Jaguar is an ab initio quantum chemical program that specializes in fast electronic structure predictions for molecular systems of medium and large size. Jaguar focuses on computational methods with reasonable computational scaling with the size of the system, such as density functional theory (DFT) and local second-order Moller–Plesset perturbation theory. The favorable scaling of the methods and the high efficiency of the program make it possible to conduct routine computations involving several thousand molecular orbitals. This performance is achieved through a utilization of the pseudospectral approximation and several levels of parallelization. The speed advantages are beneficial for applying Jaguar in biomolecular computational modeling. Additionally, owing to its superior wave function guess for transition-metal-containing systems, Jaguar finds applications in inorganic and bioinorganic chemistry. The emphasis on larger systems and transition metal elements paves the way toward developing Jaguar for its use in materials science modeling. The article describes the historical and new features of Jaguar, such as improved parallelization of many modules, innovations in ab initio pKa prediction, and new semiempirical corrections for nondynamic correlation errors in DFT. Jaguar applications in drug discovery, materials science, force field parameterization, and other areas of computational research are reviewed. Timing benchmarks and other results obtained from the most recent Jaguar code are provided. The article concludes with a discussion of challenges and directions for future development of the program. © 2013 Wiley Periodicals, Inc.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/qua.24481

Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences

This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.

Aromatic rings in chemical and biological recognition: energetics and structures.

Organic chemists tend to consider the conformation of compounds as a consequence of repulsive steric interactions. In other words, “the steric effect” means “repulsive” in many cases. Thus, folded conformations observed in organic molecules have been often regarded as unusual, while the reason remained undecided. However, accurate determinations by modern spectroscopic methods, recent crystallographic data, and high-level ab initio MO calculations have demonstrated that the folded conformation is by no means exceptional. We will show that the gauche or folded conformation prevails in organic compounds bearing at least an electronegative or π-group in the molecule. We consider that the above phenomenon finds its origin, in most cases, in nonconventional hydrogen bonds such as the CH/X (X ) O, halogen, etc.) and the XH/π (X ) O, N, C, etc.) hydrogen bonds. * To whom correspondence should be addressed. E-mail: shu@ hiroshima-u.ac.jp. ‡ Hiroshima University. § Yokohama National University. ⊥ The CHPI Institute. Chem. Rev. 2010, 110, 6049–6076 6049

Relevance of Weak Hydrogen Bonds in the Conformation of Organic Compounds and Bioconjugates: Evidence from Recent Experimental Data and High-Level ab Initio MO Calculations

There is great need for stand-alone luminescence-based chemosensors that exemplify selectivity, sensitivity, and applicability and that overcome the challenges that arise from complex, real-world media. Discussed herein are recent developments toward these goals in the field of supramolecular luminescent chemosensors, including macrocycles, polymers, and nanomaterials. Specific focus is placed on the development of new macrocycle hosts since 2010, coupled with considerations of the underlying principles of supramolecular chemistry as well as analytes of interest and common luminophores. State-of-the-art developments in the fields of polymer and nanomaterial sensors are also examined, and some remaining unsolved challenges in the area of chemosensors are discussed.

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Supramolecular Luminescent Sensors

Optical band gaps of organic semiconductor materials

The structure of the indole−benzene dimer has been investigated using experimental techniques, namely, UV spectroscopy and infrared−ultraviolet (IR/UV) double resonance spectroscopy, combined with quantum chemical calculations such as MP2 and dispersion corrected DFT methods. The red shift of the indole N−H stretch frequency in the dimer provides direct evidence that the experimentally observed indole−benzene dimer is an N−H···π bound hydrogen bonded complex. Theoretical investigations suggest that the potential energy surface (PES) of the complex is rather flat along the coordinate describing the tilt angle between the molecular planes of indole and benzene, with several minima of similar energies, namely, parallel displaced (PD), right-angle T-shaped (T), and other intermediate structures which can be categorized as tilted T-shaped (T′) and tilted parallel displaced (PD′) structures. Three different computational methods, namely, RI-MP2, RI-B97-D, and PBE1-DCP, are used to arrive at a new structural ass...

