Structure and dynamics of mesogens using intermolecular potentials derived from ab initio calculations

A method for the calculation of the two-body intermolecular potential which can be applied to large molecules is presented. Each monomer is fragmented in a number of moieties whose interaction energies are used to recover the interaction energy of the whole dimer. For these reasons this strategy has been called fragmentation reconstruction method (FRM). By a judicious choice of the fragmentation scheme it is shown that very accurate interaction energies can be obtained. The sampling of the potential energy surface of a dimer is then used to obtain intermolecular force fields at several levels of complexity, suitable to be employed in bulk phase computer simulations. Applications are presented for benzene and for some mesogenic molecules which constitute the principal interest of the authors. A number of properties ranging from phase stability, thermodynamic quantities, orientational order parameter and collective dynamics properties are computed and discussed.     

Extrapolation of the linear and nonlinear polarizabilities from ab initio finite oligomer calculations

Different definitions of property per unit cell and different fitting functions are employed to obtain the asymptotic limit values per unit cell of the polarizability (α), the first (β), and the second (γ) hyperpolarizabilities of an infinite oligomer. A 1/n power series function is found to be suitable for the average value and logarithmic average value per unit cell definition, and an exponentially decreasing function is found to be suitable for the difference value per unit cell definition. These conclusions are derived based on an equation expressing the total energy per unit cell of a finite linear oligomer as a power series of 1/n, presented from a perturbation treatment. Several calculations of long chain systems have been carried out to reach our conclusions. An equation of p(n)/n = a + b/n + c/n² is strongly recommended for a least‐squares fitting of the properties per unit cell to achieve a stabilization behavior when the chain length is increased. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Ab initio computational study of positron emission tomography ligands interacting with lipid molecule for the prediction of nonspecific binding

Nonspecific binding is a poorly understood biological phenomenon of relevance in the study of small molecules interactions in vivo and in drug development. Nonspecific binding is thought to be correlated in part to a molecule's lipophilicity, typically estimated by measuring (or calculating) octanol-water partition coefficient. This is, however, a gross simplification of a complex phenomenon. In this article, we present a computational method whose aim is to help identify positron emission tomography (PET) ligands with low nonspecific binding characteristics by investigating the molecular basis of ligand-membrane interaction. We considered a set consisting of 10 well-studied central nervous system PET radiotracers acting on a variety of molecular targets. Quantum mechanical calculations were used to estimate the strength of the interaction between each drug molecule and one phospholipid molecule commonly present in mammalian membranes. The results indicate a correlation between the computed drug-lipid interaction energy and the in vivo nonspecific distribution volume relative to the free tracer plasma concentration, calculated using standard compartmental modeling for the analysis of PET data. Significantly, the drugs whose interaction with the lipid molecule more favorably possessed, in general, a higher nonspecific binding value, whereas for the drugs taken in consideration in this study, the water-octanol partition coefficient, log P, did not show good predictive power of the nonspecific binding. This study also illustrates how ab initio chemical methods may offer meaningful and unbiased insights for the understanding of the underlying chemical mechanisms in biological systems.     

Dissociation of sulfur oxoacids by two water molecules studied using ab initio and density functional theory calculations

Using ab initio [SCS‐MP2 and CCSD(T)] and density functional theory (M062X) calculations, we have studied the geometries and energies of sulfur oxoacids H₂S_mO₆ (m = 2–4) and their monohydrated and dihydrated clusters. When including the results from previously reported disulfuric acid (H₂S₂O₇) cases, the gas phase acidity is ordered as H₂S₂O₆ < H₂S₃O₆ < H₂S₂O₇ < H₂S₄O₆. The intramolecular H‐bonding, which may indicate the degree of structural flexibility in this molecular series, is an important factor for the order of the gas phase acidity. All these sulfur oxoacids show dissociated (or deprotonated) geometries with only two water molecules, although the energies of the dissociated conformers are ranked differently. All of the dissociated conformers form a unique H‐bonding network structure in which the protonated first water (H₃O⁺) is triply H‐bonded to each oxygen atom of two SO₃ moieties as well as the second water, which in turn is H‐bonded to a SO₃ moiety. H₂S₃O₆ has the best molecular flexibility for adopting such an H‐bonding network structure, and thereby all the low‐lying conformers of H₂S₃O₆(H₂O)₂ are dissociated. In contrast, the least flexible H₂S₂O₆ forms such a structure with a high strain, and dissociation of H₂S₂O₆(H₂O)₂ is found from the third lowest conformer. Although the gas phase acidity of H₂S₄O₆ is the highest in this series, the lowest dissociated conformer and the lowest undissociated conformer of H₂S₄O₆(H₂O)₂ are very close in energy. This is because forming the H‐bonding network structure is somewhat difficult due to the large distance between the two SO₃ moieties.     

