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In this paper we report on our first experience with a portable, easily usable communication environment, 'Sciddle', for distributing computations over a homogeneous network of UNIX computers. We demonstrate the usefulness of the system with applications from linear algebra and quantum chemistry on a network of Ethernet-connected Sun workstations and of Internet-connected Cray supercomputers, respectively.

Profiling tools such as gprof and ssrun are used to analyze the run-time performance of a scientific application. The profiling is done in serial and in parallel mode using MPI as the communication interface. The application is a quantum chemistry program using Hartree Fock theory and Pulays DIIS method. An extensive set of test cases is taken into account in order to reach uniform conclusions. A known problem with decreased parallel scalability can thus be narrowed down to a single subroutine responsible for the reduction in Speed Up. The critical module is analyzed and a typical pitfall with triple matrix multiplications is identified. After overhauling the critical subroutine re-examination of the run-time behavior shows significantly improved performance and markedly improved parallel scalability. The lessons learned here might be of interest to other people working in similar fields with similar problems.

Electron spectra of DNA model compounds, adenosine-thymidine and guanosine-cytidine nucleoside base pairs, as well as the relevant homogeneous stacked base pair steps in A-DNA and B-DNA conformations, were investigated using ZINDO semiempirical quantum-chemical method. This work confirms that, in DNA with intact Watson–Crick hydrogen bonding and base stacking, the highest occupied molecular orbitals (HOMO) are residing on purine base residues, whereas the lowest unoccupied molecular orbitals (LUMO) — on pyrimidine base residues. In general, the present results are satisfactorily comparable with the available experimental data. The role of charge transfer excitations in the polymer DNA 260 nm spectral band is discussed.

Applying the elastic scattering Green's function theory in combination with the frontier molecular orbital theory for describing the surface-molecule coupling and hybrid density-function theory for geometrical and electronic structure calculations, we successfully reproduce the current–voltage properties of the 4,4-biphenyldithiol molecular junction, which has been measured using a lock-in technique by Lee et al.¹ We also analyze the conductance characteristics of different dimensional electrodes in contact with the molecular device, and we think that the one-dimensional formula is consistent with the experiment, and that the interaction between neighboring molecules will decrease the molecular orbital energies and draw the conductance peak positions closer to experimental results.

The Diffusion Monte Carlo (DMC) method is a powerful strategy to estimate the ground state energy E₀ of an N-body Schrödinger Hamiltonian H = -½Δ + V with high accuracy. It consists of writing E₀ as the long-time limit of an expectation value of a drift-diffusion process with a source term, and numerically simulating this process by means of a collection of random walkers. As for a number of stochastic methods, a DMC calculation makes use of an importance sampling function ψ_I which hopefully approximates some ground state ψ₀ of H. In the fermionic case, it has been observed that the DMC method is biased, except in the special case when the nodal surfaces of ψ_I coincide with those of a ground state of H. The approximation due to the fact that, in practice, the nodal surfaces of ψ_I differ from those of the ground states of H, is referred to as the Fixed Node Approximation (FNA). Our purpose in this paper is to provide a mathematical analysis of the FNA. We prove that, under convenient hypotheses, a DMC calculation performed with the importance sampling function ψ_I, provides an estimation of the infimum of the energy 〈ψ, Hψ〉 on the set of the fermionic test functions ψ that exactly vanish on the nodal surfaces of ψ_I.

The molecular ordering of a thermotropic mesogen, 4-alkenyl bicyclohexylnitrile (ALKBCHN), has been carried out on the basis of quantum mechanics and intermolecular forces. The evaluation of atomic charges and dipole moment at each atomic centre has been done through the Complete Neglect Differential Overlap (CNDO/2) method. The configurational energy has been computed using the Rayleigh-Schrodinger perturbation method. The total interaction energy values obtained through these computations were used to calculate the probability of each configuration in a dielectric medium (i.e. non-interacting and non-mesogenic solvent, benzene) at phase transition temperature (364.7 K) using the Maxwell–Boltzmann formula. It has been observed that in dielectric medium the energies/probabilities are redistributed and there is a considerable rise in the probability of interactions, although the order of preference remains the same. An attempt has been made to develop a new and interesting model of mesogen in a dielectric medium. The present article offers a theoretical support to the experimental observations.

A Comparative computational analysis of ordering in higher homologous series of p-n-alkylbenzoic acids (nBAC), having 7(7BAC); 8(8BAC) and 9(9BAC) carbon atoms in the alkyl chain, has been carried out based on quantum mechanics and intermolecular forces. The evaluation of atomic charge and dipole moment at each atomic centre has been carried out through an all-valence electron (CNDO/2) method. The modified Rayleigh-Schrodinger perturbation theory, along with multicentered-multipole expansion method, has been employed to evaluate long-range intermolecular interactions, while a "6-exp" potential function has been assumed for short-range interactions. The total interaction energy values obtained through these computations were used to calculate the probability of each configuration at room temperature, nematic-isotropic transition temperature and above transition temperature using the Maxwell-Boltzmann formula. A comparative picture of molecular parameters such as total energy, binding energy and total dipole moment has been given. A model has been developed to describe the nematogenicity of these acids in terms of their relative order with molecular parameter introduced in this paper.

