Understanding the Fe-CO bond through the electronic structure of Fe(CO)L, m = 2, 3, n = 0-3, L = Cl, Br, HO or NH.

Carbon monoxide (CO) exerts various protective effects on the body. Drugs known as CORMs (CO-releasing molecules) can continuously release small doses of CO into diseased tissues and cells. Transition metals interact strongly with the carbonyl group, and coordination compounds bearing carbonyl groups are a promising class of CORMs.

The usefulness of energy decomposition schemes to rationalize host-guest interactions.

This perspective focuses on the crucial role that energy decomposition schemes play in elucidating the physical nature of non-covalent interactions in supramolecular systems, particularly from the point of view of host-guest systems stabilized by non-covalent interactions, which are fundamental to molecular recognition. The findings reported here reveal the robustness and practical application of methods such as EDA-NOCV in rationalizing molecular recognition situations in systems such as calixarenes, cyclophanes and other box-shaped hosts, capable of incorporating different chemical species as anions and PAHs. We expect that the discussed cases in this perspective can be viewed as an initial assessment for the multidimensional nature of the weak interactions underlying supramolecular aggregations, which can be recognized in a plethora of different structures constantly synthesized and characterized by chemists around the world.

Shedding light on the electronic structure of [Ru(η-CH)(NH)] complex: a computational insight.

Ruthenophanes have been recognized as potential candidates to the design of electrically conducting polymers, particularly due to their electrochemical, structural, and spectroscopic properties. The comprehension and rationalization of the metal-ligand interaction is fundamental to pave the way for future applications as the design of new conducting materials. For that reason, this investigation sheds light on the electronic details behind the cation-π interactions present in ruthenophanes by using [Ru(η-CH)(NH)] as a model.

Use of Density Functional Based Tight Binding Methods in Vibrational Circular Dichroism.

Vibrational circular dichroism (VCD) is a spectroscopic technique used to resolve the absolute configuration of chiral systems. Obtaining a theoretical VCD spectrum requires computing atomic polar and axial tensors on top of the computationally demanding construction of the force constant matrix. In this study we evaluated a VCD model in which all necessary quantities are obtained with density functional based tight binding (DFTB) theory.

Frequency Range Selection Method for Vibrational Spectra.

Theoretical calculations of vibrational properties are widely used to explain and predict experimental spectra. However, with standard quantum chemical methods all molecular motions are considered, which is rather time-consuming for large molecules. Because typically only a specific spectral region is of experimental interest, we propose here an efficient method that allows calculation of only a selected frequency interval.

How does the total charge and isomerism influence the Ru-NO ammine complexes?

Nitric oxide plays an important role in several physiological processes. This study investigates model ruthenium ammine coordination compounds to control NO bioavailability: cis-[RuCl(NO)(NH3)4]+ (1+), cis-[RuCl(NO)(NH3)4]2+ (12+), cis-[RuCl(NO)(NH3)4]3+ (13+), trans-[RuCl(NO)(NH3)4]+ (2+), trans-[RuCl(NO)(NH3)4]2+ (22+), trans-[RuCl(NO)(NH3)4]3+ (23+), [Ru(NO)(NH3)5]+ (3+), [Ru(NO)(NH3)5]2+ (32+), and [Ru(NO)(NH3)5]3+ (33+). We employed natural population analysis (NPA) atomic charges (qNPA) and the LUMO to identify the main reduction sites in the complexes 1, 2 and 3.

Nature of the Ru-NO Coordination Bond: Kohn-Sham Molecular Orbital and Energy Decomposition Analysis.

We have analyzed structure, stability, and Ru-NO bonding of the -[RuCl(NO)(NH)] complex by using relativistic density functional theory. First, we focus on the bond dissociation energies associated with the three canonical dissociation modes leading to [RuCl(NH)]+NO, [RuCl(NH)]+NO, and [RuCl(NH)]+NO. The main objective is to understand the Ru-NO bonding mechanism in the conceptual framework of Kohn-Sham molecular orbital theory in combination with a quantitative energy decomposition analysis.

Ozone and Other 1,3-Dipoles: Toward a Quantitative Measure of Diradical Character.

Ozone and its sulfur-substituted isomers are studied by means of the Breathing Orbital Valence Bond ab initio method, with the objective of estimating their controversial diradical characters. The calculated weights of the various VB structures and their individual diabatic energies are found to be consistent with each other. All 1,3-dipoles can be described in terms of three major VB structures, one diradical and two zwitterionic ones, out of the six structures, forming a complete basis.

Photophysical properties and the NO photorelease mechanism of a ruthenium nitrosyl model complex investigated using the CASSCF-in-DFT embedding approach.

A complete state-averaged active space self-consistent field (SA-CASSCF) calculation by means of the SA-CASSCF(18,14)-in-BP86 Miller-Manby embedding approach was performed to explore the ground and excited electronic states of the trans-[RuCl(NO)(NH)] complex. Insights into the NO photodissociation mechanism and Ru-NO bonding properties are provided. In addition, spin-orbit (SO) interactions were taken into account to describe and characterize the spin-forbidden transitions observed at the low-energy regions of the trans-[RuCl(NO)(NH)] UV-Vis spectrum.

