Abstract: Dye sensitized solar cells (DSSCs) are currently attracting widespread academic and commercial interest for the conversion of sunlight into electricity because of their low cost and high DSSCs are similar to natural photosynthesis in the initial processes involving in light-harvesting and charge separation. To gain a better understanding of the role of the sensitizer, particularly of its electronic structure and excited-state properties in the efficiency of dye-sensitized solar cell devices, we have carried out Density Functional Theory (DFT) and Time Dependent DFT (TDDFT) calculations in solution of the geometry, electronic structure and optical absorption spectra of a Chl a derivative (methyl 3-devinyl-3-carboxypyropheophorbide a; Phe a) and its Mg-Phe a and Zn-Phe a -derived sensitizers. Calculations have been performed using the B3LYP exchange correlations functional, as implemented in the Gaussian03 program package. The geometries of were first optimized in vacuum using density functional 6-311G(d) method. Solvation effects were included by means of the Conductor-like polarizable continuum model (C-PCM) in the dichloromethane solvent. There are good agreement between the experimental and the TDDFT calculated absorption spectra of three Different Chlorophyllous sensitizers. From the orbital analysis and the orbital spatial orientation of HOMO and LUMO for Phe a, Mg-Phe a and Zn-Phe a -derived sensitizers, the result shows that Phe a seems to provide higher photo-to-electric conversion efficiencies.

Abstract: We studied the description of charge-transfer excitations in [CuL₂]⁺ (L=6,6′-dimethyl-2,2′-bipyridine-4,4′-bis(propenoic acid)) dye sensitizer. This dye was studied using density functional theory (DFT), and the electronic absorption spectrum was investigated via time-dependent DFT (TD-DFT) with several hybrid functional, both in the gas phase and in acetonitrile solution. We also have investigated HOMO and LUMO levels in gas and solvent phases for these dyes. The HOMOLUMO transition describes all lowest singlet excited states. We performed TDDFT calculations at the B3LYP/6-31G(d) level of theory. Solvation effects were included by the conductor-like polarizable continuum model (CPCM ). The excitation in the range 500-800 nm of absorption spectra confirms metal-to-ligand charge-transfer (MLCT) transitions. The results of this work suggest that the copper complexes are effective as sensitizers for DSSCs and they can replace ruthenium (II) complexes.

Abstract: The electronic, structural and spectroscopic properties of the Coumarin NKX-2697 dye in gas and water solvent by the conductor-like polarizable continuum model (CPCM) to account for soulate-solvent interactions have been investigated by means of combined DFT/TD-DFT calculations. Using time dependent density functional theory (TD-DFT), we calculate excitation energies and oscillator strengths. The spectra in the range of 470-1100 nm were found to originate from transitions.We also have investigated HOMO and LUMO levels in gas and solvent phases for this dye. Inclusion of the solvent leads to important changes of the energies and composition of the molecular orbitals of the dye.

Abstract: Molecular geometries, electronic structures, and optical absorption spectra were investigated using density functional theory (DFT) at the HF/3-21G and B3LYP/3-21G levels for heteroleptic ruthenium dye, both in the gas phase and in water solution. The vertical excitation energies were calculated within the framework of the time-dependent DFT (TD-DFT) approach, whereas the solvent effects were taken into account using the conductor like polarizable continuum model (CPCM). Our results show that the three highest occupied molecular orbitals (HOMOs) are composed of Ru 4d orbitals. The spectra in the range of 350-600 nm were found to originate from metal-to-ligand charge-transfer (MLCT) transitions. The solvent effects lead to changes in both the geometries and the absorption spectra. The results of this work suggest that Ruthenium-based complexes might be effective sensitizers for next-generation dye-Sensitized Photoelectrochemical Cell.

Abstract: At the explanation of the spectra peculiarities of phenylsulfones by general formula C₆H₅SO₂R the arguments in favour of intramolecular effect of functional groups position in the fragment R through the spatial on the value of phenyl protons chemical shifts ð_i^Hhave been adduced.

