Light-Controlled Anticancer Activity and Cellular Uptake of a Photoswitchable Cisplatin Analogue.

A photoactive analogue of cisplatin was synthesized with two arylazopyrazole ligands, able to undergo -/- photoisomerizations. The photoisomer showed a dark half-life of 9 days. The cytotoxicities of both photoisomers of the complex were determined in several cancer and normal cell lines and compared to that of cisplatin.

Ab Initio Study of H-Bond Dynamics in Three-Component Crystals Comprising (DABCOH ) Polycationic Chains.

In this work, the dynamic character of hydrogen-bond (H-bond) networks in two three-component crystals comprising polycationic chains was described. The first studied system was 1,4-diazabicyclo[2.2.

Near-Infrared fluorescent unsymmetrical aza-BODIPYs: Synthesis, photophysics and TD-DFT calculations.

In view of the ever-growing demand for efficient NIR fluorophores for biomedical applications, we herein report the synthesis and properties of four unsymmetrical aza-BODIPYs exhibiting NIR fluorescence. Highly desirable photophysical and photochemical properties were induced in these molecules due to the presence of both strongly electron-withdrawing p-nitrophenyl rings (p-NOPh-) and mildly electron-donating p-methoxyphenyl rings (p-MeOPh-) within the aza-BODIPY core. In particular, upon excitation with λ the unsymmetrical aza-BODIPYs studied exhibited NIR emission with λ ranging from 699 nm to 718 nm in toluene.

Unravelling the nature of a toluene-fumaronitrile complex.

In this research, the occurrence and anomalous increase of an additional absorption band observed in the spectrum of fumaronitrile dissolved in toluene are explained and characterized. The formation of a stable ground-state complex between these two molecules is evidenced by both experimental and theoretical studies. TD-DFT calculations show that the presence of an unexpected signal in the absorption spectra originates from the photoinduced intermolecular charge-transfer process occurring within this system.

A comparison of the hydrogen bond interaction dynamics in the adenine and thymine crystals: BOMD and spectroscopic study.

In this work we present the comparison study of Adenine and Thymine crystals based on the hydrogen bond dynamics. The ab initio molecular dynamics have been used as the base for the further studied interactions observed inside crystals. The generated power spectra, as well as the fluctuation of the interaction energies, showed large differences between hydrogen bond networks in the considered crystals.

Path Integral Calculation of the Hydrogen/Deuterium Kinetic Isotope Effect in Monoamine Oxidase A-Catalyzed Decomposition of Benzylamine.

Monoamine oxidase A (MAO A) is a well-known enzyme responsible for the oxidative deamination of several important monoaminergic neurotransmitters. The rate-limiting step of amine decomposition is hydride anion transfer from the substrate α-CH2 group to the N5 atom of the flavin cofactor moiety. In this work, we focus on MAO A-catalyzed benzylamine decomposition in order to elucidate nuclear quantum effects through the calculation of the hydrogen/deuterium (H/D) kinetic isotope effect.

Comparison of the Hydrogen Bond Interaction Dynamics in the Guanine and Cytosine Crystals: Ab Initio Molecular Dynamics and Spectroscopic Study.

In this work, we present the comparison study of guanine and cytosine crystals based on the hydrogen bond (HB) dynamics. The ab initio molecular dynamics gave us a base for detailed analysis. The analysis of the trajectories by power spectrum generation, as well as the fluctuation of the interaction energies, showed large differences between HB networks in the considered crystals.

Understanding the Structure of the Hydrogen Bond Network and Its Influence on Vibrational Spectra in a Prototypical Aprotic Ionic Liquid.

Analysis of the hydrogen bond network in aprotic ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (EMIM-TFSI) has been performed based on structures obtained from ab initio or classical molecular dynamics simulations. Statistics of different donor and acceptor atoms and the amount of chelating or bifurcated bonds has been presented. Most of the hydrogen bonds in EMIM-TFSI are formed with oxygen atoms as hydrogen acceptors; and the most probable bifurcated bonds are those with a mixed pair of oxygen and nitrogen acceptors.

Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics.

Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations.

ETS-NOCV decomposition of the reaction force for double-proton transfer in formamide-derived systems.

The analysis of the electronic-structure changes along IRC paths for double-proton-transfer reactions in the formamide dimer (R1), formamide-thioformamide system (R2), and the thioformamide dimer (R3) was performed based on the extended-transition-state natural orbitals for chemical valence (ETS-NOCV) partitioning of the reaction force, considering the intra-fragments strain and the inter-fragments interaction terms, and further-the electrostatic, Pauli-repulsion and orbital interaction components, with the latter being decomposed into the NOCV components. Two methods of the system partitioning into the fragments were considered ('reactant perspective'/bond-formation, 'product perspective' / bond-breaking). In agreement with previous studies, the results indicate that the major changes in the electronic structure occur in the transition state region; the bond-breaking processes are, however, initiated already in the reactant region, prior to entering the TS region.

