How well can density functional methods describe hydrogen bonds to pi acceptors?

1,2,4-Triazine-based Materials: Spectroscopic Investigation, DFT, NBO, and TD-DFT Calculations as Well As Dye-sensitized Solar Cells Applications

In this manuscript, we report four series for 1,2,4-triazine derivatives as dye-sensitized solar cells (DSSCs). Density functional theory (DFT) methods via utilizing Becke's three-parameter functional and LeeeYangeParr functional (B3LYP) level with 6-31G (d, p) basis set to investigate their modeling molecular structures. Optimized molecular structures for studied molecular structures are obtained using the DFT/B3LYP/6-31G (d, p) method. In addition, the time-dependant density functional theory (TD-DFT) is used to study the optoelectronic properties and absorption spectra using DFT/CAM-B3LYP/ 6-31G +  + (d, p) level in the Gaussian 09 program. The highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), energy gap (E_g), light harvest efficiency (LHE), and open-circuit voltage (Voc) of the studied molecular structures are calculated and illustrated. These properties indicate that these molecular modeling structures as good candidates for utilization in organic DSSCs.

Phenolic 3° Phosphine Oxides as a Class of Metal-Free Catalysts for the Activation of C–O Bonds in Aliphatic Alcohols: Direct Synthesis of Catalyst Candidates, and Kinetic Studies

It was recently reported that a (2-hydroxybenzyl)phosphine oxide (2-HOBPO) can serve as a phosphorus-centered catalyst for the stereo-invertive coupling of aliphatic alcohols and acidic pronucleophiles (akin to a Mitsunobu reaction, but without additional reagents). Herein, we report an improved synthesis, which provides direct access to systematically varied 2-HOBPOs in a single step from commercially available precursors (salicylaldehydes and secondary phosphines). The efficiency and generality of the synthetic method enabled limited structure–activity relationship (SAR) studies, from which it was determined that substituents on both the phenolic and phosphine oxide portions can exert significant influence on the turnover frequency (TOF) of each catalyst. Importantly, for all catalytically active 2-HOBPOs examined, the molecularity of catalyst in the rate law of the alcohol coupling was determined to be <1. Thus, for high catalyst loadings, differences in catalytic activity between 2-HOBPOs appear to be dominated by differences in catalytic auto-inhibition, while for low catalyst loadings, differences are attributed to inherent differences in the energetic span of the catalytic cycle, ignoring off-cycle species, in good agreement with density functional theory (DFT) modeling at the ωB97X-D/6-311G(d,p) level.

Isotope Effects on the Vaporization of Organic Compounds from an Aqueous Solution-Insight from Experiment and Computations

An isotope fractionation analysis of organic groundwater pollutants can assess the remediation at contaminated sites yet needs to consider physical processes as potentially confounding factors. This study explores the predictability of water–air partitioning isotope effects from experiments and computational predictions for benzene and trimethylamine (both H-bond acceptors) as well as chloroform (H-bond donor). A small, but significant, isotope fractionation of different direction and magnitude was measured with ε = −0.12‰ ± 0.07‰ (benzene), ε_C = 0.49‰ ± 0.23‰ (triethylamine), and ε_H = 1.79‰ ± 0.54‰ (chloroform) demonstrating that effects do not correlate with expected hydrogen-bond functionalities. Computations revealed that the overall isotope effect arises from contributions of different nature and extent: a weakening of intramolecular vibrations in the condensed phase plus additional vibrational modes from a complexation with surrounding water molecules. Subtle changes in benzene contrast with a stronger coupling between intra- and intermolecular modes in the chloroform–water system and a very local vibrational response with few atoms involved in a specific mode of triethylamine. An energy decomposition analysis revealed that each system was affected differently by electrostatics and dispersion, where dispersion was dominant for benzene and electrostatics dominated for chloroform and triethylamine. Interestingly, overall stabilization patterns in all studied systems originated from contributions of dispersion rather than other energy terms.

London Dispersion Helps Refine Steric A-Values: Dispersion Energy Donor Scales

We suggest a scale of dispersion energy donors (DEDs) that allows for direct comparisons with steric effects. This scale is based on the classic A-values and allows groups to reorient to minimize strain, thereby providing an advantage over raw group polarizabilities. The A-value can no longer be considered purely a steric factor. Even for groups that do not participate in charge transfer or electrostatic interactions, the A-value includes Pauli repulsion (steric hindrance) and attractive London dispersion (LD) interactions. Although the common assumption is that, at the distances found in monosubstituted cyclohexanes, steric demands are the key factors influencing conformer preferences, we show in this computational study that there is a non-negligible LD part. We use this system to build a DED scale and a complementary steric scale. These scales are quantitatively comparable, as they are based on the same system, and allow for comparison of the two competing interactions in experimentally relevant settings. In addition, we show that LD interactions can be used to explain puzzling data regarding relative group sizes.

