Nanoparticles: Taking a Unique Position in Medicine

The human nature of curiosity, wonder, and ingenuity date back to the age of humankind. In parallel with our history of civilization, interest in scientific approaches to unravel mechanisms underlying natural phenomena has been developing. Recent years have witnessed unprecedented growth in research in the area of pharmaceuticals and medicine. The optimism that nanotechnology (NT) applied to medicine and drugs is taking serious steps to bring about significant advances in diagnosing, treating, and preventing disease-a shift from fantasy to reality. The growing interest in the future medical applications of NT leads to the emergence of a new field for nanomaterials (NMs) and biomedicine. In recent years, NMs have emerged as essential game players in modern medicine, with clinical applications ranging from contrast agents in imaging to carriers for drug and gene delivery into tumors. Indeed, there are instances where nanoparticles (NPs) enable analyses and therapies that cannot be performed otherwise. However, NPs also bring unique environmental and societal challenges, particularly concerning toxicity. Thus, clinical applications of NPs should be revisited, and a deep understanding of the effects of NPs from the pathophysiologic basis of a disease may bring more sophisticated diagnostic opportunities and yield more effective therapies and preventive features. Correspondingly, this review highlights the significant contributions of NPs to modern medicine and drug delivery systems. This study also attempted to glimpse the future impact of NT in medicine and pharmaceuticals.

Protobranching as repulsion-induced attraction: a prototype for geminal stabilization

Noncovalent interactions are traditionally defined within the context of their attractive components, such as electrostatics and dispersion. Sources of molecular strain are derived through the destabilization of Coulombic and exchange repulsion. Due to this binary designation, the underlying origin of geminal stability with respect to alkanes (referred to as protobranching) has been an active subject for debate between these competing perspectives. We recast this stabilization as a complementary (Gestalt) interaction between dispersion and exchange repulsion, each impacting the other. We use triplet hydrogen and argon dimer as foundational van der Waals adducts to develop a procedure for the visualization and quantification of both exchange repulsion, Δρ_SCF, and medium-range correlation, ΔΔρ, as perturbations in electron density. We use the framework of the DFT-D3 correction to reproduce the shape of the dispersion potential at medium range and successfully model the trend in stability for the eighteen isomers of octane with a diverse series of functionals: BLYP, B3LYP, BP86, PBE, and PBE0. Collectively, our findings show that protobranching is a manifestation of steric repulsion-reduction in vibrational enthalpy and medium-range electron correlation.

London dispersion in molecular chemistry--reconsidering steric effects

London dispersion, which constitutes the attractive part of the famous van der Waals potential, has long been underappreciated in molecular chemistry as an important element of structural stability, and thus affects chemical reactivity and catalysis. This negligence is due to the common notion that dispersion is weak, which is only true for one pair of interacting atoms. For increasingly larger structures, the overall dispersion contribution grows rapidly and can amount to tens of kcal mol(-1) . This Review collects and emphasizes the importance of inter- and intramolecular dispersion for molecules consisting mostly of first row atoms. The synergy of experiment and theory has now reached a stage where dispersion effects can be examined in fine detail. This forces us to reconsider our perception of steric hindrance and stereoelectronic effects. The quantitation of dispersion energy donors will improve our ability to design sophisticated molecular structures and much better catalysts.

Nano-scale displacement sensing based on van der Waals interactions

We propose that a nano-scale displacement sensor with high resolution in weak-force systems can be realized based on vertically stacked two-dimensional (2D) atomic corrugated layer materials bound through van der Waals (vdW) interactions. Using first-principles calculations, we found that the electronic structures of bi-layer blue phosphorus (BLBP) vary appreciably with lateral and vertical interlayer displacements. The variation of the electronic structure is attributed to the change of the interlayer distance dz for both the lateral and vertical displacement. For lateral displacement, the change of dz is induced by atomic layer corrugation. Despite the different stacking configurations of BLBP, we find that the change of the indirect band gap is proportional to dz(-2). Furthermore, this dz(-2) dependence is found to be applicable to other graphene-like corrugated bi-layer materials such as MoS2. BLBP represents a large family of bi-layer 2D atomic corrugated materials for which the electronic structure is sensitive to the interlayer vertical and lateral displacement, and thus could be used for a nano-scale displacement sensor. This can be done by monitoring the tunable electronic structure using absorption spectroscopy. Because this type of sensor is established on atomic layers coupled through vdW interactions, it provides unique applications in the measurements of nano-scale displacement induced by tiny external forces.

