resulting in a lowering of the energy barrier for the second dehydrogenation process per dimer. These results will be useful for the design of future hydrogen-storage media.

To understand the autoionization of pure water and the solvation of ammonia in water, we investigated the undissociated and dissociated (ion-pair) structures of (H2O) n and NH3(H2O)n-1 (n = 5, 8, 9, 21) using density functional theory (DFT) and second order Moller-Plesset perturbation theory (MP2). The stability, thermodynamic properties, and infrared spectra were also studied. The dissociated (ion-pair) form of the clusters tends to favor the solvent-separated ion-pair of H3O+/NH4+ and OH-. As for the NH3(H2O)20 cluster, the undissociated structure has the internal conformation, in contrast to the surface conformation for the (H2O)21 cluster, whereas the dissociated structure of NH3(H2O)20 has the surface conformation. As the cluster size of (H2O)n/NH3(H2O)n-1 increases, the difference in standard free energy between undissociated and dissociated (ion-pair) clusters is asymptotically well corroborated with the experimental free energy change at infinite dilution of H3O+/NH4+ and OH-. The predicted NH and OH stretching frequencies of the undissociated and dissociated (ion-pair) clusters are discussed.

In this mini-review we briefly describe intermolecular interactions ranging from hydrogen bonding to ionic interactions to aromatic interactions. Manifestation of these interaction forces is in the design and realization of various ionophores with chemo-sensing capability for biologically important cations and anions. We also explain how the understanding of hydrogen bonding and π-interactions has led to the design of self-assembled organic nanotubes. We further discuss the conformational changes between stacked and edge-to-face conformers in benzoquinone-benzene complexes, which are controlled by alternating electrochemical potential. The resulting flapping motion illustrates a promising pathway toward the design of nanomechanical devices.

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.

The spectral properties of protonated water clusters, especially the difference between Eigen (H3O+) and Zundel (H5O2+) conformers and the difference between their unhydrated and dominant hydrated forms are investigated with the first principles molecular dynamics simulations as well as with the high level ab initio calculations. The vibrational modes of the excess proton in H3O+ are sensitive to the hydration, while those in H5O2+ are sensitive to the messenger atom such as Ar (which was assumed to be weakly bound to the water cluster during acquisitions of experimental spectra). The spectral feature around approximately 2700 cm-1 (experimental value: 2665 cm-1) for the Eigen moiety appears when H3O+ is hydrated. This feature corresponds to the hydrating water interacting with H3O+, so it cannot appear in the Eigen core. Thus, H3O+ alone would be somewhat different from the Eigen forms in water. For the Zundel form (in particular, H5O2+), there have been some differences in spectral features among different experiments as well as between experiments and theory. When an Ar messenger atom is introduced at a specific temperature corresponding to the experimental condition, the calculated vibrational spectra for H5O2+.Ar are in good agreement with the experimental infrared spectra showing the characteristic Zundel frequency at approximately 1770 cm-1. Thus, the effect of hydration, messenger atom Ar, and temperature are crucial to elucidating the nature of vibrational spectra of Eigen and Zundel forms and to assigning the vibrational modes of small protonated water clusters.

By linking the urea moiety at the 1,8 positions of the carbazole fragment, we synthesized host systems 1, 2, and 3 having both chromogenic and fluorogenic signaling subunits. The spectral changes in both the signaling subunits could be easily analyzed via a simple 2-dimensional (2D) analytic approach described here, which enables us to differentiate the given set of anions. Structural studies are also reported.

[structure: see text] Quinoxaline derivatives (1-4) bearing two imidazolium moieties are found to strongly bind anions and show unique charge-transfer fluorescent responses to pyrophosphate and acetate, whereas they show excimer formation with other anions. Anion-binding studies are investigated with fluorescence and 1H NMR analysis, single-crystal X-ray analysis, and theoretical calculations.

The Hinsberg test to recognize the type of amine (1 degrees -3 degrees amines), which has been established for more than 100 years and well documented in textbooks, is not possible without conducting complicated organic reactions. We report for the first time unique chemosensors that are capable of showing selective color changes toward 1 degrees -3 degrees amines as a color version of the Hinsberg test. This simple and straightforward qualitative analysis, using the synthesized novel compounds herein, can be considered a new innovative tool for discriminating 1 degrees -3 degrees amines as an alternative to the historical Hinsberg test.

The imidazole-based ligands, bis(imidazol-1-yl)methane (Bizm, 1a) and (pyrenyl)bis(imidazol-1-yl) methane (Pbizm, 2a) were prepared. With LiClO4, these two compounds formed two novel organic−inorganic hybrid materials: a 3D network polymer Li(Bizm)·ClO4 (1b) and a 1D chain polymer Li(Pbizm)2·ClO4 (2b). The intriguing topological and physiochemical characteristics of 1b and 2b are reported on the basis of the X-ray single-crystal structure analysis and Li ion binding studies.

A new water-soluble imidazolium anthracene derivative not only differentiates two structurally similar compounds GTP and ATP but also acts as potential fluorescent chemosensors (as a quencher and an enhancer, respectively) for GTP and ATP in 100% aqueous solution (pH = 7.4, 10 mM HEPES).