Quantum biochemical analysis of the TtgR regulator and effectors

The recent expansion of multidrug-resistant (MDR) pathogens poses significant challenges in treating healthcare-associated infections. Although antibacterial resistance occurs by numerous mechanisms, active efflux of the drugs is a critical concern. A single species of efflux pump can produce a simultaneous resistance to several drugs. One of the best-studied efflux pumps is the TtgABC: a tripartite resistance-nodulation-division (RND) efflux pump implicated in the intrinsic antibiotic resistance in Pseudomonas putida DOT-T1E. The expression of the TtgABC gene is down-regulated by the HTH-type transcriptional repressor TtgR. In this context, by employing quantum chemistry methods based on the Density Functional Theory (DFT) within the Molecular Fragmentation with Conjugate Caps (MFCC) approach, we investigate the coupling profiles of the transcriptional regulator TtgR in complex with quercetin (QUE), a natural polyphenolic flavonoid, tetracycline (TAC), and chloramphenicol (CLM), two broad-spectrum antimicrobial agents. Our quantum biochemical computational results show the: [i] convergence radius, [ii] total binding energy, [iii] relevance (energetically) of the ligands regions, and [iv] most relevant amino acids residues of the TtgR-QUE/TAC/CLM complexes, pointing out distinctions and similarities among them. These findings improve the understanding of the binding mechanism of effectors and facilitate the development of new chemicals targeting TtgR, helping in the battle against the rise of resistance to antimicrobial drugs. These advances are crucial in the ongoing fight against rising antimicrobial drug resistance, providing hope for a future where healthcare-associated infections can be more beneficially treated.

Lattice thermal conductivity of 2D nanomaterials: a simple semi-empirical approach

Extracting reliable information on certain physical properties of materials, such as thermal transport, can be computationally very demanding. Aiming to overcome such difficulties in the particular case of lattice thermal conductivity (LTC) of 2D nanomaterials, we propose a simple, fast, and accurate semi-empirical approach for LTC calculation. The approach is based on parameterized thermochemical equations and Arrhenius-like fitting procedures, thus avoiding molecular dynamics or ab initio protocols, which frequently require computationally expensive simulations. As a proof of concept, we obtain the LTC of some prototypical physical systems, such as graphene (and other 2D carbon allotropes), hexagonal boron nitride (hBN), silicene, germanene, binary, and ternary BNC lattices and two examples of the fullerene network family. Our obtained values are in good agreement with other theoretical and experimental estimations, nonetheless, being derived in a rather straightforward way, at a fraction of the usual computational cost.

On the mechanical properties and fracture patterns of the nonbenzenoid carbon allotrope (biphenylene network): a reactive molecular dynamics study

Recently, a new two-dimensional carbon allotrope named biphenylene network (BPN) was experimentally realized. The BPN structure consists of four-, six-, and eight-membered rings of sp²-hybridized carbon atoms. In this work, we carried out fully-atomistic reactive (ReaxFF) molecular dynamics simulations to study the mechanical properties and fracture patterns of non-defective and defective (nanocracks) BPN. Results show that, under uniaxial tensile loading, BPN is converted into four distinct morphologies before fracture starts. This conversion process is dependent on the stretching direction. Some of the formed structures contain mainly eight-membered rings, which have different shapes in each morphology. In one of them, a graphitization process occurs before the complete fracture. Importantly, in the presence of nanocracks, no new morphologies are formed. BPN exhibits a distinct fracture process when contrasted to graphene. After the critical strain threshold, the graphene transitions from an elastic to a brittle regime, while BPN can exhibit different inelastic stages. These stages are associated with the appearance of new morphologies. However, BPN shares some of the exceptional graphene properties. BPN Young's modulus and melting point are comparable to graphene, about 1019.4 GPa and 4024 K, respectively.