The internal rotations of nitrotyl around the bond C–C in Z- and E-benzaldoximes and their various substituted species have been investigated theoretically by the method of density functional theory (DFT) at the B3LYP/6-31G* level. The corresponding rotation transition states have been optimized. The potential barriers and the rates of the internal rotations of various species have been calculated. The rotation barrier of Z-benzaldoxime is lower than that of E-isomer. The para-substitution has only a small influence on the rotation barriers. The conjugations are consolidated in the acidic and basic species of both Z- and E-isomers. The experimental NMR spectrums of Z- and E-benzaldoxime are explained based on the calculation results.

The accurate prediction of the strength of protein–ligand interactions is a very difficult problem despite impressive advances in the field of biomolecular modeling. There are good reasons to believe that quantum mechanical methods can help with this task, but the application of such methods in the context of scoring is still in its infancy. Here we benchmark several wave function theory (WFT), density functional theory (DFT) and semiempirical quantum mechanical (SQM) approaches against high-level theoretical references for realistic test cases. Based on our findings for systematically generated model systems of real protein/ligand complexes from the PDB-bind database, we can recommend SCS-MP2 and B2-PLYP-D3 as reference methods, TPSS-D3+D_abc/def-TZVPP as the best DFT approach and PM6-DH+ as a fast and accurate alternative to full ab initio treatments.

The detailed mechanism of NO oxidation catalyzed by ZSM5 supported Mn/Co–Al/Ce is investigated and revealed by Quantum Chemistry Calculation. A three-step catalytic mechanism for NO oxidation is proposed and studied. Theoretical results show that, the activate energies of reactions catalyzed by ZSM-5 supported Mn/Co (71.1kJ/mol/80.6kJ/mol) are much lower than that obtained from the direct NO oxidation. This indicates that the ZSM-5 supported Mn/Co has an obvious catalytic effect. When the active center Si is replaced by Al and Ce, the activation energies are further decreased to about 40kJ/mol. This indicates that the doping of Al and Ce can obviously improve the catalytic effect. The theoretical study illustrates that the catalysts for NO oxidation not only relate to the supported transition metal such as Co and Mn, but also highly relate to the activity centers such as Al and Ce.

Since there is no exact solution for problems in physics and chemistry, extrapolation methods may assume a key role in quantitative quantum chemistry. Two topics where it bears considerable impact are addressed, both at the heart of computational quantum chemistry: electronic structure and reaction dynamics. In the first, the problem of extrapolating the energy obtained by solving the electronic Schrödinger equation to the limit of the complete one-electron basis set is addressed. With the uniform-singlet-and-triplet-extrapolation (USTE) scheme at the focal point, the emphasis is on recent updates covering from the energy itself to other molecular properties. The second topic refers to extrapolation of quantum mechanical reactive scattering probabilities from zero total angular momentum to any of the values that it may assume when running quasiclassical trajectories, QCT/QM-$\alpha$J. With the extrapolation guided in both cases by physically motivated asymptotic theories, realism is seeked by avoiding unsecure jumps into the unknown. Although, mostly review oriented, a few issues are addressed for the first time here and there. Prospects for future work conclude the overview.

Quantum chemistry program based on Multiresolution Multiwavelet (MRMW) basis set is much simpler and can be more efficient than the conventional one based on Gaussian basis set in molecular geometry optimization because the Hellmann Fynman Theorem (HFT) holds for the complete space which MRMW provides. It is numerically shown that large Gaussian basis sets can provide the chemical information with chemical accuracy for very small molecular systems despite the incompleteness of their basis set. However, even for the relatively small size molecule of CH₄, the error from the basis set incompleteness results in an error larger than an acceptable chemical accuracy. The advantage of the MRMW complete basis set in vibrational analysis is also discussed.

Quantum chemistry methods were used to study the meta-tetra(hydroxyphenyl)chlorin (mTHPC) and its isomers. The mTHPC (Foscan®) is a commercial chlorin, used in photodynamic therapy (PDT) and is classified as a second-generation drug in PDT. The present work is to obtain quantum chemistry properties which can explain the high efficiency of the mTHPC compared with its isomers (ortho and para) and other chlorins. Based in the chemical hardness and ionization potential obtained from HOMO and LUMO orbitals energy, our results show that all chlorins have similar reactivity. Moreover, all chlorins have approximately the same capacity to storage energy in the triplet excited state, with energy differences between the ground state and the triplet excited state of 1.38, 1.39 and 1.36 eV for oTHPC, mTHPC and pTHPC, respectively. The calculated UV spectra (a very important quantity which can be correlated with the photosensitizer (PS) efficiency property), shows that the present chlorins all have a peak at 622 nm. Finally, after analysis of the dipole moment differences, between the three isomers, an explanation about the greater mTHPC efficiency in PDT, was possible. Due to its greater lipophilic character, mTHPC is absorbed by tumor cells to a greater degree than oTHPC and pTHPC. Our findings are consistent with literature and can be used to help new drug design for use in PDT.

