GPU Linear Algebra Libraries and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations

Unique magnetic and thermoelectric properties of chemically functionalized narrow carbon polymers

We analyze magnetic, transport and thermoelectric properties of narrow carbon polymers, which are chemically functionalized with nitroxide groups. Numerical calculations of the electronic band structure and the corresponding transmission function are based on density functional theory. Transport and thermoelectric parameters are calculated in the linear response regime, with particular interest in charge and spin thermopowers (charge and spin Seebeck effects). Such nanoribbons are shown to have thermoelectric properties described by large thermoelectric efficiency, which makes these materials promising from the application point of view.

Deeper insight into the properties of the newly synthesized macrocycles as drug receptors – some preliminary quantum chemical studies

We present the results of our experimental and theoretical studies on 1,10-N,N′-bis-(β-d-ureidocellobiosyl)-4,7,13-trioxa-1,10-diazacyclopentadecane, its complex with aspirin and the corresponding host–guest interactions.

Ethyl 2,2-dimethyl-4-oxo-6-phenyl-3,4-dihydro-2H-pyran-5-carboxylate

The title compound, C16H18O4, is a derivative of 3,4-dihydro-2H-pyran-4-one. The plane of the pyranone ring system forms a dihedral angle of 42.76 (10)° with that of the phenyl group. The crystal structure is stabilized by C—H...O interactions that enclose anR21(6) ring motif and link the molecules into chains along thecaxis. A short intramolecular O...O contact [2.942 (3) Å] gives rise to anS(5) motif.

Palladium-Mediated Catalysis Leads to Intramolecular Narcissistic Self-Sorting on a Cavitand Platform

Palladium-catalyzed aminocarbonylation reactions have been used to directly convert a tetraiodocavitand intermediate into the corresponding carboxamides and 2-ketocarboxamides. When complex mixtures of the amine reactants are employed in competition experiments using polar solvents, such as DMF, no "mixed" products possessing structurally different amide fragments are detected either by ¹H or ¹³C NMR. Only highly symmetrical cavitands are sorted out of a large number of potentially feasible products, which represents a rare example of intramolecular, narcissistic self-sorting. Our experimental results along with thermodynamic energy analysis suggest that the observed self-sorting is a symmetry-driven, kinetically controlled process.

Influence of Metal, Ligand and Solvent on Supramolecular Polymerizations with Transition-Metal Compounds: A Theoretical Study

The nature of intermolecular interactions governing supramolecular polymerizations is very important for controlling their cooperativity. In order to address this problem, supramolecular columns made of Pt^II and Pd^II complexes of oligo(phenylene ethynylene)-based pyridine (OPE) and tetrazolylpyridine ligands (TEP) were investigated through the dispersion-corrected PM6 method. Aromatic, CH-π, M-Cl and metallophilic interactions helped stabilize the supramolecules studied, and their geometries and associated cooperativities were in excellent agreement with experimental data. The OPE ligand and/or the presence of Pt^II led to stronger metallophilic interactions and also to cooperative supramolecular polymerizations, which clearly suggests that metallophilic interactions are a key factor for controlling cooperativity. The results indicate that sequential monomer addition is in general less spontaneous than the combination of two larger preformed stacks. The present theoretical investigations contribute to the further understanding of the relation between the thermodynamics of supramolecular polymerizations and the nature of different synthons.

Crystal and geometry-optimized structure, and Hirshfeld surface analysis of 1-(2-bromo-eth-yl)indoline-2,3-dione

In the title compound, C10H8BrNO2, the isatin (1H-indole-2,3-dione) moiety is nearly planar (r.m.s. deviation = 0.026 Å). In the crystal, mol-ecules are linked by C-H⋯O hydrogen bonds, forming layers parallel to the ab plane, and enclosing R44(24) loops. There are a low percentage (19.3%) of inter-molecular H⋯H contacts in the structure, as estimated by the analysis of Hirshfeld surfaces. This could be due to the presence of the Br atom, present in the bromo-ethyl-ene group, which makes ca 18.7% Br⋯H contacts.