Spatial assignment of symmetry adapted perturbation theory interaction energy components: The atomic SAPT partition

We develop a physically-motivated assignment of symmetry adapted perturbation theory for intermolecular interactions (SAPT) into atom-pairwise contributions (the A-SAPT partition). The basic precept of A-SAPT is that the many-body interaction energy components are computed normally under the formalism of SAPT, following which a spatially-localized two-body quasiparticle interaction is extracted from the many-body interaction terms. For electrostatics and induction source terms, the relevant quasiparticles are atoms, which are obtained in this work through the iterative stockholder analysis (ISA) procedure. For the exchange, induction response, and dispersion terms, the relevant quasiparticles are local occupied orbitals, which are obtained in this work through the Pipek-Mezey procedure. The local orbital atomic charges obtained from ISA additionally allow the terms involving local orbitals to be assigned in an atom-pairwise manner. Further summation over the atoms of one or the other monomer allows for a chemically intuitive visualization of the contribution of each atom and interaction component to the overall noncovalent interaction strength. Herein, we present the intuitive development and mathematical form for A-SAPT applied in the SAPT0 approximation (the A-SAPT0 partition). We also provide an efficient series of algorithms for the computation of the A-SAPT0 partition with essentially the same computational cost as the corresponding SAPT0 decomposition. We probe the sensitivity of the A-SAPT0 partition to the ISA grid and convergence parameter, orbital localization metric, and induction coupling treatment, and recommend a set of practical choices which closes the definition of the A-SAPT0 partition. We demonstrate the utility and computational tractability of the A-SAPT0 partition in the context of side-on cation-π interactions and the intercalation of DNA by proflavine. A-SAPT0 clearly shows the key processes in these complicated noncovalent interactions, in systems with up to 220 atoms and 2845 basis functions.

Folded conformations due to arene interactions in dissymmetric and symmetric butylidene-linker models based on pyrazolo[3,4-d]pyrimidine, purine and 7-deazapurine

The butylidene-linker models 1-[2-(2,6-dimethylsulfanyl-9H-purin-9-yl)-2-methylidenepropyl]-4,6-bis(methylsulfanyl)-1H-pyrazolo[3,4-d]pyrimidine, C18H20N8S4, (XI), 7,7'-(2-methylidenepropane-1,3-diyl)bis[3-methyl-2-methylsulfanyl-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one], C20H22N6O2S2, (XIV), and 7-[2-(4,6-dimethylsulfanyl-1H-pyrazolo[3,4-d]pyrimidin-1-yl)-2-methylidenepropyl]-3-methyl-2-methylsulfanyl-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one, C19H21N7OS3, (XV), show folded conformations in solution, as shown by (1)H NMR analysis. This folding carries over to the crystalline state. Intramolecular π-π interactions are observed in all three compounds, but only (XIV) shows additional intramolecular C-H···π interactions in the solid state. As far as can be established, this is the first report incorporating the pyrrolo[2,3-d]pyrimidine nucleus for such a study. In addition to the π-π interactions, the crystal structures are also stabilized by other weak intermolecular C-H···S/N/O and/or S···N/S interactions.

Spectroscopic probe on N-H⋯N, N-H⋯O and controversial C-H⋯O contact in A-T base pair: a DFT study

DNA base pair A-T has been investigated by IR and NMR spectroscopy using DFT methods. The results have been analyzed in terms of infrared vibrational frequencies and (1)H NMR chemical shifts. Different types of interactions N-H⋯N, N-H⋯O and C-H⋯O types have been investigated in DNA base pairs. Although, previous reports argued about the third C-H⋯O type interaction in A-T base pair, such typical interaction has been analyzed thoroughly by IR and NMR spectroscopy using DFT methods. Our results show that the CH⋯O interaction in the A-T base pair is a weak interaction compared to normal hydrogen bond interactions.