On the Mechanical Properties of Popgraphene-Based Nanotubes: a Reactive Molecular Dynamics Study

Carbon-based tubular materials have sparked a great interest in future electronics and optoelectronics device applications. In this work, we computationally studied the mechanical properties of nanotubes generated from popgraphene (PopNTs). Popgraphene is a 2D carbon allotrope composed of 5-8-5 rings. We carried out fully atomistic reactive (ReaxFF) molecular dynamics for PopNTs of different chiralities ( n , 0 and 0 , n ) and/or diameters and at different temperatures (from 300 up to 1200 K). Results showed that the tubes are thermally stable (at least up to 1200 K). All tubes presented stress/strain curves with a quasi-linear behavior followed by an abrupt drop of stress values. Interestingly, armchair-like PopNTs ( 0 , n ) can stand a higher strain load before fracturing when contrasted to the zigzag-like ones ( n , 0 ). Moreover, it was obtained that Young's modulus (Y_Mod ) (750-900 GPa) and ultimate strength (σ_US ) (120-150 GPa) values are similar to the ones reported for conventional armchair and zigzag carbon nanotubes. Y_Mod values obtained for PopNTs are not significantly temperature-dependent. While the σ_US values for the 0 , n showed a quasi-linear dependence with the temperature, the n , 0 exhibited no clear trends.

Virtually imprinted polymers (VIPs): understanding molecularly templated materialsviamolecular dynamics simulations

Theoretical model of molecularly imprinted polymers based on molecular dynamics simulations.

Efficient prediction of suitable functional monomers for molecular imprintingvialocal density of states calculations

Computational screening of suitable functional monomersvialocal density of states calculations.

Dynamics of the formation of carbon nanotube serpentines

Recently, Geblinger et al. [Nat. Nanotechnol. 3, 195 (2008)] reported the experimental realization of carbon nanotube S-like shaped nanostructures, the so-called carbon nanotube serpentines. We report here results from multimillion fully atomistic molecular dynamics simulations of their formation. We consider one-μm-long carbon nanotubes placed on stepped substrates with and without a catalyst nanoparticle on the top free end of the tube. A force is applied to the upper part of the tube during a short period of time and turned off; then the system is set free to evolve in time. Our results show that these conditions are sufficient to form robust serpentines and validates the general features of the "falling spaghetti model" proposed to explain their formation.

Graphene to fluorographene and fluorographane: a theoretical study

We report here a fully reactive molecular dynamics study on the structural and dynamical aspects of the fluorination of graphene membranes (fluorographene). Our results show that fluorination tends to produce defective areas on the graphene membranes with significant distortions of carbon-carbon bonds. Depending on the amount of incorporated fluorine atoms, large membrane holes were observed due to carbon atom losses. These results may explain the broad distribution of the structural lattice parameter values experimentally observed. We have also investigated the effects of mixing hydrogen and fluorine atoms on the graphene functionalization. Our results show that, when in small amounts, the presence of hydrogen atoms produces a significant decrease in the rate of fluorine incorporation onto the membrane. On the other hand, when fluorine is the minority element, it produces a significant catalytic effect on the rate of hydrogen incorporation. We have also observed the spontaneous formation of new hybrid structures with different stable configurations (chair-like, zigzag-like and boat-like) which we named fluorographane.

On the unzipping of multiwalled carbon nanotubes

Graphene nanoribbons (GNRs) are very interesting structures which can retain graphene's high carrier mobility while presenting a finite bandgap. These properties make GNRs very valuable materials for the building of nanodevices. Unzipping carbon nanotubes (CNTs) is considered one of the most promising approaches for GNR controlled and large-scale production, although some of the details of the CNT unzipping processes are not completely known. In this work we have investigated CNT unzipping processes through fully atomistic molecular dynamics simulations using reactive force fields (ReaxFF). Multiwalled CNTs of different dimensions and chiralities under induced mechanical stretching were considered. Our results show that fracture patterns and stress profiles are highly CNT chirality dependent. Our results also show that the 'crests' (partially unzipped CNT regions presenting high curvature), originating from defective CNT areas, can act as a guide for the unzipping processes, which can explain the almost perfectly linear cuts frequently observed in unzipped CNTs.