Performance of heterogeneous computing with graphics processing unit and many integrated core for hartree potential calculations on a numerical grid

We investigated the performance of heterogeneous computing with graphics processing units (GPUs) and many integrated core (MIC) with 20 CPU cores (20×CPU). As a practical example toward large scale electronic structure calculations using grid-based methods, we evaluated the Hartree potentials of silver nanoparticles with various sizes (3.1, 3.7, 4.9, 6.1, and 6.9 nm) via a direct integral method supported by the sinc basis set. The so-called work stealing scheduler was used for efficient heterogeneous computing via the balanced dynamic distribution of workloads between all processors on a given architecture without any prior information on their individual performances. 20×CPU + 1GPU was up to ∼1.5 and ∼3.1 times faster than 1GPU and 20×CPU, respectively. 20×CPU + 2GPU was ∼4.3 times faster than 20×CPU. The performance enhancement by CPU + MIC was considerably lower than expected because of the large initialization overhead of MIC, although its theoretical performance is similar with that of CPU + GPU. © 2016 Wiley Periodicals, Inc.

The molecular shape and the field similarities as criteria to interpret SAR studies for fragment-based design of platinum(IV) anticancer agents. Correlation of physicochemical properties with cytotoxicity

Molecular shape similarity and field similarity have been used to interpret, in a qualitative way, the structure-activity relationships in a selected series of platinum(IV) complexes with anticancer activity. MM and QM calculations have been used to estimate the electron density, electrostatic potential maps, partial charges, dipolar moments and other parameters to correlate the stereo-electronic properties with the differential biological activity of complexes. Extended Electron Distribution (XED) field similarity has been also evaluated for the free 1,4-diamino carrier ligands, in a fragment-based drug design approach, comparing Connolly solvent excluded surface, hydrophobicity field surface, Van der Waals field surface, nucleophilicity field surface, electrophilicity field surface and the extended electron-distribution maxima field points. A consistency has been found when comparing the stereo-electronic properties of the studied series of platinum(IV) complexes and/or the free ligands evaluated and their in vitro anticancer activity.

Spectacular enhancement of thermoelectric phenomena in chemically synthesized graphene nanoribbons with substitution atoms

We analyze theoretically the transport and thermoelectric properties of graphene nanoribbons of a specific geometry, which have been synthesized recently from polymers [Cai, et al., Nature, 2011, 466, 470]. When such nanoribbons are modified at one of the two edges by Al or N substitutions, they acquire a ferromagnetic moment localized at the modified edge. We present numerical results on the electronic structure and thermoelectric properties (including also spin thermoelectricity) of the modified nanoribbons. The results show that such nanoribbons can display large thermoelectric efficiency in certain regions of chemical potential, where the corresponding electric and spin figures of merit achieve unusually large values. The enhancement of thermoelectric efficiency follows from a reduced phonon heat conductance of the nanoribbons and from their peculiar electronic band structure. Thus, such nanoribbons are promising for practical applications in nanoelectronic and spintronic devices.

Centrosymmetric resonance-assisted intermolecular hydrogen bonding chains in the enol form of β-diketone: Crystal structure and theoretical study

Isobenzofuran-1(3H)-ones (phtalides) are heterocycles that present a benzene ring fused to a γ-lactone functionality. This structural motif is found in several natural and synthetic compounds that present relevant biological activities. In the present investigation, the 3-(2-hydroxy-4,4-dimethyl-6-oxocyclohexen-1-yl)isobenzofuran-1(3H)-one was characterized by single-crystal X-ray analysis. In the crystal structure, there are two molecules per asymmetric unit. One of them exhibits resonance assisted hydrogen bonds (RAHBs). Semi-empirical and DFT calculations were performed to obtain electronic structure and π-delocalization parameters, in order to better understand the energy stabilization of RAHBs in the crystal packing of the studied molecule. The structural parameters showed good agreement between theoretical and experimental data. The theoretical investigation revealed that the RAHBs stabilization energy is directly related to the electronic delocalization of the enol form fragment. In addition, RAHBs significantly affected the HOMO and charge distribution around the conjugated system.

