Very Strong Hydrogen Bond in Nitrophthalic Cocrystals.

This work presents the studies of a very strong hydrogen bond (VSHB) in biologically active phthalic acids. Research on VSHB comes topical due to its participation in many biological processes. The studies cover the modelling of intermolecular interactions and phthalic acids with 2,4,6-collidine and N,N-dimethyl-4-pyridinamine complexes with aim to obtain a VSHB.

Renewed spectroscopic and theoretical research of hydrogen bonding in ascorbic acid.

The studies of two isomers of ascorbic acid and their deuteroanalogues, presented in the paper, have been accomplished by vibrational spectroscopy methods and quantum-chemical simulations. The spectroscopic research of L-ascorbic and D-isoascorbic acids have been carried out by the infrared (IR) and Raman (R) techniques. On the basis of the obtained results the spectral interpretation of the hydrogen bonded groups of ascorbic acids has been performed.

Inter- vs. Intra-Molecular Hydrogen Bond in Complexes of Nitrophthalic Acids with Pyridine.

This study covers the analysis of isomeric forms of nitrophthalic acids with pyridine. This work dwells on the complementary experimental (X-ray, IR and Raman) and theoretical (Car-Parrinello Molecular Dynamics (CPMD) and Density Functional Theory (DFT)) studies of the obtained complexes. The conducted studies showed that steric repulsion between the nitro group in ortho-position and the carboxyl group causes significant isomeric changes.

UV Laser-Induced Phototransformations of Matrix-Isolated 5-Chloro-3-nitro-2-hydroxyacetophenone.

Conformational changes of 5-chloro-3-nitro-2-hydroxyacetophenone were studied by experimental and theoretical methods. Phototransformations of the compound were induced in low-temperature argon matrices by using UV radiation, which was followed by FT-IR measurements. Two types of changes within the molecule were detected: rotations of the hydroxyl and acetyl groups.

Comparison of Proton Acceptor and Proton Donor Properties of HO and HO in Organic Crystals of Drug-like Compounds: Peroxosolvates vs. Crystallohydrates.

Two new peroxosolvates of drug-like compounds were synthesized and studied by a combination of X-ray crystallographic, Raman spectroscopic methods, and periodic DFT computations. The enthalpies of H-bonds formed by hydrogen peroxide (HO) as a donor and an acceptor of protons were compared with the enthalpies of analogous H-bonds formed by water (HO) in isomorphic (isostructural) hydrates. The enthalpies of H-bonds formed by HO as a proton donor turned out to be higher than the values of the corresponding H-bonds formed by HO.

Spectroscopic Identification of Hydrogen Bond Vibrations and Quasi-Isostructural Polymorphism in N-Salicylideneaniline.

The -hydroxy aryl base 2-[(E)-(phenylimino)methyl]phenol and its deutero-derivative have been studied by the inelastic incoherent neutron scattering (IINS), infrared (IR) and Raman experimental methods, as well as by Density Functional Theory (DFT) and Density-Functional Perturbation Theory (DFPT) simulations. The assignments of vibrational modes within the 3500-50 cm spectral region made it possible to state that the strong hydrogen bond in the studied compound can be classified as the so-called quasi-aromatic bond. The isotopic substitution supplemented by the results of DFT calculations allowed us to identify vibrational bands associated with all five major hydrogen bond vibrations.

Polymorphism and Conformational Equilibrium of Nitro-Acetophenone in Solid State and under Matrix Conditions.

Conformational and polymorphic states in the nitro-derivative of -hydroxy acetophenone have been studied by experimental and theoretical methods. The potential energy curves for the rotation of the nitro group and isomerization of the hydroxyl group have been calculated by density functional theory (DFT) to estimate the barriers of the conformational changes. Two polymorphic forms of the studied compound were obtained by the slow and fast evaporation of polar and non-polar solutions, respectively.

Combination of "Buttressing" and "Clothespin" Effects for Reaching the Shortest NHN Hydrogen Bond in Proton Sponge Cations.

A series of previously unknown 2,4,5-tri- and 2,4,5,7-tetrasubstituted 1,8-bis(dimethylamino)naphthalenes and their salts with HBF containing bulky spherically shaped substituents (Me, Br, and SiMe) in the naphthalene ring has been synthesized. Using XRD analysis of 11 samples, the influence of the so-called "buttressing" and "clothespin" effects on their molecular structure and the NHN hydrogen bond geometry in the solid cations were investigated. The combined action of both effects has been shown to significantly increase the compression of the hydrogen bond.

Inter- vs. Intramolecular Hydrogen Bond Patterns and Proton Dynamics in Nitrophthalic Acid Associates.

Noncovalent interactions are among the main tools of molecular engineering. Rational molecular design requires knowledge about a result of interplay between given structural moieties within a given phase state. We herein report a study of intra- and intermolecular interactions of 3-nitrophthalic and 4-nitrophthalic acids in the gas, liquid, and solid phases.

Modeling Biologically Important NH···π Interactions Using -Disubstituted Naphthalenes.