The influence of the metal cations and microhydration on the reaction trajectory of the N3 ↔ O2 thymine proton transfer: Quantum mechanical study.

This study involves the intramolecular proton transfer (PT) process on a thymine nucleobase between N3 and O2 atoms. We explore a mechanism for the PT assisted by hexacoordinated divalent metals cations, namely Mg , Zn , and Hg . Our results point out that this reaction corresponds to a two-stage process.

ETS-NOCV Decomposition of the Reaction Force: The HCN/CNH Isomerization Reaction Assisted by Water.

The partitioning of the reaction force based on the extended-transition-state natural orbital for chemical valence (ETS-NOCV) scheme has been proposed. This approach, together with the analysis of reaction electronic flux (REF), has been applied in a description of the changes in the electronic structure along the IRC pathway for the HCN/CNH isomerization reaction assisted by water. Two complementary ways of partitioning the system into molecular fragments have been considered ("reactant perspective" and "product perspective").

Infrared Spectroscopy and Born-Oppenheimer Molecular Dynamics Simulation Study on Deuterium Substitution in the Crystalline Benzoic Acid.

In this study we present complementary computational and experimental studies of hydrogen bond interaction in crystalline benzoic acid and its deuterated and partially deuterated derivatives. The experimental part of the presented work includes preparation of partially deuterated samples and measurement of attenuated total reflection (ATR)-FTIR spectra. Analysis of the geometrical parameters and time course of dipole moment of crystalline benzoic acid and its deuterated and partially deuterated derivatives by Born-Oppenheimer molecular dynamics (BOMD) enabled us to deeply analyze the IR spectra.

Explicit Solvent Modeling of IR and UV-Vis Spectra of 1-Ethyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide Ionic Liquid.

Explicit solvent modeling of absorption spectra of 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide has been performed. Fourier transform of the autocorrelation function of the dipole moment calculated from ab initio molecular dynamics (AIMD) simulations has been used to obtain the IR spectrum of the bulk liquid. A sequential molecular dynamics (MD)/time-dependent density functional theory procedure has been applied to calculate the UV-vis spectrum.

Born-Oppenheimer Molecular Dynamics Study on Proton Dynamics of Strong Hydrogen Bonds in Aspirin Crystals, with Emphasis on Differences between Two Crystal Forms.

In this study, the proton dynamics of hydrogen bonds for two forms of crystalline aspirin was investigated by the Born-Oppenheimer molecular dynamics (BOMD) method. Analysis of the geometrical parameters of hydrogen bonds using BOMD reveals significant differences in hydrogen bonding between the two crystalline forms of aspirin, Form I and Form II. Analysis of the trajectory for Form I shows spontaneous proton transfer in cyclic dimers, which is absent in Form II.

Car-Parrinello Molecular Dynamics Simulations of Infrared Spectra of Crystalline Vitamin C with Analysis of Double Minimum Proton Potentials for Medium-Strong Hydrogen Bonds.

We studied proton dynamics of a hydrogen bonds of the crystalline l-ascorbic acid. Our approach was based on the Car-Parrinello molecular dynamics. The focal point of our study was simulation of the infrared spectra of l-ascorbic acid associated with the O-H stretching modes that are very sensitive to the strength of hydrogen bonding.

Analysis of the bonding between two M(μ-NAr(#)) monomers in the dimeric metal(II) imido complexes {M(μ-NAr(#))}2 [M = Si, Ge, Sn, Pb; Ar(#) = C6H3-2,6-(C6H2-2,4,6-R3)2]. The stabilizing role played by R = Me and iPr.

The nature of the bonding between the two M(μ-NAr(#)) imido monomers [M = Si, Ge, Sn, Pb; Ar(#) = C6H3-2,6-(C6H2-2,4,6-R3)2; R = Me, iPr] in the {M(μ-NAr(#))}2 dimer is investigated with the help of a newly developed energy and density decomposition scheme as well as molecular dynamics. The approach combines the extended transition state energy decomposition method with the natural orbitals for chemical valence density decomposition scheme within the same theoretical framework. The dimers are kept together by two σ bonds and two π bonds.

Car-Parrinello simulation of the vibrational spectrum of a medium strong hydrogen bond by two-dimensional quantization of the nuclear motion: application to 2-hydroxy-5-nitrobenzamide.

The nature of medium strong intra- and intermolecular hydrogen bonding in 2-hydroxy-5-nitrobenzamide in the crystal phase was examined by infrared spectroscopy and Car-Parrinello molecular dynamics simulation. The focal point of our study was the part of the infrared spectra associated with the O-H and N-H stretching modes that are very sensitive to the strength of hydrogen bonding. For spectra calculations we used an isolated dimer and the fully periodic crystal environment.