WebMTA: a web-interface for ab initio geometry optimization of large molecules using molecular tailoring approach

A web-interface for geometry optimization of large molecules using a linear scaling method, i.e., cardinality guided molecular tailoring approach (CG-MTA), is presented. CG-MTA is a cut-and-stitch, fragmentation-based method developed in our laboratory, for linear scaling of conventional ab initio techniques. This interface provides limited access to CG-MTA-enabled GAMESS. It can be used to obtain fragmentation schemes for a given spatially extended molecule depending on the maximum allowed fragment size and minimum cut radius values provided by the user. Currently, we support submission of single point or geometry optimization jobs at Hartree-Fock and density functional theory levels of theory for systems containing between 80 to 200 first row atoms and comprising up to 1000 basis functions. The graphical user interface is built using HTML and Python at the back end. The back end farms out the jobs on an in-house Linux-based cluster running on Pentium-4 Class or higher machines using an @Home-based parallelization scheme (http://chem.unipune.ernet.in/ approximately tcg/mtaweb/).     

Complete basis set ab initio and hybrid density functional theory exploration of the potential energy surface in the reaction between an amino radical and nitrogen oxide

The potential energy surface for the reaction involving NH₂ plus NO was explored with a quadratic complete basis set ab initio approach and three hybrid density functional theory methods, the target being to accurately estimate activation barriers and the relative stability of the nitrogen–oxygen isomers. The computational results were compared with previously performed ab initio calculations and new, more accredited values for the NH₂NO rearrangement to HNNOH and for the HNNOH decomposition reaction were suggested. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66 : 409–414, 1998     

Ab initio calculations and Franck-Condon simulation of the absorption spectra of GeCl2 including anharmonicity.

Geometrical parameters, vibrational frequencies and relative electronic energies of the X1A1, ?3B1 and A1B1 states of GeCl2 have been calculated at the CCSD(T) and/or CASSCF/MRCI level with basis sets of up to aug-cc-pV5Z quality. Core electron correlation and relativistic contributions were also investigated. RCCSD(T)/ aug-cc-pVQZ potential energy functions (PEFs) of the X1A1 and ?3B, states, and a CASSCF/MRCl/aug-cc-pVQZ PEF of the A1B1 state of GeCl2 are reported. Anharmonic vibrational wavefunctions of these electronic states of GeCl2, obtained variationally using the computed PEFs, are employed to calculate the Franck-Condon factors (FCFs) of the ?-X and A-X transitions of GeCl2. Simulated absorption spectra of these transitions based on the computed FCFs are compared with the corresponding experimental laser-induced fluorescence (LIF) spectra of Karolczak et al. [J. Chem. Phys. 1993, 98, 60-70]. Excellent agreement is obtained between the simulated absorption spectrum and observed LIF spectrum of the ?-X transition of GeCl2, which confirms the molecular carrier, the electronic states involved and the vibrational assignments of the LIF spectrum. However, comparison between the simulated absorption spectrum and experimental LIF spectrum of the A-X transition of GeCl2 leads to a revision of vibrational assignments of the LIF spectrum and suggests that the X1A1 state of GeCl2 was prepared in the experimental work, with a non-Boltzmann vibrational population distribution. The X(0,0,1) level is populated over 4000 times more than expected from a Boltzmann distribution at 60 K, which is appropriate for the relative population of the other low-lying vibrational levels, such as the X(1,0,0) and X(0,1,0) levels.     

Electron delocalization and electrostatic repulsion at the origin of the strong spin coupling in mixed-valence keggin polyoxometalates: ab initio calculations of the one- and two-electron processes

We present here a general theoretical procedure to treat the problem of electron delocalization and magnetic interactions in high-nuclearity mixed valence clusters based on polyoxometalates. The main interactions between the delocalized electrons of mixed-valence polyoxometalate anions are extracted from valence spectroscopy ab initio calculations on embedded fragments. Electron transfer, magnetic coupling and exchange transfer parameters between nearest and next-nearest-neighbor metal ions, as well as the value of the electrostatic repulsion between pairs of metal ions are determined. These parameters are introduced in a model Hamiltonian that considers the whole anion. It thus provides macroscopic properties that should be compared with the experimental data. This method is applied to a two-electron-reduced polyoxowolframate Keggin anion. The results demonstrate that the electron transfer processes, combined with the Coulombic repulsion between the "extra" electrons, induce a strong antiferromagnetic coupling between the two delocalized spins providing a definite explanation of the diamagnetic properties of these high nuclearity mixed-valence clusters.     