For the first time, systematic studies of 8-aryl and 8-pyrrolyl derivatives of 1-aminonaphthalene as simple, synthetically available, and nicely preorganized models were conducted for a better understanding the properties of NH···π interactions involved in the stabilization of the secondary and tertiary protein structures as well as the recognition of guest molecules by biological receptors. It was shown that the NH···π binding is especially effective when the NH-donor is a positively charged group, for example, MeNH, and the π-donor is an electron-rich aromatic substituent, in particular, the 1-pyrrolyl or the 4-hydroxyphenyl group. Using protonated tetrafluoroborate salts, a strong counterion effect was demonstrated by means of theoretical calculations.

H/D Isotope Effects on H-NMR Chemical Shifts in Cyclic Heterodimers and Heterotrimers of Phosphinic and Phosphoric Acids.

Hydrogen-bonded heterocomplexes formed by POOH-containing acids (diphenylphosphoric , dimethylphosphoric , diphenylphosphinic , and dimethylphosphinic ) are studied by the low-temperature (100 K) H-NMR and P-NMR using liquefied gases CDF/CDFCl as a solvent. Formation of cyclic dimers and cyclic trimers consisting of molecules of two different acids is confirmed by the analysis of vicinal H/D isotope effects (changes in the bridging proton chemical shift, δH, after the deuteration of a neighboring H-bond). Acids and (or and ) form heterotrimers with very strong (short) H-bonds (δH ca.

Nucleophilic Substitution of Hydrogen Atom in Initially Inactivated Pyrrole Ring.

It has been found that 1-dialkylamino-8-(pyrrolyl-1)naphthalenes 1 and 6, upon treatment with an equimolar amount of HBF under ambient conditions, produce 1-dialkylammonium salts which are transformed into 7,7-dialkyl-7 H-pyrrolo[1,2- a]perimidine-7-ium tetrafluoroborates 5 and 7, respectively. The reaction proceeds in a highly selective manner and represents the first case of nucleophilic substitution of hydrogen in the initially inactivated pyrrole ring. The scope and limitations of the transformation, apparently operating due to the joint action of the "proximity effect" and proton catalysis, are outlined.

Neutral Pyrrole Nitrogen Atom as a π- and Mixed n,π-Donor in Hydrogen Bonding.

9-Dimethylaminobenzo[ g]indoles 3-6 and 1-dimethylamino-8-(pyrrolyl-1)naphthalene 7 were examined as possible models for establishing the ability of the pyrrole nitrogen atom to participate in [NHN] hydrogen bonding as a proton acceptor. Indoles 3-5 (to a lesser extent 6) form rather stable tetrafluoroborates, with the proton mostly located on the NMe group but simultaneously engaged in the formation of a charged intramolecular [NHN] hydrogen bond (IHB) with the pyrrole N atom. The theoretically estimated energies of IHB in salts 3HBF-6HBF vary between 7.

Impact of the Keto-Enol Tautomeric Equilibrium on the BODIPY Chromophore.

An intramolecular tautomeric fluorescent BODIPY sensor has been designed and synthesized. The obtained BODIPY dye is a combination of the 4-bora- 3a, 4a-diaza- s-indacene core and a diketone fragment. The study of conformational equilibria in the ground and excited states has been completed for a broad range of solvent polarity by steady state and NMR methods as well as by DFT and TD-DFT calculations.

Some Brief Notes on Theoretical and Experimental Investigations of Intramolecular Hydrogen Bonding.

A review of selected literature data related to intramolecular hydrogen bonding in -hydroxyaryl Schiff bases, -hydroxyaryl ketones, -hydroxyaryl amides, proton sponges and -hydroxyaryl Mannich bases is presented. The paper reports on the application of experimental spectroscopic measurements (IR and NMR) and quantum-mechanical calculations for investigations of the proton transfer processes, the potential energy curves, tautomeric equilibrium, aromaticity etc. Finally, the equilibrium between the intra- and inter-molecular hydrogen bonds in amides is discussed.

Calculations of BODIPY dyes in the ground and excited states using the M06-2X and PBE0 functionals.

A number of fluorescent dyes based on BODIPY (4,4'-difluoro-4-bora-3a,4a-diaza-s-indacene) have been studied theoretically. This paper presents the results of calculations of these BODIPY dyes in their ground and excited states, performed using DFT and TD-DFT methods, respectively. The influences of N,N-dimethylaminobenzyl, ortho-fluorophenol, and methyl substituents as well as the solvent polarity on the positions of the absorption and emission bands of the dyes were analyzed.

Ring lithiation of 1,8-bis(dimethylamino)naphthalene: another side of the 'proton sponge coin'.

It has been found that 1,8-bis(dimethylamino)naphthalene (DMAN), unlike N,N-dimethylaniline, undergoes ring metallation in the n-BuLi-TMEDA-Et2O system with a low selectivity and in poor total yields. The situation is significantly improved in the t-BuLi-TMEDA-n-hexane system when 3- and 4-lithium derivatives become the only reaction products obtained in good yields. The formation of 3-Li-DMAN is especially desired since no method of direct meta-functionalization of DMAN is known to date.