Structure of the Indole−Benzene Dimer Revisited

In this article, hydrogen bonding interaction between p-cresol (p-CR) and cyclic ether, tetrahydrofuran (THF) and thioether, tetrahydrothiophene (THT) has been investigated. Two-color resonantly enhanced two-photon ionization in conjunction with the fluorescence detected IR (FDIR) spectroscopy was used to record the changes in the OH stretching frequency in these complexes. The FDIR spectra showed existence of a single conformer of the p-CR·THF and two conformers of the p-CR·THT complex. With the help of computed IR spectra and atoms-in-molecules analysis, the two conformers of p-CR·THT were assigned as the complex of p-CR with THT (C2)/THT (CS). The redshift of OH stretching frequency for the p-CR·THF complex was greater compared to those for the conformers of the p-CR·THT complex. The binding energies of the p-CR·THF and p-CR·THT complexes were computed to be 7.42 and 6.15 kcal/mole. These were of the same order as those for the acyclic analogs, diethylether (DEE), and diethylsulfide (DES), of the solve...

OH···X (X = O, S) hydrogen bonding in thetrahydrofuran and tetrahydrothiophene.

In this work, we present spectroscopic investigations of hydrogen bonded complexes of CHF3 and CHCl3 with p-cresol and p-cyanophenol. The systems were chosen as the potential candidates bound by C–H···Y type hydrogen bonds that are known to exhibit unconventional blue shifts in the C–H stretching frequency. The two phenol derivatives chosen offer multiple hydrogen bonding acceptor sites. They also differ from each other in regard to the electron-donating/withdrawing ability of the para substituents which could dictate the global minimum structure in each case. The complexes were formed using the supersonic jet expansion method and were investigated using a variant of the IR-UV double resonance technique, namely fluorescence depletion IR (FDIR) spectroscopy. It was found that in the case of p-cresol the complexes were C–H···π bound in which the C–H stretch was blue-shifted. In the case of p-cyanophenol the complexes were C–H···N bound. In its fluoroform complex the C–H frequency was blue-shifted by 27 cm–1...

C-H···Y hydrogen bonds in the complexes of p-cresol and p-cyanophenol with fluoroform and chloroform.

In this work, the vibronic spectroscopy of the p-aminophenol–water 1:1 complex is presented. The S1 vibrational energy levels of the complex were characterized by REMPI spectroscopy up to 2500 cm−1 above the band origin. The dispersed fluorescence spectra were recorded for the B.O., 6a01 and I02 excitations to characterize the vibrational levels in the S0 state of the complex. Stimulated ion depletion spectroscopy was carried out to determine the higher vibrational levels of the ground state all the way up to ∼3075 cm−1. The structure and the vibrational levels of the AP–W1 complex were calculated ab initio at the HF level and DFT with B3LYP functional for S0, and CIS level for S1 using 6-31G** basis set. The structure of the AP–W1 complex compared well with the earlier calculations for this case as well as the other ROH–water (R=aromatic group) complexes reported in the literature. However, the redshift in the electronic band origin was almost half of that observed in other cases. A good correlation was ...

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Vibronic spectroscopy of the H-bonded aminophenol–water complex

Infrared chemiluminescence from the HF, HCl, and OH products has been used to measure the nascent vibrational distributions and the rate constants at 300 K for the title reactions in a fast flow reactor. The ClO reaction was observed as a secondary step in the ClO2 and Cl2O systems. The reactions proceeding by a direct mechanism, Cl2O, ClNO, OF2, and CF3OF release relatively small fractions, ∼0.37, of the available energy as HCl or HF vibrational energy with narrow distributions, in accord with the dynamics associated with the H atoms on a repulsive potential surface. The ClO2 and NO2 reactions, which proceed by short lived intermediates, release a larger fraction of vibrational energy to OH and with broad distributions. Although the data for the ClO reaction are not definitive, the OH formation channel is the more important by a factor of 4–5. The NO2 reaction was studied in direct comparison with Cl2 to choose the best Einstein coefficients of OH by comparing the OH and HCl formation rate constants.

Sanjay Wategaonkar

Papers

Structure of the Indole−Benzene Dimer Revisited

OH···X (X = O, S) hydrogen bonding in thetrahydrofuran and tetrahydrothiophene.

C-H···Y hydrogen bonds in the complexes of p-cresol and p-cyanophenol with fluoroform and chloroform.

Vibronic spectroscopy of the H-bonded aminophenol–water complex

Infrared chemiluminescence studies of H atom reactions with Cl2O, ClNO, F2O, CF3OF, ClO2, NO2, and ClO