Recent Progress in Treating Protein-Ligand Interactions with Quantum-Mechanical Methods

We review the first successes and failures of a “new wave” of quantum chemistry-based approaches to the treatment of protein/ligand interactions. These approaches share the use of “enhanced”, dispersion (D), and/or hydrogen-bond (H) corrected density functional theory (DFT) or semi-empirical quantum mechanical (SQM) methods, in combination with ensemble weighting techniques of some form to capture entropic effects. Benchmark and model system calculations in comparison to high-level theoretical as well as experimental references have shown that both DFT-D (dispersion-corrected density functional theory) and SQM-DH (dispersion and hydrogen bond-corrected semi-empirical quantum mechanical) perform much more accurately than older DFT and SQM approaches and also standard docking methods. In addition, DFT-D might soon become and SQM-DH already is fast enough to compute a large number of binding modes of comparably large protein/ligand complexes, thus allowing for a more accurate assessment of entropic effects.

Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications

Semiempirical (SE) methods can be derived from either Hartree-Fock or density functional theory by applying systematic approximations, leading to efficient computational schemes that are several orders of magnitude faster than ab initio calculations. Such numerical efficiency, in combination with modern computational facilities and linear scaling algorithms, allows application of SE methods to very large molecular systems with extensive conformational sampling. To reliably model the structure, dynamics, and reactivity of biological and other soft matter systems, however, good accuracy for the description of noncovalent interactions is required. In this review, we analyze popular SE approaches in terms of their ability to model noncovalent interactions, especially in the context of describing biomolecules, water solution, and organic materials. We discuss the most significant errors and proposed correction schemes, and we review their performance using standard test sets of molecular systems for quantum chemical methods and several recent applications. The general goal is to highlight both the value and limitations of SE methods and stimulate further developments that allow them to effectively complement ab initio methods in the analysis of complex molecular systems.

Control over the Self-Assembly Modes of Pt(II) Complexes by Alkyl Chain Variation: From Slipped to Parallel π-Stacks

We report the self-assembly of a new family of hydrophobic, bis(pyridyl) Pt(II) complexes featuring an extended oligophenyleneethynylene-derived π-surface appended with six long (dodecyloxy (2)) or short (methoxy (3)) side groups. Complex 2, containing dodecyloxy chains, forms fibrous assemblies with a slipped arrangement of the monomer units (dPt⋅⋅⋅Pt ≈14 Å) in both nonpolar solvents and the solid state. Dispersion-corrected PM6 calculations suggest that this organization is driven by cooperative π-π, C-H⋅⋅⋅Cl and π-Pt interactions, which is supported by EXAFS and 2D NMR spectroscopic analysis. In contrast, nearly parallel π-stacks (dPt⋅⋅⋅Pt ≈4.4 Å) stabilized by multiple π-π and C-H⋅⋅⋅Cl contacts are obtained in the crystalline state for 3 lacking long side chains, as shown by X-ray analysis and PM6 calculations. Our results reveal not only the key role of alkyl chain length in controlling self-assembly modes but also show the relevance of Pt-bound chlorine ligands as new supramolecular synthons.

1-Benzyl-5-methylindoline-2,3-dione

The title compound, C16H13NO2, is an isatin (indole-2,3-dione) derivative. The isatin moiety is almost planar with an r.m.s. deviation of 0.022 Å, and its mean plane makes a dihedral angle of 74.19 (12)° with the benzyl ring. In the crystal, molecules are linked by C—H...O hydrogen bonds, formingC(6) chains propagating along thea-axis direction. The chains are linkedviaC—H...π interactions, forming slabs parallel to theabplane. Within the slabs there are weak π–π interactions present involving inversion-related isatin moieties.

Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Benchmarks for Ground-State Properties

The semiempirical orthogonalization-corrected OMx methods (OM1, OM2, and OM3) go beyond the standard MNDO model by including additional interactions in the electronic structure calculation. When augmented with empirical dispersion corrections, the resulting OMx-Dn approaches offer a fast and robust treatment of noncovalent interactions. Here we evaluate the performance of the OMx and OMx-Dn methods for a variety of ground-state properties using a large and diverse collection of benchmark sets from the literature, with a total of 13035 original and derived reference data. Extensive comparisons are made with the results from established semiempirical methods (MNDO, AM1, PM3, PM6, and PM7) that also use the NDDO (neglect of diatomic differential overlap) integral approximation. Statistical evaluations show that the OMx and OMx-Dn methods outperform the other methods for most of the benchmark sets.

Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Theory, Implementation, and Parameters

Semiempirical orthogonalization-corrected methods (OM1, OM2, and OM3) go beyond the standard MNDO model by explicitly including additional interactions into the Fock matrix in an approximate manner (Pauli repulsion, penetration effects, and core–valence interactions), which yields systematic improvements both for ground-state and excited-state properties. In this Article, we describe the underlying theoretical formalism of the OMx methods and their implementation in full detail, and we report all relevant OMx parameters for hydrogen, carbon, nitrogen, oxygen, and fluorine. For a standard set of mostly organic molecules commonly used in semiempirical method development, the OMx results are found to be superior to those from standard MNDO-type methods. Parametrized Grimme-type dispersion corrections can be added to OM2 and OM3 energies to provide a realistic treatment of noncovalent interaction energies, as demonstrated for the complexes in the S22 and S66×8 test sets.

Fluorescein Tri-Aldehyde Promotes the Selective Detection of Homocysteine

Elevated homocysteine levels are a well-known independent risk factor for cardiovascular disease. To date, relatively few selective fluorescent probes for homocysteine detection have been reported. The lack of sensing reagents and remaining challenges largely derive from issues of sensitivity and/or selectivity. For example, homocysteine is a structural homologue of the more abundant (ca, 20-25 fold) aminothiol cysteine, differing only by an additional methylene group side chain. Fluorescein tri-aldehyde, described herein, has been designed and synthesized as a sensitive and selective fluorophore for the detection of homocysteine in human plasma samples. It responds to analytes selectively via a photoinduced electron transfer (PET) inhibition process that is modulated by predictable analyte-dye product hybridization and ionization states. Mulliken population analysis of fluorescein tri-aldehyde and its reaction products reveals that the characteristic formation of multiple cationic of homocysteine-derived heterocycles leads to enhanced relative negative charge build up on the proximal phenolate oxygen of the fluorophore as a contributing factor to selective emission enhancement.

Heat of formation distributions of components involved in bi-component cocrystals and simple binary eutectic mixtures

The distributions of heat of formation characterizing a set of 3226 cocrystals.

BODIPY atropisomer interconversion, face discrimination, and superstructure appending

Atropisomerism and atropisomer interconversion in the BODIPY series are presented. It was used to synthesize a picket-fence-like BODIPY and to examine the BODIPY face discrimination. Pickets are aimed at preventing π-stacking of the BODIPY platform.

Optical anisotropy and sign reversal in layer-by-layer assembled films from chiral nanoparticles

Chiral anisotropy and related optical effects at the nanoscale represent some of the most dynamic areas of nanomaterials today. Translation of optical activity of chiral semiconductor and metallic nanoparticles (NPs) into optoelectronic devices requires preparation of thin films from chiral NPs on both flat and curved surfaces. In this paper we demonstrate that chiral NP films can be made via layer-by-layer assembly (LBL) using negatively charged chiral CdS NPs, stabilized by d- and l-cysteine and positively charged polyelectrolytes, as building blocks. LBL coatings from NPs combine simplicity of preparation and strong optical activity. Circular extinction measurements using circular dichroism instruments indicate that the film possess four chiroptical bands at 280, 320, 350, and 390 nm. The latter two bands at 390 and 350 nm are associated with the band gap transitions (chiral excitons), while the former two are attributed to transitions involving surface ligands. When NPs are assembled in LBL films, the rotatory activity and the sign for circular extinction associated with the electronic transition in the inorganic core of the NPs is conserved. However, this is not true for circular extinction bands at short wavelengths: the sign of the rotatory optical activity is reversed. This effect is attributed to the change of the conformation of surface ligands in the polyelectrolyte matrix, which was confirmed both by semi-empirical and density functional (DFT) quantum mechanical calculations. Circular dichroism spectra calculated using a DFT algorithm closely match the experimental spectra of CdS NPs. These findings indicate that the spectroscopic methods sensitive to chirality of the surface ligands can be used to investigate fine structural changes in the surface layer of nanocolloids. Strong rotatory optical activity of nanostructured semiconductor films opens the possibilities for new polarization-based optical devices.