London Dispersion Helps Refine Steric A-Values: The Halogens

Halogens are rarely considered as dispersion energy donors for organic reaction design. Here, we re-examine one of the textbook examples for assessing steric hindrance, the A-value, and demonstrate that even in this system, halogens cannot be treated solely as classic repulsive hard spheres. A significant part of the steric demand of the halogens is compensated by attractive London dispersion (LD) interactions, explaining the experimental lack of a clear trend when going down the halogens' row. Beyond monohalogenated cyclohexanes, dihalo- and perhalocyclohexanes also show significant LD interactions. We also explored several other small organic systems containing halogens. Our findings show that organic chemists should treat halogens as possible sources of LD interactions in reaction design, as these atoms can change the landscape of the potential energy surface and reverse trends of conformer stabilities and reaction selectivities.

Charge Transfer Complexes of Ketotifen with 2,3-Dichloro-5,6-dicyano-p-benzoquinone and 7,7,8,8-Tetracyanoquodimethane: Spectroscopic Characterization Studies

The reactions of ketotifen fumarate (KT) with 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ) and 7,7,8,8-tetracyanoquinodimethane (TCNQ) as π acceptors to form charge transfer (CT) complexes were evaluated in this study. Experimental and theoretical approaches, including density function theory (DFT), were used to obtain the comprehensive, reliable, and accurate structure elucidation of the developed CT complexes. The CT complexes (KT-DDQ and KT-TCNQ) were monitored at 485 and 843 nm, respectively, and the calibration curve ranged from 10 to 100 ppm for KT-DDQ and 2.5 to 40 ppm for KT-TCNQ. The spectrophotometric methods were validated for the determination of KT, and the stability of the CT complexes was assessed by studying the corresponding spectroscopic physical parameters. The molar ratio of KT:DDQ and KT:TCNQ was estimated at 1:1 using Job's method, which was compatible with the results obtained using the Benesi-Hildebrand equation. Using these complexes, the quantitative determination of KT in its dosage form was successful.

Novel complexes with ONNO tetradentate coumarin schiff-base donor ligands: x-ray structures, DFT calculations, molecular dynamics and potential anticarcinogenic activity

The synthesis of eight novel Zn(II), Co(II), Cu(II), Ni(II) and Pt(II) complexes (2-9) derived from the ONNO tetradentate coumarin Schiff-Base donor ligands, L₁ and the novel L₂, was performed. All compounds were characterized by analytical, spectrometry and spectroscopy techniques. Complexes 2-4 were also characterized by DFT calculations and the structures of 5 and 6 were determined by single-crystal X-ray diffraction analysis. A cytotoxicity study was carried out through an MTT assay in the carcinogenic cell line HeLa and the noncarcinogenic cell lines HFF-1 and HaCaT. The results indicated that among all the evaluated compounds, 2 and 6 presented the best anticarcinogenic potential against HeLa cells with an IC₅₀ of 3.5 and 4.1 µM, respectively. In addition, classical molecular dynamics simulations were performed on the synthesized coordination compounds bound to G4 DNA architectures in the scope of shedding light on their inhibition mode and the most conserved interactions that may lead to the biological activity of the compounds.

Permeation of second row neutral elements through Al12P12 and B12P12 nanocages; a first-principles study

Both exohedral and endohedral complexes of second row elements doped X₁₂Y₁₂ (X = B, Al and Y = P) nano-cages are evaluated for thermodynamic stabilities, electronic properties and kinetic barriers. Interaction energies are calculated to deeply perceive the stability of these complexes. Further, interconversion of exohedral and endohedral complexes is explored through an unprecedented approach, where 2nd row elements translate into nano-cages through boundary crossing. Subsequently, the kinetic barriers for encapsulation and decapsulation are also investigated through PES scanning of all elements by passing through hexagon of nano-cages. Systematic investigations revealed that due to larger diameter, AlP nanocage exhibits low encapsulation barriers in comparison to BP nano-cage. Such as; the encapsulation barrier of F@AlP (7.57 kcal mol^-1) is lower than that of F@BP (129.78 kcal mol^-1). Moreover, distortion of nano-cages due to translation of elements is also estimated by distortion energies. Large distortion energies of 113.81/118.39 kcal mol^-1 are noticed for exo-B@AlP/exo-C@BP complexes. In addition, the electronic properties for all the complexes are probed and depicted that the endohedral doping have remarkable influence on the electronic properties of the nanocage in comparison to exohedral doping. NBO charge analysis shows that Be metal delivers charges of 0.08 |e|/0.03 |e| to the AlP/BP nanocage, causing the later more electron rich. Contrary to Be, all other doped atoms show negative charges.