Electronic properties of Fibonacci and random Si-Ge chains

In this paper we address a theoretical calculation of the electronic spectra of an Si-Ge atomic chain that is arranged in a Fibonacci quasi-periodic sequence, by using a semi-empirical quantum method based on the Hückel extended model. We apply the Fibonacci substitutional sequences in the atomic building blocks A(Si) and B(Ge) through the inflation rule or a recursion relation. In our ab initio calculations we use only a single point, which is sufficient for considering all the orbitals and charge distribution across the entire system. Although the calculations presented here are more complete than the models adopted in the literature which take into account the electronic interaction only up to the second and third neighbors, an interesting property remains in their electronic spectra: the fractality (which is the main signature of this kind of system). We discuss this fractality of the spectra and we compare them with the random arrangement of the Si-Ge atomic chain, and with previous results based on the tight-binding approximation of the Schrödinger equation considering up to the nearest neighbor.

Ordered phases of encapsulated diamondoids into carbon nanotubes

Diamondoids are hydrogen-terminated nanosized diamond fragments that are present in petroleum crude oil at low concentrations. These fragments are found as oligomers of the smallest diamondoid, adamantane (C(10)H(16)). Due to their small size, diamondoids can be encapsulated into carbon nanotubes to form linear arrangements. We have investigated the encapsulation of diamondoids into single walled carbon nanotubes with diameters between 1.0 and 2.2 nm using fully atomistic simulations. We performed classical molecular dynamics and energy minimizations calculations to determine the most stable configurations. We observed molecular ordered phases (e.g. double, triple, 4- and 5-stranded helices) for the encapsulation of adamantane, diamantane, and dihydroxy diamantane. Our results also indicate that the functionalization of diamantane with hydroxyl groups can lead to an improvement on the molecular packing factor when compared to non-functionalized compounds. Comparisons to hard-sphere models revealed differences, especially when more asymmetrical diamondoids were considered. For larger diamondoids (i.e., adamantane tetramers), we have not observed long-range ordering but only a tendency to form incomplete helical structures. Our calculations predict that thermally stable (at least up to room temperature) complex ordered phases of diamondoids can be formed through encapsulation into carbon nanotubes.

Mechanical deformation of nanoscale metal rods: when size and shape matter

Face centered cubic metals deform mainly by propagating partial dislocations generating planar fault ribbons. How do metals deform if the size is smaller than the fault ribbons? We studied the elongation of Au and Pt nanorods by in situ electron microscopy and ab initio calculations. Planar fault activation barriers are so low that, for each temperature, a minimal rod size is required to become active for releasing elastic energy. Surface effects dominate deformation energetics; system size and shape determine the preferred fault gliding directions which induce different tensile and compressive behavior.

Adsorption configuration effects on the surface diffusion of large organic molecules: the case of Violet Lander

Violet Lander (C(108)H(104)) is a large organic molecule that when deposited on Cu(110) surface exhibits lock-and-key like behavior [Otero et al., Nature Mater. 3, 779 (2004)]. In this work, we report a detailed fully atomistic molecular mechanics and molecular dynamics study of this phenomenon. Our results show that it has its physical basis on the interplay of the molecular hydrogens and the Cu(110) atomic spacing, which is a direct consequence of the matching between molecule and surface dimensions. This information could be used to find new molecules capable of displaying lock-and-key behavior with new potential applications in nanotechnology.

Temperature effects on the atomic arrangement and conductance of atomic-size gold nanowires generated by mechanical stretching

We have studied the changes induced by thermal effects in the structural and transport response of Au nanowires generated by mechanical elongation. We have used time-resolved atomic resolution transmission electron microscopy imaging and quantum conductance measurement using a mechanically controllable break junction. Our results showed remarkable differences in the NW evolution for experiments realized at 150 and 300 K, which modifies drastically the conductance response during elongation. Molecular dynamics and electronic transport calculations were used to consistently correlate the observed structural and conductance behavior. These results emphasize that it is essential to take into account the precise atomic arrangement of nanocontacts generated by mechanical stretching to understand electrical transport properties. Also, our study shows that much care must be taken when comparing results obtained in different experimental conditions, mainly different temperatures.