How computational methods and relativistic effects influence the study of chemical reactions involving Ru-NO complexes?

Two treatments of relativistic effects, namely effective core potentials (ECP) and all-electron scalar relativistic effects (DKH2), are used to obtain geometries and chemical reaction energies for a series of ruthenium complexes in B3LYP/def2-TZVP calculations. Specifically, the reaction energies of reduction (A-F), isomerization (G-I), and Cl negative trans influence in relation to NH (J-L) are considered. The ECP and DKH2 approaches provided geometric parameters close to experimental data and the same ordering for energy changes of reactions A-L.

Computationally Designed 1,2,4-Triazolylidene-Derived N-Heterocyclic Olefins for CO Capture, Activation, and Storage.

In this article, triazolylidene-derived N-heterocyclic olefins (trNHOs) are designed using computational quantum tools, and their potential to promote CO sequestration is tested and discussed in detail. The low barrier heights related to the trNHO-mediated process indicate that the tailored compounds are very promising for fast CO sequestration. The systematic analysis of the presence of distinct substitutes at different N positions of the trNHO ring allows us to rationalize their effect on the carboxylation process and reveal the best N-substituted trNHO systems for CO sequestration and improved trNHO carboxylates for faster CO capture/release.

Computational study of the interaction between NO, NO, and NO with HO.

In this computational study the interaction of NO, NO, and NO with HO: [NO--HO], 1 , [NO--HO], 1 , and [NO--HO], 1 was analysed. The optimized geometries indicate that the relative position of NO and HO depends on the total charge: (ON--H-OH), (NO--H-OH), and (ON--OH). Moreover, atomic spin density along with frontier molecular orbitals help to identify the preferred reduction or oxidation sites on the nitric oxide.

Microhydration effects on geometric properties and electronic absorption spectra of ortho-aminobenzoic acid.

TD-DFT and a combination of polarized continuum model (PCM) and microhydration methods helped to simulate the optical electronic absorption spectrum of ortho-aminobenzoic acid (o-Abz). The microhydration method involved the use of different numbers, from 1 to 5, of first solvation layer water molecules. We examined how implicit and explicit water affected the energies of the HOMO-LUMO transition in the o-Abz/water systems.

Effects of the protonation state in the interaction of an HIV-1 reverse transcriptase (RT) amino acid, Lys101, and a non nucleoside RT inhibitor, GW420867X.

Interactions between an inhibitor and amino acids from a binding pocket could help not only to understand the nature of these interactions, but also to support the design of new inhibitors. In this paper, we explore the key interaction between a second generation non-nucleoside reverse transcriptase inhibitor (NNRTI), GW420867X, and HIV-1 RT amino acid Lys101 (K101), by quantum mechanical methods. The neutral, protonated, and zwitterionic complexes of GW420867X-K101 were studied.

Electronic structure and gas-phase chemistry of protonated α- and β-quinonoid compounds: a mass spectrometry and computational study.

Rationale: The use of quinonoid compounds against tropical diseases and as antitumor agents has prompted the search for new naturally occurring and synthetic derivatives. Among these quinonoid compounds, lapachol and its isomers (α- and β-lapachone) serve as models for the synthesis of new compounds with biological activity, and the use of electrospray ionization tandem mass spectrometry (ESI-MS/MS) analysis as a tool to elucidate and characterize these products has furnished important information about these compounds.

Methods: ESI-MS/MS analysis under collision-induced dissociation conditions was used to describe the fragmentation mechanisms for protonated 1,4-naphthoquinone, 1,2-naphthoquinone, α-lapachone, and β-lapachone.

Gas-phase reactivity of 2-hydroxy-1,4-naphthoquinones: a computational and mass spectrometry study of lapachol congeners.

In order to understand the influence of alkyl side chains on the gas-phase reactivity of 1,4-naphthoquinone derivatives, some 2-hydroxy-1,4-naphthoquinone derivatives have been prepared and studied by electrospray ionization tandem mass spectrometry in combination with computational quantum chemistry calculations. Protonation and deprotonation sites were suggested on the basis of gas-phase basicity, proton affinity, gas-phase acidity (ΔG(acid) ), atomic charges and frontier orbital analyses. The nature of the intramolecular interaction as well as of the hydrogen bond in the systems was investigated by the atoms-in-molecules theory and the natural bond orbital analysis.

Triboelectricity: macroscopic charge patterns formed by self-arraying ions on polymer surfaces.

Tribocharged polymers display macroscopically patterned positive and negative domains, verifying the fractal geometry of electrostatic mosaics previously detected by electric probe microscopy. Excess charge on contacting polyethylene (PE) and polytetrafluoroethylene (PTFE) follows the triboelectric series but with one caveat: net charge is the arithmetic sum of patterned positive and negative charges, as opposed to the usual assumption of uniform but opposite signal charging on each surface. Extraction with n-hexane preferentially removes positive charges from PTFE, while 1,1-difluoroethane and ethanol largely remove both positive and negative charges.