Abstract: 2- and 3-nitrobenzofurans are studied in polar thermal Diels-Alder reactions whit normal electron demand using several and structural different dienes. A very strong electron-acceptor group, such as nitro group, push the dienophilic character of these heterocyclic compounds and owing to this substituent is easily extruded under thermal conditions make this reaction sequence a simple method of organic compound's families with heteroatom rings preparation. This work is specifically concerned with theoretical studies using DFT methods. 2-nitrobenzofuran and 3-nitrobenzofuran react as dienophile against isoprene, 1-trimethylsilyloxy-1,3-butadiene, the Danishesfky diene and the Rawal's diene, taking part in a normal demand DA cycloaddition reactions. These reactions could be considered a domino process that is initialized by a polar D-A reaction, and the latter concerted elimination of nitrous acid from the [4 + 2] cycloadduct yields the corresponding dibenzofurans.

Abstract: The process of anion transport trough a synthetic ion channel based in anion···π interactions is studied by means of computational methods. Employing two models for the units forming the channel, the calculations indicate that stable complexes are formed with any of bromide, chloride, fluoride or hydroxide anions. All these complexes exhibit strong interactions in the gas phase. When studied in water no favourable complexation was obtained for any of the anions studied, so anion···π interactions, though strong, are not capable of overcoming the cost of anion dehydration. However, it has been found that a process of hydroxide displacement by another anion is indeed favourable in water.

Abstract: The structural data and vibrational frequencies of 1- and 2-silaallenes have been studied computationally using the Gaussian 03 suite of programs. All of 15 normal modes were assigned to one of six types of motion (symmetrical stretching, antisymmetrical stretching, scissoring, rocking, wagging, twisting) determined by a group of quantum chemical analysis. Predicted geometric features, vibrational frequencies, and infrared intensities are also reported herein.

Abstract: The formation of complexes between alkaline cations and molecular bowls (MBs), curved conjugated systems related with fullerene (C 60 ), is studied using DFT calculations. The series of MBs is constructed starting with benzene and additional hexagonal or pentagonal rings are added symmetrically to complete the C 60 structure. All the MBs studied form stable cation–π complexes by both of its sides: concave and convex. In all cases complexes with the cation in the convex side are more stable than their corresponding partner inside the bowl. The stability of the complexes is determined by the polarizing power of the cation and by the molecular electrostatic potential and the polarizability of the bowl. Additionally, size effects are observed when bulky cations are placed in the concave side of the largest bowls.

Abstract: There are many of pathogen parasite species with different susceptibility profile to antiparasitic drugs. Unfortunately, almost QSAR models predict the biological activity of drugs against only one parasite species. Consequently, predicting the probability with which a drug is active against different species with a single unify model is a goal of the major importance. In so doing, we use Markov Chains theory to calculate new multi-target spectral moments to fit a QSAR model that predict by the first time a mt-QSAR model for 500 drugs tested in the literature against 16 parasite species and other 207 drugs no tested in the literature using spectral moments. The data was processed by Linear Discriminant Analysis (LDA) classifying drugs as active or non-active against the different tested parasite species. The model correctly classifies 311 out of 358 active compounds (86.9%) and 2328 out of 2577 non-active compounds (90.3%) in training series. Overall training performance was 89.9%. Validation of the model was carried out by means of external predicting series. In these series the model classified correctly 157 out 190, 82.6% of antiparasitic compounds and 1151 out of 1277 non-active compounds (90.1%). Overall predictability performance was 89.2%. In addition we developed four types of non Linear Artificial Neural Networks (ANN) and we compared with the mt-QSAR model. The improved ANN model had an overall training performance was 87%. The present work report the first attempts to calculate within a unify framework probabilities of antiparasitic action of drugs against different parasite species based on spectral moment analysis.