Conformational state of β-hydroxynaphthylamides: Barriers for the rotation of the amide group around CN bond and dynamics of the morpholine ring.

Three β-hydroxynaphthylamides (morpholine, pyrrolidine and dimethylamine derivatives) have been synthesized and their conformational state was analyzed by NMR, X-ray and DFT calculations. In aprotic solution the molecules contain intramolecular OHO hydrogen bonds, which change into intermolecular ones in solid state. The energy barriers for the amide group rotation around the CN bond were estimated from the line shape analysis of (1)H and (13)C NMR signals.

Solvatochromism of BODIPY-Schiff dye.

A boron-dipyrrin chromophore connected with an o-hydroxyaryl aldimine by a diazo bridge (BODIPY-Schiff dye) has been developed. The photophysical properties of the BODIPY-Schiff dye have been investigated with UV, steady-state, and time-resolved fluorimetry. The spectral features have been characterized with respect to density functional theory and time-dependent density functional theory.

Comparison of resonance assisted and charge assisted effects in strengthening of hydrogen bonds in dipyrrins.

This paper deals with the study of two types of hydrogen bonding: a quasi-aromatic hydrogen bonding in dipyrromethene and the ionic one in dipyrromethane. The study focuses on two phenomena-the proton transfer process and tautomeric equilibrium. Metric parameters and spectroscopic assignments have been calculated; this allowed a further comparison of spectral features calculated with four methods (Car-Parrinello molecular dynamics (CPMD), ab initio, density functional theory (DFT), and numerical calculation of anharmonic vibrational levels via a solution of the corresponding 1D Schrödinger equation).

Impact of proton transfer phenomena on the electronic structure of model Schiff bases: an AIM/NBO/ELF study.

Understanding of the electronic structure evolution due to a proton dynamics is a key issue in biochemistry and material science. This paper reports on density functional theory calculations of Schiff bases containing short, strong intramolecular hydrogen bonds where the bridged proton is located: (i) at the donor site, (ii) strongly delocalized, and (iii) at the acceptor site. The mobility of the bridged proton and its influence on the molecular structure and properties of the chosen Schiff base derivatives have been investigated on the basis of Atoms in Molecules, Natural Bond Orbitals, and Electron Localization Function theories.

Photochromic cycle of 2'-hydroxyacetophenone azine studied by absorption and emission spectroscopy in different solvents.

This paper reports on the investigations of the synthesized di-(o-hydroxyaryl ketoimine) compound by the steady state absorption and emission techniques as well as picosecond time resolved emission and femtosecond transient absorption methods in different solvents. The results of the experimental observation have been supported by the theoretical DFT and TD-DFT calculations. The theoretical data have revealed the completed influence of the environmental polarity on particular conformers of studied compound.

H/D isotope effects in hydrogen bonded systems.

An extremely strong H/D isotope effect observed in hydrogen bonded A-H…B systems is connected with a reach diversity of the potential shape for the proton/deuteron motion. It is connected with the anharmonicity of the proton/deuteron vibrations and of the tunneling effect, particularly in cases of short bridges with low barrier for protonic and deuteronic jumping. Six extreme shapes of the proton motion are presented starting from the state without possibility of the proton transfer up to the state with a full ionization.

Triple hydrogen bonding in a circular arrangement: ab initio, DFT and first-principles MD studies of tris-hydroxyaryl enamines.

First-principles Car-Parrinello molecular dynamics, ab initio (MP2) and density functional schemes have been used to explore the tautomeric equilibrium in three tris(amino(R)methylidene)cyclohexane-1,3,5-triones (R = hydrogen, methyl or phenyl group). The dynamic nature of the cyclic hydrogen bonding has been studied by the first-principles MD method. The comparison of the results obtained by aforesaid methods has been accomplished on the basis of calculations of structural and spectroscopic characteristics of the compounds.

Rational design, synthesis, and spectroscopic and photophysical properties of a visible-light-excitable, ratiometric, fluorescent near-neutral pH indicator based on BODIPY.

A visible-light-excitable, ratiometric, brightly fluorescent pH indicator for measurements in the pH range 5-7 has been designed and synthesized by conjugatively linking the BODIPY fluorophore at the 3-position to the pH-sensitive ligand imidazole through an ethenyl bridge. The probe is available as cell membrane permeable methyl ester 8-(4-carbomethoxyphenyl)-4,4-difluoro-3-[2-(1H-imidazol-4-yl)ethenyl]-1,5,7-trimethyl-3a,4a-diaza-4-bora-s-indacene (I) and corresponding water-soluble sodium carboxylate, sodium 8-(4-carboxylatophenyl)-4,4-difluoro-3-[2-(1H-imidazol-4-yl)ethenyl]-1,5,7-trimethyl-3a,4a-diaza-4-bora-s-indacene (II). The fluorescence quantum yield Φ(f) of ester I is very high (0.