Topologically closed macromolecules made of single walled carbon nanotubes-'super'-fullerenes

We propose and theoretically investigated a new class of topologically closed macromolecules built using single walled carbon nanotubes. These macromolecules are based on the fullerene architecture. Classical molecular dynamics simulations were used to predict their stability, thermal, vibrational, and mechanical properties. These macromolecules, named 'super'-fullerenes, present high porosity, low density (approximately 1 g/cm3), and high surface area (approximately equal 2500 m2/g). Our results predict gas phase specific heat of about 0.4 Jg(-1)K(-1) at room temperature and high flexibility under compressive strains. These properties make these hypothetical macromolecules good candidates for gas storage material and biomolecular sieves.

Curved graphene nanoribbons: structure and dynamics of carbon nanobelts

Carbon nanoribbons (CNRs) are graphene (planar) structures with a large aspect ratio. Carbon nanobelts (CNBs) are small graphene nanoribbons rolled up into spiral-like structures, i.e. carbon nanoscrolls (CNSs) with a large aspect ratio. In this work we investigated the energetics and dynamical aspects of CNBs formed from rolling up CNRs. We have carried out molecular dynamics simulations using reactive empirical bond-order potentials. Our results show that, similarly to CNSs, CNB formation is dominated by two major energy contributions, the increase in the elastic energy due to the bending of the initial planar configuration (decreasing structural stability) and the energetic gain due to van der Waals interactions of the overlapping surface of the rolled layers (increasing structural stability). Beyond a critical diameter value these scrolled structures can be even more stable (in terms of energy) than their equivalent planar configurations. In contrast to CNSs that require energy-assisted processes (sonication, chemical reactions, etc) to be formed, CNBs can be spontaneously formed from low temperature driven processes. Long CNBs (length of approximately 30.0 nm) tend to exhibit self-folded racket-like conformations with formation dynamics very similar to the one observed for long carbon nanotubes. Shorter CNBs will be more likely to form perfect scrolled structures. Possible synthetic routes to fabricate CNBs from graphene membranes are also addressed.

C60-derived nanobaskets: stability, vibrational signatures, and molecular trapping

C(60)-derived nanobaskets, with chemical formulae (symmetry point group) C(40)H(10) (C(5v)), C(39)H(12) (C(3v)), C(46)H(12) (C(2v)), were investigated. Molecular dynamic simulations (MDSs) indicate that the molecules preserve their bonding frame for temperatures up to 300 K (simulation time 100 ps), and maintain atomic cohesion for at least 4 ps at temperatures up to 3500 K. The infrared spectra of the C(60)-derived nanobaskets were simulated through density functional theory (DFT) calculations, allowing for the attribution of infrared signatures specific to each carbon nanobasket. The possibility of using C(60)-derived nanobaskets as molecular containers is demonstrated by performing a DFT study of their bonding to hydrogen, water, and L-alanine. The carbon nanostructures presented here show a higher bonding energy (approximately 1.0 eV), suggesting that a family of nanostructures, C(n)-derived (n = 60,70,76,80, etc) nanobaskets, could work as molecular containers, paving the way for future developments such as tunable traps for complex molecular systems.

Defects in graphene-based twisted nanoribbons: structural, electronic, and optical properties

We present some computational simulations of graphene-based nanoribbons with a number of half-twists varying from 0 to 4 and two types of defects obtained by removing a single carbon atom from two different sites. Optimized geometries are found by using a mix of classical quantum semiempirical computations. According with the simulations results, the local curvature of the nanoribbons increases at the defect sites, especially for a higher number of half-twists. The HOMO-LUMO energy gap of the nanostructures has significant variation when the number of half-twists increases for the defective nanoribbons. At the quantum semiempirical level, the first optically active transitions and oscillator strengths are calculated using the full configuration interaction (CI) framework, and the optical absorption in the UV/vis range (electronic transitions) and in the infrared (vibrational transitions) are achieved. Distinct nanoribbons show unique spectral signatures in the UV/vis range, with the first absorption peaks in wavelengths ranging from the orange to the violet. Strong absorption is observed in the ultraviolet region, although differences in their infrared spectra are hardly discernible.