Structures and interligand interaction pattern of phosphoramidite Pd complexes by NMR spectroscopy: modulations in extended interaction surfaces as stereoselection mode of a privileged class of ligands

During the last decade, phosphoramidites have been established as a so-called privileged class of ligands in various transition metal catalyses. However, the interactions responsible for their favorable properties have hitherto remained elusive. To address this issue, the formation trends, structural features, and interligand interaction patterns of several trans- and cis-[PdLL'Cl2] complexes have been investigated by NMR spectroscopy. The energetic contribution of their interligand interactions has been measured experimentally using the supramolecular balance for transition-metal complexes. The resulting energetics combined with an analysis of the electrostatic potential surfaces reveal that in phosphoramidites not only the aryl groups but the complete (CH)CH3 Ph moieties of the amine side chains form extended quasi-planar CH-π and π-π interaction surfaces. Application of the supramolecular balance has shown that modulations in these extended interaction surfaces cause energetic differences that are relevant to enantioselective catalysis. In addition, the energetics of these interligand interactions are quite independent of the actual structures of the complexes. This is shown by similar formation and aggregation trends of complexes with the same ligand but different structures. The extended quasi-planar electrostatic interaction surface of the (CH)CH3 Ph moiety explains the known pattern of successful ligand modulation and the substrate specificity of phosphoramidites. Thus, we propose modulations in these extended CH-π and π-π interaction areas as a refined stereoselection mode for these ligands. Based on the example of phosphoramidites, this study reveals three general features potentially applicable to various ligands in asymmetric catalysis. First, specific combinations of alkyl and aryl moieties can be used to create extended anisotropic interaction areas. Second, modulations in these interaction surfaces cause energetic differences that are relevant to catalytic applications. Third, bulky substituents with matching complementary interaction surfaces should not only be considered in terms of steric hindrance but also in terms of attractive and repulsive interactions, a feature that may often be underestimated in asymmetric catalysis.

Pyrazolo[3,4-d]pyrimidines as inhibitor of anti-coagulation and inflammation activities of phospholipase A 2 : insight from molecular docking studies

Phospholipase A2 (PLA2), isolated from Daboia russelli pulchella (Russell's viper), is enzymatically active as well as induces several pharmacological disorders including neurotoxicity, myotoxicity, cardiotoxicity, anti-coagulant, hemolytic, and platelet effects. Indomethacin reduces the effects of anti-coagulant and pro-inflammatory actions of PLA2. Pyrazolo[3,4-d]pyrimidines constitute a class of naturally occurring fused uracils that posses diverse biological activities. The in-silico docking studies of nine pyrazolo[3,4-d]pyrimidine molecules have been carried out with the X-ray crystal structure of Russell's viper PLA2 (PDB ID: 3H1X) to predict the binding affinity, molecular recognition, and to explicate the binding modes, using AUTODOCK and GLIDE (Standard precision and Extra precision) modules, respectively. Docking results through each method make obvious that pyrazolo[3,4-d]pyrimidine molecules with trimethylene linker can bind with both anti-coagulation and enzymatic regions of PLA2.

On the Performance of Local Density Approximation in Describing the Adsorption of Electron Donating/Accepting Molecules on Graphene

In order to asses performance of the LDA in describing physisorption on graphene, adsorptions of TCNE, TCNQ, TNF, TTF, and DMPD as well as four benzene derivatives on C(54)H(18) and C(110)H(30) were explored with a variety of DFTs such as MPWB1K, M06-2X, PBE-D and LSDA. Although it is well known that the LDA considerably overestimate non-covalent interaction, the LSDA predicted adsorption energies except for TCNE on C(110)H(30) are systematically lower than those from the M06-2X by 0.4-3.2 kcal/mol, and they are more significantly lower than those from the PBE-D for all the molecules by 3-6 kcal/mol. However, the LSDA adsorption energy sequence is consistent with that from the PBE-D, TNF~TCNQ>TCNE~DMPD>TTF. Moreover, the domain interaction between the electron donor and acceptor molecules with graphene through cooperative π···π, C-H···π and N-H···π were visualized with sign(λ(2))×ρ, and the relationships between the binding energy with London force, molecular electronegativity, and frontier orbital level were extensively discussed.

Theoretical study of the structures and hydrogen-bond properties of new alternated heterocyclic compounds

The conformational preferences of a new bis-pyrrole derivative and its bis-pyridazine precursor have been investigated through quantum chemistry calculations (HF, DFT(MPWB1K), LMP2) and observations in the solid state. The global energetic minima are planar for both structures, with the conformational preferences being explained by pi-electronic conjugation between the aromatic systems and the occurrence of intramolecular hydrogen bonds (HB). For the bis-pyridazine derivative, the all-anti preferred conformation results from CH...Nsp(2) HB whereas the all-syn conformation of the bis-pyrrole is partly due to NH...Nsp(2) HB. For both systems, the validity of the theoretical conformational features is confirmed through the excellent agreement with the experimental data available. Calculations of electrostatic potential computed on the molecular surface of the various structures and their building blocks allow the variations to be rationalized in terms of molecular structure and are used to analyze the HB donor and acceptor sites of the compounds. The HB interaction sites predicted from the quantum chemical calculations are confirmed through the HB interactions observed in relevant crystal structures.