Accurate prediction of heats of formation by a combined method of B3LYP and neural network correction

Recently, we proposed the X1 method which combines the B3LYP/6‐311+G(3df,2p)//B3LYP/6‐311+G(d,p) method with a neural network correction for an accurate yet efficient prediction of heats of formation (Wu and Xu, J Chem Phys 2007, 127, 214105). In this contribution, we discuss in detail how to set up the X1 neural network. We give examples, showing how to apply the X1 method and how the applicability of X1 can be extended. The overall mean absolute deviation of the X1 method from experiment for the 488 heats of formation is 1.52 kcal/mol compared with 9.44 kcal/mol for the original B3LYP results. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

FA(I):A(+) and FA(II):Cu(+) laser activity and photographic sensitization at the low coordinated surfaces of AgBr ab initio calculations

The twofold potentials of F(A)(I):Au(+) and F(A)(II)Cu(+) color centers at the low coordinated surfaces of AgBr thin films in providing tunable laser activity and photographic sensitization were investigated using ab initio methods of molecular electronic structure calculations. Clusters of variable size were embedded in simulated Coulomb fields that closely approximated the Madelung fields of the host surfaces, and the nearest neighbor ions to the F(A) defect site were allowed to relax to equilibrium in each case. Based on the calculated Stokes shifted optical transition bands and horizontal shifts along the configuration coordinate diagrams, both F(A)(I):Au(+) and F(A)(II):Cu(+) color centers were found to be laser active. The laser activity faded quickly as the bromide ion coordination decreased from 5 (flat) to 4 (edge) to 3 (corner) and as the size of the impurity cation increased from Cu(+) to Au(+). The latter relation was explainable in terms of the axial perturbation of the impurity cation. The smallest calculated Stokes-shift at the corner surface suggested that emission had the same oscillator strength as absorption. All relaxed excited states RESs of the defect containing surfaces were deep below the lower edges of the conduction bands of the defect free ground state surfaces, indicating that F(A)(I):Au(+) and F(A)(II):Cu(+) are suitable laser defects. The probability of orientational destruction of the two centers attributed to the assumed RES saddle point ion configurations along the <110> axis was found to be directly proportional to the size of the impurity cation, with activation energy barriers of about 0.655-3.294 eV for Cu(+), and about 1.887-3.404 eV for Au(+). The possibility of exciton (energy) transfer from the sites of higher coordination to those of lower coordination is demonstrated. The more laser active F(A)(II):Cu(+) center was more easily formed than the less laser active F(A)(I):Au(+) center. The Glasner-Tompkins empirical relation was generalized to include F(A) centers at the low coordinated surfaces of silver bromide thin film. As far as color photographic sensitization is concerned, the lowest unoccupied molecular orbitals of the selected dye molecules in the excited states were high enough for electron injection. F(A) defect formation and rotational diffusion of silver clusters reduced the energy gaps between the excited dye molecules and the lower edges of the conduction bands and allowed for hole injection. About 54-60% of the reduction of silver ions at the flat surface of AgBr was attributed to the host anions and F(A) defect formation, leaving about 40-46% for the reduction of photoelectrons as well as the electrons of the developer or dye molecules. The unrelaxed rotational diffusions of the central Ag(4) by 90 degrees decreased the latter percentage, but were severely hindered by activation energy barriers.     