An intramolecular oxa-Michael reaction on α,β-unsaturated α-amino-δ-hydroxycarboxylic acid esters. Synthesis of functionalized 1,3-dioxanes

A highly diastereoselective intramolecular oxa-Michael reaction on α,β-unsaturated α-amino-δ-hydroxycarboxylic acid esters is presented; 1,3-dioxanes functionalized in positions 2,4 and 6 were obtained in good yields and with excellent selectivities; an experimental and computational study was carried out to understand the reaction course in terms of yields and selectivities. This reaction proceeds under mild reaction conditions using highly electrophilic aldehydes and ketones.

Growth, Hirshfeld surfaces, spectral, quantum chemical calculations, photoconductivity and chemical etching analyses of nonlinear optical p-toluidine p-toluenesulfonate single crystal

A single crystal of p-toluidine p-toluenesulfonate (PTPT) has been grown by slow evaporation solution technique (SEST) at room temperature. Single crystal X-ray analysis confirms that grown crystal belongs to the monoclinic structure with space group P2₁. Intermolecular interactions and fingerprint plots of PTPT molecules are executed by Hirshfeld surface analysis. It was found that H···H (44.2%) contacts have maximum intermolecular interactions contributions in the total Hirshfeld surface area. The characteristic absorption band occurs at below 290 nm. The functional groups were identified using FTIR and FT-Raman analyses and compared with theoretical values. The title molecule contains fourteen CH bonds and three OH bonds. The calculated HOMO and LUMO energy values are -6.125 eV and -1.157 eV, respectively. The chemical potential (μ) and electronegativity (χ) values are estimated to be -3.4938 eV and 3.4938 eV, respectively. The strongest negative hyperconjugation occurs due to the charge transfer from the occupied orbital (σ) to the unoccupied orbital (π*) which is calculated for the σ(N20-C21) → π*(N20-O18). The green and red lines in the total density of states (TDOS) spectrum indicate the occupied orbital and virtual orbital levels, respectively. Photoconductivity studies have been done for the grown crystal. It is observed that the dark current is greater than photocurrent. It shows negative photoconductivity nature of PTPT crystal. The etching analysis was executed on (001) plane of PTPT crystal. It has rectangular shape etch pits patterns.

Exploiting hydrogen bonding interactions to probe smaller linear and cyclic diamines binding to G-quadruplexes: a DFT and molecular dynamics study

This report reveals that hydrogen bonding interactions between the ligand and G-quadruplex can initiate an alternative binding motif to typical π-stacking interactions.

Looking for the interactions between omeprazole and amoxicillin in a disordered phase. An experimental and theoretical study

In this paper, co-grinding mixtures of omeprazole-amoxicillin trihydrate (CGM samples) and omeprazole-anhydrous amoxicillin (CGMa samples) at 3:7, 1:1 and 7:3 molar ratios, respectively, were studied with the aim of obtaining a co-amorphous system and determining the potential intermolecular interactions. These systems were fully characterized by differential scanning calorimetry (DSC), FT-infrared spectroscopy (FTIR), X-ray powder diffraction (PXRD), scanning electron microscopy (SEM) and solid state Nuclear Magnetic Resonance (ssNMR). The co-grinding process was not useful to get a co-amorphous system but it led to obtaining the 1:1 CGMa disordered phase. Moreover, in this system both FTIR and ssNMR analysis strongly suggest intermolecular interactions between the sulfoxide group of omeprazole and the primary amine of amoxicillin anhydrous. The solubility measurements were performed in simulated gastric fluid (SGF) to prove the effect of the co-grinding process. Complementarily, we carried out density functional theory calculations (DFT) followed by quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses in order to shed some light on the principles that guide the possible formation of heterodimers at the molecular level, which are supported by spectroscopic experimental findings.