Synthesis, antibacterial evaluation and QSAR analysis of Schiff base complexes derived from [2,2′-(ethylenedioxy)bis(ethylamine)] and aromatic aldehydes

A novel series of Schiff base complexes (1–34) were synthesized which exhibited good antibacterial activity and compound 30 was found to be the most potent antibacterial agent.

Adsorption of doxorubicin on citrate-capped gold nanoparticles: insights into engineering potent chemotherapeutic delivery systems

Gold nanomaterials have received great interest for their use in cancer theranostic applications over the past two decades. Many gold nanoparticle-based drug delivery system designs rely on adsorbed ligands such as DNA or cleavable linkers to load therapeutic cargo. The heightened research interest was recently demonstrated in the simple design of nanoparticle-drug conjugates wherein drug molecules are directly adsorbed onto the as-synthesized nanoparticle surface. The potent chemotherapeutic, doxorubicin often serves as a model drug for gold nanoparticle-based delivery platforms; however, the specific interaction facilitating adsorption in this system remains understudied. Here, for the first time, we propose empirical and theoretical evidence suggestive of the main adsorption process where (1) hydrophobic forces drive doxorubicin towards the gold nanoparticle surface before (2) cation-π interactions and gold-carbonyl coordination between the drug molecule and the cations on AuNP surface facilitate DOX adsorption. In addition, biologically relevant compounds, such as serum albumin and glutathione, were shown to enhance desorption of loaded drug molecules from AuNP at physiologically relevant concentrations, providing insight into the drug release and in vivo stability of such drug conjugates.

An investigation on the chemistry of the R2P = P ligand: reactions of a phosphanylphosphinidene complex of tungsten(VI) with electrophilic reagents

The nucleophilic properties of the title compound [(2,6-i-Pr2C6H3N)2(Cl)W(η(2)-t-Bu2P = P)]Li·3DME (1) were investigated in reactions with selected electrophilic reagents such as MeI, M(CO)5THF (M = Cr, Mo, W), AlCl3, and GaCl3. Methylation of 1 by MeI yields phosphanylphosphido complexes [(2,6-i-Pr2C6H3N)2W(X)(1,2-η-t-Bu2P = P-CH3)] (X = Cl, I) (2-Cl/2-I) with the formation of a new P-C bond. Moreover, 1 reacts with electrophilic compounds [(OC)5M·THF] (M = Cr, Mo, W) to yield a series of novel dinuclear phosphanylphosphinidene complexes [(2,6-i-Pr2C6H3N)2(Cl)W(1,2-η-t-Bu2P = P-M(CO)5)]Li·3DME (3, 4, 5) with very long P-M distances. Adducts [(2,6-i-Pr2C6H3N)2(Cl)W(1,2-η-t-Bu2P = P-MCl3)]Li·3DME (6, 7) formed by reaction of 1 with GaCl3 and AlCl3 are labile and dissociate into 1 and MCl3 (M = Ga, Al). The outcomes of reactions were monitored by (31)P-NMR spectroscopy. Furthermore, the structures of the isolated complexes 2-Cl/2-I, 3, 4, and [(2,6-i-Pr2C6H3N)2(Cl)W(1,2-η-t-Bu2P = P-W(t-Bu2PH)(CO)3COLi·2DME] (5-P) were confirmed unambiguously by X-ray diffraction studies.