Observation of the smallest metal nanotube with a square cross-section

Understanding the mechanical properties of nanoscale systems requires a range of measurement techniques and theoretical approaches to gather the relevant physical and chemical information. The arrangements of atoms in nanostructures and macroscopic matter can be different, principally due to the role of surface energy, but the interplay between atomic and electronic structure in association with applied mechanical stress can also lead to surprising differences. For example, metastable structures such as suspended chains of atoms and helical wires have been produced by stretching metal junctions. Here, we report the spontaneous formation of the smallest possible metal nanotube with a square cross-section during the elongation of silver nanocontacts. Ab initio calculations and molecular simulations indicate that the hollow wire forms because this configuration allows the surface energy to be minimized, and also generates a soft structure capable of absorbing a huge tensile deformation.

Carbon nanotubes as reinforcement elements of composite nanotools

Nanotechnology is stimulating the development of nanomanipulators, including tips to interact with individual nanosystems. Fabricating nanotips fulfilling the requirements of shape (size, aspect ratio), mechanical, magnetic, and electrical properties is a material science challenge. Here, we report the generation of reinforced carbon-carbon composite nanotools using a nanotube (CNTs) covered by an amorphous carbon matrix (shell); the CNT tip protruded and remained uncoated to preserve apex size. Unsuitable properties such as flexibility and vibration could be controlled without deteriorating the CNT size, strength, and resilience. Nanomanipulation experiments and molecular dynamics simulations have been used to study the mechanical response of these composite beams under bending efforts. AFM probes based on these C-C composite high aspect ratio tips generated excellent image resolution and showed no degradation after acquiring several hundred (400) images.

Entanglement and the nonlinear elastic behavior of forests of coiled carbon nanotubes

Helical or coiled nanostructures have been objects of intense experimental and theoretical studies due to their special electronic and mechanical properties. Recently, it was experimentally reported that the dynamical response of a foamlike forest of coiled carbon nanotubes under mechanical impact exhibits a nonlinear, non-Hertzian behavior, with no trace of plastic deformation. The physical origin of this unusual behavior is not yet fully understood. In this Letter, based on analytical models, we show that the entanglement among neighboring coils in the superior part of the forest surface must be taken into account for a full description of the strongly nonlinear behavior of the impact response of a drop ball onto a forest of coiled carbon nanotubes.

Size limit of defect formation in pyramidal Pt nanocontacts

We report high resolution transmission electron microscopy and ab initio calculation results for defect formation in sharp pyramidal Pt nanocontacts. Our results show that there is a size limit to the existence of twins (extended structural defects). These defects are always present but blocked away from the tip axes. They may act as scattering planes, influencing the electron conductance for Pt nanocontacts at room temperature and Ag/Au nanocontacts at low temperature (<150 K).

Molecular dynamics simulation of single wall carbon nanotubes polymerization under compression

Single wall carbon nanotubes (SWCNTs) often aggregate into bundles of hundreds of weakly interacting tubes. Their cross-polymerization opens new possibilities for the creation of new super-hard materials. New mechanical and electronic properties are expected from these condensed structures, as well as novel potential applications. Previous theoretical results presented geometric modifications involving changes in the radial section of the compressed tubes as the explanation to the experimental measurements of structural changes during tube compression. We report here results from molecular dynamics simulations of the SWCNTs polymerization for small diameter arm chair tubes under compression. Hydrostatic and piston-type compression of SWCNTs have been simulated for different temperatures and rates of compression. Our results indicate that large diameter tubes (10,10) are unlike to polymerize while small diameter ones (around 5 A) polymerize even at room temperature. Other interesting results are the observation of the appearance of spontaneous scroll-like structures and also the so-called tubulane motifs, which were predicted in the literature more than a decade ago.

Experimental realization of suspended atomic chains composed of different atomic species

Research into nanostructured materials frequently relates to pure substances. This contrasts with industrial applications, where chemical doping or alloying is often used to enhance the electrical or mechanical properties of materials. However, the controlled preparation of doped nanomaterials has been much more difficult than expected because the increased surface-area-to-volume ratio can, for instance, lead to the expulsion of impurities (self-purification). For nanostructured alloys, the influence of growth methods and the atomic structure on self-purification is still open to investigation. Here, we explore, experimentally and with molecular dynamics simulations, to what extent alloying persists in the limit that a binary metal is mechanically stretched to a linear chain of atoms. Our results reveal a gradual evolution of the arrangement of the different atomic elements in the narrowest region of the chain, where impurities may be expelled to the surface or enclosed during elongation.