In spite of the numerous experimental and theoretical studies on green fluorescent protein and its modifications, there is still no definitive answer to the central question: why such systems exhibit enhanced fluorescence. Based upon detailed quantum-chemical estimations, we advocate the following hypothesis. In the green fluorescent protein ground electronic state, the protein surrounding strains the chromophore with respect to its native intramolecular conformational preference in vacuo or in solution. Absorbing a photon of the proper wavelength not only causes a joint proton–electron transfer in and around the chromophore, but also increases the intrinsic strain of the latter. Since conformational relaxation of such a structure will not require any additional energy input, the energy gained by the chromophore cannot be dissipated into the chromophore's internal non-radiative degrees of freedom, and thus it returns as a fluorescence emission.

We adopted the verified quantum chemistry approach to demonstrate the possible frictionless transport of solid He-4 with high shear viscosity in a confined 3 nm (diameter) nanopore. Both the sharp decrease of flow resistance and sudden increase of shear viscosity of solid ⁴He in nanodomains near the onset of possible supersolidity are illustrated.

Recent years have seen vast improvements in the ability of rigorous quantum-mechanical methods to treat systems of interest to molecular biology. In this review article, we survey common computational methods used to study such large, weakly bound systems, starting from classical simulations and reaching to quantum chemistry and density functional theory. We sketch their underlying frameworks and investigate their strengths and weaknesses when applied to potentially large biomolecules. In particular, density functional theory — a framework that can treat thousands of atoms on firm theoretical ground — can now accurately describe systems dominated by weak van der Waals interactions. This newfound ability has rekindled interest in using this tried-and-true approach to investigate biological systems of real importance. In this review, we focus on some new methods within the density functional theory that allow for accurate inclusion of the weak interactions that dominate binding in biological macromolecules. Recent work utilizing these methods to study biologically relevant systems will be highlighted, and a vision for the future of density functional theory within molecular biology will be discussed.

Breast cancer is the most common cancer among women worldwide. Breast cancer is caused by the overexpression of genes that facilitate breast cell proliferation. Estrogen receptor alpha (ER$\alpha$) mediation is mostly responsible for the development of malignant tumors by regulating the transcription of various genes as a transcription factor. ER$\alpha$ is regarded as an important receptor for the proliferation of this disease and its inhibition is necessary for the treatment of breast cancer. In our study, the aim is to find out potential inhibitors for ER$\alpha$ by docking 100 anticancer constituents of different halogen-based derivatives against ER$\alpha$. Among the 100 $X$-based derivatives, 20 ligands were selected based on the interaction energy ranging from $-$6.7kcal/mol to $-$8.2kcal/mol and lower values of inhibition constant (0.92–11.77$\mu \mathrm{\text{mol}}$). We have performed a comprehensive analysis of five most popular ligands (L17, L57, L61, L67, and L70) among these 20 selected derivatives. The interaction analysis is mainly stabilized by making different interactions including hydrogen bonding, hydrophobic, electrostatic, and halogen bonding with the active site of ER$\alpha$. A quantum study based on frontier molecular orbitals (FMOs), molecular electrostatic potential (MEP), and global chemical reactivity descriptor (GCRD) is carried out to explore the structural chemistry of our most popular ligands which indicates that they are quite reactive and kinetically stable. Additionally, we also assess the ADMET profiles to predict the toxicity and drug-likeness of our lead compounds. Our selected ligands have the highest absorption and good clearance rate and have no AMES toxicity, skin sensitization, and hepatotoxicity. Molecular dynamics simulations were run to check the conformational stability of apo form of ER$\alpha$ and complex state, at 60-ns time scale. The molecular dynamics simulations are based on the plots of RMSD, RMSF, $R_g$, SASA, and the number of H-bonds. The results of RMSD and RMSF showed that the lead compounds L17, L57, L61, L67, and L70 are most stable and have no significant residual fluctuations and deviation. The analysis of the plots of $R_g$, SASA, and the number of H-bonds revealed that the complexes L17, L57, and L70 are most stable. So, the lead anticancer compounds L17, L57, L61, L67, and L70 are the most promising inhibitors against ER$\alpha$ of breast cancer. The comprehensive analysis of all studied parameters highlighted that our selected ligands have great potential to inhibit ER$\alpha$. So, it can be concluded that the selected halogen-based derivatives can promote rational drug design for the target therapies of ER$\alpha$ of breast cancer.