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

The method of dispersion correction as an add-on to standard Kohn-Sham density functional theory (DFT-D) has been refined regarding higher accuracy, broader range of applicability, and less empiricism. The main new ingredients are atom-pairwise specific dispersion coefficients and cutoff radii that are both computed from first principles. The coefficients for new eighth-order dispersion terms are computed using established recursion relations. System (geometry) dependent information is used for the first time in a DFT-D type approach by employing the new concept of fractional coordination numbers (CN). They are used to interpolate between dispersion coefficients of atoms in different chemical environments. The method only requires adjustment of two global parameters for each density functional, is asymptotically exact for a gas of weakly interacting neutral atoms, and easily allows the computation of atomic forces. Three-body nonadditivity terms are considered. The method has been assessed on standard benchmark sets for inter- and intramolecular noncovalent interactions with a particular emphasis on a consistent description of light and heavy element systems. The mean absolute deviations for the S22 benchmark set of noncovalent interactions for 11 standard density functionals decrease by 15%-40% compared to the previous (already accurate) DFT-D version. Spectacular improvements are found for a tripeptide-folding model and all tested metallic systems. The rectification of the long-range behavior and the use of more accurate C(6) coefficients also lead to a much better description of large (infinite) systems as shown for graphene sheets and the adsorption of benzene on an Ag(111) surface. For graphene it is found that the inclusion of three-body terms substantially (by about 10%) weakens the interlayer binding. We propose the revised DFT-D method as a general tool for the computation of the dispersion energy in molecules and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems.

Carboxylic acids: versatile building blocks and mediators for two-dimensional supramolecular self-assembly

Two-dimensional (2D) supramolecular self-assembly of various organic molecules at the liquid-solid interface is presented and discussed with a focus on compounds that are primarily functionalized by carboxylic groups. The main analytical tool utilized is scanning tunneling microscopy (STM), a high-resolution real-space technique capable of readily providing full crystallographic information (i.e., not only lattice parameters but also number, type, and orientation of molecules within the unit cell). Carboxylic groups are of particular interest because their combined donor and acceptor character with regard to hydrogen bonds provides reliable intermolecular cross-linking, thereby facilitating the self-assembly of well-ordered, stable monolayers. By means of various homomeric (monomolecular) and heteromeric (here, bimolecular) examples, this feature article illustrates the influence of both molecular structure and external conditions (type of solvent, concentration, etc.) on monolayer self-assembly at the liquid-solid interface. A very intriguing aspect of interfacial self-assembly is that many systems are thermodynamically controlled (i.e., adsorbed molecules at the surface are in equilibrium with molecules dissolved in the supernatant liquid phase). This offers the unique possibility not only to steer the system reliably by intensive thermodynamic parameters such as temperature and concentration but also to gain fundamental knowledge about decisive processes and steps in supramolecular self-assembly.

Scaled MP3 non-covalent interaction energies agree closely with accurate CCSD(T) benchmark data

Scaled MP3 interaction energies calculated as a sum of MP2/CBS (complete basis set limit) interaction energies and scaled third-order energy contributions obtained in small or medium size basis sets agree very closely with the estimated CCSD(T)/CBS interaction energies for the 22 H-bonded, dispersion-controlled and mixed non-covalent complexes from the S22 data set. Performance of this so-called MP2.5 (third-order scaling factor of 0.5) method has also been tested for 33 nucleic acid base pairs and two stacked conformers of porphine dimer. In all the test cases, performance of the MP2.5 method was shown to be superior to the scaled spin-component MP2 based methods, e.g. SCS-MP2, SCSN-MP2 and SCS(MI)-MP2. In particular, a very balanced treatment of hydrogen-bonded compared to stacked complexes is achieved with MP2.5. The main advantage of the approach is that it employs only a single empirical parameter and is thus biased by two rigorously defined, asymptotically correct ab-initio methods, MP2 and MP3. The method is proposed as an accurate but computationally feasible alternative to CCSD(T) for the computation of the properties of various kinds of non-covalently bound systems.