Density Functionals for Noncovalent Interaction Energies of Biological Importance

Forty density functionals and one wavefunction method are assessed against a recently published database of accurate noncovalent interaction energies of biological importance. The comparison shows that two newly developed density functional theory (DFT) methods, PWB6K and M05-2X, give the best performance for this benchmark database of 22 noncovalent complexes, including both hydrogen-bonding and dispersion-dominated complexes. In contrast, the more popular B3LYP and PBEh functionals fail to describe the interactions in the dispersion-dominated complexes. The local spin density approximation and BHandH functionals give good performance for dispersion-dominated interactions at the expense of a large error for hydrogen bonding. PWB6K and M05-2X constitute a new generation of DFT methods based on simultaneously optimized exchange and correlation functionals that include kinetic energy density in both the exchange and correlation functional, and the present study confirms that they have greatly improved performance for noncovalent interactions as compared to previous DFT methods. We interpret this as being due to an improved treatment of medium-range correlation effects by the exchange-correlation functional. We recommend the PWB6K and M05-2X methods for investigating large biological systems and soft materials.

Water on BN doped benzene: a hard test for exchange-correlation functionals and the impact of exact exchange on weak binding

Density functional theory (DFT) studies of weakly interacting complexes have recently focused on the importance of van der Waals dispersion forces, whereas the role of exchange has received far less attention. Here, by exploiting the subtle binding between water and a boron and nitrogen doped benzene derivative (1,2-azaborine) we show how exact exchange can alter the binding conformation within a complex. Benchmark values have been calculated for three orientations of the water monomer on 1,2-azaborine from explicitly correlated quantum chemical methods, and we have also used diffusion quantum Monte Carlo. For a host of popular DFT exchange-correlation functionals we show that the lack of exact exchange leads to the wrong lowest energy orientation of water on 1,2-azaborine. As such, we suggest that a high proportion of exact exchange and the associated improvement in the electronic structure could be needed for the accurate prediction of physisorption sites on doped surfaces and in complex organic molecules. Meanwhile to predict correct absolute interaction energies an accurate description of exchange needs to be augmented by dispersion inclusive functionals, and certain non-local van der Waals functionals (optB88- and optB86b-vdW) perform very well for absolute interaction energies. Through a comparison with water on benzene and borazine (B3N3H6) we show that these results could have implications for the interaction of water with doped graphene surfaces, and suggest a possible way of tuning the interaction energy.

Distortion–interaction analysis along the reaction pathway to reveal the reactivity of the Alder-ene reaction of enes

The reactivity of uncatalyzed Alder-ene type reactions of hetero-substituted propylene is interpreted by distortion–interaction analysis of both the transition states and the complete reaction pathways.

An experimental and theoretical study on the regioselective synthesis of a new class of spiropyrrolothiazoles with quinoxaline motifs via a 1,3-dipolar cycloaddition reaction. An evaluation of DFT methods

Evaluation of B3LYP/6-31G(d,p), wB97xD/6-31G(d,p) and M06-2X/6-31G(d,p) methods revealed the importance of π/π interactions in regio- and stereoselectivity of cycloaddition reactions.

Experimental measurement and theory of substituent effects in π-hydrogen bonding: complexes of substituted phenols with benzene

IR spectroscopic experiments and theoretical DFT computations reveal the effects of aromatic substituents on π-hydrogen bonding between monosubstituted phenol derivatives and benzene. Simultaneous formation of two π-hydrogen bonds (red-shifting O-H···π and blue-shifting ortho-C-H···π) contribute to the stability of these complexes. The interaction of the acidic phenol O-H proton-donating group with the benzene π-system dominates the complex formation. The experimental shifts of O-H stretching frequencies for the different phenol complexes vary in the range 45-74 cm(-1). Strong effects on hydrogen-bonding energies and frequency shifts of electron-withdrawing aromatic substituents and very weak influence of electron-donating groups have been established. Experimental quantities and theoretical parameters are employed in rationalizing the properties of these complexes. The acidities of the proton-donating phenols describe quantitatively the hydrogen-bonding process. The results obtained provide clear evidence that, when the structural variations are in the proton-donating species, the substituent effects on π-hydrogen bonding follow classic mechanisms, comprising both resonance and direct through-space influences. The performance of three alternative DFT functionals (B3LYP, B97-D, and PBE0 combined with the 6-311++G(2df,2p) basis set) in predicting the O-H frequency shifts upon complexation is examined. For comparison, O-H frequency shifts for several complexes were also determined at MP2/6-31++G(d,p).

Intramolecular excimer formation in hexakis(pyrenyloxy)cyclotriphosphazene: photophysical properties, crystal structure, and theoretical investigation

A hexakis(pyrenyloxy)cyclotriphosphazene was synthesized by the reaction of N₃P₃Cl₆ with 2-hydroxypyrene, and its excimer emission has been investigated.