Application of the atoms in molecules theory and computational chemistry in mass spectrometry analysis of 1,4-naphthoquinone derivatives.

Mass spectrometry analysis of 2-(acylamino)-1,4-naphthoquinone derivatives was carried out using electrospray ionization ion source in combination with tandem mass spectrometry. Protonated molecules were dissociated by application of the collision-induced dissociation (CID), and the protonation sites were suggested on the basis of the HOMO, molecular electrostatic potential map (MEP), proton affinity, and Fukui functions calculated by B3LYP/6-31+G(d,p). The main fragmentation mechanisms undergone by the protonated ions were elucidated on the basis of energy, geometry, and topology analysis of equilibrium geometries.

Reactivity, photolability, and computational studies of the ruthenium nitrosyl complex with a substituted cyclam fac-[Ru(NO)Cl2(κ3N4,N8,N11(1-carboxypropyl)cyclam)]Cl·H2O.

Chemical reactivity, photolability, and computational studies of the ruthenium nitrosyl complex with a substituted cyclam, fac-[Ru(NO)Cl(2)(κ(3)N(4),N(8),N(11)(1-carboxypropyl)cyclam)]Cl·H(2)O ((1-carboxypropyl)cyclam = 3-(1,4,8,11-tetraazacyclotetradecan-1-yl)propionic acid)), (I) are described. Chloride ligands do not undergo aquation reactions (at 25 °C, pH 3). The rate of nitric oxide (NO) dissociation (k(obs-NO)) upon reduction of I is 2.

Generation of naphthoquinone radical anions by electrospray ionization: solution, gas-phase, and computational chemistry studies.

Radical anions are present in several chemical processes, and understanding the reactivity of these species may be described by their thermodynamic properties. Over the last years, the formation of radical ions in the gas phase has been an important issue concerning electrospray ionization mass spectrometry studies. In this work, we report on the generation of radical anions of quinonoid compounds (Q) by electrospray ionization mass spectrometry.

Fragmentation studies and electrospray ionization mass spectrometry of lapachol: protonated, deprotonated and cationized species.

Electrospray ionization mass spectrometric analysis of lapachol (2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinone) was accomplished in order to elucidate the gas-phase dissociation reactions of this important biologically active natural product. The occurrence of protonated and cationized species in the positive mode and of deprotonated species in the negative mode was explored by means of collision-induced dissociation (CID) experiments. For the protonated molecule, the H(2)O and C(4)H(8) losses occur by two competitive channels.

Gas-phase fragmentation of gamma-lactone derivatives by electrospray ionization tandem mass spectrometry.

Fragmentation reactions of beta-hydroxymethyl-, beta-acetoxymethyl- and beta-benzyloxymethyl-butenolides and the corresponding gamma-butyrolactones were investigated by electrospray ionization tandem mass spectrometry (ESI-MS/MS) using collision-induced dissociation (CID). This study revealed that loss of H(2)O [M+H-8](+) is the main fragmentation process for beta-hydroxymethylbutenolide (1) and beta-hydroxymethyl-gamma-butyrolactone (2). Loss of ketene ([M+H-42](+)) is the major fragmentation process for protonated beta-acetoxymethyl-gamma-butyrolactone (4), but not for beta-acetoxymethylbutenolide (3).

Gas-phase dissociation of 1,4-naphthoquinone derivative anions by electrospray ionization tandem mass spectrometry.

Gas-phase dissociation pathways of deprotonated 1,4-naphthoquinone (NQ) derivatives have been investigated by electrospray ionization tandem mass spectrometry (ESI-MS/MS). The major decomposition routes have been elucidated on the basis of quantum chemical calculations at the B3LYP/6-31 + G(d,p) level. Deprotonation sites have been indicated by analysis of natural charges and gas-phase acidity.

On an electrode modified by a supramolecular ruthenium mixed valence (Ru(II)/Ru(III)) diphosphine-porphyrin assembly.

Three novel polymetallic ruthenium (III) meso-tetra(4-pyridyl)porphyrins containing peripheral "RuCl(3)(dppb)" moieties have been prepared and characterized. The X-ray structure of the tetraruthenated {NiTPyP[RuCl(3)(dppb)](4)} porphyrin complex crystallizes in the triclinic space group P1. This structure is discussed and compared with the crystal data for the mer-[RuCl(3)(dppb)(py)].

Computational study of steric and spectroscopic characteristics of bi-chromophoric cyanine dyes: comparison with experimental data.

The spectral and energetic characteristics of four bi-chromophoric cyanine dyes (BCDs) which possess angles between chromophores 180 degrees , 150 degrees , 120 degrees and 90 degrees , were studied using quantum chemical calculations in comparison with experimental data. It was demonstrated that for BCD with 180 degrees , 150 degrees and 90 degrees trans-trans isomers possess the lowest energy, while for BCD with 120 degrees the trans-trans and cis-trans isomers have comparable energies and in the temperature range from 273K up to 373K both isomers of this dye are present. It was also demonstrated that the splitting of the spectra of cyanine dyes with two chromophores (BCD) was determined by two effects: the dipole-dipole chromophore interaction and the electron tunneling through the central heterocycle.