Molecular structure of aniline in the gaseous phase: A concerted study by electron diffraction and ab initio molecular orbital calculations

The molecular structure of free aniline has been investigated by gas-phase electron diffraction and ab initio MO calculations at the HF and MP2 levels of theory, using the 6-31G^*(6D) basis set. Least-squares refinement of a model withC _s symmetry, with constraints from MP2 calculations, has led to an accurate determination of the C-C-C angle at theipso position of the benzene ring, =119.0±0.2 (where the uncertainty represents total error). This parameter provides information on the extent of the interaction between the nitrogen lone pair and the system of the benzene ring, and could not be determined accurately by microwave spectroscopy. The angles at theortho, meta, andpara positions of the ring are 120.3±0.1, 120.7±0.1, and 119.0±0.3, respectively. Important bond distances are r _g(C-C)=1.398±0.003 å andr _g(C-N) =1.407±0.003 å. The effective dihedral angle between the H-N-H plane and the ring plane, averaged over the large-amplitude inversion motion of the amino group, is ¦¦=44±4. The equilibrium dihedral angle is calculated to be 41.8 at the HF level and 43.6 at the MP2 level, in agreement with far-infrared spectroscopic information. The MO calculations predict that the differencer(C_ortho-C_meta) -r(C_ipso-C_ortho) is 0.008–0.009 å. They also indicate that the nitrogen atom is displaced from the ring plane, on the side opposite to the amino hydrogens. The displacement is 0.049 å at the HF level and 0.072 å at the MP2 level. The two calculations, however, yield very different patterns for the minute deviations from planarity of the ring carbons.     

A combined ab initio/Franck-Condon study of the A-X single-vibronic-level emission spectrum of CCl2 and the photodetachment spectrum of CCl2 -.

State-of-the-art ab initio calculations have been carried out on the X1A1, ?3B1 and A1B1 states of CCl2 and the X2B1 state of CCl2-. Franck-Condon factors including anharmonicity have been calculated, between the CCl2 states, and between the CCl2- X2B1 state and the CCl2 states. They are used to simulate the A-X single-vibronic-level (SVL) emission spectra of CCl2 determined by M.-L. Lui et al. [PCCP 2003, 5, 352] and the 364 nm laser photodetachment spectrum of CCl2- obtained by R. L. Schwartz et al. [J. Phys. Chem. A 1999, 103, 8213]. Comparison between simulated and observed spectra confirms the vibrational assignments of the X2B1 SVL emission spectra and the T0 position of the A1B1 state of CCl2. For the photodetachment spectrum of CCl2-, spectral simulation shows that the higher binding energy ?3B1(CCl2) <-- X2B1(CCl2-) band is well separated from the X1A1(CCl2) <-- X2B1(CCl2-) band. It is concluded that the observed second band, which overlaps heavily with the X1A1(CCl2) <-- X2B1(CCl2-) band in the photodetachment spectrum of CCl2- cannot be assigned to the CCl2(?3B1) + e --> CCl2-(X2B1) detachment process. Further ab initio calculations carried out in the present investigation support the suggestion that the second band in the 364 nm photodetachment spectrum of CCl2- is due to detachment from an excited state of CCl2-, a linear quartet state, to a triplet state of CCl2. These calculations identify the anionic state to be the lowest 4Sigmag- (4Sigma-) state, which photodetaches vertically to the 3Sigmag- (3Sigma-; adiabatically ?3B1) and/or 3Pi(u) (3Pi) states of CCl2 to give the second band observed in the 364 nm photodetachment spectrum of CCl2-.     

Vibrational spectroscopy investigation using ab initio and density functional theory analysis on the structure of 2-amino-4,6-dimethoxypyrimidine

The FTIR and FT-Raman spectra of 2-amino-4,6-dimethoxypyrimidine (2A46DMP) has been recorded in the region 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The optimized geometry, frequency and intensity of the vibrational bands of 2A46DMP were obtained by the ab initio and DFT levels of theory with complete relaxation in the potential energy surface using 6-31G(d,p) and 6-311G(d,p) basis sets. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed bar type spectrograms.     

Separation of organic acid compounds from biological samples by zinc oxide nanoparticles–chitosan using genetic algorithm based on response surface methodology and artificial neural network

In this study, zinc oxide nanoparticles–chitosan based on solid phase extraction and high performance liquid chromatography was developed for the separation of organic compounds including citric, tartaric and oxalic acids from biological samples. For simulation and optimization of this method, the hybrids of genetic algorithm with response surface methodology (RSM) and artificial neural network (ANN) have been used. The predictive capability and generalization of both predictive models (RSM and ANN) were compared by unseen data. The results have shown the superiority of ANN compared with RSM. At the optimum conditions, the limits of detections of 2.2–2.9 µg L⁻¹ were obtained for the analytes. The developed procedure was then applied to the extraction and determination of organic acid compounds from biological samples. Copyright © 2014 John Wiley & Sons, Ltd.