Abstract: A QSAR study has been performed on a series of substituted pyrido[3,2-b]pyrazinones as potent and selective PDE-5 Inhibitors. The compounds in the selected series were characterized by spatial, molecular and electrotopological descriptors using QSAR module of molecular design suite (V-Life MDS^TM 3.5). Correlations between inhibitory activities and calculated predictor variables were established through partial least square regression (stepwise forward) method. The generated QSAR models reveal that the topology of the molecules crucially influences the desired inhibitory activity of pyrido[3,2-b]pyrazinones. PDE-5 inhibition can be well defined by the models generated and the molecules are more selective towards PDE –5 while PDE –6 and PDE –11 inhibitory activities cannot be well delineated by the help of generated QSAR models. So PDE-5 selective compounds can be synthesized based on the assumption of the present QSAR analysis. The best model shows 90% correlation for PDE-5 inhibitory activity which explains good reliability of the model. However cross correlated regression coefficients (Q²) 0.5959 further validate the model significance. The present study imply that the PDE-5 inhibition can be augmented primarily by increasing molecular refractivity and number of carbons connected to the aromatic rings, single bonds and by decreasing number of carbons connected to the double bonds.

Abstract: Herein we present results of a Quantitative Structure-Activity Relationship (QSAR) studies to classify and design, in a rational way, new antitrypanosomal compounds by using non-stochastic and stochastic bond-based quadratic indices. A data set of 440 organic chemicals, 143 with antitrypanosomal activity and 297 having other clinical uses, is used to develop QSAR models based on Linear Discriminant Analysis (LDA). Non-stochastic model correctly classifies more than 93% and 95% of chemicals in both training and external prediction groups, respectively. On the other hand, the stochastic model shows an accuracy of about the 87% for both series. As an experiment of virtual lead generation, the present approach is finally satisfactorily applied to the virtual evaluation of 9 already synthesized in house compounds. The in vitro antitrypanosomal activity of this series against epimastigote forms of Trypanosoma cruzi is assayed. The model is able to predict correctly the behaviour for the majority of these compounds. Four compounds (FER16, FER32, FER33 and FER 132) showed more than 70% of epimastigote inhibition at a concentration of 100µg/mL (86.74%, 78.12%, 88.85% and 72.10%, respectively) and two of these chemicals, FER16 (78.22% of AE) and FER33 (81.31% of AE), also showed good activity at a concentration of 10µg/mL. At the same concentration, compound FER16 showed lower value of cytotoxicity (15.44%), and compound FER33 showed very low value of 1.37%. Taking into account all these results, we can say that these three compounds can be optimized in forthcoming works, but we consider that compound FER33 is the best candidate. Even though none of them resulted more active than Nifurtimox, the current results constitute a step forward in the search for efficient ways to discover new lead antitrypanosomals.

Abstract: DFT computations were carried out to characterize the ¹⁷Oand ²H electric field gradient, EFG, in various bisphosphonic acids derivatives. The computations were performed at the B3LYP level with 6-311++G (d, P) standard basis set. Calculated EFG tensors were used to determine the ¹⁷O and ²H nuclear quadrupole coupling constant, c and asymmetry parameter, η. The results showed that various substituents have a strong effect on the Nuclear Quadrupole Resonance (NQR) parameters (c, η) of ¹⁷O in contrast with ²H NQR parameters. The NQR parameters were studied in order to find the correlation between electronic structure and activity of structure. Investigations showed that substitutions on the carbon atom in P-C-P are important in bisphosphonates drug properties.

Abstract: A new proton transfer compound of 2, 9-dimethyl-1, 10-phenantroline and d-tartaric acid was synthesized and studied by using DFT and ab initio HF methods. The chemical formulas for the proton transfer ion pair is (dmpH) ₂⁺ (d-tartH) ₂^–.9H₂O, where dmp = 2, 9-dimethyl-1, 10-phenantroline and d-tartH₂ = d-tartaric acid. In this crystal structure, d-hydrogen tartrate anions are joined together in a head-to-tail fashion via short hydrogen. A number of intermolecular O–H···O, N-H···O and C–H···O hydrogen bonding interactions, as well as π–π stacking, play important roles in this crystal structure. The geometrical parameters of (dmpH)₂⁺(d-tartH)₂^– , 9H₂Oion pair have been optimazed with the B3LYP method of density functional theory (DFT) and ab initio Hartree-Fock (HF) methods for comparison. Theoretical calculations confirm a number of intermolecular O–H···O, N-H···O and C–H···O hydrogen bonding interactions, as well as π–π stacking, play important roles in this crystal structure.