Mechanical properties of amorphous nanosprings

Helical amorphous nanosprings have attracted particular interest due to their special mechanical properties. In this work we present a simple model, within the framework of the Kirchhoff rod model, for investigating the structural properties of nanosprings having asymmetric cross section. We have derived expressions that can be used to obtain the Young's modulus and Poisson's ratio of the nanospring material composite. We also address the importance of the presence of a catalyst in the growth process of amorphous nanosprings in terms of the stability of helical rods.

Indication of unusual pentagonal structures in atomic-size Cu nanowires

We present a study of the structural and quantum conductance properties of atomic-size copper nanowires generated by mechanical stretching. The atomistic evolution was derived from time-resolved electron microscopy observations and molecular dynamics simulations. We have analyzed the quantum transport behavior by means of conductance measurements and theoretical calculations. The results suggest the formation of an unusual and highly stable pentagonal Cu nanowire with a diameter of approximately 0.45 nm and approximately 4.5 conductance quanta.

Benzo[c]quinolizin-3-ones Theoretical Investigation: SAR Analysis and Application to Nontested Compounds

We investigate with the use of theoretical methodologies the activity of a set of 41 benzo[c]quinolizin-3-ones (BC3), some of them explored as selective inhibitors of the human 5alpha-reductase steroid. For the structure-activity study we have considered dividing the molecules into groups of tested and nontested compounds. Semiempirical calculations and pattern recognition methods such as Electronic Indices Methodology (EIM), Principal Components Analysis (PCA), Hierarchical Cluster Analysis (HCA), and K-Nearest Neighbors (KNN) have been applied to search for a correlation between experimental activity and theoretical descriptors. Our results show that it is possible to directly correlate some molecular quantum descriptors with BC3 biological activity. This information can be used in principle to identify active/inactive untested compounds and/or to design new active compounds.

Theoretical investigation of electromechanical effects for graphyne carbon nanotubes

We present a theoretical study of the electronic and mechanical properties of graphyne-based nanotubes (GNTs). These semiconducting nanotubes result from the elongation of one-third of the covalent interconnections of graphite-based nanotubes by the introduction of yne groups. The effect of charge injection on the dimensions of GNTs was investigated using tight-binding calculations. Low amounts of electron injection are predicted to cause qualitatively different responses for armchair and zigzag graphyne nanotubes. Although the behavior is qualitatively similar to the usual carbon nanotubes, the charge-induced strains are predicted to be smaller for the GNTs than for ordinary single walled carbon nanotubes.

A structure-activity study of taxol, taxotere, and derivatives using the electronic indices methodology (EIM)

Among the new families of effective anticancer drugs, the natural product paclitaxel (Taxol/Bristol-Myers-Squibb) and its semisynthetic derivative docetaxel (Taxotere/Rhone-Poulenc Rorer) are probably the most promising agents under investigation. Surprisingly considering their importance no detailed quantum mechanical studies have been carried out for these drugs. In this work we report the first structure--activity relationship (SAR) studies for 20 taxoid structures using molecular descriptors from all-electron quantum methods. The used methods were the pattern-recognition Principal Component Analysis (PCA), Hierarchical Clustering Analysis (HCA), and the recently developed Electronic Indices Methodology (EIM). The combined use of EIM with PCA/HCA methodologies was able to correctly classify active and inactive taxoids with 100% of accuracy using only a few "universal" quantum molecular descriptors. It was possible to identify the electronic features defining active molecules. This information can be used to select and design new active compounds. The combined use of EIM with PCA/HCA can be a new and very efficient tool in the field of computer assisted drug design.

Molecular-dynamics simulations of carbon nanotubes as gigahertz oscillators

Recently, Zheng and Jiang [Phys. Rev. Lett. 88, 045503 (2002)]] have proposed that multiwalled carbon nanotubes could be the basis for a new generation of nano-oscillators in the several gigahertz range. In this Letter, we present the first molecular dynamics simulation for these systems. Different nanotube types were considered in order to verify the reliability of such devices as gigahertz oscillators. Our results show that these nano-oscillators are dynamically stable when the radii difference values between inner and outer tubes are of approximately 3.4 A. Frequencies as large as 38 GHz were observed, and the calculated force values are in good agreement with recent experimental investigations.