Abstract: A systematic investigation of the Ge(CH₃)₂, CH₃GeSiH₃, CH₃GeGeH₃, XGeCY₃ (X; Y = H, F, Cl, Br) species was carried out using the DFT functionals BLYP, B3LYP and BHHLYP. Predicted are the singlet-triplet energy gaps and four types of neutral-anion separations: adiabatic electron affinity (EA_ad), zero-point vibrational energy corrected EA_ad(ZPVE), vertical electron affinity (EA_vert), and vertical detachment energy (VDE). The basis sets used for all atoms are of double-ζ plus polarization quality with additional s- and p-type diffuse functions denoted DZP++. The geometries are fully optimized with each functional independently. Vibrational frequency analyses are performed to compute zero-point energy corrections and to determine the nature of the stationary points. The EA_ad(ZPVE) values (eV) obtained with the BHLYP functional is Ge(CH₃)₂ = 0.46 eV, CH₃GeSiH₃ = 1.22 eV and CH₃GeGeH₃ = 1.26 eV, and FGeCCl₃ = 1.66 eV. The singlet-triplet splittings range from 1.28 eV (HGeCF₃) to 2.22 eV (FGeCCl₃). The XGeCY₃ (Y = Br) species are most often characterized by three-membered cyclic systems involving the divalent germanium atom, the carbon atom and a halogen atom. The predicted results are helpful for the synthesis, characterizations, and applications of these germylene derivatives.

Abstract: Isomerization reactions between nitroso oxide and nitrocompounds in both triplet and singlet states were studied with quantum chemistry methods. Calculated activation parameters for different paths of the isomerization reactions. It was shown that both in the singlet and triplet states the said reaction proceeds to the nitrocompound formation direction.

Abstract: The aromaticities of all possible dinitro, diamino substituted diaza derivatives of benzene; pyrazine, pyrimidine and pyridazine, have been investigated by computational calculations at the level of B3LYP/6-31G(d,p). The NICS (0), NICS (0.5), NICS (1.0) data have been reported herein. 2_5,6A_2,4N and 3_2,3A_5,6N are found to be the most aromatic structures among all. The results indicated that, the more closer the nitro groups to the aza points, the more aromatic the structure.

Abstract: The 1,3-dipolar cycloaddition (1,3-DC) and Diels-Alder (DA) reactions of substituted pyridinium-3-olates and pyrazinium-3-olates with methyl acrylate are studied using DFT method at the B3LYP/6-31G(d) level of theory. The molecular mechanism of the possible stereo- and regiochemical pathways is characterized both in the condensed and solvent phases. It is found that 1,3-DC is the favourable pathway for the reaction of pyridinium-3-olates with methyl acrylate and the thermodynamically more stable 6-substituted 8-azabicyclo[3.2.1]oct-3-en-2-ones are formed preferentially. This research is further extended to substituted pyrazinium-3-olates. Reactions of unsubstituted pyrazinium-3-olate and 1-methyl pyrazinium-3-olate with both ethene and methyl acrylate show a preference for the DA cycloaddition reaction. However, the addition of methyl acrylate to substituted pyrazinium-3-olates results in competitive mechanistic pathways and the preferred cycloaddition pathway is dependent on the location of the methyl group on the pyrazinium ring. The presence of a methyl substituent on C5 of the pyrazinium-3-olate favours the 1,3-DC over the DA reaction as the 2,6 positions are not sterically crowded. However, when methyl groups are present at the C2 and C6 positions, cycloaddition occurs via a Diels-Alder route which is free from encumbrance and hence bond formation at the C5 position is more enhanced.

Abstract: The polymer-bound phosphonium salts are known as disinfectants, being important for drugs with prolonged activity and less toxicity, antifouling coatings and fiber finishing, water and air disinfection. The toxicity (expressed as the logarithm of oral lethal dose for mouse) was related to the structural features of a series of organic phosphonium salts by MLR. The structure of these compounds was modeled by molecular mechanics calculations and descriptors were then derived from the minimized structures. The structural features thus derived important for compound toxicity were derived by MLR combined with genetic algorithm for variable selection. Phosphonium salts toxicity was influenced by their electron distribution and steric factors.