Identifying relevant molecular descriptors related to carcinogenic activity of polycyclic aromatic hydrocarbons (PAHs) using pattern recognition methods

Polycyclic Aromatic Hydrocarbons (PAHs) constitute an important family of molecules capable of inducing chemical carcinogenesis. In this work we report structure-activity relationship (SAR) studies for 81 PAHs using the pattern-recognition methods Principal Component Analysis (PCA), Hierarchical Clustering Analysis (HCA) and Neural Networks (NN). The used molecular descriptors were obtained from the semiempirical Parametric Method 3 (PM3) calculations. We have developed a new procedure that is capable of identifying the PAHs' carcinogenic activity with an accuracy higher than 80%. PCA selected molecular descriptors that can be directly correlated with some models proposed to PAHs' metabolic activation mechanism leading to the formation of PAHs-DNA adducts. PCA, HCA and NN validate the energy separation between the highest occupied molecular orbital and its next lower level as a major descriptor defining the carcinogenic activity. This descriptor has been only recently discussed in the literature as one new possible universal parameter for defining the biological activity of several classes of compounds.

A semiempirical study on the electronic structure of 10-deacetylbaccatin-III

We performed a conformational and electronic analysis for 10-deacetylbaccatin-III (DBAC) using well-known semiempirical methods (parametric method 3 (PM3) and Zerner's intermediate neglect of differential overlap (ZINDO)) coupled to the concepts of total and local density of states (LDOS). Our results indicate that regions presented by paclitaxel (Taxol) as important for the biological activity can be traced out by the electronic features present in DBAC. These molecules differ only by a phenylisoserine side chain. Compared to paclitaxel, DBAC has a simpler structure in terms of molecular size and number of degrees of freedom (d.f.). This makes DBAC a good candidate for a preliminary investigation of the taxoid family. Our results question the importance of the oxetane group, which seems to be consistent with recent experimental data.

Structure--activity relationship studies of substituted 17alpha-acetoxyprogesterone hormones

Recently a new methodology, called electronic indices methodology (EIM), based on local density of state calculations (LDOS) using topological and semiempirical methods, was proposed to identify the biological activity of polycyclic aromatic hydrocarbons (PAHs). In this work we apply the concepts of the EIM approach to classify the progestational activity of 21 17alpha-acetoxyprogesterones (steroid hormones) (APs). The EIM approach pointed to a few descriptors, which correctly classify the active/inactive compounds of this class (approximately 90%). We show that these descriptors arise naturally from principal component analysis (PCA) and neural network (NN) calculations. Moreover, using only the parameters from EIM, instead of a large set of descriptors that have been used before to describe the biological activity of these hormones, we slightly improve and simplify PCA and NN results. Finally, the molecular region related to the chemical activity of these hormones naturally appears in our theoretical analysis, from the local density of states of the frontier orbitals. This shows the generality of the principles of EIM approach, and confirms that the combination of these distinct methodologies can be an efficient and powerful tool in the structure-activity studies of many different classes of compounds.

Structure-activity relationship studies of carcinogenic activity of polycyclic aromatic hydrocarbons using calculated molecular descriptors with principal component analysis and neural network methods

Recently a new methodology based on local density of state (LDOS) calculations using topological and semiempirical methods was proposed to identify the carcinogenic activity of polycyclic aromatic hydrocarbons (PAHs). In this work we perform a comparative study of this methodology with principal component analysis (PCA) and neural networks (NN). The PCA and NN results show that LDOS quantum chemical descriptors are relevant descriptors to identify the carcinogenic activity of methylated and non-methylated PAHs. Also, we show that the combination of these distinct methodologies can be an efficient and powerful tool in the structure-activity studies of PAHs compounds. We have studied 81 methylated and non-methylated PAHs, and our study shows that with the use of these methods it is possible to correctly predict the carcinogenic activity of PAHs with accuracy higher than 80%.